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Series GSE90486 Query DataSets for GSE90486
Status Public on Dec 16, 2016
Title Dissecting immune circuits by linking CRISPR pooled screens with single cell RNA-seq [SET1]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
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 Transcriptional and CRISPR profiles from single myeloid cells, infected with lentiviral vectors carrying different gRNAs, were generated by deep sequencing of tens of thousands of single cells, sequenced in several batches in an Illumina Nextseq 500.

Experiment was paired-end, but read2 was used to read cell and molecule barcodes only.

Additional details about experimental design (associating each single cell with its amplification batch and index sorting readout) available as Series supplementary file.
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)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (62)
GSM2402740 AB1118
GSM2402741 AB1120
GSM2402742 AB1121
This SubSeries is part of SuperSeries:
GSE90488 Dissecting immune circuits by linking CRISPR pooled screens with single cell RNA-seq
BioProject PRJNA354870
SRA SRP093880

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
GSE90486_RAW.tar 63.8 Mb (http)(custom) TAR (of TXT)
GSE90486_experimental_design.txt.gz 197.2 Kb (ftp)(http) TXT
GSE90486_gRNA_UGI_lists.xls.gz 10.3 Kb (ftp)(http) XLS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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