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Sample GSM3596322 Query DataSets for GSM3596322
Status Public on Jun 09, 2019
Title GM12878-GM18502 MIXTURE
Sample type SRA
Source name LCL cell line
Organism Homo sapiens
Characteristics cell type: LCL
cell line: GM12878-GM18502
Biomaterial provider Coriell Cell Repositories
Coriell Cell Repositories
Growth protocol GM12878 and GM18502 were purchased from the Coriell Institute for Medical Research. Cells were cultured in the Roswell Park Memorial Institute (RPMI) Medium 1640 supplemented with 2mM L-glutamine and 20% of non-inactivated fetal bovine serum in T25 tissue culture flasks. Flasks with 20 mL medium were incubated on upright position at 37°C under 5% carbon dioxide. Cell cultures were split every three days for maintenance.
Extracted molecule polyA RNA
Extraction protocol Single-cell sample preparation was conducted according to Sample Preparation Demonstrated Protocol provided by 10X Genomics as follows: 1 mL of cell suspensions from each cell line (day 4, stable phase) was pelleted in Eppendorf tubes by centrifugation (400g, 5min). The supernatant was discarded, and the cells pellet was then resuspended in 1X PBS with 0.04% BSA, followed by two washing procedures by centrifugation (150g, 3min). After the second wash, cells were resuspended in ~500 uL 1X PBS with 0.04% BSA followed by gently pipetting mix 10-15 times.
Libraries were prepared using the Chromium Controller (10X Genomics, CA) in conjunction with the single-cell 3’ v2 kit. Briefly, the cell suspensions were diluted in nuclease-free water according to manufacturer instructions to achieve a targeted cell count of 5,000 for each cell line. The cDNA synthesis, barcoding and library preparation were then carried out according to the manufacturer's instructions. Libraries were sequenced in the North Texas Genome Center facilities on a Novaseq 6000 sequencer (Illumina, San Diego).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Data processing Mapping of reads to transcripts and cells
Quality Control
Cell cycle phase and population assignment
Genome_build: hg38
Supplementary_files_format_and_content: QC files include common quality control measures for scRNA-Seq including UMI count per cell and percentage of mitochondrial transcripts. Barcodes, Genes and Matrix files are the output of the 10X pipeline.
Submission date Feb 08, 2019
Last update date Sep 20, 2019
Contact name Daniel Camilo Osorio
Organization name The University of Texas at Austin
Street address 1601 Trinity St
City Austin
State/province TX
ZIP/Postal code 78701
Country USA
Platform ID GPL24676
Series (1)
GSE126321 Single-cell RNA sequencing of lymphoblastoid cell lines of European and African ancestries
BioSample SAMN10904683
SRA SRX5353464

Supplementary file Size Download File type/resource
GSM3596322_MIX_barcodes.tsv.gz 23.3 Kb (ftp)(http) TSV
GSM3596322_MIX_cellLineage.tsv.gz 26.2 Kb (ftp)(http) TSV
GSM3596322_MIX_cellQC.tsv.gz 71.5 Kb (ftp)(http) TSV
GSM3596322_MIX_genes.tsv.gz 258.6 Kb (ftp)(http) TSV
GSM3596322_MIX_matrix.mtx.gz 63.0 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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