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Sample GSM3976571 Query DataSets for GSM3976571
Status Public on May 22, 2020
Title Th17(23)_miR-22-/- RNA-seq rep2
Sample type SRA
Source name TH17(23) cells
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: Th17(23)
genotype: mir-22 KO
Growth protocol Naïve CD4+ T cells were isolated from lymph nodes or spleen of mice using a CD4+ CD62L+ T cell isolation kit II (Miltenyi Biotec) according to the manufacturer’s instruction. Naïve CD4+ T cells were stimulated with plate-bound anti-CD3ε mAb (5 µg/ml) in the presence of anti-CD28 mAb (2 µg/ml) in a 48-well plate under neutral conditions (10 µg/ml anti–IL-4 mAb and 10 µg/ml anti–IFN-γ mAb), IL-6 conditions (10 ng/ml IL-6, 10 µg/ml anti–IL-4 mAb, and 10 µg/ml anti–IFN-γ mAb), TH17 (23) conditions (20 ng/ml IL-6, 20 ng/ml IL-1β, 20 ng/ml IL-23, 10 µg/ml anti–IL-4 mAb, and 10 µg/ml anti–IFN-γ mAb).
Extracted molecule total RNA
Extraction protocol Naive CD4+ T cells from control and miR-22-/- mice were differentiated under pathogenic TH17 (23) differentiation condition. Total RNA was prepared from these cells using Trizol reagent (Invitrogen). RNA-seq libraries were prepared using a TruSeq Stranded Total RNA Library Prep Kit (Illumina). For GFP+ TH17 cells sorted from in vivo suspensions, 50,000 cells were resuspended in 700 ul Trizol reagent, total RNA was prepared by miRNeasy Micro Kit (Qiagen), RNA-seq libraries were prepared using SMART-Seq v4 Ultra Low Input RNA Kit (clontech). Sequencing was performed on an Illumina HiSeq X Ten System in a 150 bp/150 bp Paired end mode.
RNA libraries were prepared for sequencing using standard Illumina protocols
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
Data processing Basecalls performed using CASAVA version 1.4
RNA-seq reads were mapped to mm10 with refGene annotation downloaded from UCSC Genome Browser using TopHat2 v2.1.0. Gene expression level were counted by htseq-count 0.11.0. Differential expressed genes were called by DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: TAB-delimited text file included the raw reads count for each gene from RNA-seq sample.
Submission date Jul 25, 2019
Last update date May 22, 2020
Contact name Zhijun Han
Organization name Southern University of Science and Technology
Street address No 1088,xueyuan Rd., Nanshan District
City Shenzhen
State/province Guangdong
ZIP/Postal code 518055
Country China
Platform ID GPL21273
Series (1)
GSE134895 The microRNA miR-22 represses T helper 17 cell pathogenicity by targeting PTEN-regulated pathways
BioSample SAMN12365022
SRA SRX6592076

Supplementary file Size Download File type/resource
GSM3976571_Ko3.readscount.txt.gz 97.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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