|
| Status |
Public on May 19, 2014 |
| Title |
RNA-Seq: 48h Normox |
| Sample type |
SRA |
| |
|
| Source name |
SK-N-BE(2)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SK-N-BE(2)
treatment: normoxia
|
| Treatment protocol |
1% O2 or 20% O2 for 48 hours
|
| Growth protocol |
DMEM with 10% FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
hMe-SEAL followed previously described methods(Song et al., Nature Biotechnology, 2011). RNA extracted with Trizol reagent.
Standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RNA-Seq
|
| Data processing |
hMe-Seal: DNA reads were aligned using BWA aligner
hMe-SEAL: Peaks called using MACS1.4
RNA-Seq: Reads aligned with tophat2 and bowtie2
RNA-Seq: Cufflinks (cufflinks, cuffcompare, cuffdiff) for expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: wig for DNA data; tab-delimited output of FPKM for RNA
|
| |
|
| Submission date |
Feb 26, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Christopher Mariani |
| E-mail(s) |
christopher.mariani@gmail.com
|
| Organization name |
University of Chicago
|
| Street address |
900 E 57 St
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE55391 |
TET1-mediated hydroxymethylation facilitates hypoxic gene induction in neuroblastoma |
|
| Relations |
| BioSample |
SAMN02665662 |
| SRA |
SRX476316 |
