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Series GSE90063 Query DataSets for GSE90063
Status Public on Dec 16, 2016
Title Perturb-seq: Dissecting molecular circuits with scalable single cell RNA profiling of pooled genetic screens
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Methods: We create a CRISPR vector containing a polyadenylated RNA barcode and couple it with droplet scRNA-seq to get a large scale transcriptional measurements of perturbations
Results: We were able to perform regulatory inference of gene function, observe nonlinear interactions, and perform downsampling analysis to show that gene signature effects can be seen with as few as 10's of cells while gene level phenotypes, depending on effects size would require 100's of cells
Conclusion: Perturb-seq presents a scalable paradigm for obtaining rich genomic profiles of perturbations
Overall design scRNA-seq with pooled CRISPR-KO perturbations in 200,000 cells across six screens unstimulated BMDC, BMDC stimulated at 3hr, TFs in K562 at 7 and 13 days post trasnduction, and 13 days at a higher MOI of perturbations,

*Note: that the raw SRA data consists of BAM files not FASTQ files
Contributor(s) Dixit A, Parnas O, Li B, Chen J, Fulco CP, Jerby-Arnon L, Marjanovic ND, Dionne D, Burks T, Raychndhury R, Adamson B, Norman TM, Lander ES, Weissman JS, Friedman N, Regev A
Citation(s) 27984732
Submission date Nov 18, 2016
Last update date May 15, 2019
Contact name Atray Dixit
Organization name MIT
Street address 415 Main Street
City Cambridge
State/province MA
ZIP/Postal code 02139
Country USA
Platforms (2)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (6)
GSM2396856 DC 3hr
GSM2396857 DC 0hr
GSM2396858 K562 TFs, 7 days
BioProject PRJNA354362
SRA SRP093670

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
GSE90063_RAW.tar 1.4 Gb (http)(custom) TAR (of CSV, TXT)
GSE90063_dc0hr_umi_wt.txt.gz 3.2 Mb (ftp)(http) TXT
GSE90063_dc3hr_umi_wt.txt.gz 2.0 Mb (ftp)(http) TXT
GSE90063_k562_umi_wt.txt.gz 8.4 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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