|
| Status |
Public on Aug 03, 2015 |
| Title |
TEAD4_rep2_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
2c-140612_ep_GTGGCC_L005_R1_001.fastq.gz
2c-140612_ep_GTGGCC_L006_R1_001.fastq.gz
|
| 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 (http://genome.ucsc.edu/FAQ/FAQformat.html#format12)
|
| |
|
| Submission date |
Feb 19, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Silvio Bicciato |
| E-mail(s) |
silvio.bicciato@unipd.it
|
| 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 |
|
| Relations |
| BioSample |
SAMN03354182 |
| SRA |
SRX883583 |
