|
| Status |
Public on Oct 19, 2017 |
| Title |
40minE2_BS |
| Sample type |
SRA |
| |
|
| Source name |
MCF-7
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF-7
estradiol treatment (min): 40min
tissue: breast adenocarcinoma
|
| Treatment protocol |
Hormone starved cells were treated either with etoh (ctrl) or 100nM estradiol for 40min.
|
| Growth protocol |
MCF-7 cells, normally grown in DMEM (10% FCS), were placed in hormone-free medium i.e. high glucose DMEM without phenol red supplemented with 5% charcoal stripped FCS for 72h before induction.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted with Qiagen kit.
According to the instructions of the SureSelect MethylSeq Target Enrichment System (Agilent).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Bisulfite converted gDNA
|
| Data processing |
Reads were mapped with bowtie2.
Reads deduplication and methylation calling with Bismark (Krueger and Andrews, Bioinformatics 2011).
Genome_build: hg19
Supplementary_files_format_and_content: etoh.BS.bed; 40minE2.BS.bed; Score column in the bed files represents b-value (b-value*1000).
|
| |
|
| Submission date |
Jun 03, 2015 |
| Last update date |
Oct 19, 2022 |
| Contact name |
Evgenia Ntini |
| E-mail(s) |
ntinievgenia@gmail.com
|
| Organization name |
IMBB-FORTH
|
| Street address |
Nik. Plastira 100
|
| City |
Heraklion |
| ZIP/Postal code |
71305 |
| Country |
Greece |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE69505 |
Bisulfite sequencing coupled to target enrichment in MCF-7 |
| GSE69507 |
Chromatin-release of the long ncRNA A-ROD is required for transcriptional activation of its target gene DKK1 |
|
| Relations |
| BioSample |
SAMN03758678 |
| SRA |
SRX1047274 |
