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Series GSE90487 Query DataSets for GSE90487
Status Public on Dec 16, 2016
Title Dissecting immune circuits by linking CRISPR pooled screens with single cell RNA-seq [SET2]
Organism Mus musculus
Experiment type Other
Summary In multicellular organisms, dedicated regulatory circuits control cell-type diversity and response. The crosstalk and redundancies within these circuits and substantial cellular heterogeneity pose a major research challenge. We present CRISP-seq, an integrated method for massively parallel single-cell RNA-seq and CRISPR pooled screens. We show that profiling the perturbation and transcriptome in the same cell, enables to elucidate, the function of multiple factors and their interactions. In this benchmarking study, we applied this technology to probe regulatory circuits of innate immunity. By sampling tens of thousands of perturbed cells in vitro and in mice, we identified interactions and redundancies between developmental and signaling-dependent factors controlling the commitment toward different cell lineages or the inflammatory and antiviral pathways. CRISP-seq thereby emerges as a broadly applicable, comprehensive, and unbiased approach for elucidating mammalian regulatory circuits.
Overall design DNA sequencing of guide RNA targeted loci for several CRISPR pools. Libraries were generated using primer flanking the target region for bulk population of cells, and sequenced on the Illumina MiSeq.
Contributor(s) Amit I, Jaitin DA, Weiner A, Yoffe I
Citation(s) 27984734
Submission date Nov 24, 2016
Last update date May 15, 2019
Contact name Ido Amit
Phone 972-8-9343338
Organization name Weizmann Institute of Science
Department Immunology
Street address 234 Herzl st.
City Rehovot
ZIP/Postal code 760001
Country Israel
Platforms (1)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (8)
This SubSeries is part of SuperSeries:
GSE90488 Dissecting immune circuits by linking CRISPR pooled screens with single cell RNA-seq
BioProject PRJNA354871
SRA SRP093881

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
GSE90487_RAW.tar 90.0 Kb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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