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| 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
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| 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
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| 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
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| 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 |
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| Submission date |
Nov 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Atray Dixit |
| E-mail(s) |
acdixit@mit.edu
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| Organization name |
MIT
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| Street address |
415 Main Street
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
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| Platforms (2) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA354362 |
| SRA |
SRP093670 |
| 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 Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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