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Sample GSM7731944 Query DataSets for GSM7731944
Status Public on Apr 01, 2024
Title SI-Bone_marrow_recipient-1
Sample type SRA
Source name Small intestine lamina propria
Organism Mus musculus
Characteristics tissue: Small intestine lamina propria
cell type: CD4+ T cells
genotype: Rag1-/-
treatment: transplant of mixed bone marrow from CD45.1+ WT and CD45.2+ Bcl3-/- mice
Treatment protocol Rag1-/- mice were irradiated and then injected with 1x10^7 bone marrow cells from either WT CD45.1+ or Bcl3-/- CD45.2 mice in a 50:50 ratio. Mice were analyzed after 16 weeks.
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.
Prior to sorting cells were labeled with anti-CD45.1 TotalSeq-B0178 and anti-CD45.2 TotalSeqB0157 antibodies for feature barcoding. Library was prepared according to manufacturer's instructions (Chromium Next GEM Single Cell 3' Kit v3.1; 10X Genomics).
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description BMR1
10X Genomics
Data processing Demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger software v6.1.1 (
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)
GSE241606 Single-cell gene expression profiling of CD4+ T cells from small intestine lamina propria of mixed Bcl3-/- CD45.2+ and WT CD45.1+ bone marrow recipients [Mixed-bone-marrow_10XscRNAseq]
GSE241611 CD4+ T cells and Bcl3
BioSample SAMN37131268
SRA SRX21474999

Supplementary file Size Download File type/resource
GSM7731944_BMR1_barcodes.tsv.gz 49.6 Kb (ftp)(http) TSV
GSM7731944_BMR1_features.tsv.gz 272.9 Kb (ftp)(http) TSV
GSM7731944_BMR1_matrix.mtx.gz 78.8 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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