|
Status |
Public on Oct 19, 2017 |
Title |
etoh_BS |
Sample type |
SRA |
|
|
Source name |
MCF-7
|
Organism |
Homo sapiens |
Characteristics |
cell line: MCF-7 estradiol treatment (min): 0min 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 |
SAMN03758677 |
SRA |
SRX1047273 |