|
| Status |
Public on Sep 13, 2018 |
| Title |
PP2A cKO2 |
| Sample type |
SRA |
| |
|
| Source name |
In vitro polarized Th17 cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
time of collection: Polarized for 2 days
restimulation: Restimulate with PMA/Iono
genotype/variation: PP2A cKO
|
| Treatment protocol |
Cells were restimulated with 50ng/ml PMA and 500ng/ml Ionomycin for 4 hours.
|
| Growth protocol |
For polarization experiments, naïve cells were cultured at 1×106/ml with irradiated autologous antigen presenting cells (APCs) at a ratio of 1:3. Then the cells were primed for 2 days with soluble anti-CD3 (2µg/ml) and anti-CD28 (2 µg/ml),TGFβ1 (2 ng/ml), IL-6 (20 ng/ml) in the presence of anti-IL4 antibody (10 µg/ml) and anti-IFNγ antibody (10 µg/ml).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
According to the instructions of RNAeasy Plus Mini kit (Qiagen).
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
K2
|
| Data processing |
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Sep 12, 2018 |
| Last update date |
Sep 13, 2018 |
| Contact name |
Xuexiao Jin |
| E-mail(s) |
shirleyj@zju.edu.cn
|
| Organization name |
Zhejiang University
|
| Street address |
866 Yuhangtang Road
|
| City |
Hangzhou |
| ZIP/Postal code |
310058 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE119836 |
PP2A is essential for Th17 differentiaiton |
|
| Relations |
| BioSample |
SAMN10036370 |
| SRA |
SRX4671879 |
