|
| Status |
Public on Apr 26, 2023 |
| Title |
1_WT1_Th17_us |
| Sample type |
SRA |
| |
|
| Source name |
CD4 T cell
|
| Organism |
Mus musculus |
| Characteristics |
strain: activated CD4 T cells
tissue: spleen and lymph nodes
genotype: wild-type
|
| Treatment protocol |
Naïve cells were activated under Th17 culture conditions (20 ng/ml IL-6; 5 ng/ml human TGFb; 10 ng/ml IL-1b, 10 ug/ml anti-IL-4, and 10 ug/ml anti-IFNg) for 5 days.
|
| Growth protocol |
naïve CD4+ T cells isolated from spleen/lymph nodes were actiated with 2 ug/ml anti-CD3 and 0.5 ug/ml anti-CD28
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction using miRNeasy Mini Kit (Qiagen)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RNA-seq
1_WT_Th17_us.bw
|
| Data processing |
The raw reads were trimmed of the adaptors and aberrant reads were removed by TrimGalore (version 0.4.5). The quality controlled reads were mapped onto the mouse genome build mm9 using Tophat2 (version 2.0.12). BAM files were sorted using SAMtools (version 0.1.18) (Li et al., 2009), and reads were counted for each gene using HTSeq (version 0.7.2) (Anders et al., 2015)
Differential expression analysis was performed using DESeq2 (version 1.18.1) (Love et al., 2014) using R (version 3.4.3).
Genome_build: mm9
Supplementary_files_format_and_content: bw
|
| |
|
| Submission date |
Feb 24, 2021 |
| Last update date |
Apr 26, 2023 |
| Contact name |
Min Gao |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Alabama at Birmingham
|
| Street address |
1900 University Blvd, THT Building Suite #130G
|
| City |
Birmingham |
| State/province |
AL |
| ZIP/Postal code |
35294 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE167418 |
Batf stabilizes Th17 cell development via limiting STAT5 signaling pathway (RNA-Seq) |
| GSE167420 |
Batf stabilizes Th17 cell development via limiting STAT5 signaling pathway |
|
| Relations |
| BioSample |
SAMN18050588 |
| SRA |
SRX10162887 |
