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Sample GSM7731943 Query DataSets for GSM7731943
Status Public on Apr 01, 2024
Title SI-WT-4
Sample type SRA
Source name Small intestine lamina propria
Organism Mus musculus
Characteristics tissue: Small intestine lamina propria
cell type: CD4+ T cells
strain: C57Bl/6
genotype: Wildtype
Extracted molecule total RNA
Extraction protocol Small intestine was extracted from mice and Peyer's patches were removed. Then intestine was opened longitudinally, washed in PBS and cut into 0.5-1 cm pieces. The pieces were then incubated in ice cold PBS with 30 mM EDTA for 30 min and thoroughly washed in PBS. Afterwards they were cut into smaller pieces and digested three times for 10 min, 20 min and 30 min in RPMI 1640 containing 25 mM HEPES, 0.5 mg/ml Collagenase D and 10 µg/ml DNaseI. Disintegrated supernatants were collected in RPMI1640 + 10% FCS in between digestion steps. Cells were then filtered to remove clumps and Percoll density gradient centrifugation (40%/80%) was performed to purify lymphocytes. Cells were stained with antibodies against CD45, CD3 and CD4 and before sorting 7AAD was added to label dead cells. They were then sorted for CD45+CD3+CD4+7AAD- using the FACS Aria III and collected in PBS with 0.04% BSA.
Library was prepared according to manufacturer's instructions (Chromium Single Cell 5' Library; 10X Genomics).
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description GEX4
10X Genomics
Data processing Demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger software v3.0.2 (
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).
Submission date Aug 23, 2023
Last update date Apr 01, 2024
Contact name Caspar Ohnmacht
Organization name Helmholtz Munich
Department Institute for Allergy Research
Street address Ingolstädter Landstraße 1
City Oberschleißheim
ZIP/Postal code 85764
Country Germany
Platform ID GPL17021
Series (2)
GSE241605 Single-cell gene expression profiling of CD4+ T cells from the murine small intestine lamina propria [steady-state_SI-Treg_10XscRNAseq]
GSE241611 CD4+ T cells and Bcl3
BioSample SAMN37131165
SRA SRX21475005

Supplementary file Size Download File type/resource
GSM7731943_GEX4_barcodes.tsv.gz 27.1 Kb (ftp)(http) TSV
GSM7731943_GEX4_features.tsv.gz 272.8 Kb (ftp)(http) TSV
GSM7731943_GEX4_matrix.mtx.gz 36.2 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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