GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE96583 Query DataSets for GSE96583
Status Public on Jun 13, 2017
Title Multiplexing droplet-based single cell RNA-sequencing using genetic barcodes
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Here, we introduce an in-silico algorithm demuxlet that harnesses naturally occurring genetic variation in a pool of cells from unrelated individuals to discover the sample identity of each cell and identify droplets containing cells from two different individuals (doublets). These two capabilities enable a simple multiplexing design that increases single cell library construction throughput by experimental design where cells from genetically diverse samples are multiplexed and captured at 2-10x over standard workflows. We further demonstrate the utility of sample multiplexing by characterizing the interindividual variability in cell type-specific responses of ~15k PBMCs to interferon-beta, a potent cytokine. Our computational tool enables sample multiplexing of droplet-based single cell RNA-seq for large-scale studies of population variation and could be extended to other single cell datasets that incorporate natural or synthetic DNA barcodes.
Overall design HiSeq 2500 data for sequencing of PBMCs from SLE patients and 2 controls. We collected 1M cells each from frozen PBMC samples that were Ficoll isolated and prepared using the 10x Single Cell instrument according to standard protocol. Samples A, B, and C were prepared on the instrument directly following thaw, while samples 2.1 and 2.2 were cultured for 6 hours with (B) or without (A) IFN-beta stimulation prior to loading on the 10x Single Cell instrument.
Contributor(s) Targ S
Citation(s) 29227470
Submission date Mar 14, 2017
Last update date May 15, 2019
Contact name Sasha Targ
Phone 6508144110
Organization name UCSF IHG
Street address 513 Parnassus Ave S-965
City San Francisco
State/province California
ZIP/Postal code 94143
Country USA
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (5)
GSM2560245 batch 1 sample A
GSM2560246 batch 1 sample B
GSM2560247 batch 1 sample C
BioProject PRJNA381100
SRA SRP102802

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE96583_RAW.tar 72.7 Mb (http)(custom) TAR (of MAT, MTX, TSV)
GSE96583_batch1.genes.tsv.gz 251.2 Kb (ftp)(http) TSV 364.0 Kb (ftp)(http) TSV
GSE96583_batch2.genes.tsv.gz 270.6 Kb (ftp)(http) TSV 738.6 Kb (ftp)(http) TSV
GSE96583_genes.txt.gz 186.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap