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Sample GSM4782043 Query DataSets for GSM4782043
Status Public on Sep 30, 2020
Title Mal_Subject 1_VDJ+GEX scRNA-seq
Sample type SRA
 
Source name Peripheral mononuclear blood cells (PBMCs)
Organism Homo sapiens
Characteristics disease state: Malaria
age: 18 years
Sex: Female
tissue: Blood
Growth protocol Peripheral blood draw was done, and mononuclear cells were isolated by ficoll gradient purification. B cells were isolated with the EasySep Human B cell isolation kit on a RoboSep platform
Extracted molecule total RNA
Extraction protocol Cells were encapsulated in droplets using the Chromium Controller (10X Genomics). Reverse transcription and cDNA amplification were performed using the Chromium Single Cell 5’ kit (10X Genomics). All steps were done according to manufacturer’s instructions. 100 ng of cDNA (25% of generated cDNA) was used as input for library preparation.
Libraries were sequenced using the Illumina Hiseq3000 platform 8 lanes of sequencing at 26bp-8bp-98bp according to 10X Genomics sequencing recommendations.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing The sample replicates were split into 8 Hiseq 2500 sequencing anes and library pool contained 1/10 of VDJ and 9/10 of gene expression.S1 flow cell for sequencing. Count matrix and VDJ contig files were generated using Cell Ranger v3.0 (10X Genomics). Further, the resultant counts matrices were processed using an inhouse single-cell RNA-seq pipeline that uses Seurat v 3.0
Genome_build: Human - hg38
Supplementary_files_format_and_content: CSV files are generated from CellrangerV3.0 and Integrated matrix file is generated by integrating VDJ contig file with the gene expression matrix SeuratV3.0
 
Submission date Sep 15, 2020
Last update date Mar 29, 2021
Contact name Arun Boddapati
E-mail(s) [email protected]
Organization name Yerkes National Primate research center
Department Genomics Core
Street address 954 Gatewood Road, NE
City Atlanta
State/province GA
ZIP/Postal code 30329
Country USA
 
Platform ID GPL21290
Series (2)
GSE149729 Chronic Malaria drives functional heterogenity in B cell subpopilations and expansion of unswitched atypical memory B cells
GSE157967 Shared transcriptional profiles at the single cell level of atypical memory B cells suggest common drivers of expansion and function in malaria, HIV and autoimmune diseases [Malaria VDJ+GEX scRNA-seq]
Relations
BioSample SAMN16134304

Supplementary file Size Download File type/resource
GSM4782043_VDJ_Mal_subject1.csv.gz 41.0 Mb (ftp)(http) CSV
Processed data provided as supplementary file
Raw data not provided for this record

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