|
| Status |
Public on Jul 28, 2021 |
| Title |
WT_colitis_colon CD4+ T cells_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
WT_colitis
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Rora_fl/fl
cell type: colon CD4+ T cells
|
| Treatment protocol |
The cells were re-stimulated with PMA and ionomycin for 2 hours before RNA extraction.
|
| Growth protocol |
For the in vivo isolated CD4+ T cells, naïve CD4+ T cells from Rora_fl/fl (WT) or Cd4_cre Rora_fl/fl (KO) mice were transferred into Tcrbd-/- recipient mice for 6 weeks, and the CD4+ T cells were isolated from colon tissues for sequencing. For in vitro polarized Th17 cells, naïve CD4+ T cells were activated with plate-bound anti-CD3 and anti-CD28 and cultured with TGF-β+IL-6 or IL-6+IL-1β+IL-23 for 4 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was extracted with Trizol (Life Technologies) according to manufacturer’s instructions
RNA-seq library was constructed for deep sequencing by BGI Genomics.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
Low quality reads and adaptor sequences were removed by Trim Galore
The clean reads were aligned to mm10 by bowtie2 with default parameter and uniquely mapping reads were summarized by featureCounts
FPKM (Fragments Per Kilobase of exon model per Million mapped reads) were calculated using edgeR TMM normalization
Differentially expressed genes were identified by at least 2fold change and fdr adjusted p-value 0.05 using Deseq2
Genome_build: mm10
Supplementary_files_format_and_content: counts
|
| |
|
| Submission date |
Mar 04, 2021 |
| Last update date |
Jul 28, 2021 |
| Contact name |
Chen Dong |
| Organization name |
Tsinghua University
|
| Department |
Institute for Immunology and School of Medicine
|
| Lab |
Dongchen's lab
|
| Street address |
Haidian District
|
| City |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
| |
|
| Platform ID |
GPL23479 |
| Series (2) |
| GSE168216 |
RORα is critical for mTORC1 activity in T cell-mediated colitis [RNA-seq] |
| GSE168219 |
RORα is critical for mTORC1 activity in T cell-mediated colitis. |
|
| Relations |
| BioSample |
SAMN18139226 |
| SRA |
SRX10237399 |
