|
| Status |
Public on Sep 12, 2017 |
| Title |
4C_control_off |
| Sample type |
SRA |
| |
|
| Source name |
cell line
|
| Organism |
Homo sapiens |
| Characteristics |
time: 0h
mycn level: mycnLow
treatment: no_doxorubicin_treatment
|
| Treatment protocol |
Cells were treated with 0.1µg/ml Doxorubicin for 72 hours. After treatment the medium with DOX was washed out and replaced with a normal growth medium.
|
| Growth protocol |
MYCN-high (without doxycycline) and MCN-low cells (with doxycycline) were grown in RPMI1640 media supplemented with 100 U/ml Penicillin and 10% FCS in 10cm2 dishes.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted from 106 cells using RNeasy mini kit (Qiagen) with a separate step for DNAse I digestion (Qiagen). ERCC Spike-in control mix-1 (Life technologies) was added to each sample prior to processing (1 μl of a 1:10 dilution of mix-1). RNA from each sample was processed using the RiboGold kit (Epicentre) to remove rRNA
The rRNA-depleted was used to prepare libraries for sequencing using ScriptSeq Complete Gold Kit low input (Epicenter).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
RTA 1.17.21.3
Raw reads were aligned to hg19 genome by STAR (v2.4.0h1)
counts of genes were generated by Htseq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with counts for each samples
|
| |
|
| Submission date |
Apr 27, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Tatsiana Ryl |
| Organization name |
German Cancer Research Center
|
| Department |
Theoretical Systems Biology
|
| Street address |
Im Neuenheimer Feld 280
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE98274 |
RNA-Seq of SHEP TET21N cells upon Doxorubicin treatment |
|
| Relations |
| BioSample |
SAMN06841285 |
| SRA |
SRX2766674 |
