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Sample GSM2467221 Query DataSets for GSM2467221
Status Public on Apr 18, 2017
Title MCF7_E2_5min_ERalpha
Sample type SRA
 
Source name MCF7
Organism Homo sapiens
Characteristics tissue: mammary gland
cell line: MCF7
chip antibody: F3A6 (to ERalpha, Gronemeyer)
treatment: 5min
Treatment protocol MCF-7 cells were mock treated or with 10nM 17b-E2 at a series of time points.
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 using the Transcription factor protocol. Settings: 20 min cross-linking and 20min sonication for H3K4me3 and H2A.Zac, 15min resp. 10min for F3A6 (to ERalpha). 100 µl chromatin and 2.5µl antibody. Pooled 2 samples.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
 
Description 2730
Data processing Mapping was done using the GenomatixMapper software (version 3.4) onto the hg19 whole genome for the given time points. No trimming was applied to the reads. Only reads mapping uniquely to the genome with at most 2 mismatches were reported.
Genome_build: NCBI build37
Supplementary_files_format_and_content: tag files in bed format
 
Submission date Jan 24, 2017
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 Netherlands
 
Platform ID GPL10999
Series (1)
GSE94023 MCF7 breast cancer cell response to estradiol
Relations
BioSample SAMN06252900
SRA SRX2513517

Supplementary file Size Download File type/resource
GSM2467221_5minERa_relaxed_1e-11_no_lambda_peaks.bed.gz 684.6 Kb (ftp)(http) BED
GSM2467221_MCF7_5min_ERa_2012-03_unique.bed.gz 442.3 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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