|
| Status |
Public on Oct 12, 2014 |
| Title |
miR-155-/- Th17 |
| Sample type |
SRA |
| |
|
| Source name |
in vitro polarized CD4+ Th17 cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: primary CD4+ T cells
genotype/variation: miR-155-/-
|
| Growth protocol |
Naïve CD4+CD62LhighCD44lowCD25- T cells were isolated from the lymph nodes of mice and cultured for 4 days under Th17 polarizing conditions that include IL-6, IL-21, IL-1β,TGFβ and blocking for IFNγ, IL-4 and IL-12 (p40). T cells were co-cultured with irradiated splenocytes at a 1:5 T cell to APC ratio and T cell activation was achieved by addition of soluble antibodies for CD3 and CD28. The cells were then harvested and RNA was extracted using the miRVana kit from Applied Biosystems. We then took three biological replicates and pooled them into equal concentrations for library preparation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Library preparation was performed starting with 4ug of total RNA using the TruSeq RNA sample prep kit following manufacturer's protocol (Illumina). Briefy, Oligo-dT purified mRNA was fragmented and subjected to first and second strand cDNA sythesis. cDNA fragments were blunt-ended, ligated to Illumina adaptors, and PCR amplified to enrich for the fragments ligated to adaptors. The resulting cDNA libraries were verified and quantified on Agilent Bioanalyser.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to mouse whole genome version mm9 using TopHat with option --coverage-search --microexon-search --max-multihits 20
Read counts were performed using in-house codes
Genome_build: mm9
|
| |
|
| Submission date |
Apr 12, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Gokhul Krishna Kilaru |
| E-mail(s) |
gokhul.kilaru@utsouthwestern.edu
|
| Phone |
214-648-4158
|
| Organization name |
University of Texas Southwestern Medical Center
|
| Department |
Department of Neuroscience
|
| Lab |
Joseph S. Takahashi
|
| Street address |
6000 Harry Hines Boulevard
|
| City |
Dallas |
| State/province |
TEXAS |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE37228 |
miR-155 promotes Th17 development by targeting Jarid2 |
|
| Relations |
| SRA |
SRX141249 |
| BioSample |
SAMN00854949 |
