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Sample GSM6697669 Query DataSets for GSM6697669
Status Public on Nov 15, 2023
Title sgRNA Library-transduced OT-I cells B2S6
Sample type SRA
 
Source name sgRNA Library-transduced OT-I cells at day 7 post adoptive transfer from B16-OVA tumor
Organism Mus musculus
Characteristics cell type: sgRNA Library transduced OT-I cells
strain: C57BL/6
Growth protocol OT-I cells transduced with indicatd sgRNA Library were sorted from B16-OVA tumor after adoptive transfer
Extracted molecule total RNA
Extraction protocol CD8+ OT-I T cells were sorted at day 7 post adoptive transfer from B16-OVA tumor and loaded onto the Chromium Controller according to their respective cell counts to target 9000 single cell GEMs (gel beads in emulsion) per sample.
Libraries were prepared using the Chromium Single Cell 3’ v3 Library, CRISPR screening library and Gel Bead Kit (10x Genomics)
scRNA-seq and direct capture CRISPR
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description sgRNA Library-transduced OT-I cells
Data processing The Cell Ranger 6.0 Single-Cell Software Suite (10x Genomics) was implemented to process the raw sequencing data from the Illumina HiSeq run.
This pipeline performed de-multiplexing, alignment (mm10 and CRISPR library), and barcode processing to generate gene-cell and sgRNA-cell matrices used for downstream analysis.
Assembly: mm10
Supplementary files format and content: cell ranger gene expression and sgRNA count matrix for single cells in each sample
 
Submission date Oct 31, 2022
Last update date Nov 15, 2023
Contact name Hongbo Chi
E-mail(s) hongbo.chi@stjude.org
Organization name St Jude Children's Research Hospital
Department Immunology
Street address 262 Danny Thomas Place
City Memphis
State/province TN
ZIP/Postal code 38105
Country USA
 
Platform ID GPL21103
Series (2)
GSE216800 Single-cell CRISPR screens in vivo map T cell fate regulomes in cancer
GSE216909 Single-cell CRISPR screens in vivo map T cell fate regulomes in cancer [scCRISPR]
Relations
BioSample SAMN31535984
SRA SRX18089653

Supplementary file Size Download File type/resource
GSM6697669_S6_B2.tar.gz 88.4 Mb (ftp)(http) TAR
GSM6697669_feature_reference.csv.gz 12.9 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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