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Sample GSM2402783 Query DataSets for GSM2402783
Status Public on Dec 16, 2016
Title AB1680
Sample type SRA
 
Source name single cell-sorted mouse donor (Cas9-GFP+) in vivo myeloid cells from the spleen
Organism Mus musculus
Characteristics strain: wild-type and transgenic Cas9-GFP C57BL/6
organ: spleen
selection marker: GFP+BFP+CD3-TCRb-CD19-NK-1.1-Ly6g-
treatment: mice injected with lypopolysacharide (LPS), 4 hours before experiment
grna in the infecting vector: in vivo mix (BFP)
Treatment protocol Cells were infected on day 2 post plating with lentivirus vectors, each containing one gRNA and one fluorescent selection marker. On day 7, cells were challenged with LPS for 4 hours before harvest.
Growth protocol Bone marrows were flushed from hind leg bones from euthanized 6 to 8 weeks-old mice housed at the Weizmann Institute animal facility. Cell suspensions were obtained, red blood cells lysed, and cells grown on 6-well petri dishes on media supplemented with GM-CSF.
Extracted molecule polyA RNA
Extraction protocol Cells were scrapped from the plate and stained with FACS markers antibodies as indicated above (selection marker).
3' end mRNA libraries were prepared for sequencing using CRISP-seq (Jaitin et al., Cell 2016), which includes a module of MARS-seq (Jaitin et al., Science 2014) and a module of UGI-seq.
single cell RNA-seq and UGI-seq for gene expression quantitation and gRNA identification, respectively.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description Donor LSK cells infected with a mix of Cebpb, Rela, Irf8, Stat1, Stat2, and two control (Oris and LacOp) gRNAs (BFP) lentiviruses
Data processing bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample; single cell expression matrix
 
Submission date Nov 24, 2016
Last update date May 15, 2019
Contact name Ido Amit
E-mail(s) ido.amit@weizmann.ac.il
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
 
Platform ID GPL19057
Series (2)
GSE90486 Dissecting immune circuits by linking CRISPR pooled screens with single cell RNA-seq [SET1]
GSE90488 Dissecting immune circuits by linking CRISPR pooled screens with single cell RNA-seq
Relations
BioSample SAMN06053602
SRA SRX2373891

Supplementary file Size Download File type/resource
GSM2402783_AB1680.txt.gz 962.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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