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Sample GSM2839455 Query DataSets for GSM2839455
Status Public on Nov 06, 2017
Title Salmonella/H.poly infection (H.poly day10 - Mouse1)
Sample type SRA
 
Source name WT Mouse intestinal epithelial cells
Organism Mus musculus
Characteristics strain: C57BL/6
treatment: Infection with 200 third-stage larvae of H. polygyrus
time point: 10 days after infection
genotype: Wild-type
Extracted molecule total RNA
Extraction protocol 3' polyA RNA seq
10X Genomics Chromium Prep
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing 3' polyA RNA-seq
CellRanger 1.0
PCA (prcomp in R)
kNN-based graph clustering (R code)
Genome_build: mm10
Supplementary_files_format_and_content: 3' polyA RNA-seq. The expression levels for each gene (rows) in each single cell (column) in UMI counts as calculated using the CellRanger pipeline. Each column header provides the sequencing batch id, the cell barcode, and the cell type as identified by cluster analysis. Each ID is seperated by '_'
 
Submission date Nov 03, 2017
Last update date May 15, 2019
Contact name Adam Haber
E-mail(s) ahaber@hsph.harvard.edu
Organization name Harvard T. H. Chan School of Public Health
Street address 665 Huntington Ave, HSPH Building 1, Room 305
City Boston
State/province Massachusetts
ZIP/Postal code 02115
Country USA
 
Platform ID GPL19057
Series (1)
GSE92332 A single-cell survey of the small intestinal epithelium
Relations
BioSample SAMN07976258
SRA SRX3361134

Supplementary file Size Download File type/resource
GSM2839455_SH_Hpoly_Day10_Rep1_barcodes.tsv.gz 6.1 Kb (ftp)(http) TSV
GSM2839455_SH_Hpoly_Day10_Rep1_genes.tsv.gz 211.0 Kb (ftp)(http) TSV
GSM2839455_SH_Hpoly_Day10_Rep1_matrix.mtx.gz 6.5 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Processed data provided as supplementary file
Processed data are available on Series record
Raw data are available in SRA

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