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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 31, 2023 |
| Title |
Treg_F_Rep3 |
| Sample type |
SRA |
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| Source name |
Spleen
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| Organism |
Mus musculus |
| Characteristics |
strain: Foxp3 YFP/cre
cell type: T cells
phenotype: Treg
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| Extracted molecule |
total RNA |
| Extraction protocol |
Spleens were removed, gently dissociated on ice, and cells were antibody-stained and sorted by FACS (Aria III). Cells were activated in vitro with plate-bound anti-CD3 (2μg/ml), anti-CD28 (2μg/ml) and IL-2 (10 ng/mL) for 72h. RNA was harvested and isolated using NucleoZOL reagent and columns. QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina was used with 500 ng of total RNA for the construction of sequencing libraries. UMI were added to the protocol.
Libraries were prepared for sequencing using standard protocols
3'-RNA-Seq
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
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| Description |
healthy
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| Data processing |
After initial QCs using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and FastQ Screen (https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/), fastq files were processed using a local Snakemake workflow including the following main steps.
First, raw reads were trimmed from their UMI index, poly A and adapter sequences using a combination of dedicated scripts and cutadapt (v2.10).
Next, filtered reads were submitted for mapping (STAR v2.5.3a) on the Mouse Reference genome (GRCm38).
Collapsing of reads originating from the same fragment was achieved with umi_tools (v 1.0.0) and counting was perfomed with featureCounts (subread v2.0.0).
Assembly: GRCm38 (mm10)
Supplementary files format and content: Table with raw gene counts for every gene and every sample
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| Submission date |
Oct 19, 2022 |
| Last update date |
May 31, 2023 |
| Contact name |
Etienne Moussay |
| E-mail(s) |
[email protected]
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| Organization name |
Luxembourg Institute of Health
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| Department |
Cancer Research
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| Street address |
6 rue Nicolas-Ernest Barblé
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| City |
Luxembourg |
| ZIP/Postal code |
1210 |
| Country |
Luxembourg |
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| Platform ID |
GPL21626 |
| Series (1) |
| GSE216131 |
Gene expression in murine T cells from Ebi3-WT or Ebi3-KO mice |
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| Relations |
| BioSample |
SAMN31368312 |
| SRA |
SRX17957476 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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