!Series_title	"Chronic opioid treatment arrests neurodevelopment and alters synaptic activity in human midbrain organoids"
!Series_geo_accession	"GSE260711"
!Series_status	"Public on Mar 05 2024"
!Series_submission_date	"Mar 01 2024"
!Series_last_update_date	"Jun 26 2024"
!Series_pubmed_id	"38549185"
!Series_summary	"Understanding the impact of long-term opioid exposure on the embryonic brain is critical due to the surging number of pregnant mothers with opioid dependency, but has been limited by human brain inaccessibility and cross-species differences in animal models. Here we establish a human midbrain model that uses hiPSC-derived midbrain organoids and apply it to assess cell-type-specific responses to acute and chronic fentanyl treatment and fentanyl withdrawal. Single-cell mRNA sequencing of 25,510 cells from organoids in different treatment groups indicated that chronic fentanyl treatment arrests neuronal subtype specification during early midbrain development and alters synaptic activity and neuron projection. In contrast, acute fentanyl treatment increases dopamine release but does not significantly alter gene expression related to cell lineage development. These results provide the first examination of the effects of opioid exposure on human midbrain development at the single cell level."
!Series_overall_design	"Midbrain organoids derived from human FA11 iPSC cells were cultured and later treated with or without fentanyl. The acute treatment with Fentanyl was administered at a concentration of 74nM for a duration of 4 hours , on day 53 (KH002_D53_AC_FTY). The chronic treatment with Fentanyl was administered at a concentration of 74nM for a duration of 77 days, from Day 1 to Day 77 (KH004_D77_FTY). Withdrawal sample was treated with Fentanyl (74nM for 77 days, Day 1 to Day 77) and then replaced with fresh media for 2 days (KH005_D79_WD)."
!Series_type	"Expression profiling by high throughput sequencing"
!Series_contributor	"Kim,,Hye Sung"
!Series_contributor	"Xiao,,Yang"
!Series_contributor	"Xu,,Bin"
!Series_contributor	"Leong,,Kam"
!Series_sample_id	"GSM8122883 GSM8122884 GSM8122885 GSM8122886 GSM8122887 "
!Series_contact_name	"Kam,,Leong"
!Series_contact_laboratory	"Kam Leong Lab"
!Series_contact_department	"Biomedical Engineering"
!Series_contact_institute	"Columbia University"
!Series_contact_address	"3600 Broadway, RM450C"
!Series_contact_city	"New York"
!Series_contact_state	"NY"
!Series_contact_zip/postal_code	"10032"
!Series_contact_country	"USA"
!Series_supplementary_file	"ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE260nnn/GSE260711/suppl/GSE260711_RAW.tar"
!Series_platform_id	"GPL24676"
!Series_platform_taxid	"9606"
!Series_sample_taxid	"9606"
!Series_relation	"BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1082742"

!Sample_title	"KH001_D53_UT"	"KH002_D53_AC_FTY"	"KH003_D77_UT"	"KH004_D77_FTY"	"KH005_D79_WD"
!Sample_geo_accession	"GSM8122883"	"GSM8122884"	"GSM8122885"	"GSM8122886"	"GSM8122887"
!Sample_status	"Public on Mar 05 2024"	"Public on Mar 05 2024"	"Public on Mar 05 2024"	"Public on Mar 05 2024"	"Public on Mar 05 2024"
!Sample_submission_date	"Mar 01 2024"	"Mar 01 2024"	"Mar 01 2024"	"Mar 01 2024"	"Mar 01 2024"
!Sample_last_update_date	"Mar 05 2024"	"Mar 05 2024"	"Mar 05 2024"	"Mar 05 2024"	"Mar 05 2024"
!Sample_type	"SRA"	"SRA"	"SRA"	"SRA"	"SRA"
!Sample_channel_count	"1"	"1"	"1"	"1"	"1"
!Sample_source_name_ch1	"Midbrain Organoids"	"Midbrain Organoids"	"Midbrain Organoids"	"Midbrain Organoids"	"Midbrain Organoids"
!Sample_organism_ch1	"Homo sapiens"	"Homo sapiens"	"Homo sapiens"	"Homo sapiens"	"Homo sapiens"
!Sample_characteristics_ch1	"tissue: Midbrain Organoids"	"tissue: Midbrain Organoids"	"tissue: Midbrain Organoids"	"tissue: Midbrain Organoids"	"tissue: Midbrain Organoids"
!Sample_characteristics_ch1	"cell line: FA11"	"cell line: FA11"	"cell line: FA11"	"cell line: FA11"	"cell line: FA11"
!Sample_characteristics_ch1	"cell type: Midbrain Organoids"	"cell type: Midbrain Organoids"	"cell type: Midbrain Organoids"	"cell type: Midbrain Organoids"	"cell type: Midbrain Organoids"
!Sample_characteristics_ch1	"time: Day 53"	"time: Day 53"	"time: Day 77"	"time: Day 77"	"time: Day 79"
!Sample_characteristics_ch1	"fentanyl treatment: Untreated"	"fentanyl treatment: Yes"	"fentanyl treatment: Untreated"	"fentanyl treatment: Yes"	"fentanyl treatment: Yes"
!Sample_characteristics_ch1	"fentanyl treatment_duration: 0"	"fentanyl treatment_duration: 4 Hours"	"fentanyl treatment_duration: 0"	"fentanyl treatment_duration: 77 Days"	"fentanyl treatment_duration: 77 Days"
!Sample_treatment_protocol_ch1	"Midbrain organoids derived from human FA11 iPSC cells were cultured and later treated with or without fentanyl. The acute treatment with Fentanyl was administered at a concentration of 74nM for a duration of 4 hours , on day 53 (KH002_D53_AC_FTY). The chronic treatment with Fentanyl was administered at a concentration of 74nM for a duration of 77 days, from Day 1 to Day 77 (KH004_D77_FTY). Withdrawal sample was treated with Fentanyl (74nM for 77 days, Day 1 to Day 77) and then replaced with fresh media for 2 days (KH005_D79_WD)."	"Midbrain organoids derived from human FA11 iPSC cells were cultured and later treated with or without fentanyl. The acute treatment with Fentanyl was administered at a concentration of 74nM for a duration of 4 hours , on day 53 (KH002_D53_AC_FTY). The chronic treatment with Fentanyl was administered at a concentration of 74nM for a duration of 77 days, from Day 1 to Day 77 (KH004_D77_FTY). Withdrawal sample was treated with Fentanyl (74nM for 77 days, Day 1 to Day 77) and then replaced with fresh media for 2 days (KH005_D79_WD)."	"Midbrain organoids derived from human FA11 iPSC cells were cultured and later treated with or without fentanyl. The acute treatment with Fentanyl was administered at a concentration of 74nM for a duration of 4 hours , on day 53 (KH002_D53_AC_FTY). The chronic treatment with Fentanyl was administered at a concentration of 74nM for a duration of 77 days, from Day 1 to Day 77 (KH004_D77_FTY). Withdrawal sample was treated with Fentanyl (74nM for 77 days, Day 1 to Day 77) and then replaced with fresh media for 2 days (KH005_D79_WD)."	"Midbrain organoids derived from human FA11 iPSC cells were cultured and later treated with or without fentanyl. The acute treatment with Fentanyl was administered at a concentration of 74nM for a duration of 4 hours , on day 53 (KH002_D53_AC_FTY). The chronic treatment with Fentanyl was administered at a concentration of 74nM for a duration of 77 days, from Day 1 to Day 77 (KH004_D77_FTY). Withdrawal sample was treated with Fentanyl (74nM for 77 days, Day 1 to Day 77) and then replaced with fresh media for 2 days (KH005_D79_WD)."	"Midbrain organoids derived from human FA11 iPSC cells were cultured and later treated with or without fentanyl. The acute treatment with Fentanyl was administered at a concentration of 74nM for a duration of 4 hours , on day 53 (KH002_D53_AC_FTY). The chronic treatment with Fentanyl was administered at a concentration of 74nM for a duration of 77 days, from Day 1 to Day 77 (KH004_D77_FTY). Withdrawal sample was treated with Fentanyl (74nM for 77 days, Day 1 to Day 77) and then replaced with fresh media for 2 days (KH005_D79_WD)."
!Sample_growth_protocol_ch1	"Generation of midbrain organoids was explained in detail in the manuscript Methods session."	"Generation of midbrain organoids was explained in detail in the manuscript Methods session."	"Generation of midbrain organoids was explained in detail in the manuscript Methods session."	"Generation of midbrain organoids was explained in detail in the manuscript Methods session."	"Generation of midbrain organoids was explained in detail in the manuscript Methods session."
!Sample_molecule_ch1	"total RNA"	"total RNA"	"total RNA"	"total RNA"	"total RNA"
!Sample_extract_protocol_ch1	"Five independent samples of midbrain organoids were gently dissociated to single cells with papain enzymatic dissociation (Worthington Biochemical Corporation). After filtering cell clumps with a cell strainer (35 µm mesh), suspended single cells were encapsulated with barcoded beads in oil droplets by 10X Genomics Chromium technology."	"Five independent samples of midbrain organoids were gently dissociated to single cells with papain enzymatic dissociation (Worthington Biochemical Corporation). After filtering cell clumps with a cell strainer (35 µm mesh), suspended single cells were encapsulated with barcoded beads in oil droplets by 10X Genomics Chromium technology."	"Five independent samples of midbrain organoids were gently dissociated to single cells with papain enzymatic dissociation (Worthington Biochemical Corporation). After filtering cell clumps with a cell strainer (35 µm mesh), suspended single cells were encapsulated with barcoded beads in oil droplets by 10X Genomics Chromium technology."	"Five independent samples of midbrain organoids were gently dissociated to single cells with papain enzymatic dissociation (Worthington Biochemical Corporation). After filtering cell clumps with a cell strainer (35 µm mesh), suspended single cells were encapsulated with barcoded beads in oil droplets by 10X Genomics Chromium technology."	"Five independent samples of midbrain organoids were gently dissociated to single cells with papain enzymatic dissociation (Worthington Biochemical Corporation). After filtering cell clumps with a cell strainer (35 µm mesh), suspended single cells were encapsulated with barcoded beads in oil droplets by 10X Genomics Chromium technology."
!Sample_extract_protocol_ch1	"Library was performed according to the manufacter’s instructions (Chromium single cell 3’ v2 protocol, 10x Genomics)."	"Library was performed according to the manufacter’s instructions (Chromium single cell 3’ v2 protocol, 10x Genomics)."	"Library was performed according to the manufacter’s instructions (Chromium single cell 3’ v2 protocol, 10x Genomics)."	"Library was performed according to the manufacter’s instructions (Chromium single cell 3’ v2 protocol, 10x Genomics)."	"Library was performed according to the manufacter’s instructions (Chromium single cell 3’ v2 protocol, 10x Genomics)."
!Sample_taxid_ch1	"9606"	"9606"	"9606"	"9606"	"9606"
!Sample_description	"Chromium 10x Genomics"	"Chromium 10x Genomics"	"Chromium 10x Genomics"	"Chromium 10x Genomics"	"Chromium 10x Genomics"
!Sample_data_processing	"The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0."	"The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0."	"The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0."	"The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0."	"The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0."
!Sample_data_processing	"Assembly: GRCh38"	"Assembly: GRCh38"	"Assembly: GRCh38"	"Assembly: GRCh38"	"Assembly: GRCh38"
!Sample_data_processing	"Supplementary files format and content: Expression matrix of each sample."	"Supplementary files format and content: Expression matrix of each sample."	"Supplementary files format and content: Expression matrix of each sample."	"Supplementary files format and content: Expression matrix of each sample."	"Supplementary files format and content: Expression matrix of each sample."
!Sample_data_processing	"Supplementary files format and content: For each sample, ""features.tsv.gz"" corresponded to gene names. ""barcodes.tsv.gz"" corresponded to cell barcodes. ""matrix.mtx.gz"" was the expression counts in sparce matrix."	"Supplementary files format and content: For each sample, ""features.tsv.gz"" corresponded to gene names. ""barcodes.tsv.gz"" corresponded to cell barcodes. ""matrix.mtx.gz"" was the expression counts in sparce matrix."	"Supplementary files format and content: For each sample, ""features.tsv.gz"" corresponded to gene names. ""barcodes.tsv.gz"" corresponded to cell barcodes. ""matrix.mtx.gz"" was the expression counts in sparce matrix."	"Supplementary files format and content: For each sample, ""features.tsv.gz"" corresponded to gene names. ""barcodes.tsv.gz"" corresponded to cell barcodes. ""matrix.mtx.gz"" was the expression counts in sparce matrix."	"Supplementary files format and content: For each sample, ""features.tsv.gz"" corresponded to gene names. ""barcodes.tsv.gz"" corresponded to cell barcodes. ""matrix.mtx.gz"" was the expression counts in sparce matrix."
!Sample_platform_id	"GPL24676"	"GPL24676"	"GPL24676"	"GPL24676"	"GPL24676"
!Sample_contact_name	"Kam,,Leong"	"Kam,,Leong"	"Kam,,Leong"	"Kam,,Leong"	"Kam,,Leong"
!Sample_contact_laboratory	"Kam Leong Lab"	"Kam Leong Lab"	"Kam Leong Lab"	"Kam Leong Lab"	"Kam Leong Lab"
!Sample_contact_department	"Biomedical Engineering"	"Biomedical Engineering"	"Biomedical Engineering"	"Biomedical Engineering"	"Biomedical Engineering"
!Sample_contact_institute	"Columbia University"	"Columbia University"	"Columbia University"	"Columbia University"	"Columbia University"
!Sample_contact_address	"3600 Broadway, RM450C"	"3600 Broadway, RM450C"	"3600 Broadway, RM450C"	"3600 Broadway, RM450C"	"3600 Broadway, RM450C"
!Sample_contact_city	"New York"	"New York"	"New York"	"New York"	"New York"
!Sample_contact_state	"NY"	"NY"	"NY"	"NY"	"NY"
!Sample_contact_zip/postal_code	"10032"	"10032"	"10032"	"10032"	"10032"
!Sample_contact_country	"USA"	"USA"	"USA"	"USA"	"USA"
!Sample_data_row_count	"0"	"0"	"0"	"0"	"0"
!Sample_instrument_model	"Illumina NovaSeq 6000"	"Illumina NovaSeq 6000"	"Illumina NovaSeq 6000"	"Illumina NovaSeq 6000"	"Illumina NovaSeq 6000"
!Sample_library_selection	"cDNA"	"cDNA"	"cDNA"	"cDNA"	"cDNA"
!Sample_library_source	"transcriptomic single cell"	"transcriptomic single cell"	"transcriptomic single cell"	"transcriptomic single cell"	"transcriptomic single cell"
!Sample_library_strategy	"RNA-Seq"	"RNA-Seq"	"RNA-Seq"	"RNA-Seq"	"RNA-Seq"
!Sample_relation	"BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN40217978"	"BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN40217977"	"BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN40217976"	"BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN40217975"	"BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN40217974"
!Sample_relation	"SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX23811848"	"SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX23811849"	"SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX23811850"	"SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX23811851"	"SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX23811852"
!Sample_supplementary_file_1	"ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM8122nnn/GSM8122883/suppl/GSM8122883_KH001_barcodes.tsv.gz"	"ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM8122nnn/GSM8122884/suppl/GSM8122884_KH002_barcodes.tsv.gz"	"ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM8122nnn/GSM8122885/suppl/GSM8122885_KH003_barcodes.tsv.gz"	"ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM8122nnn/GSM8122886/suppl/GSM8122886_KH004_barcodes.tsv.gz"	"ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM8122nnn/GSM8122887/suppl/GSM8122887_KH005_barcodes.tsv.gz"
!Sample_supplementary_file_2	"ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM8122nnn/GSM8122883/suppl/GSM8122883_KH001_features.tsv.gz"	"ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM8122nnn/GSM8122884/suppl/GSM8122884_KH002_features.tsv.gz"	"ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM8122nnn/GSM8122885/suppl/GSM8122885_KH003_features.tsv.gz"	"ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM8122nnn/GSM8122886/suppl/GSM8122886_KH004_features.tsv.gz"	"ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM8122nnn/GSM8122887/suppl/GSM8122887_KH005_features.tsv.gz"
!Sample_supplementary_file_3	"ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM8122nnn/GSM8122883/suppl/GSM8122883_KH001_matrix.mtx.gz"	"ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM8122nnn/GSM8122884/suppl/GSM8122884_KH002_matrix.mtx.gz"	"ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM8122nnn/GSM8122885/suppl/GSM8122885_KH003_matrix.mtx.gz"	"ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM8122nnn/GSM8122886/suppl/GSM8122886_KH004_matrix.mtx.gz"	"ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM8122nnn/GSM8122887/suppl/GSM8122887_KH005_matrix.mtx.gz"
!series_matrix_table_begin
"ID_REF"	"GSM8122883"	"GSM8122884"	"GSM8122885"	"GSM8122886"	"GSM8122887"
!series_matrix_table_end
