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| Status |
Public on Aug 02, 2022 |
| Title |
Itgb7 KO-2 |
| Sample type |
SRA |
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| Source name |
small intestine
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: small intestine
age: 8-week
genotype: Itgb7-/-
cell type: epithelial cell
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| 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
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| Submission date |
Aug 02, 2019 |
| Last update date |
Aug 02, 2022 |
| Contact name |
Chen Shiyang |
| E-mail(s) |
chenshiyang2014@sibcb.ac.cn
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| Organization name |
Shanghai Institute of Biochemistry and Cell Biology (CAS)
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| Lab |
Jianfeng Chen's Lab
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| Street address |
Room 413, New biochemistry building, YueYang Road
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| City |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
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| Platform ID |
GPL21273 |
| Series (1) |
| GSE135316 |
Integrin αEβ7+ T cells direct intestinal stem cell fate decision via adhesive signaling |
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| Relations |
| BioSample |
SAMN12475873 |
| SRA |
SRX6647320 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4005172_18X098_Itgb7_KO-2_barcodes.tsv.gz |
23.0 Kb |
(ftp)(http) |
TSV |
| GSM4005172_18X098_Itgb7_KO-2_genes.tsv.gz |
212.5 Kb |
(ftp)(http) |
TSV |
| GSM4005172_18X098_Itgb7_KO-2_matrix.mtx.gz |
48.7 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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