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Status |
Public on May 22, 2020 |
Title |
Th17(23)_miR-22-/- RNA-seq rep2 |
Sample type |
SRA |
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
HiSeq X Ten |
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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.
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|
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Submission date |
Jul 25, 2019 |
Last update date |
May 22, 2020 |
Contact name |
Zhijun Han |
E-mail(s) |
hangeneral@126.com
|
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 |
|
Relations |
BioSample |
SAMN12365022 |
SRA |
SRX6592076 |