|
| Status |
Public on Nov 29, 2019 |
| Title |
Control2-TGF-β1_6h |
| Sample type |
SRA |
| |
|
| Source name |
skin fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: skin fibroblasts
disease state: control
treatment: TGF-β
time point: 6h
|
| Treatment protocol |
Cells were left untreated or treated for 2, 6, or 24 hours with IL-17A (100 ng/ml) or TGF-β1 (10 ng/ml)
|
| Growth protocol |
Skin fibroblasts were cultured in DMEM supplemented with 10% FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with the RNeasy Plus Micro Kit from QIAGEN
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Sequence reads were aligned using STAR aligner with GRCh37 reference genome.
HTSeq-count was used to generate count files.
For each individual, the fold change (FC) between unstimulated and stimulated conditions were calculated. Genes with fold change higher than 1.5 fold in all the controls were used to filter the residual responsive genes to generate heatmaps.
Genome_build: Ensembl GRCh37
Supplementary_files_format_and_content: HTSeq-count is used to get the count files, followed by DESeq2 package in R for normalization and log2 transformation.
|
| |
|
| Submission date |
Sep 09, 2019 |
| Last update date |
Nov 29, 2019 |
| Contact name |
Tanwir Habib |
| E-mail(s) |
thabib@sidra.org
|
| Organization name |
Sidra Medicine
|
| Street address |
Al Luqta Street
|
| City |
Doha |
| ZIP/Postal code |
26999 |
| Country |
Qatar |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE137108 |
Chronic mucocutaneous candidiasis and connective tissue disorder in humans with impaired JNK1-dependent responses to IL-17A/F and TGF-β [RNA-Seq] |
| GSE137110 |
Chronic mucocutaneous candidiasis and connective tissue disorder in humans with impaired JNK1-dependent responses to IL-17A/F and TGF-? |
|
| Relations |
| BioSample |
SAMN12715717 |
| SRA |
SRX6818932 |
