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Sample GSM7731985 Query DataSets for GSM7731985
Status Public on Apr 01, 2024
Title SI pTreg KO3
Sample type SRA
Source name Small intestine
Organism Mus musculus
Characteristics tissue: Small intestine
cell type: RORgt+ pTreg
genotype: Bcl3-/-
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. Spleen and lymph nodes were meshed through a 70 μm filter and then washed in DPBS. For spleens, lysis of erythrocytes was performed by incubating cells in 2 ml of ACK lysis buffer (0.15 M ammonium chloride, 10 mM potassium hydrogen carbonate, 1 mM EDTA-di sodium) for 2 min, before samples were washed and resuspended in DPBS. CD4 T cells were enriched prior to sorting using a CD4 T cell enrichment kit (Miltenyi) according to manufacturer’s protocol. 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- and depending on Foxp3 and RORgt reporter expression using the FACS Aria III.
RNA isolation of bulk Treg populations was performed using the RNeasy Plus Micro Isolation Kit (Qiagen). Cells were sorted into lysis buffer containing β-mercaptoethanol and isolation was performed according to manufacturer's instructions.
The SMART-Seq v4 ultra-low input RNA kit (Takara) was used for cDNA synthesis using the ERCC ExFold RNA Spike-In Mixes (Invitrogen). Library preparation was done using the Illumina Nextera XT DNA Library Preparation Kit. For bead cleanup AMPure XP (Beckman Coulter) were used.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Data processing Nextflow nf-Core/rnaseq
Preprocessing was performed including raw read QC, barcode extraction, trimming and removal of contaminants
Alignment and quantification using STAR via RSEM
Assembly: GRCm38
Supplementary files format and content: Gene level quantification for each sample.
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 GPL24247
Series (2)
GSE241609 Loss of Bcl3 influences gene expression in Tregs and Treg subsets [Bcl3-WT_Treg_bulkRNAseq]
GSE241611 CD4+ T cells and Bcl3
BioSample SAMN37131478
SRA SRX21481198

Supplementary file Size Download File type/resource
GSM7731985_SI-pTreg-KO3.genes.results.gz 923.1 Kb (ftp)(http) RESULTS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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