|
| Status |
Public on Jun 13, 2012 |
| Title |
ECC1_E2_R1 |
| Sample type |
SRA |
| |
|
| Source name |
Endometrial cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: 8 hour 10 nM 17β-estradiol
replicate: 1
cell line: ECC-1
|
| Treatment protocol |
Cells were treated with either 10 nM 17β-estradiol, 100 nM genistein, 100 nM bisphenol A or 0.02% DMSO (vehicle control) for 8 hours before harvesting.
|
| Growth protocol |
Both ECC-1 and T-47D were grown on phenol red-free RPMI-1640 supplemented with 10% dextran/charcoal treated fetal bovine serum for five days. RNA lysate was harvested from 100 mm dishes
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
mRNA was harvested using an mRNA-direct kit (Invitrogen), followed by DNase treatment. Non-directional libraries were then constructed as described in Gertz J, Varley KE, Davis NS, Baas BJ et al. Transposase mediated construction of RNA-seq libraries. Genome Res 2012 Jan;22(1):134-41.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
To calculate expression levels in each library, sequence reads were aligned to a database of all spliced RefSeq transcripts using Bowtie with the following parameters:-n 2 -a -m 10 -X 3000. The number of reads aligning to each transcript was multiplied by 1 million, then divided by the length of the transcript times the total number of aligned reads to calculate RPKM values.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files contain the official gene symbol, refseq id and RPKM value
|
| |
|
| Submission date |
May 24, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Jason Gertz |
| E-mail(s) |
jgertz@hudsonalpha.com
|
| Organization name |
HudsonAlpha Institute
|
| Street address |
601 Genome Way
|
| City |
Huntsville |
| State/province |
AL |
| ZIP/Postal code |
35806 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE38234 |
Genistein and bisphenol A exposure cause estrogen receptor 1 to bind thousands of binding sites in a cell type-specific manner |
|
| Relations |
| SRA |
SRX149617 |
| BioSample |
SAMN00998522 |
