|
| Status |
Public on Sep 12, 2017 |
| Title |
18h_Tet-_TAGCTT_L003 |
| Sample type |
SRA |
| |
|
| Source name |
TetM_18h
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: IMR5/75 neuroblastoma cells with tetracycline-inducible MYCN shRNA
time point: 18h
tet treatment: minus
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from 10e6 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.
rRNA-depleted RNA was used to prepare libraries with the Ultra directional RNA library prep kit for Illumina (New England Bioscience) according to manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
TetM_18h_rep1
|
| Data processing |
RTA 1.17.21.3
Raw reads were aligned to hg19 genome by Tophat (v2.0.5)
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 13, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Chunxuan Shao |
| E-mail(s) |
c.shao@Dkfz-Heidelberg.de
|
| Organization name |
German Cancer Research Center
|
| Street address |
Im Neuenheimer Feld 280
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE97774 |
Cell-cycle-resolved analysis of RNA expression in neuroblastoma cells upon MYCN knockdown |
|
| Relations |
| BioSample |
SAMN06759484 |
| SRA |
SRX2741612 |
