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Sample GSM1091921 Query DataSets for GSM1091921
Status Public on May 19, 2014
Title MCF7_No_Treat_PolII
Sample type SRA
 
Source name Breast cancer cells
Organism Homo sapiens
Characteristics cell line: MCF7
time point: none
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 SRX248447
BioSample SAMN01974745

Supplementary file Size Download File type/resource
GSM1091921_MCF7_No_Treat_PolII_unique.bed.gz 1.4 Gb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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