|
| Status |
Public on Jul 17, 2020 |
| Title |
post_KO_2 |
| Sample type |
SRA |
| |
|
| Source name |
exp2-KO-post-colitis-pool-2
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: CD4+ T-cell
genotype: Il6ra-/- Il17f/Thy1.1
|
| Treatment protocol |
2 x 10^5 each of WT (CD45.1) and Il6ra-/- (CD45.2) Thy1.1+ Th17 precursors were transferred into Rag1-/- recipients
|
| Growth protocol |
All mouse strains were bred and maintained at UAB in accordance with IACUC guidelines.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were sorted into RPMI + 10% serum, then centrifuged and resuspended in Qiazol and stored at -80C overnight. RNA was extracted the following day using Qiagen miRNeasy kit.
TruSeq Stranded mRNA Library Prep Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
IL-6Ra KO Colonic Live CD4+TCRb+CD45.2+ cells
|
| Data processing |
The raw reads were mapped onto the mouse genome build GRCm38 using STAR (version2.5.3) (Dobin et al.2013). BAM files were sorted using SAMtools (version 0.1.18) (Li et al., 2009), and reads were counted for each gene using HTSeq (version 0.7.2) (Anders et al., 2015)
Differential expression analysis was performed using DESeq2 (version 1.18.1) (Love et al., 2014) using R (version 3.4.3).
Genome_build: GRCm38-mm10
Supplementary_files_format_and_content: tab-delimited text files include htseq count values for each sample
|
| |
|
| Submission date |
May 31, 2018 |
| Last update date |
Jul 17, 2020 |
| Contact name |
Min Gao |
| E-mail(s) |
mgao@uabmc.edu
|
| Organization name |
University of Alabama at Birmingham
|
| Street address |
1900 University Blvd, THT Building Suite #130G
|
| City |
Birmingham |
| State/province |
AL |
| ZIP/Postal code |
35294 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE115141 |
Ongoing classical IL-6 signaling is required to maintain a pathogenic Th17 response in vivo |
|
| Relations |
| BioSample |
SAMN09288399 |
| SRA |
SRX4145841 |
