^DATABASE = GeoMiame
!Database_name = Gene Expression Omnibus (GEO)
!Database_institute = NCBI NLM NIH
!Database_web_link = http://www.ncbi.nlm.nih.gov/geo
!Database_email = geo@ncbi.nlm.nih.gov
^SERIES = GSE232836
!Series_title = Alterations in microbiome composition and metabolic byproducts drive behavioral and transcriptional responses to morphine
!Series_geo_accession = GSE232836
!Series_status = Public on May 18 2023
!Series_submission_date = May 18 2023
!Series_last_update_date = Jun 09 2023
!Series_pubmed_id = 34127799
!Series_summary = Recent evidence has demonstrated that the gut microbiome has marked effects on neuronal function and behavior. Disturbances to microbial populations within the gut have been linked to myriad models of neuropsychiatric disorders. However, the role of the microbiome in substance use disorders remains understudied. Here we show that male mice with their gut microbiome depleted by nonabsorbable antibiotics (Abx) exhibit decreased formation of morphine conditioned place preference across a range of doses (2.5-15 mg/kg), have decreased locomotor sensitization to morphine, and demonstrate marked changes in gene expression within the nucleus accumbens (NAc) in response to high-dose morphine (20 mg/kg × 7 days). Replacement of short-chain fatty acid (SCFA) metabolites, which are reduced by microbiome knockdown, reversed the behavioral and transcriptional effects of microbiome depletion. This identifies SCFA as the crucial mediators of microbiome-brain communication responsible for the effects on morphine reward caused by microbiome knockdown. These studies add important new behavioral, molecular, and mechanistic insight to the role of gut-brain signaling in substance use disorders
!Series_overall_design = RNA-seq profiling of Nac from male mice with their gut microbiome depleted by nonabsorbable antibiotics (Abx) and treated with morphine.
!Series_type = Expression profiling by high throughput sequencing
!Series_contributor = Rebecca,S,Hofford
!Series_contributor = Nicholas,L,Mervosh
!Series_contributor = Tanner,J,Euston
!Series_contributor = Katherine,R,Meckel
!Series_contributor = Amon,T,Orr
!Series_contributor = Drew,D,Kiraly
!Series_sample_id = GSM7384342
!Series_sample_id = GSM7384343
!Series_sample_id = GSM7384344
!Series_sample_id = GSM7384345
!Series_sample_id = GSM7384346
!Series_sample_id = GSM7384347
!Series_sample_id = GSM7384348
!Series_sample_id = GSM7384349
!Series_sample_id = GSM7384350
!Series_sample_id = GSM7384351
!Series_sample_id = GSM7384352
!Series_sample_id = GSM7384353
!Series_sample_id = GSM7384354
!Series_sample_id = GSM7384355
!Series_sample_id = GSM7384356
!Series_sample_id = GSM7384357
!Series_sample_id = GSM7384358
!Series_sample_id = GSM7384359
!Series_sample_id = GSM7384360
!Series_sample_id = GSM7384361
!Series_sample_id = GSM7384362
!Series_sample_id = GSM7384363
!Series_contact_name = Drew,,Kiraly
!Series_contact_email = dkiraly@wakehealth.edu
!Series_contact_phone = 2032282275
!Series_contact_department = Physiology, Pharmacology, Psychiatry
!Series_contact_institute = Wake Forest University School of Medicine
!Series_contact_address = 115 South Chestnut Street
!Series_contact_city = Winston-Salem
!Series_contact_state = NC
!Series_contact_zip/postal_code = 27101
!Series_contact_country = USA
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE232nnn/GSE232836/suppl/GSE232836_Non-normalizedData.csv.gz
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE232nnn/GSE232836/suppl/GSE232836_NormalizedData.csv.gz
!Series_platform_id = GPL17021
!Series_platform_taxid = 10090
!Series_sample_taxid = 10090
!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA974044
^PLATFORM = GPL17021
!Platform_title = Illumina HiSeq 2500 (Mus musculus)
!Platform_geo_accession = GPL17021
!Platform_status = Public on Apr 16 2013
!Platform_submission_date = Apr 16 2013
!Platform_last_update_date = Mar 21 2019
!Platform_technology = high-throughput sequencing
!Platform_distribution = virtual
!Platform_organism = Mus musculus
!Platform_taxid = 10090
!Platform_contact_name = ,,GEO
!Platform_contact_country = USA
!Platform_data_row_count = 0
^SAMPLE = GSM7384342
!Sample_title = Otc0363_H2O_Saline_3
!Sample_geo_accession = GSM7384342
!Sample_status = Public on May 18 2023
!Sample_submission_date = May 18 2023
!Sample_last_update_date = Jun 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Nucleus accumbens (brain)
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: Nucleus accumbens (brain)
!Sample_characteristics_ch1 = Sex: male
!Sample_characteristics_ch1 = cell type: Bulk
!Sample_characteristics_ch1 = microbiome status: Normal Microbiome
!Sample_characteristics_ch1 = treatment: Saline
!Sample_treatment_protocol_ch1 = Conventionally raised mice were the ones described in the published manuscript by Hofford et al. in 2021, thus all methods for conventional mice are identical to that manuscript (Hofford et al., 2021). The conventionally raised C57BL/6J mice (7-9 weeks old, Jackson Laboratories) were group-housed in a humidity, temperature-controlled, and specific pathogen-free colony facility on a 24 hour light/dark cycle (lights on at 7AM and lights off at 7PM). All studies were performed in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals under an approved protocol from the Mt. Sinai Icahn School of Medicine Institutional Animal Care and Use Committee.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted using TRIzol reagent (Thermo Fisher #15596026) according to manufacturer’s instructions.
!Sample_extract_protocol_ch1 = cDNA was generated using the SMARTer cDNA kit (Clonetech Laboratories # 634925) from total RNA. cDNA was fragmented using Bioruptor (Diagenode) and illumina-ready, indexed sequencing libraries were made using SPRIworks HT Reagent Kit (Beckamn Coulter, Inc. # B06938).
!Sample_data_processing = Raw FASTQ files were quality checked using  FASTQC (Babraham Institute, Cambridge, UK).
!Sample_data_processing = The raw FASTQ file for each sample was aligned to the Mus musculus 10 reference genome (NCBI) with the STAR package v2.4.0 (Dobin et al., 2013).
!Sample_data_processing = For pairwise comparisons aligned non-normalized read counts were analyzed for differential gene expression using the Biojupies analysis package with default settings (Torre et al., 2018). Statistical significance was set at a threshold of FDR-corrected p value of less than 0.05. Lists of significantly differentially expressed genes were analyzed for gene ontology pathways using G:Profiler (Raudvere et al., 2019)
!Sample_data_processing = Supplementary files format and content: comma separated-values (.csv)
!Sample_data_processing = Supplementary files format and content: Normalized read counts of genes. Normalization was performed using Trimmed Mean of the M-values (TMM; edgeR R package)
!Sample_platform_id = GPL17021
!Sample_contact_name = Drew,,Kiraly
!Sample_contact_email = dkiraly@wakehealth.edu
!Sample_contact_phone = 2032282275
!Sample_contact_department = Physiology, Pharmacology, Psychiatry
!Sample_contact_institute = Wake Forest University School of Medicine
!Sample_contact_address = 115 South Chestnut Street
!Sample_contact_city = Winston-Salem
!Sample_contact_state = NC
!Sample_contact_zip/postal_code = 27101
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN35166525
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX20432562
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE232836
!Sample_data_row_count = 0
^SAMPLE = GSM7384343
!Sample_title = OtC0364_H2O_Saline_4
!Sample_geo_accession = GSM7384343
!Sample_status = Public on May 18 2023
!Sample_submission_date = May 18 2023
!Sample_last_update_date = Jun 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Nucleus accumbens (brain)
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: Nucleus accumbens (brain)
!Sample_characteristics_ch1 = Sex: male
!Sample_characteristics_ch1 = cell type: Bulk
!Sample_characteristics_ch1 = microbiome status: Normal Microbiome
!Sample_characteristics_ch1 = treatment: Saline
!Sample_treatment_protocol_ch1 = Conventionally raised mice were the ones described in the published manuscript by Hofford et al. in 2021, thus all methods for conventional mice are identical to that manuscript (Hofford et al., 2021). The conventionally raised C57BL/6J mice (7-9 weeks old, Jackson Laboratories) were group-housed in a humidity, temperature-controlled, and specific pathogen-free colony facility on a 24 hour light/dark cycle (lights on at 7AM and lights off at 7PM). All studies were performed in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals under an approved protocol from the Mt. Sinai Icahn School of Medicine Institutional Animal Care and Use Committee.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted using TRIzol reagent (Thermo Fisher #15596026) according to manufacturer’s instructions.
!Sample_extract_protocol_ch1 = cDNA was generated using the SMARTer cDNA kit (Clonetech Laboratories # 634925) from total RNA. cDNA was fragmented using Bioruptor (Diagenode) and illumina-ready, indexed sequencing libraries were made using SPRIworks HT Reagent Kit (Beckamn Coulter, Inc. # B06938).
!Sample_data_processing = Raw FASTQ files were quality checked using  FASTQC (Babraham Institute, Cambridge, UK).
!Sample_data_processing = The raw FASTQ file for each sample was aligned to the Mus musculus 10 reference genome (NCBI) with the STAR package v2.4.0 (Dobin et al., 2013).
!Sample_data_processing = For pairwise comparisons aligned non-normalized read counts were analyzed for differential gene expression using the Biojupies analysis package with default settings (Torre et al., 2018). Statistical significance was set at a threshold of FDR-corrected p value of less than 0.05. Lists of significantly differentially expressed genes were analyzed for gene ontology pathways using G:Profiler (Raudvere et al., 2019)
!Sample_data_processing = Supplementary files format and content: comma separated-values (.csv)
!Sample_data_processing = Supplementary files format and content: Normalized read counts of genes. Normalization was performed using Trimmed Mean of the M-values (TMM; edgeR R package)
!Sample_platform_id = GPL17021
!Sample_contact_name = Drew,,Kiraly
!Sample_contact_email = dkiraly@wakehealth.edu
!Sample_contact_phone = 2032282275
!Sample_contact_department = Physiology, Pharmacology, Psychiatry
!Sample_contact_institute = Wake Forest University School of Medicine
!Sample_contact_address = 115 South Chestnut Street
!Sample_contact_city = Winston-Salem
!Sample_contact_state = NC
!Sample_contact_zip/postal_code = 27101
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN35166524
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX20432563
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE232836
!Sample_data_row_count = 0
^SAMPLE = GSM7384344
!Sample_title = OtC0365_H2O_Saline_5
!Sample_geo_accession = GSM7384344
!Sample_status = Public on May 18 2023
!Sample_submission_date = May 18 2023
!Sample_last_update_date = Jun 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Nucleus accumbens (brain)
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: Nucleus accumbens (brain)
!Sample_characteristics_ch1 = Sex: male
!Sample_characteristics_ch1 = cell type: Bulk
!Sample_characteristics_ch1 = microbiome status: Normal Microbiome
!Sample_characteristics_ch1 = treatment: Saline
!Sample_treatment_protocol_ch1 = Conventionally raised mice were the ones described in the published manuscript by Hofford et al. in 2021, thus all methods for conventional mice are identical to that manuscript (Hofford et al., 2021). The conventionally raised C57BL/6J mice (7-9 weeks old, Jackson Laboratories) were group-housed in a humidity, temperature-controlled, and specific pathogen-free colony facility on a 24 hour light/dark cycle (lights on at 7AM and lights off at 7PM). All studies were performed in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals under an approved protocol from the Mt. Sinai Icahn School of Medicine Institutional Animal Care and Use Committee.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted using TRIzol reagent (Thermo Fisher #15596026) according to manufacturer’s instructions.
!Sample_extract_protocol_ch1 = cDNA was generated using the SMARTer cDNA kit (Clonetech Laboratories # 634925) from total RNA. cDNA was fragmented using Bioruptor (Diagenode) and illumina-ready, indexed sequencing libraries were made using SPRIworks HT Reagent Kit (Beckamn Coulter, Inc. # B06938).
!Sample_data_processing = Raw FASTQ files were quality checked using  FASTQC (Babraham Institute, Cambridge, UK).
!Sample_data_processing = The raw FASTQ file for each sample was aligned to the Mus musculus 10 reference genome (NCBI) with the STAR package v2.4.0 (Dobin et al., 2013).
!Sample_data_processing = For pairwise comparisons aligned non-normalized read counts were analyzed for differential gene expression using the Biojupies analysis package with default settings (Torre et al., 2018). Statistical significance was set at a threshold of FDR-corrected p value of less than 0.05. Lists of significantly differentially expressed genes were analyzed for gene ontology pathways using G:Profiler (Raudvere et al., 2019)
!Sample_data_processing = Supplementary files format and content: comma separated-values (.csv)
!Sample_data_processing = Supplementary files format and content: Normalized read counts of genes. Normalization was performed using Trimmed Mean of the M-values (TMM; edgeR R package)
!Sample_platform_id = GPL17021
!Sample_contact_name = Drew,,Kiraly
!Sample_contact_email = dkiraly@wakehealth.edu
!Sample_contact_phone = 2032282275
!Sample_contact_department = Physiology, Pharmacology, Psychiatry
!Sample_contact_institute = Wake Forest University School of Medicine
!Sample_contact_address = 115 South Chestnut Street
!Sample_contact_city = Winston-Salem
!Sample_contact_state = NC
!Sample_contact_zip/postal_code = 27101
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN35166523
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX20432564
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE232836
!Sample_data_row_count = 0
^SAMPLE = GSM7384345
!Sample_title = OtC0366_H2O_Saline_6
!Sample_geo_accession = GSM7384345
!Sample_status = Public on May 18 2023
!Sample_submission_date = May 18 2023
!Sample_last_update_date = Jun 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Nucleus accumbens (brain)
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: Nucleus accumbens (brain)
!Sample_characteristics_ch1 = Sex: male
!Sample_characteristics_ch1 = cell type: Bulk
!Sample_characteristics_ch1 = microbiome status: Normal Microbiome
!Sample_characteristics_ch1 = treatment: Saline
!Sample_treatment_protocol_ch1 = Conventionally raised mice were the ones described in the published manuscript by Hofford et al. in 2021, thus all methods for conventional mice are identical to that manuscript (Hofford et al., 2021). The conventionally raised C57BL/6J mice (7-9 weeks old, Jackson Laboratories) were group-housed in a humidity, temperature-controlled, and specific pathogen-free colony facility on a 24 hour light/dark cycle (lights on at 7AM and lights off at 7PM). All studies were performed in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals under an approved protocol from the Mt. Sinai Icahn School of Medicine Institutional Animal Care and Use Committee.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted using TRIzol reagent (Thermo Fisher #15596026) according to manufacturer’s instructions.
!Sample_extract_protocol_ch1 = cDNA was generated using the SMARTer cDNA kit (Clonetech Laboratories # 634925) from total RNA. cDNA was fragmented using Bioruptor (Diagenode) and illumina-ready, indexed sequencing libraries were made using SPRIworks HT Reagent Kit (Beckamn Coulter, Inc. # B06938).
!Sample_data_processing = Raw FASTQ files were quality checked using  FASTQC (Babraham Institute, Cambridge, UK).
!Sample_data_processing = The raw FASTQ file for each sample was aligned to the Mus musculus 10 reference genome (NCBI) with the STAR package v2.4.0 (Dobin et al., 2013).
!Sample_data_processing = For pairwise comparisons aligned non-normalized read counts were analyzed for differential gene expression using the Biojupies analysis package with default settings (Torre et al., 2018). Statistical significance was set at a threshold of FDR-corrected p value of less than 0.05. Lists of significantly differentially expressed genes were analyzed for gene ontology pathways using G:Profiler (Raudvere et al., 2019)
!Sample_data_processing = Supplementary files format and content: comma separated-values (.csv)
!Sample_data_processing = Supplementary files format and content: Normalized read counts of genes. Normalization was performed using Trimmed Mean of the M-values (TMM; edgeR R package)
!Sample_platform_id = GPL17021
!Sample_contact_name = Drew,,Kiraly
!Sample_contact_email = dkiraly@wakehealth.edu
!Sample_contact_phone = 2032282275
!Sample_contact_department = Physiology, Pharmacology, Psychiatry
!Sample_contact_institute = Wake Forest University School of Medicine
!Sample_contact_address = 115 South Chestnut Street
!Sample_contact_city = Winston-Salem
!Sample_contact_state = NC
!Sample_contact_zip/postal_code = 27101
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN35166522
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX20432565
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE232836
!Sample_data_row_count = 0
^SAMPLE = GSM7384346
!Sample_title = OtC0367_H2O_Saline_8
!Sample_geo_accession = GSM7384346
!Sample_status = Public on May 18 2023
!Sample_submission_date = May 18 2023
!Sample_last_update_date = Jun 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Nucleus accumbens (brain)
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: Nucleus accumbens (brain)
!Sample_characteristics_ch1 = Sex: male
!Sample_characteristics_ch1 = cell type: Bulk
!Sample_characteristics_ch1 = microbiome status: Normal Microbiome
!Sample_characteristics_ch1 = treatment: Saline
!Sample_treatment_protocol_ch1 = Conventionally raised mice were the ones described in the published manuscript by Hofford et al. in 2021, thus all methods for conventional mice are identical to that manuscript (Hofford et al., 2021). The conventionally raised C57BL/6J mice (7-9 weeks old, Jackson Laboratories) were group-housed in a humidity, temperature-controlled, and specific pathogen-free colony facility on a 24 hour light/dark cycle (lights on at 7AM and lights off at 7PM). All studies were performed in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals under an approved protocol from the Mt. Sinai Icahn School of Medicine Institutional Animal Care and Use Committee.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted using TRIzol reagent (Thermo Fisher #15596026) according to manufacturer’s instructions.
!Sample_extract_protocol_ch1 = cDNA was generated using the SMARTer cDNA kit (Clonetech Laboratories # 634925) from total RNA. cDNA was fragmented using Bioruptor (Diagenode) and illumina-ready, indexed sequencing libraries were made using SPRIworks HT Reagent Kit (Beckamn Coulter, Inc. # B06938).
!Sample_data_processing = Raw FASTQ files were quality checked using  FASTQC (Babraham Institute, Cambridge, UK).
!Sample_data_processing = The raw FASTQ file for each sample was aligned to the Mus musculus 10 reference genome (NCBI) with the STAR package v2.4.0 (Dobin et al., 2013).
!Sample_data_processing = For pairwise comparisons aligned non-normalized read counts were analyzed for differential gene expression using the Biojupies analysis package with default settings (Torre et al., 2018). Statistical significance was set at a threshold of FDR-corrected p value of less than 0.05. Lists of significantly differentially expressed genes were analyzed for gene ontology pathways using G:Profiler (Raudvere et al., 2019)
!Sample_data_processing = Supplementary files format and content: comma separated-values (.csv)
!Sample_data_processing = Supplementary files format and content: Normalized read counts of genes. Normalization was performed using Trimmed Mean of the M-values (TMM; edgeR R package)
!Sample_platform_id = GPL17021
!Sample_contact_name = Drew,,Kiraly
!Sample_contact_email = dkiraly@wakehealth.edu
!Sample_contact_phone = 2032282275
!Sample_contact_department = Physiology, Pharmacology, Psychiatry
!Sample_contact_institute = Wake Forest University School of Medicine
!Sample_contact_address = 115 South Chestnut Street
!Sample_contact_city = Winston-Salem
!Sample_contact_state = NC
!Sample_contact_zip/postal_code = 27101
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN35166521
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX20432566
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE232836
!Sample_data_row_count = 0
^SAMPLE = GSM7384347
!Sample_title = OtC0368_H2O_Saline_9
!Sample_geo_accession = GSM7384347
!Sample_status = Public on May 18 2023
!Sample_submission_date = May 18 2023
!Sample_last_update_date = Jun 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Nucleus accumbens (brain)
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: Nucleus accumbens (brain)
!Sample_characteristics_ch1 = Sex: male
!Sample_characteristics_ch1 = cell type: Bulk
!Sample_characteristics_ch1 = microbiome status: Normal Microbiome
!Sample_characteristics_ch1 = treatment: Saline
!Sample_treatment_protocol_ch1 = Conventionally raised mice were the ones described in the published manuscript by Hofford et al. in 2021, thus all methods for conventional mice are identical to that manuscript (Hofford et al., 2021). The conventionally raised C57BL/6J mice (7-9 weeks old, Jackson Laboratories) were group-housed in a humidity, temperature-controlled, and specific pathogen-free colony facility on a 24 hour light/dark cycle (lights on at 7AM and lights off at 7PM). All studies were performed in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals under an approved protocol from the Mt. Sinai Icahn School of Medicine Institutional Animal Care and Use Committee.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted using TRIzol reagent (Thermo Fisher #15596026) according to manufacturer’s instructions.
!Sample_extract_protocol_ch1 = cDNA was generated using the SMARTer cDNA kit (Clonetech Laboratories # 634925) from total RNA. cDNA was fragmented using Bioruptor (Diagenode) and illumina-ready, indexed sequencing libraries were made using SPRIworks HT Reagent Kit (Beckamn Coulter, Inc. # B06938).
!Sample_data_processing = Raw FASTQ files were quality checked using  FASTQC (Babraham Institute, Cambridge, UK).
!Sample_data_processing = The raw FASTQ file for each sample was aligned to the Mus musculus 10 reference genome (NCBI) with the STAR package v2.4.0 (Dobin et al., 2013).
!Sample_data_processing = For pairwise comparisons aligned non-normalized read counts were analyzed for differential gene expression using the Biojupies analysis package with default settings (Torre et al., 2018). Statistical significance was set at a threshold of FDR-corrected p value of less than 0.05. Lists of significantly differentially expressed genes were analyzed for gene ontology pathways using G:Profiler (Raudvere et al., 2019)
!Sample_data_processing = Supplementary files format and content: comma separated-values (.csv)
!Sample_data_processing = Supplementary files format and content: Normalized read counts of genes. Normalization was performed using Trimmed Mean of the M-values (TMM; edgeR R package)
!Sample_platform_id = GPL17021
!Sample_contact_name = Drew,,Kiraly
!Sample_contact_email = dkiraly@wakehealth.edu
!Sample_contact_phone = 2032282275
!Sample_contact_department = Physiology, Pharmacology, Psychiatry
!Sample_contact_institute = Wake Forest University School of Medicine
!Sample_contact_address = 115 South Chestnut Street
!Sample_contact_city = Winston-Salem
!Sample_contact_state = NC
!Sample_contact_zip/postal_code = 27101
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN35166520
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX20432567
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE232836
!Sample_data_row_count = 0
^SAMPLE = GSM7384348
!Sample_title = OtC0369_Abx_Saline_1
!Sample_geo_accession = GSM7384348
!Sample_status = Public on May 18 2023
!Sample_submission_date = May 18 2023
!Sample_last_update_date = Jun 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Nucleus accumbens (brain)
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: Nucleus accumbens (brain)
!Sample_characteristics_ch1 = Sex: male
!Sample_characteristics_ch1 = cell type: Bulk
!Sample_characteristics_ch1 = microbiome status: Depleted Microbiome
!Sample_characteristics_ch1 = treatment: Saline
!Sample_treatment_protocol_ch1 = Conventionally raised mice were the ones described in the published manuscript by Hofford et al. in 2021, thus all methods for conventional mice are identical to that manuscript (Hofford et al., 2021). The conventionally raised C57BL/6J mice (7-9 weeks old, Jackson Laboratories) were group-housed in a humidity, temperature-controlled, and specific pathogen-free colony facility on a 24 hour light/dark cycle (lights on at 7AM and lights off at 7PM). All studies were performed in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals under an approved protocol from the Mt. Sinai Icahn School of Medicine Institutional Animal Care and Use Committee.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted using TRIzol reagent (Thermo Fisher #15596026) according to manufacturer’s instructions.
!Sample_extract_protocol_ch1 = cDNA was generated using the SMARTer cDNA kit (Clonetech Laboratories # 634925) from total RNA. cDNA was fragmented using Bioruptor (Diagenode) and illumina-ready, indexed sequencing libraries were made using SPRIworks HT Reagent Kit (Beckamn Coulter, Inc. # B06938).
!Sample_data_processing = Raw FASTQ files were quality checked using  FASTQC (Babraham Institute, Cambridge, UK).
!Sample_data_processing = The raw FASTQ file for each sample was aligned to the Mus musculus 10 reference genome (NCBI) with the STAR package v2.4.0 (Dobin et al., 2013).
!Sample_data_processing = For pairwise comparisons aligned non-normalized read counts were analyzed for differential gene expression using the Biojupies analysis package with default settings (Torre et al., 2018). Statistical significance was set at a threshold of FDR-corrected p value of less than 0.05. Lists of significantly differentially expressed genes were analyzed for gene ontology pathways using G:Profiler (Raudvere et al., 2019)
!Sample_data_processing = Supplementary files format and content: comma separated-values (.csv)
!Sample_data_processing = Supplementary files format and content: Normalized read counts of genes. Normalization was performed using Trimmed Mean of the M-values (TMM; edgeR R package)
!Sample_platform_id = GPL17021
!Sample_contact_name = Drew,,Kiraly
!Sample_contact_email = dkiraly@wakehealth.edu
!Sample_contact_phone = 2032282275
!Sample_contact_department = Physiology, Pharmacology, Psychiatry
!Sample_contact_institute = Wake Forest University School of Medicine
!Sample_contact_address = 115 South Chestnut Street
!Sample_contact_city = Winston-Salem
!Sample_contact_state = NC
!Sample_contact_zip/postal_code = 27101
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN35166519
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX20432568
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE232836
!Sample_data_row_count = 0
^SAMPLE = GSM7384349
!Sample_title = OtC0370_Abx_Saline_2
!Sample_geo_accession = GSM7384349
!Sample_status = Public on May 18 2023
!Sample_submission_date = May 18 2023
!Sample_last_update_date = Jun 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Nucleus accumbens (brain)
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: Nucleus accumbens (brain)
!Sample_characteristics_ch1 = Sex: male
!Sample_characteristics_ch1 = cell type: Bulk
!Sample_characteristics_ch1 = microbiome status: Depleted Microbiome
!Sample_characteristics_ch1 = treatment: Saline
!Sample_treatment_protocol_ch1 = Conventionally raised mice were the ones described in the published manuscript by Hofford et al. in 2021, thus all methods for conventional mice are identical to that manuscript (Hofford et al., 2021). The conventionally raised C57BL/6J mice (7-9 weeks old, Jackson Laboratories) were group-housed in a humidity, temperature-controlled, and specific pathogen-free colony facility on a 24 hour light/dark cycle (lights on at 7AM and lights off at 7PM). All studies were performed in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals under an approved protocol from the Mt. Sinai Icahn School of Medicine Institutional Animal Care and Use Committee.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted using TRIzol reagent (Thermo Fisher #15596026) according to manufacturer’s instructions.
!Sample_extract_protocol_ch1 = cDNA was generated using the SMARTer cDNA kit (Clonetech Laboratories # 634925) from total RNA. cDNA was fragmented using Bioruptor (Diagenode) and illumina-ready, indexed sequencing libraries were made using SPRIworks HT Reagent Kit (Beckamn Coulter, Inc. # B06938).
!Sample_data_processing = Raw FASTQ files were quality checked using  FASTQC (Babraham Institute, Cambridge, UK).
!Sample_data_processing = The raw FASTQ file for each sample was aligned to the Mus musculus 10 reference genome (NCBI) with the STAR package v2.4.0 (Dobin et al., 2013).
!Sample_data_processing = For pairwise comparisons aligned non-normalized read counts were analyzed for differential gene expression using the Biojupies analysis package with default settings (Torre et al., 2018). Statistical significance was set at a threshold of FDR-corrected p value of less than 0.05. Lists of significantly differentially expressed genes were analyzed for gene ontology pathways using G:Profiler (Raudvere et al., 2019)
!Sample_data_processing = Supplementary files format and content: comma separated-values (.csv)
!Sample_data_processing = Supplementary files format and content: Normalized read counts of genes. Normalization was performed using Trimmed Mean of the M-values (TMM; edgeR R package)
!Sample_platform_id = GPL17021
!Sample_contact_name = Drew,,Kiraly
!Sample_contact_email = dkiraly@wakehealth.edu
!Sample_contact_phone = 2032282275
!Sample_contact_department = Physiology, Pharmacology, Psychiatry
!Sample_contact_institute = Wake Forest University School of Medicine
!Sample_contact_address = 115 South Chestnut Street
!Sample_contact_city = Winston-Salem
!Sample_contact_state = NC
!Sample_contact_zip/postal_code = 27101
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN35166518
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX20432569
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE232836
!Sample_data_row_count = 0
^SAMPLE = GSM7384350
!Sample_title = OtC0371_Abx_Saline_3
!Sample_geo_accession = GSM7384350
!Sample_status = Public on May 18 2023
!Sample_submission_date = May 18 2023
!Sample_last_update_date = Jun 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Nucleus accumbens (brain)
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: Nucleus accumbens (brain)
!Sample_characteristics_ch1 = Sex: male
!Sample_characteristics_ch1 = cell type: Bulk
!Sample_characteristics_ch1 = microbiome status: Depleted Microbiome
!Sample_characteristics_ch1 = treatment: Saline
!Sample_treatment_protocol_ch1 = Conventionally raised mice were the ones described in the published manuscript by Hofford et al. in 2021, thus all methods for conventional mice are identical to that manuscript (Hofford et al., 2021). The conventionally raised C57BL/6J mice (7-9 weeks old, Jackson Laboratories) were group-housed in a humidity, temperature-controlled, and specific pathogen-free colony facility on a 24 hour light/dark cycle (lights on at 7AM and lights off at 7PM). All studies were performed in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals under an approved protocol from the Mt. Sinai Icahn School of Medicine Institutional Animal Care and Use Committee.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted using TRIzol reagent (Thermo Fisher #15596026) according to manufacturer’s instructions.
!Sample_extract_protocol_ch1 = cDNA was generated using the SMARTer cDNA kit (Clonetech Laboratories # 634925) from total RNA. cDNA was fragmented using Bioruptor (Diagenode) and illumina-ready, indexed sequencing libraries were made using SPRIworks HT Reagent Kit (Beckamn Coulter, Inc. # B06938).
!Sample_data_processing = Raw FASTQ files were quality checked using  FASTQC (Babraham Institute, Cambridge, UK).
!Sample_data_processing = The raw FASTQ file for each sample was aligned to the Mus musculus 10 reference genome (NCBI) with the STAR package v2.4.0 (Dobin et al., 2013).
!Sample_data_processing = For pairwise comparisons aligned non-normalized read counts were analyzed for differential gene expression using the Biojupies analysis package with default settings (Torre et al., 2018). Statistical significance was set at a threshold of FDR-corrected p value of less than 0.05. Lists of significantly differentially expressed genes were analyzed for gene ontology pathways using G:Profiler (Raudvere et al., 2019)
!Sample_data_processing = Supplementary files format and content: comma separated-values (.csv)
!Sample_data_processing = Supplementary files format and content: Normalized read counts of genes. Normalization was performed using Trimmed Mean of the M-values (TMM; edgeR R package)
!Sample_platform_id = GPL17021
!Sample_contact_name = Drew,,Kiraly
!Sample_contact_email = dkiraly@wakehealth.edu
!Sample_contact_phone = 2032282275
!Sample_contact_department = Physiology, Pharmacology, Psychiatry
!Sample_contact_institute = Wake Forest University School of Medicine
!Sample_contact_address = 115 South Chestnut Street
!Sample_contact_city = Winston-Salem
!Sample_contact_state = NC
!Sample_contact_zip/postal_code = 27101
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN35166517
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX20432570
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE232836
!Sample_data_row_count = 0
^SAMPLE = GSM7384351
!Sample_title = OtC0372_Abx_Saline_4
!Sample_geo_accession = GSM7384351
!Sample_status = Public on May 18 2023
!Sample_submission_date = May 18 2023
!Sample_last_update_date = Jun 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Nucleus accumbens (brain)
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: Nucleus accumbens (brain)
!Sample_characteristics_ch1 = Sex: male
!Sample_characteristics_ch1 = cell type: Bulk
!Sample_characteristics_ch1 = microbiome status: Depleted Microbiome
!Sample_characteristics_ch1 = treatment: Saline
!Sample_treatment_protocol_ch1 = Conventionally raised mice were the ones described in the published manuscript by Hofford et al. in 2021, thus all methods for conventional mice are identical to that manuscript (Hofford et al., 2021). The conventionally raised C57BL/6J mice (7-9 weeks old, Jackson Laboratories) were group-housed in a humidity, temperature-controlled, and specific pathogen-free colony facility on a 24 hour light/dark cycle (lights on at 7AM and lights off at 7PM). All studies were performed in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals under an approved protocol from the Mt. Sinai Icahn School of Medicine Institutional Animal Care and Use Committee.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted using TRIzol reagent (Thermo Fisher #15596026) according to manufacturer’s instructions.
!Sample_extract_protocol_ch1 = cDNA was generated using the SMARTer cDNA kit (Clonetech Laboratories # 634925) from total RNA. cDNA was fragmented using Bioruptor (Diagenode) and illumina-ready, indexed sequencing libraries were made using SPRIworks HT Reagent Kit (Beckamn Coulter, Inc. # B06938).
!Sample_data_processing = Raw FASTQ files were quality checked using  FASTQC (Babraham Institute, Cambridge, UK).
!Sample_data_processing = The raw FASTQ file for each sample was aligned to the Mus musculus 10 reference genome (NCBI) with the STAR package v2.4.0 (Dobin et al., 2013).
!Sample_data_processing = For pairwise comparisons aligned non-normalized read counts were analyzed for differential gene expression using the Biojupies analysis package with default settings (Torre et al., 2018). Statistical significance was set at a threshold of FDR-corrected p value of less than 0.05. Lists of significantly differentially expressed genes were analyzed for gene ontology pathways using G:Profiler (Raudvere et al., 2019)
!Sample_data_processing = Supplementary files format and content: comma separated-values (.csv)
!Sample_data_processing = Supplementary files format and content: Normalized read counts of genes. Normalization was performed using Trimmed Mean of the M-values (TMM; edgeR R package)
!Sample_platform_id = GPL17021
!Sample_contact_name = Drew,,Kiraly
!Sample_contact_email = dkiraly@wakehealth.edu
!Sample_contact_phone = 2032282275
!Sample_contact_department = Physiology, Pharmacology, Psychiatry
!Sample_contact_institute = Wake Forest University School of Medicine
!Sample_contact_address = 115 South Chestnut Street
!Sample_contact_city = Winston-Salem
!Sample_contact_state = NC
!Sample_contact_zip/postal_code = 27101
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN35166516
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX20432571
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE232836
!Sample_data_row_count = 0
^SAMPLE = GSM7384352
!Sample_title = OtC0373_Abx_Saline_5
!Sample_geo_accession = GSM7384352
!Sample_status = Public on May 18 2023
!Sample_submission_date = May 18 2023
!Sample_last_update_date = Jun 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Nucleus accumbens (brain)
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: Nucleus accumbens (brain)
!Sample_characteristics_ch1 = Sex: male
!Sample_characteristics_ch1 = cell type: Bulk
!Sample_characteristics_ch1 = microbiome status: Depleted Microbiome
!Sample_characteristics_ch1 = treatment: Saline
!Sample_treatment_protocol_ch1 = Conventionally raised mice were the ones described in the published manuscript by Hofford et al. in 2021, thus all methods for conventional mice are identical to that manuscript (Hofford et al., 2021). The conventionally raised C57BL/6J mice (7-9 weeks old, Jackson Laboratories) were group-housed in a humidity, temperature-controlled, and specific pathogen-free colony facility on a 24 hour light/dark cycle (lights on at 7AM and lights off at 7PM). All studies were performed in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals under an approved protocol from the Mt. Sinai Icahn School of Medicine Institutional Animal Care and Use Committee.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted using TRIzol reagent (Thermo Fisher #15596026) according to manufacturer’s instructions.
!Sample_extract_protocol_ch1 = cDNA was generated using the SMARTer cDNA kit (Clonetech Laboratories # 634925) from total RNA. cDNA was fragmented using Bioruptor (Diagenode) and illumina-ready, indexed sequencing libraries were made using SPRIworks HT Reagent Kit (Beckamn Coulter, Inc. # B06938).
!Sample_data_processing = Raw FASTQ files were quality checked using  FASTQC (Babraham Institute, Cambridge, UK).
!Sample_data_processing = The raw FASTQ file for each sample was aligned to the Mus musculus 10 reference genome (NCBI) with the STAR package v2.4.0 (Dobin et al., 2013).
!Sample_data_processing = For pairwise comparisons aligned non-normalized read counts were analyzed for differential gene expression using the Biojupies analysis package with default settings (Torre et al., 2018). Statistical significance was set at a threshold of FDR-corrected p value of less than 0.05. Lists of significantly differentially expressed genes were analyzed for gene ontology pathways using G:Profiler (Raudvere et al., 2019)
!Sample_data_processing = Supplementary files format and content: comma separated-values (.csv)
!Sample_data_processing = Supplementary files format and content: Normalized read counts of genes. Normalization was performed using Trimmed Mean of the M-values (TMM; edgeR R package)
!Sample_platform_id = GPL17021
!Sample_contact_name = Drew,,Kiraly
!Sample_contact_email = dkiraly@wakehealth.edu
!Sample_contact_phone = 2032282275
!Sample_contact_department = Physiology, Pharmacology, Psychiatry
!Sample_contact_institute = Wake Forest University School of Medicine
!Sample_contact_address = 115 South Chestnut Street
!Sample_contact_city = Winston-Salem
!Sample_contact_state = NC
!Sample_contact_zip/postal_code = 27101
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN35166515
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX20432572
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE232836
!Sample_data_row_count = 0
^SAMPLE = GSM7384353
!Sample_title = OtC0374_Abx_Saline_6
!Sample_geo_accession = GSM7384353
!Sample_status = Public on May 18 2023
!Sample_submission_date = May 18 2023
!Sample_last_update_date = Jun 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Nucleus accumbens (brain)
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: Nucleus accumbens (brain)
!Sample_characteristics_ch1 = Sex: male
!Sample_characteristics_ch1 = cell type: Bulk
!Sample_characteristics_ch1 = microbiome status: Depleted Microbiome
!Sample_characteristics_ch1 = treatment: Saline
!Sample_treatment_protocol_ch1 = Conventionally raised mice were the ones described in the published manuscript by Hofford et al. in 2021, thus all methods for conventional mice are identical to that manuscript (Hofford et al., 2021). The conventionally raised C57BL/6J mice (7-9 weeks old, Jackson Laboratories) were group-housed in a humidity, temperature-controlled, and specific pathogen-free colony facility on a 24 hour light/dark cycle (lights on at 7AM and lights off at 7PM). All studies were performed in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals under an approved protocol from the Mt. Sinai Icahn School of Medicine Institutional Animal Care and Use Committee.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted using TRIzol reagent (Thermo Fisher #15596026) according to manufacturer’s instructions.
!Sample_extract_protocol_ch1 = cDNA was generated using the SMARTer cDNA kit (Clonetech Laboratories # 634925) from total RNA. cDNA was fragmented using Bioruptor (Diagenode) and illumina-ready, indexed sequencing libraries were made using SPRIworks HT Reagent Kit (Beckamn Coulter, Inc. # B06938).
!Sample_data_processing = Raw FASTQ files were quality checked using  FASTQC (Babraham Institute, Cambridge, UK).
!Sample_data_processing = The raw FASTQ file for each sample was aligned to the Mus musculus 10 reference genome (NCBI) with the STAR package v2.4.0 (Dobin et al., 2013).
!Sample_data_processing = For pairwise comparisons aligned non-normalized read counts were analyzed for differential gene expression using the Biojupies analysis package with default settings (Torre et al., 2018). Statistical significance was set at a threshold of FDR-corrected p value of less than 0.05. Lists of significantly differentially expressed genes were analyzed for gene ontology pathways using G:Profiler (Raudvere et al., 2019)
!Sample_data_processing = Supplementary files format and content: comma separated-values (.csv)
!Sample_data_processing = Supplementary files format and content: Normalized read counts of genes. Normalization was performed using Trimmed Mean of the M-values (TMM; edgeR R package)
!Sample_platform_id = GPL17021
!Sample_contact_name = Drew,,Kiraly
!Sample_contact_email = dkiraly@wakehealth.edu
!Sample_contact_phone = 2032282275
!Sample_contact_department = Physiology, Pharmacology, Psychiatry
!Sample_contact_institute = Wake Forest University School of Medicine
!Sample_contact_address = 115 South Chestnut Street
!Sample_contact_city = Winston-Salem
!Sample_contact_state = NC
!Sample_contact_zip/postal_code = 27101
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN35166514
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX20432573
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE232836
!Sample_data_row_count = 0
^SAMPLE = GSM7384354
!Sample_title = OtC0376_H2O_Morphine_2
!Sample_geo_accession = GSM7384354
!Sample_status = Public on May 18 2023
!Sample_submission_date = May 18 2023
!Sample_last_update_date = Jun 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Nucleus accumbens (brain)
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: Nucleus accumbens (brain)
!Sample_characteristics_ch1 = Sex: male
!Sample_characteristics_ch1 = cell type: Bulk
!Sample_characteristics_ch1 = microbiome status: Normal Microbiome
!Sample_characteristics_ch1 = treatment: Morphine (20mg/kg/day/7 days)
!Sample_treatment_protocol_ch1 = Conventionally raised mice were the ones described in the published manuscript by Hofford et al. in 2021, thus all methods for conventional mice are identical to that manuscript (Hofford et al., 2021). The conventionally raised C57BL/6J mice (7-9 weeks old, Jackson Laboratories) were group-housed in a humidity, temperature-controlled, and specific pathogen-free colony facility on a 24 hour light/dark cycle (lights on at 7AM and lights off at 7PM). All studies were performed in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals under an approved protocol from the Mt. Sinai Icahn School of Medicine Institutional Animal Care and Use Committee.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted using TRIzol reagent (Thermo Fisher #15596026) according to manufacturer’s instructions.
!Sample_extract_protocol_ch1 = cDNA was generated using the SMARTer cDNA kit (Clonetech Laboratories # 634925) from total RNA. cDNA was fragmented using Bioruptor (Diagenode) and illumina-ready, indexed sequencing libraries were made using SPRIworks HT Reagent Kit (Beckamn Coulter, Inc. # B06938).
!Sample_data_processing = Raw FASTQ files were quality checked using  FASTQC (Babraham Institute, Cambridge, UK).
!Sample_data_processing = The raw FASTQ file for each sample was aligned to the Mus musculus 10 reference genome (NCBI) with the STAR package v2.4.0 (Dobin et al., 2013).
!Sample_data_processing = For pairwise comparisons aligned non-normalized read counts were analyzed for differential gene expression using the Biojupies analysis package with default settings (Torre et al., 2018). Statistical significance was set at a threshold of FDR-corrected p value of less than 0.05. Lists of significantly differentially expressed genes were analyzed for gene ontology pathways using G:Profiler (Raudvere et al., 2019)
!Sample_data_processing = Supplementary files format and content: comma separated-values (.csv)
!Sample_data_processing = Supplementary files format and content: Normalized read counts of genes. Normalization was performed using Trimmed Mean of the M-values (TMM; edgeR R package)
!Sample_platform_id = GPL17021
!Sample_contact_name = Drew,,Kiraly
!Sample_contact_email = dkiraly@wakehealth.edu
!Sample_contact_phone = 2032282275
!Sample_contact_department = Physiology, Pharmacology, Psychiatry
!Sample_contact_institute = Wake Forest University School of Medicine
!Sample_contact_address = 115 South Chestnut Street
!Sample_contact_city = Winston-Salem
!Sample_contact_state = NC
!Sample_contact_zip/postal_code = 27101
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN35166513
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX20432574
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE232836
!Sample_data_row_count = 0
^SAMPLE = GSM7384355
!Sample_title = OtC0377_H2O_Morphine_3
!Sample_geo_accession = GSM7384355
!Sample_status = Public on May 18 2023
!Sample_submission_date = May 18 2023
!Sample_last_update_date = Jun 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Nucleus accumbens (brain)
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: Nucleus accumbens (brain)
!Sample_characteristics_ch1 = Sex: male
!Sample_characteristics_ch1 = cell type: Bulk
!Sample_characteristics_ch1 = microbiome status: Normal Microbiome
!Sample_characteristics_ch1 = treatment: Morphine (20mg/kg/day/7 days)
!Sample_treatment_protocol_ch1 = Conventionally raised mice were the ones described in the published manuscript by Hofford et al. in 2021, thus all methods for conventional mice are identical to that manuscript (Hofford et al., 2021). The conventionally raised C57BL/6J mice (7-9 weeks old, Jackson Laboratories) were group-housed in a humidity, temperature-controlled, and specific pathogen-free colony facility on a 24 hour light/dark cycle (lights on at 7AM and lights off at 7PM). All studies were performed in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals under an approved protocol from the Mt. Sinai Icahn School of Medicine Institutional Animal Care and Use Committee.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted using TRIzol reagent (Thermo Fisher #15596026) according to manufacturer’s instructions.
!Sample_extract_protocol_ch1 = cDNA was generated using the SMARTer cDNA kit (Clonetech Laboratories # 634925) from total RNA. cDNA was fragmented using Bioruptor (Diagenode) and illumina-ready, indexed sequencing libraries were made using SPRIworks HT Reagent Kit (Beckamn Coulter, Inc. # B06938).
!Sample_data_processing = Raw FASTQ files were quality checked using  FASTQC (Babraham Institute, Cambridge, UK).
!Sample_data_processing = The raw FASTQ file for each sample was aligned to the Mus musculus 10 reference genome (NCBI) with the STAR package v2.4.0 (Dobin et al., 2013).
!Sample_data_processing = For pairwise comparisons aligned non-normalized read counts were analyzed for differential gene expression using the Biojupies analysis package with default settings (Torre et al., 2018). Statistical significance was set at a threshold of FDR-corrected p value of less than 0.05. Lists of significantly differentially expressed genes were analyzed for gene ontology pathways using G:Profiler (Raudvere et al., 2019)
!Sample_data_processing = Supplementary files format and content: comma separated-values (.csv)
!Sample_data_processing = Supplementary files format and content: Normalized read counts of genes. Normalization was performed using Trimmed Mean of the M-values (TMM; edgeR R package)
!Sample_platform_id = GPL17021
!Sample_contact_name = Drew,,Kiraly
!Sample_contact_email = dkiraly@wakehealth.edu
!Sample_contact_phone = 2032282275
!Sample_contact_department = Physiology, Pharmacology, Psychiatry
!Sample_contact_institute = Wake Forest University School of Medicine
!Sample_contact_address = 115 South Chestnut Street
!Sample_contact_city = Winston-Salem
!Sample_contact_state = NC
!Sample_contact_zip/postal_code = 27101
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN35166512
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX20432575
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE232836
!Sample_data_row_count = 0
^SAMPLE = GSM7384356
!Sample_title = OtC0378_H2O_Morphine_4
!Sample_geo_accession = GSM7384356
!Sample_status = Public on May 18 2023
!Sample_submission_date = May 18 2023
!Sample_last_update_date = Jun 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Nucleus accumbens (brain)
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: Nucleus accumbens (brain)
!Sample_characteristics_ch1 = Sex: male
!Sample_characteristics_ch1 = cell type: Bulk
!Sample_characteristics_ch1 = microbiome status: Normal Microbiome
!Sample_characteristics_ch1 = treatment: Morphine (20mg/kg/day/7 days)
!Sample_treatment_protocol_ch1 = Conventionally raised mice were the ones described in the published manuscript by Hofford et al. in 2021, thus all methods for conventional mice are identical to that manuscript (Hofford et al., 2021). The conventionally raised C57BL/6J mice (7-9 weeks old, Jackson Laboratories) were group-housed in a humidity, temperature-controlled, and specific pathogen-free colony facility on a 24 hour light/dark cycle (lights on at 7AM and lights off at 7PM). All studies were performed in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals under an approved protocol from the Mt. Sinai Icahn School of Medicine Institutional Animal Care and Use Committee.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted using TRIzol reagent (Thermo Fisher #15596026) according to manufacturer’s instructions.
!Sample_extract_protocol_ch1 = cDNA was generated using the SMARTer cDNA kit (Clonetech Laboratories # 634925) from total RNA. cDNA was fragmented using Bioruptor (Diagenode) and illumina-ready, indexed sequencing libraries were made using SPRIworks HT Reagent Kit (Beckamn Coulter, Inc. # B06938).
!Sample_data_processing = Raw FASTQ files were quality checked using  FASTQC (Babraham Institute, Cambridge, UK).
!Sample_data_processing = The raw FASTQ file for each sample was aligned to the Mus musculus 10 reference genome (NCBI) with the STAR package v2.4.0 (Dobin et al., 2013).
!Sample_data_processing = For pairwise comparisons aligned non-normalized read counts were analyzed for differential gene expression using the Biojupies analysis package with default settings (Torre et al., 2018). Statistical significance was set at a threshold of FDR-corrected p value of less than 0.05. Lists of significantly differentially expressed genes were analyzed for gene ontology pathways using G:Profiler (Raudvere et al., 2019)
!Sample_data_processing = Supplementary files format and content: comma separated-values (.csv)
!Sample_data_processing = Supplementary files format and content: Normalized read counts of genes. Normalization was performed using Trimmed Mean of the M-values (TMM; edgeR R package)
!Sample_platform_id = GPL17021
!Sample_contact_name = Drew,,Kiraly
!Sample_contact_email = dkiraly@wakehealth.edu
!Sample_contact_phone = 2032282275
!Sample_contact_department = Physiology, Pharmacology, Psychiatry
!Sample_contact_institute = Wake Forest University School of Medicine
!Sample_contact_address = 115 South Chestnut Street
!Sample_contact_city = Winston-Salem
!Sample_contact_state = NC
!Sample_contact_zip/postal_code = 27101
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN35166511
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX20432576
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE232836
!Sample_data_row_count = 0
^SAMPLE = GSM7384357
!Sample_title = OtC0379_H2O_Morphine_5
!Sample_geo_accession = GSM7384357
!Sample_status = Public on May 18 2023
!Sample_submission_date = May 18 2023
!Sample_last_update_date = Jun 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Nucleus accumbens (brain)
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: Nucleus accumbens (brain)
!Sample_characteristics_ch1 = Sex: male
!Sample_characteristics_ch1 = cell type: Bulk
!Sample_characteristics_ch1 = microbiome status: Normal Microbiome
!Sample_characteristics_ch1 = treatment: Morphine (20mg/kg/day/7 days)
!Sample_treatment_protocol_ch1 = Conventionally raised mice were the ones described in the published manuscript by Hofford et al. in 2021, thus all methods for conventional mice are identical to that manuscript (Hofford et al., 2021). The conventionally raised C57BL/6J mice (7-9 weeks old, Jackson Laboratories) were group-housed in a humidity, temperature-controlled, and specific pathogen-free colony facility on a 24 hour light/dark cycle (lights on at 7AM and lights off at 7PM). All studies were performed in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals under an approved protocol from the Mt. Sinai Icahn School of Medicine Institutional Animal Care and Use Committee.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted using TRIzol reagent (Thermo Fisher #15596026) according to manufacturer’s instructions.
!Sample_extract_protocol_ch1 = cDNA was generated using the SMARTer cDNA kit (Clonetech Laboratories # 634925) from total RNA. cDNA was fragmented using Bioruptor (Diagenode) and illumina-ready, indexed sequencing libraries were made using SPRIworks HT Reagent Kit (Beckamn Coulter, Inc. # B06938).
!Sample_data_processing = Raw FASTQ files were quality checked using  FASTQC (Babraham Institute, Cambridge, UK).
!Sample_data_processing = The raw FASTQ file for each sample was aligned to the Mus musculus 10 reference genome (NCBI) with the STAR package v2.4.0 (Dobin et al., 2013).
!Sample_data_processing = For pairwise comparisons aligned non-normalized read counts were analyzed for differential gene expression using the Biojupies analysis package with default settings (Torre et al., 2018). Statistical significance was set at a threshold of FDR-corrected p value of less than 0.05. Lists of significantly differentially expressed genes were analyzed for gene ontology pathways using G:Profiler (Raudvere et al., 2019)
!Sample_data_processing = Supplementary files format and content: comma separated-values (.csv)
!Sample_data_processing = Supplementary files format and content: Normalized read counts of genes. Normalization was performed using Trimmed Mean of the M-values (TMM; edgeR R package)
!Sample_platform_id = GPL17021
!Sample_contact_name = Drew,,Kiraly
!Sample_contact_email = dkiraly@wakehealth.edu
!Sample_contact_phone = 2032282275
!Sample_contact_department = Physiology, Pharmacology, Psychiatry
!Sample_contact_institute = Wake Forest University School of Medicine
!Sample_contact_address = 115 South Chestnut Street
!Sample_contact_city = Winston-Salem
!Sample_contact_state = NC
!Sample_contact_zip/postal_code = 27101
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN35166510
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX20432577
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE232836
!Sample_data_row_count = 0
^SAMPLE = GSM7384358
!Sample_title = OtC0380_H2O_Morphine_6
!Sample_geo_accession = GSM7384358
!Sample_status = Public on May 18 2023
!Sample_submission_date = May 18 2023
!Sample_last_update_date = Jun 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Nucleus accumbens (brain)
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: Nucleus accumbens (brain)
!Sample_characteristics_ch1 = Sex: male
!Sample_characteristics_ch1 = cell type: Bulk
!Sample_characteristics_ch1 = microbiome status: Normal Microbiome
!Sample_characteristics_ch1 = treatment: Morphine (20mg/kg/day/7 days)
!Sample_treatment_protocol_ch1 = Conventionally raised mice were the ones described in the published manuscript by Hofford et al. in 2021, thus all methods for conventional mice are identical to that manuscript (Hofford et al., 2021). The conventionally raised C57BL/6J mice (7-9 weeks old, Jackson Laboratories) were group-housed in a humidity, temperature-controlled, and specific pathogen-free colony facility on a 24 hour light/dark cycle (lights on at 7AM and lights off at 7PM). All studies were performed in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals under an approved protocol from the Mt. Sinai Icahn School of Medicine Institutional Animal Care and Use Committee.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted using TRIzol reagent (Thermo Fisher #15596026) according to manufacturer’s instructions.
!Sample_extract_protocol_ch1 = cDNA was generated using the SMARTer cDNA kit (Clonetech Laboratories # 634925) from total RNA. cDNA was fragmented using Bioruptor (Diagenode) and illumina-ready, indexed sequencing libraries were made using SPRIworks HT Reagent Kit (Beckamn Coulter, Inc. # B06938).
!Sample_data_processing = Raw FASTQ files were quality checked using  FASTQC (Babraham Institute, Cambridge, UK).
!Sample_data_processing = The raw FASTQ file for each sample was aligned to the Mus musculus 10 reference genome (NCBI) with the STAR package v2.4.0 (Dobin et al., 2013).
!Sample_data_processing = For pairwise comparisons aligned non-normalized read counts were analyzed for differential gene expression using the Biojupies analysis package with default settings (Torre et al., 2018). Statistical significance was set at a threshold of FDR-corrected p value of less than 0.05. Lists of significantly differentially expressed genes were analyzed for gene ontology pathways using G:Profiler (Raudvere et al., 2019)
!Sample_data_processing = Supplementary files format and content: comma separated-values (.csv)
!Sample_data_processing = Supplementary files format and content: Normalized read counts of genes. Normalization was performed using Trimmed Mean of the M-values (TMM; edgeR R package)
!Sample_platform_id = GPL17021
!Sample_contact_name = Drew,,Kiraly
!Sample_contact_email = dkiraly@wakehealth.edu
!Sample_contact_phone = 2032282275
!Sample_contact_department = Physiology, Pharmacology, Psychiatry
!Sample_contact_institute = Wake Forest University School of Medicine
!Sample_contact_address = 115 South Chestnut Street
!Sample_contact_city = Winston-Salem
!Sample_contact_state = NC
!Sample_contact_zip/postal_code = 27101
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN35166509
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX20432578
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE232836
!Sample_data_row_count = 0
^SAMPLE = GSM7384359
!Sample_title = OtC0381_Abx_Morphine_1
!Sample_geo_accession = GSM7384359
!Sample_status = Public on May 18 2023
!Sample_submission_date = May 18 2023
!Sample_last_update_date = Jun 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Nucleus accumbens (brain)
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: Nucleus accumbens (brain)
!Sample_characteristics_ch1 = Sex: male
!Sample_characteristics_ch1 = cell type: Bulk
!Sample_characteristics_ch1 = microbiome status: Depleted Microbiome
!Sample_characteristics_ch1 = treatment: Morphine (20mg/kg/day/7 days)
!Sample_treatment_protocol_ch1 = Conventionally raised mice were the ones described in the published manuscript by Hofford et al. in 2021, thus all methods for conventional mice are identical to that manuscript (Hofford et al., 2021). The conventionally raised C57BL/6J mice (7-9 weeks old, Jackson Laboratories) were group-housed in a humidity, temperature-controlled, and specific pathogen-free colony facility on a 24 hour light/dark cycle (lights on at 7AM and lights off at 7PM). All studies were performed in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals under an approved protocol from the Mt. Sinai Icahn School of Medicine Institutional Animal Care and Use Committee.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted using TRIzol reagent (Thermo Fisher #15596026) according to manufacturer’s instructions.
!Sample_extract_protocol_ch1 = cDNA was generated using the SMARTer cDNA kit (Clonetech Laboratories # 634925) from total RNA. cDNA was fragmented using Bioruptor (Diagenode) and illumina-ready, indexed sequencing libraries were made using SPRIworks HT Reagent Kit (Beckamn Coulter, Inc. # B06938).
!Sample_data_processing = Raw FASTQ files were quality checked using  FASTQC (Babraham Institute, Cambridge, UK).
!Sample_data_processing = The raw FASTQ file for each sample was aligned to the Mus musculus 10 reference genome (NCBI) with the STAR package v2.4.0 (Dobin et al., 2013).
!Sample_data_processing = For pairwise comparisons aligned non-normalized read counts were analyzed for differential gene expression using the Biojupies analysis package with default settings (Torre et al., 2018). Statistical significance was set at a threshold of FDR-corrected p value of less than 0.05. Lists of significantly differentially expressed genes were analyzed for gene ontology pathways using G:Profiler (Raudvere et al., 2019)
!Sample_data_processing = Supplementary files format and content: comma separated-values (.csv)
!Sample_data_processing = Supplementary files format and content: Normalized read counts of genes. Normalization was performed using Trimmed Mean of the M-values (TMM; edgeR R package)
!Sample_platform_id = GPL17021
!Sample_contact_name = Drew,,Kiraly
!Sample_contact_email = dkiraly@wakehealth.edu
!Sample_contact_phone = 2032282275
!Sample_contact_department = Physiology, Pharmacology, Psychiatry
!Sample_contact_institute = Wake Forest University School of Medicine
!Sample_contact_address = 115 South Chestnut Street
!Sample_contact_city = Winston-Salem
!Sample_contact_state = NC
!Sample_contact_zip/postal_code = 27101
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN35166508
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX20432579
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE232836
!Sample_data_row_count = 0
^SAMPLE = GSM7384360
!Sample_title = OtC0382_Abx_Morphine_2
!Sample_geo_accession = GSM7384360
!Sample_status = Public on May 18 2023
!Sample_submission_date = May 18 2023
!Sample_last_update_date = Jun 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Nucleus accumbens (brain)
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: Nucleus accumbens (brain)
!Sample_characteristics_ch1 = Sex: male
!Sample_characteristics_ch1 = cell type: Bulk
!Sample_characteristics_ch1 = microbiome status: Depleted Microbiome
!Sample_characteristics_ch1 = treatment: Morphine (20mg/kg/day/7 days)
!Sample_treatment_protocol_ch1 = Conventionally raised mice were the ones described in the published manuscript by Hofford et al. in 2021, thus all methods for conventional mice are identical to that manuscript (Hofford et al., 2021). The conventionally raised C57BL/6J mice (7-9 weeks old, Jackson Laboratories) were group-housed in a humidity, temperature-controlled, and specific pathogen-free colony facility on a 24 hour light/dark cycle (lights on at 7AM and lights off at 7PM). All studies were performed in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals under an approved protocol from the Mt. Sinai Icahn School of Medicine Institutional Animal Care and Use Committee.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted using TRIzol reagent (Thermo Fisher #15596026) according to manufacturer’s instructions.
!Sample_extract_protocol_ch1 = cDNA was generated using the SMARTer cDNA kit (Clonetech Laboratories # 634925) from total RNA. cDNA was fragmented using Bioruptor (Diagenode) and illumina-ready, indexed sequencing libraries were made using SPRIworks HT Reagent Kit (Beckamn Coulter, Inc. # B06938).
!Sample_data_processing = Raw FASTQ files were quality checked using  FASTQC (Babraham Institute, Cambridge, UK).
!Sample_data_processing = The raw FASTQ file for each sample was aligned to the Mus musculus 10 reference genome (NCBI) with the STAR package v2.4.0 (Dobin et al., 2013).
!Sample_data_processing = For pairwise comparisons aligned non-normalized read counts were analyzed for differential gene expression using the Biojupies analysis package with default settings (Torre et al., 2018). Statistical significance was set at a threshold of FDR-corrected p value of less than 0.05. Lists of significantly differentially expressed genes were analyzed for gene ontology pathways using G:Profiler (Raudvere et al., 2019)
!Sample_data_processing = Supplementary files format and content: comma separated-values (.csv)
!Sample_data_processing = Supplementary files format and content: Normalized read counts of genes. Normalization was performed using Trimmed Mean of the M-values (TMM; edgeR R package)
!Sample_platform_id = GPL17021
!Sample_contact_name = Drew,,Kiraly
!Sample_contact_email = dkiraly@wakehealth.edu
!Sample_contact_phone = 2032282275
!Sample_contact_department = Physiology, Pharmacology, Psychiatry
!Sample_contact_institute = Wake Forest University School of Medicine
!Sample_contact_address = 115 South Chestnut Street
!Sample_contact_city = Winston-Salem
!Sample_contact_state = NC
!Sample_contact_zip/postal_code = 27101
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN35166507
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX20432580
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE232836
!Sample_data_row_count = 0
^SAMPLE = GSM7384361
!Sample_title = OtC0383_Abx_Morphine_3
!Sample_geo_accession = GSM7384361
!Sample_status = Public on May 18 2023
!Sample_submission_date = May 18 2023
!Sample_last_update_date = Jun 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Nucleus accumbens (brain)
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: Nucleus accumbens (brain)
!Sample_characteristics_ch1 = Sex: male
!Sample_characteristics_ch1 = cell type: Bulk
!Sample_characteristics_ch1 = microbiome status: Depleted Microbiome
!Sample_characteristics_ch1 = treatment: Morphine (20mg/kg/day/7 days)
!Sample_treatment_protocol_ch1 = Conventionally raised mice were the ones described in the published manuscript by Hofford et al. in 2021, thus all methods for conventional mice are identical to that manuscript (Hofford et al., 2021). The conventionally raised C57BL/6J mice (7-9 weeks old, Jackson Laboratories) were group-housed in a humidity, temperature-controlled, and specific pathogen-free colony facility on a 24 hour light/dark cycle (lights on at 7AM and lights off at 7PM). All studies were performed in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals under an approved protocol from the Mt. Sinai Icahn School of Medicine Institutional Animal Care and Use Committee.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted using TRIzol reagent (Thermo Fisher #15596026) according to manufacturer’s instructions.
!Sample_extract_protocol_ch1 = cDNA was generated using the SMARTer cDNA kit (Clonetech Laboratories # 634925) from total RNA. cDNA was fragmented using Bioruptor (Diagenode) and illumina-ready, indexed sequencing libraries were made using SPRIworks HT Reagent Kit (Beckamn Coulter, Inc. # B06938).
!Sample_data_processing = Raw FASTQ files were quality checked using  FASTQC (Babraham Institute, Cambridge, UK).
!Sample_data_processing = The raw FASTQ file for each sample was aligned to the Mus musculus 10 reference genome (NCBI) with the STAR package v2.4.0 (Dobin et al., 2013).
!Sample_data_processing = For pairwise comparisons aligned non-normalized read counts were analyzed for differential gene expression using the Biojupies analysis package with default settings (Torre et al., 2018). Statistical significance was set at a threshold of FDR-corrected p value of less than 0.05. Lists of significantly differentially expressed genes were analyzed for gene ontology pathways using G:Profiler (Raudvere et al., 2019)
!Sample_data_processing = Supplementary files format and content: comma separated-values (.csv)
!Sample_data_processing = Supplementary files format and content: Normalized read counts of genes. Normalization was performed using Trimmed Mean of the M-values (TMM; edgeR R package)
!Sample_platform_id = GPL17021
!Sample_contact_name = Drew,,Kiraly
!Sample_contact_email = dkiraly@wakehealth.edu
!Sample_contact_phone = 2032282275
!Sample_contact_department = Physiology, Pharmacology, Psychiatry
!Sample_contact_institute = Wake Forest University School of Medicine
!Sample_contact_address = 115 South Chestnut Street
!Sample_contact_city = Winston-Salem
!Sample_contact_state = NC
!Sample_contact_zip/postal_code = 27101
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN35166506
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX20432581
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE232836
!Sample_data_row_count = 0
^SAMPLE = GSM7384362
!Sample_title = OtC0384_Abx_Morphine_4
!Sample_geo_accession = GSM7384362
!Sample_status = Public on May 18 2023
!Sample_submission_date = May 18 2023
!Sample_last_update_date = Jun 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Nucleus accumbens (brain)
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: Nucleus accumbens (brain)
!Sample_characteristics_ch1 = Sex: male
!Sample_characteristics_ch1 = cell type: Bulk
!Sample_characteristics_ch1 = microbiome status: Depleted Microbiome
!Sample_characteristics_ch1 = treatment: Morphine (20mg/kg/day/7 days)
!Sample_treatment_protocol_ch1 = Conventionally raised mice were the ones described in the published manuscript by Hofford et al. in 2021, thus all methods for conventional mice are identical to that manuscript (Hofford et al., 2021). The conventionally raised C57BL/6J mice (7-9 weeks old, Jackson Laboratories) were group-housed in a humidity, temperature-controlled, and specific pathogen-free colony facility on a 24 hour light/dark cycle (lights on at 7AM and lights off at 7PM). All studies were performed in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals under an approved protocol from the Mt. Sinai Icahn School of Medicine Institutional Animal Care and Use Committee.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted using TRIzol reagent (Thermo Fisher #15596026) according to manufacturer’s instructions.
!Sample_extract_protocol_ch1 = cDNA was generated using the SMARTer cDNA kit (Clonetech Laboratories # 634925) from total RNA. cDNA was fragmented using Bioruptor (Diagenode) and illumina-ready, indexed sequencing libraries were made using SPRIworks HT Reagent Kit (Beckamn Coulter, Inc. # B06938).
!Sample_data_processing = Raw FASTQ files were quality checked using  FASTQC (Babraham Institute, Cambridge, UK).
!Sample_data_processing = The raw FASTQ file for each sample was aligned to the Mus musculus 10 reference genome (NCBI) with the STAR package v2.4.0 (Dobin et al., 2013).
!Sample_data_processing = For pairwise comparisons aligned non-normalized read counts were analyzed for differential gene expression using the Biojupies analysis package with default settings (Torre et al., 2018). Statistical significance was set at a threshold of FDR-corrected p value of less than 0.05. Lists of significantly differentially expressed genes were analyzed for gene ontology pathways using G:Profiler (Raudvere et al., 2019)
!Sample_data_processing = Supplementary files format and content: comma separated-values (.csv)
!Sample_data_processing = Supplementary files format and content: Normalized read counts of genes. Normalization was performed using Trimmed Mean of the M-values (TMM; edgeR R package)
!Sample_platform_id = GPL17021
!Sample_contact_name = Drew,,Kiraly
!Sample_contact_email = dkiraly@wakehealth.edu
!Sample_contact_phone = 2032282275
!Sample_contact_department = Physiology, Pharmacology, Psychiatry
!Sample_contact_institute = Wake Forest University School of Medicine
!Sample_contact_address = 115 South Chestnut Street
!Sample_contact_city = Winston-Salem
!Sample_contact_state = NC
!Sample_contact_zip/postal_code = 27101
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN35166505
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX20432582
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE232836
!Sample_data_row_count = 0
^SAMPLE = GSM7384363
!Sample_title = OtC0385_Abx_Morphine_5
!Sample_geo_accession = GSM7384363
!Sample_status = Public on May 18 2023
!Sample_submission_date = May 18 2023
!Sample_last_update_date = Jun 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Nucleus accumbens (brain)
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: Nucleus accumbens (brain)
!Sample_characteristics_ch1 = Sex: male
!Sample_characteristics_ch1 = cell type: Bulk
!Sample_characteristics_ch1 = microbiome status: Depleted Microbiome
!Sample_characteristics_ch1 = treatment: Morphine (20mg/kg/day/7 days)
!Sample_treatment_protocol_ch1 = Conventionally raised mice were the ones described in the published manuscript by Hofford et al. in 2021, thus all methods for conventional mice are identical to that manuscript (Hofford et al., 2021). The conventionally raised C57BL/6J mice (7-9 weeks old, Jackson Laboratories) were group-housed in a humidity, temperature-controlled, and specific pathogen-free colony facility on a 24 hour light/dark cycle (lights on at 7AM and lights off at 7PM). All studies were performed in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals under an approved protocol from the Mt. Sinai Icahn School of Medicine Institutional Animal Care and Use Committee.
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = RNA was extracted using TRIzol reagent (Thermo Fisher #15596026) according to manufacturer’s instructions.
!Sample_extract_protocol_ch1 = cDNA was generated using the SMARTer cDNA kit (Clonetech Laboratories # 634925) from total RNA. cDNA was fragmented using Bioruptor (Diagenode) and illumina-ready, indexed sequencing libraries were made using SPRIworks HT Reagent Kit (Beckamn Coulter, Inc. # B06938).
!Sample_data_processing = Raw FASTQ files were quality checked using  FASTQC (Babraham Institute, Cambridge, UK).
!Sample_data_processing = The raw FASTQ file for each sample was aligned to the Mus musculus 10 reference genome (NCBI) with the STAR package v2.4.0 (Dobin et al., 2013).
!Sample_data_processing = For pairwise comparisons aligned non-normalized read counts were analyzed for differential gene expression using the Biojupies analysis package with default settings (Torre et al., 2018). Statistical significance was set at a threshold of FDR-corrected p value of less than 0.05. Lists of significantly differentially expressed genes were analyzed for gene ontology pathways using G:Profiler (Raudvere et al., 2019)
!Sample_data_processing = Supplementary files format and content: comma separated-values (.csv)
!Sample_data_processing = Supplementary files format and content: Normalized read counts of genes. Normalization was performed using Trimmed Mean of the M-values (TMM; edgeR R package)
!Sample_platform_id = GPL17021
!Sample_contact_name = Drew,,Kiraly
!Sample_contact_email = dkiraly@wakehealth.edu
!Sample_contact_phone = 2032282275
!Sample_contact_department = Physiology, Pharmacology, Psychiatry
!Sample_contact_institute = Wake Forest University School of Medicine
!Sample_contact_address = 115 South Chestnut Street
!Sample_contact_city = Winston-Salem
!Sample_contact_state = NC
!Sample_contact_zip/postal_code = 27101
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN35166504
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX20432583
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE232836
!Sample_data_row_count = 0
