|
| Status |
Public on Mar 23, 2022 |
| Title |
RNA-seq_Sscr_fibro_5aza1_1 |
| Sample type |
SRA |
| |
|
| Source name |
Primary dermal fibroblasts
|
| Organism |
Sus scrofa |
| Characteristics |
Sex: Female
genome build: susScr11
treatment: Treated 5-AzadC 1 microM
tissue: Primary dermal fibroblasts
|
| Treatment protocol |
Fibroblasts were treated with 1 µM final concentration of 5-AzadC (Sigma A3656) for 72 hours and the medium was renewed every day.
|
| Growth protocol |
Primary dermal fibroblasts were grown in DMEM-GlutaMax supplemented with 10% fetal bovine serum and 50U/mL penicillin-streptomycin in a humidified atmosphere containing 5% CO2 at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA samples were prepared using the AllPrep DNA/RNA Mini Kit (Qiagen).
RNA-seq libraries were prepared from 150 to 350 ng of total RNA using the TruSeq Stranded Total RNA Library Prep Gold kit (Illumina), according to the manufacturer's instructions. Briefly, cytoplasmic and mitochondrial ribosomal RNA (rRNA) was removed using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. The depleted RNA was fragmented using divalent cations at 94°C and cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. cDNA fragments were blunted, adenylated and ligated to adapters using T4 DNA Ligase. The cDNA libraries were generated with 12 cycles of PCR amplification, purified using AMPure XP beads (Beckman-Coulter) and checked for quality and quantified using capillary electrophoresis
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Reads were aligned to the corresponding genome with HISAT2 v2.0.5 using default parameters and Ensembl transcriptome index.
For data visualization, BigWig files of normalized read counts per base were generated with bamToBed from bedtools and bedGraphToBigWig from UCSC using only reads that map uniquely in the genome.
genome build: hg38, mm10, oryCun2, canFam3, bosTau8, susScr11, galGal6
processed data files format and content: We provide bigWig files for visualization of RNA-seq tracks.
|
| |
|
| Submission date |
May 27, 2021 |
| Last update date |
Mar 23, 2022 |
| Contact name |
Michael Weber |
| Organization name |
CNRS
|
| Department |
UMR7242 Biotechnology and Cell Signalling
|
| Street address |
300 Bd Sebastien Brant
|
| City |
Illkirch |
| ZIP/Postal code |
67412 |
| Country |
France |
| |
|
| Platform ID |
GPL22475 |
| Series (1) |
| GSE175615 |
Conservation and divergence of DNA methylation patterns and functions in vertebrates |
|
| Relations |
| BioSample |
SAMN19365345 |
| SRA |
SRX11003214 |
