|
| Status |
Public on May 26, 2023 |
| Title |
WT 3 3h [3hWT3] |
| Sample type |
SRA |
| |
|
| Source name |
CD4+ T cells from spleen of WT #3 3h stimulation
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL6
genotype/variation: WT
treatment: 3h stimulation with anti-CD3/CD28
tissue: spleen
cell type: CD4+ T cells
|
| Treatment protocol |
Stimulation with anti-CD3/CD28 between 0 h and 24 h
|
| Growth protocol |
Culture in RP10 between 0 and 24 h
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The CD4+ T cells were washed with PBS and pelleted. Then the cells were resuspended in RLT buffer from the RNeasy Mini kit (Qiagen) and from there we followed the protocol of the kit.
Sequencing libraries were prepared following the protocol "TruSeqStrandedmRNASamplePreparationGuide(Part#15031047Rev.E)" with the "TruSeq stranded mRNAseq library preparation kit” (Illumina Inc., Cat.#RS-122-2101orRS-122-2102(SetAorB,respectively))
mRNA stranded library sequencing
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
3hWT3_lib_00040AAA_ACAGTG
|
| Data processing |
FASTQ files were aligned to Genome data base using STAR software [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905/],and read counts obtained for each gene
Differential Expression was estimated using DESeq2 [https://www.ncbi.nlm.nih.gov/pubmed/25516281] and edgeR [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2796818/]
Genome_build: Mus_musculus.GRCm38.94.gtf
Supplementary_files_format_and_content: A matrix is generated as a plain text file (*.txt), in which each column is a sample, each row is a gene (ensembl_ID), and in each cell indicates the number of raw counts obtained by STAR per sample and gene.
|
| |
|
| Submission date |
Jun 04, 2020 |
| Last update date |
May 26, 2023 |
| Contact name |
Ana Maria Aransay |
| E-mail(s) |
amaransay@cicbiogune.es
|
| Phone |
0034944061325
|
| Organization name |
CIC bioGUNE
|
| Department |
Genome Analysis Platform
|
| Street address |
Parque tecnologico de Bizkaia, Building 801-A
|
| City |
Derio |
| State/province |
BIZKAIA |
| ZIP/Postal code |
48160 |
| Country |
Spain |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE151782 |
AIM2 negatively regulate FOXP3 expression in mouse CD4+ T cells |
|
| Relations |
| BioSample |
SAMN15098861 |
| SRA |
SRX8468808 |
