|
| Status |
Public on Mar 21, 2018 |
| Title |
DMS0-2_S4 |
| Sample type |
SRA |
| |
|
| Source name |
ARN8
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: ARN8
replicate: rep2
treatment: DMSO
|
| Treatment protocol |
The cells were treated with 5 μM of compound A and 20 μM of compound M for 5h. DMSO was used as vehicle, with final concentration of 0.05%.
|
| Growth protocol |
150,000 cells per well were seeded in a 6 well plates, and were incubated for 24h before treatment at 37°C, 5% CO2. ARN8 cells were grown and incuabted in DMEM supplemented with 10% fetal bovine serum and 1% penycilin/streptomycin mix.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The cells were harvested by trypsinization as suggested by the mirVana™ miRNA Isolation Kit for isolation of total RNA (Life Technologies, AM1560)
Libraries were generated using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina BaseSpace FASTQ Generation. Version: 1.0.0
quality check on raw sequencing reads was performed using FastQC 0.11.2
We used trimmomatic 0.32 to filter reads for quality score and read length. Reads with average quality below 20 (within 4-base wide sliding window) and/or shorter than 36 bases were removed
star 2.4.1c was used to align the reads to the reference genome
Genome_build: Homo_sapiens.GRCh38.83
Supplementary_files_format_and_content: tab-delimited text file providing values for each sample.
|
| |
|
| Submission date |
Oct 03, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Vicent Pelechano |
| E-mail(s) |
vicente.pelechano.garcia@ki.se
|
| Organization name |
ScilifeLab - Karolinska Institutet
|
| Department |
MTC
|
| Street address |
Nobels väg 16
|
| City |
Solna |
| ZIP/Postal code |
SE-17177 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE87577 |
Transcriptional study of ARN8 cells treated with novel DHODH inhibitors |
|
| Relations |
| BioSample |
SAMN05859785 |
| SRA |
SRX2208199 |
