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Sample GSM1614034 Query DataSets for GSM1614034
Status Public on Aug 03, 2015
Title TEAD4_rep1_ChIPSeq
Sample type SRA
Source name MDA-MB-231 breast cancer cells
Organism Homo sapiens
Characteristics cell line: MDA-MB-231
chip antibody: TEF-3 (N-G2) (SCBT, sc-101184, lot C2812)
Growth protocol MDA MB 231 cells were cultured in DMEM:F12 + 10% FBS.
Extracted molecule genomic DNA
Extraction protocol Cross-linked chromatin was sheared by sonication and immunoprecipitated with YAP, TAZ, TEAD4 and JUN antibodies. DNA was purified by phenol/chloroform extraction and ethanol precipitation.
NuGEN Ovation Ultralow Library Prep System kit
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
Description Pooling of IgG_rep3_ChIPSeq and IgG_rep4_ChIPSeq was used as control for Peak calling within the IDR framework
processed data file: MDA-MB-231_TEAD4_IDR_0.01.narrowPeak
Data processing Basecalls performed using CASAVA version v1.8.2
Raw reads were aligned using Bowtie (version 0.12.7) (Langmead et al., 2009) to build version hg19 of the human genome retaining only uniquely mapped reads. Redundant reads were removed using SAMtools
The IDR (Irreproducible Discovery Rate) framework was used to assess the reproducibility of replicate experiments and to obtain a single set of peak calls for each TF (Landt et al., 2012)
MACS2 version 2.0.10 (Zhang et al., 2008) was used to call peaks in individual replicates using IgG ChIP-seq as control sample and an IDR threshold of 0.01 was applied for all datasets to identify an optimal and robust number of peaks
Genome_build: hg19
Supplementary_files_format_and_content: NarrowPeak files contain the genomic locations of peaks identified using MACS2 and the IDR framework. NarrowPeak format is a BED6+4 format (
Submission date Feb 19, 2015
Last update date May 15, 2019
Contact name Silvio Bicciato
Phone +39-049-827-6108
Organization name University of Padova
Department Molecular Medicine
Street address via U. Bassi 59/b
City Padova
ZIP/Postal code 35131
Country Italy
Platform ID GPL16791
Series (2)
GSE66081 Widespread association between YAP/TAZ/TEAD and AP-1 at enhancers drives oncogenic growth [ChIP-Seq]
GSE66083 Widespread association between YAP/TAZ/TEAD and AP-1 at enhancers drives oncogenic growth
BioSample SAMN03354188
SRA SRX883582

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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