|
| Status |
Public on Oct 10, 2015 |
| Title |
Th2cell-TSA_RNA_exp2 |
| Sample type |
SRA |
| |
|
| Source name |
Five-day cultured Th2 cells generated from primary splenic CD4_T cells were treated with trichostatin A (TSA)
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: Th2 cell
treatment: TSA
|
| Growth protocol |
Splenic CD4_T cells were stimulated under Th2 culture conditions (15 ng/ml IL-2, 10 ng/ml IL-4) for 5 days in vitro. For TSA treatment, splenic CD4 cells were cultured under Th2 conditions and 10 nM TSA (Sigma, St Louis, MO) was added in the culture on day 2 and after another 3-days of culture, Th2 cells were collected for analysis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total cellular RNA was extracted with TRIzol reagent (Invitrogen).
TruSeq RNA Sample Prep Kit v2 (Illumina) was used according to the manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
TSA-treated_Th2_cells
|
| Data processing |
Read sequences (50 bp) were aligned to the mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011) using Bowtie (version 0.12.8) and TopHat (version 1.3.2).
Fragments per kilobase of exon per million mapped reads (FPKM) for each gene were calculated using Cufflinks (version 2.0.2).
Genome_build: mm10
Supplementary_files_format_and_content: Text files include FPKM values for each Sample
|
| |
|
| Submission date |
Oct 07, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Atsushi Onodera |
| Organization name |
Chiba University
|
| Department |
Immunology
|
| Street address |
Chuo-ku Inohana 1-8-1
|
| City |
Chiba |
| ZIP/Postal code |
260-8670 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18480 |
| Series (2) |
| GSE73813 |
Spatial interplay between Polycomb and Trithorax complexes controls transcriptional activity in T lymphocytes [RNA-Seq] |
| GSE73825 |
Spatial interplay between Polycomb and Trithorax complexes controls transcriptional activity in T lymphocytes |
|
| Relations |
| BioSample |
SAMN04151788 |
| SRA |
SRX1310212 |
