GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM3384874 Query DataSets for GSM3384874
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
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
BioSample SAMN10036370
SRA SRX4671879

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap