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Sample GSM3983393 Query DataSets for GSM3983393
Status Public on Sep 24, 2019
Title Lin- HSPC, Stag2 KO, XA4
Sample type SRA
 
Source name Lin- HSPC
Organism Mus musculus
Characteristics cell type: Lin- HSPC
genotype: Stag2 KO
Extracted molecule polyA RNA
Extraction protocol Sequencing librairies were prepared using 10X Chromium Single Cell 3' Solution V2
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing R1 read: contains the cell barcode (first 16 nt) and UMI (next 10 nt).
R2 read: contains the RNA sequence.
RNA-seq data was processed from raw fastq files to count matrices with SEQC (see https://github.com/ambrosejcarr/seqc.git)
SEQC provides cell (barcodes) by gene matrices as a standard format and first column (CLUSTER) represents Phenograph clustering of the data.
Genome_build: mm38
Supplementary_files_format_and_content: Cell x gene unnormalized count matrices in gzipped csv format
 
Submission date Jul 29, 2019
Last update date Sep 25, 2019
Contact name Richard Koche
E-mail(s) kocher@mskcc.org
Organization name Memorial Sloan Kettering Cancer Center
Street address 417 E. 68th St.
City New York
State/province New York
ZIP/Postal code 10065
Country USA
 
Platform ID GPL24247
Series (2)
GSE134997 Stag1 and Stag2 regulate cell fate decisions in hematopoiesis through non-redundant topological control [II]
GSE135031 Stag1 and Stag2 regulate cell fate decisions in hematopoiesis through non-redundant topological control
Relations
BioSample SAMN12389654
SRA SRX6606896

Supplementary file Size Download File type/resource
GSM3983393_XA4_dense.csv.gz 10.4 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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