|
| Status |
Public on May 19, 2014 |
| Title |
MCF7_E2_5min_PolII_rep |
| Sample type |
SRA |
| |
|
| Source name |
Breast cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF7
time point: 5 min
cell type: Pleural effusion
passages: 14-17
chip antibody: Homemade Anti-Pol II Monoclonal
|
| Treatment protocol |
MCF-7 cells were mock treated or with 10nM 17b-E2 to nine time points (5', 10', 20', 40', 80', 160', 320')
|
| Growth protocol |
MCF-7 cells were cultured in DMEM with 10% FCS at 37 °C. Cells were maintained in DMEM w/o phenol red and 5% charcoal stripped FCS for 72 hours before induction
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody
End repair was performed using the precipitated DNA of ∼6 million cells using Klenow and T4 PNK. A 3′ protruding A base was generated using Taq polymerase and adapters were ligated. The DNA was loaded on gel and a band corresponding to ∼200 bp (ChIP fragment + adapters) was excised. The DNA was isolated, amplified by PCR, and used for cluster generation on the Illumina 1G genome analyzer. The 32 bp tags were mapped to the human genome hg19 using the eland program allowing one mismatch. The 32 bp sequence reads were directionally extended to 133 bp, corresponding to the length of the original fragments used for sequencing. For each base pair in the genome the number of overlapping sequence reads was determined and averaged over a 10 bp window and visualized in the University of California Santa Cruz genome browser (http://genome.ucsc.edu).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The data was processed using the genomatix mining station (GMS). Align and convert to bed files.
Genome_build: hg19
|
| |
|
| Submission date |
Mar 01, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
H.G. Stunnenberg |
| E-mail(s) |
h.stunnenberg@ncmls.ru.nl
|
| Phone |
+31-24-3610520
|
| Organization name |
Radboud University
|
| Department |
Department of Molecular Biology (274)
|
| Street address |
Geert Grooteplein 28
|
| City |
Nijmegen |
| ZIP/Postal code |
6525 GA |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE44800 |
A Probabilistic Model of Transcription Dynamics applied to Estrogen Signalling in Breast Cancer Cells |
|
| Relations |
| SRA |
SRX248440 |
| BioSample |
SAMN01974738 |
