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Sample GSM4984088 Query DataSets for GSM4984088
Status Public on Oct 14, 2021
Title KD2_rep1
Sample type SRA
Source name Tfh-like cell
Organism Mus musculus
Characteristics treatment: pMKO.1-sh-Zfp831 transfected
tissue:  Spleen+Lymph nodes
cell type: Tfh-like cell
age: 3 days in vitro
Treatment protocol PMA/ionomycin treatment or viral infection when specified
Growth protocol wild type or Mapk1-KO naïve CD4+ T cells were activated and cultured under IL-6 plus anti-IL2/IL-4/IFN-γ/TGFβ
Extracted molecule total RNA
Extraction protocol The total RNA was extracted with Trizol (Life Technologies) according to manufacturer’s instructions
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Data processing Clean reads were aligned to mm10 by bowtie2 with default parameters
Uniquely mapping reads were summarized by featureCounts(from Subread package)
RPKM (Reads Per Kilobase of exon model per Million mapped reads) were calculated using edgeR TMM normalization
Differentially expressed genes were identified by at least 1.5fold change and fdr adjusted p-value 0.05 using Deseq2
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include gene symbol and gene expression (or read count) for each sample
Submission date Dec 22, 2020
Last update date Oct 14, 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 GPL17021
Series (2)
GSE163702 Global gene expression profile of anti-CD3/CD28 or PMA/ionomycin stimulated CD4+ T cell, wild type and Mapk1-KO CD4+ T cells, and empty vector and sh-Zfp831 infected CD4+ T cells
GSE163808 ERK, differentially regulated by costimulation molecules, represses Zfp831, a critical regulator in T follicular helper cell differentiation
BioSample SAMN17137770
SRA SRX9718418

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

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