|
| Status |
Public on Jul 04, 2018 |
| Title |
DMSO treated Th1 cells Rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
DMSO treated Th1 cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: In vitro IL12 differentiated Th1 cells
treatment: DMSO treated
|
| Growth protocol |
T cells were purified and activated with plate-bound anti-Hamster IgG (MP Biomedicals) and anti-CD3 (2C11, Bio X cell) +anti-CD28 (37N, Bio X cell) in the presence of anti-IL-4 (5 _g/ml; 11B11) and IL-12 (2 ng/ml; PeproTech)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated with RNeasy plus kit
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
CD4 T cells
processed data files: RNAseq_cpx_vs_dmso_DESeq2.txt, RPM.txt
|
| Data processing |
Adaptors were first trimmed from the sequence reads with CUTADAPT
RNA seq reads were aligned to mm9 with STAR
The number of aligned reads that overlap each gene in the annotations (mm9) was counted with HTseq-count, and normalized gene expression (RPM) was determined by Deseq 2.
Differential gene expression was analyzed with Deseq
Genome_build: mm9
Supplementary_files_format_and_content: [.txt] tab-delimited text files include RPM values for each Sample and differential gene expression.
|
| |
|
| Submission date |
Jul 21, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Xing Chang |
| E-mail(s) |
changxing@sibs.ac.cn
|
| Organization name |
Shanghai Institute for Biological Sciences
|
| Street address |
320 Yueyang road
|
| City |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (2) |
| GSE84699 |
Transcriptome targets of PCBP1 in T cells |
| GSE84702 |
Iron-mediated stabilization of PCBP1 post-transcriptionally promotes GM-CSF production during autoimmune pathogenesis |
|
| Relations |
| BioSample |
SAMN05427610 |
| SRA |
SRX1969223 |
