|
| Status |
Public on Aug 12, 2020 |
| Title |
Th17_Tx_2 |
| Sample type |
SRA |
| |
|
| Source name |
In-vitro generated IL17a reporter-positive CD4+ T cells treated with desIgf1
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: spleen
cell type: CD4+ T cells
genotype: IL17a/hCD2 Ifng/Thy1.1 Foxp3/GFP Reporter
|
| Treatment protocol |
Sorted naïve CD4+ T cells were stimulated for 5 days with 5ug/mL of soluble anti-CD3, irradiated CD4-depleted splenocytes, 20ng/mL of IL6, 2.5ng/mL of TgfB, 30ng/mL of desIgf1, 10ug/mL of anti-Ifng and 10ug/mL of anti-IL4
|
| Growth protocol |
All mouse strains were bred and maintained at UAB in accordance with IACUC guidelines.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from sorted Foxp3/GFP–, Ifn-γ/Thy1.1–, IL-17a/hCD2+ T cells was isolated with Qiazol and miRNeasy micro kits according to manufacturer’s recommendations (Qiagen 217084 and 79306
TruSeq Stranded mRNA Library Prep Kit (Illumina RS-122-2103)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
In-vitro generated IL17a reporter-positive CD4+ T cells treated with desIgf1
|
| Data processing |
The raw reads were trimmed of the adaptors and aberrant reads were removed by TrimGalore (version 0.4.5). The quality controlled 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 21, 2018 |
| Last update date |
Aug 12, 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) |
| GSE114733 |
Insulin-like growth factors alter the transcriptional identity of Th17 cells |
|
| Relations |
| BioSample |
SAMN09233588 |
| SRA |
SRX4108739 |
