!Series_title	"Single cell transcriptomics reveals opioid usage evokes widespread suppression of antiviral gene program"
!Series_geo_accession	"GSE128879"
!Series_status	"Public on Apr 12 2020"
!Series_submission_date	"Mar 26 2019"
!Series_last_update_date	"Jun 08 2020"
!Series_pubmed_id	"32457298"
!Series_summary	"We report scRNA-seq of in vitro morphine treated PBMCs reveals suppression of anti-viral genes in various immune cell types."
!Series_overall_design	"PBMCs were treated in vitro with morphine for 24 hours, followed by LPS stimulation for 3 hours in vitro. We have used an antibody-based cell hashing technique to multiplex samples in droplet based scRNA-seq."
!Series_type	"Expression profiling by high throughput sequencing"
!Series_contributor	"Tanya,T,Karagiannis"
!Series_contributor	"John,P,Cleary Jr"
!Series_sample_id	"GSM3687893 GSM3687894 "
!Series_contact_name	"Christine,,Cheng"
!Series_contact_email	"chcheng@bu.eu"
!Series_contact_phone	"6173583123"
!Series_contact_institute	"Boston University"
!Series_contact_address	"24 Cummington Mall"
!Series_contact_city	"Boston"
!Series_contact_state	"Massachusetts"
!Series_contact_zip/postal_code	"02215"
!Series_contact_country	"USA"
!Series_supplementary_file	"ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE128nnn/GSE128879/suppl/GSE128879_RAW.tar"
!Series_platform_id	"GPL18573"
!Series_platform_taxid	"9606"
!Series_sample_taxid	"9606"
!Series_relation	"BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA529204"
!Series_relation	"SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP189483"

!Sample_title	"Morphine-RNA-UMI"	"Morphine-HTO"
!Sample_geo_accession	"GSM3687893"	"GSM3687894"
!Sample_status	"Public on Apr 12 2020"	"Public on Apr 12 2020"
!Sample_submission_date	"Mar 26 2019"	"Mar 26 2019"
!Sample_last_update_date	"Apr 14 2020"	"Apr 14 2020"
!Sample_type	"SRA"	"SRA"
!Sample_channel_count	"1"	"1"
!Sample_source_name_ch1	"Peripheral blood mononuclear cells"	"Peripheral blood mononuclear cells"
!Sample_organism_ch1	"Homo sapiens"	"Homo sapiens"
!Sample_characteristics_ch1	"cell type: Peripheral blood mononuclear cells"	"cell type: Peripheral blood mononuclear cells"
!Sample_characteristics_ch1	"antibodies/tags: none"	"antibodies/tags: Mock, +Morphine,Mock+LPS, +Mor+LPS"
!Sample_treatment_protocol_ch1	"400K cells per condition were revived, plated into non-tissue-culture-treated 96 well plates, and either mock treated or treated with morphine sulfate (100uM) alone for 24 hours. At the end of the incubation period cells were again treated either with medium or LPS for 3 hours, after which they were collected, washed, and each sample was “hashed” using unique oligonucleotide-barcoded antibodies to track the cells’ well/condition of origin. Samples were then normalized to 1000 cells/uL, mixed in equal measure (20uL each), and used to perform the Chromium Single Cell 3’ scRNA-seq method as described previously. Additional primers were included in the cDNA amplification step to account for the TotalSeq oligonucleotide tags. During the post-amplification cleanup, supernatant containing amplified TotalSeq tags was collected and processed parallel to the standard 10X library fraction."	"400K cells per condition were revived, plated into non-tissue-culture-treated 96 well plates, and either mock treated or treated with morphine sulfate (100uM) alone for 24 hours. At the end of the incubation period cells were again treated either with medium or LPS for 3 hours, after which they were collected, washed, and each sample was “hashed” using unique oligonucleotide-barcoded antibodies to track the cells’ well/condition of origin. Samples were then normalized to 1000 cells/uL, mixed in equal measure (20uL each), and used to perform the Chromium Single Cell 3’ scRNA-seq method as described previously. Additional primers were included in the cDNA amplification step to account for the TotalSeq oligonucleotide tags. During the post-amplification cleanup, supernatant containing amplified TotalSeq tags was collected and processed parallel to the standard 10X library fraction."
!Sample_molecule_ch1	"total RNA"	"total RNA"
!Sample_extract_protocol_ch1	"15 mL of fresh whole blood from healthy donors (Research Blood Components, Boston MA) was diluted 1:1 with warm PBS +2% FBS, mixed, and gently layered atop 30mL Ficoll-Paque density gradient medium (GE Healthcare, Ficoll Paque PLUS, Cat# 17-1440) in 50mL conical tubes. This process was repeated 7 times in processing 100mL of blood. Tubes were centrifuged for 20 min at 1200xg to separate leukocytes from red blood cells and plasma. The leukocyte-containing buffy coat was carefully transferred into new tubes, washed with warm PBS +2% FBS, counted, resuspended in DMSO and aliquoted. Isolated cells were then stored in liquid nitrogen until later experimental use."	"15 mL of fresh whole blood from healthy donors (Research Blood Components, Boston MA) was diluted 1:1 with warm PBS +2% FBS, mixed, and gently layered atop 30mL Ficoll-Paque density gradient medium (GE Healthcare, Ficoll Paque PLUS, Cat# 17-1440) in 50mL conical tubes. This process was repeated 7 times in processing 100mL of blood. Tubes were centrifuged for 20 min at 1200xg to separate leukocytes from red blood cells and plasma. The leukocyte-containing buffy coat was carefully transferred into new tubes, washed with warm PBS +2% FBS, counted, resuspended in DMSO and aliquoted. Isolated cells were then stored in liquid nitrogen until later experimental use."
!Sample_extract_protocol_ch1	"scRNA-seq libraries were prepared following Chromium Single Cell 3’ scRNA-seq method. Additional primers were included in the cDNA amplification step to account for the TotalSeq oligonucleotide tags. During the post-amplification cleanup, supernatant containing amplified TotalSeq tags was collected and processed parallel to the standard 10X library fraction."	"scRNA-seq libraries were prepared following Chromium Single Cell 3’ scRNA-seq method. Additional primers were included in the cDNA amplification step to account for the TotalSeq oligonucleotide tags. During the post-amplification cleanup, supernatant containing amplified TotalSeq tags was collected and processed parallel to the standard 10X library fraction."
!Sample_extract_protocol_ch1	"10x Genomics single cell 3' v2"	"10x Genomics single cell 3' v2"
!Sample_taxid_ch1	"9606"	"9606"
!Sample_description	"10x Genomics single cell 3' v2"	"10x Genomics single cell 3' v2"
!Sample_description	"Read 1 includes the cell barcode while Read 2 contains the cDNA fragment."	"Read 1 contains the cell barcodes while Read 2 contains the antibody/sample barcode."
!Sample_data_processing	"Each sequencing library was demultiplexed based on the sample index read and HTO barcode to generate FASTQ files for the RNA and HTO pair-end reads using Cell Ranger version 2.1.
"	"Each sequencing library was demultiplexed based on the sample index read and HTO barcode to generate FASTQ files for the RNA and HTO pair-end reads using Cell Ranger version 2.1.
"
!Sample_data_processing	"Gene-cell barcode matrices for RNA count data were generated using 10X genomics Cell Ranger 2.1
"	"Gene-cell barcode matrices for RNA count data were generated using 10X genomics Cell Ranger 2.1
"
!Sample_data_processing	"HTO count data were generated using Cite-seq-Count with reference HTO list
"	"HTO count data were generated using Cite-seq-Count with reference HTO list
"
!Sample_data_processing	"Genome_build: GRCh38
"	"Genome_build: GRCh38
"
!Sample_data_processing	"Supplementary_files_format_and_content: tab-delimited file for 10X RNA-UMI count data; comma-delimited file for HTO count data"	"Supplementary_files_format_and_content: tab-delimited file for 10X RNA-UMI count data; comma-delimited file for HTO count data"
!Sample_platform_id	"GPL18573"	"GPL18573"
!Sample_contact_name	"Christine,,Cheng"	"Christine,,Cheng"
!Sample_contact_email	"chcheng@bu.eu"	"chcheng@bu.eu"
!Sample_contact_phone	"6173583123"	"6173583123"
!Sample_contact_institute	"Boston University"	"Boston University"
!Sample_contact_address	"24 Cummington Mall"	"24 Cummington Mall"
!Sample_contact_city	"Boston"	"Boston"
!Sample_contact_state	"Massachusetts"	"Massachusetts"
!Sample_contact_zip/postal_code	"02215"	"02215"
!Sample_contact_country	"USA"	"USA"
!Sample_data_row_count	"0"	"0"
!Sample_instrument_model	"Illumina NextSeq 500"	"Illumina NextSeq 500"
!Sample_library_selection	"cDNA"	"cDNA"
!Sample_library_source	"transcriptomic"	"transcriptomic"
!Sample_library_strategy	"RNA-Seq"	"RNA-Seq"
!Sample_relation	"BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN11258657"	"BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN11258656"
!Sample_relation	"SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX5577083"	"SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX5577084"
!Sample_supplementary_file_1	"ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3687nnn/GSM3687893/suppl/GSM3687893_Morphine_RNA_count.txt.gz"	"ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3687nnn/GSM3687894/suppl/GSM3687894_Morphine_HTO_count.csv.gz"
!series_matrix_table_begin
"ID_REF"	"GSM3687893"	"GSM3687894"
!series_matrix_table_end
