GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM4005169 Query DataSets for GSM4005169
Status Public on Aug 02, 2022
Title WT-2
Sample type SRA
Source name small intestine
Organism Mus musculus
Characteristics strain: C57BL/6J
tissue: small intestine
age: 8-week
genotype: wild-type
cell type: epithelial cell
Extracted molecule total RNA
Extraction protocol Single cells were processed through the GemCode Single Cell Platform using the GemCode Gel Bead, Chip and Library Kits (V2, 10X Genomics, Pleasanton) as per the manufacturer’s protocol.
Libraries were prepared with the Chromium Single Cell 3' Reagent Version 2 Kit. Libraries were sequenced on an Illumina Hiseq Xten (2 × 150) platforms at the Omics Core of Bio-Med Big Data Center, CAS-MPG Partner Institute for Computational Biology, Shanghai, China.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
Data processing Illumina bcl2fastq v2.17.1.14 software used for basecalling.
Sequences from scRNA-seq were processed with Cell ranger (v.2.1.1) software (10X Genomics). In short, demultiplexing, UMI (unique molecular identifier) collapsing and alignment to the mm10 mouse transcriptome was performed.
Data were then normalized using a deconvolution-based method by computing size factors and to remove cell-specific biases.
Data were scaled and UMI counts regressed out with the ScaleData function.Then the Genes used for the principal component analysis. PCA was performed with RunPCA, and significant PCs determined based on the Scree plot
Differentially expressed genes for each cluster were then identified using the Wilcox test in Seurat and the top genes ( Q value <0.05 and log fold change>0.5) were used to identify different cell types.
Genome_build: mm10
Supplementary_files_format_and_content: Genes.tsv/Barcodes.tsv/Matrix.mtx files for each sample
Submission date Aug 02, 2019
Last update date Aug 02, 2022
Contact name Chen Shiyang
Organization name Shanghai Institute of Biochemistry and Cell Biology (CAS)
Lab Jianfeng Chen's Lab
Street address Room 413, New biochemistry building, YueYang Road
City Shanghai
ZIP/Postal code 200031
Country China
Platform ID GPL21273
Series (1)
GSE135316 Integrin αEβ7+ T cells direct intestinal stem cell fate decision via adhesive signaling
BioSample SAMN12475876
SRA SRX6647317

Supplementary file Size Download File type/resource
GSM4005169_18X101_WT-2_barcodes.tsv.gz 20.5 Kb (ftp)(http) TSV
GSM4005169_18X101_WT-2_genes.tsv.gz 212.5 Kb (ftp)(http) TSV
GSM4005169_18X101_WT-2_matrix.mtx.gz 47.8 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap