Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ZEB1

Cell type

Cell type Class
Breast
Cell type
MDA-MB-231
Primary Tissue
Breast
Site of Extraction
Effusion, Pleural
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

ENA first public
2020-07-22
ENA last update
2019-08-19
ENA-CHECKLIST
ERC000011
External Id
SAMEA5871631
INSDC center alias
Department of Experimental Medicine 1, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-University Erlangen-Nurnberg, Erlangen, Germany
INSDC center name
Department of Experimental Medicine 1, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-University Erlangen-Nurnberg, Erlangen, Germany
INSDC first public
2020-07-22T08:04:40Z
INSDC last update
2019-08-19T11:14:55Z
INSDC status
public
SRA accession
ERS3660117
Sample Name
E-MTAB-8258:ZEB1_ChIPseq_replicate1
Submitter Id
E-MTAB-8258:ZEB1_ChIPseq_replicate1
age
51
broker name
ArrayExpress
cell line
MDAMB231
cell type
mammary epithelial cell
common name
human
developmental stage
adult
disease
breast adenocarcinoma
genotype
wild type genotype
organism part
mammary gland
title
ZEB1_ChIPseq_replicate1

Sequenced DNA Library

library_name
ZEB1_ChIPseq_replicate1_p
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin was cross-linked by 1.5mM EGS for 30min followed by 1% formaldehyde for 10min at room temperature (RT). Crosslinking was stopped by adding glycine to a final concentration of 125mM for 5min at RT. Cells were lysed in NP40 lysis buffer containing protease inhibitors and disrupted by dounce homogenisation. MDA-MB-231 cells were purchased from the American Type Culture Collection (ATCC) and cultured under standard conditions in DMEM (Gibco) supplemented with 10 % fetal bovine serum (Gibco). Nulcei were lysed and sonicated with a Diagenode Bioruptor to a fragment size of 300 to 500bp. Chromatin was collected and precleared with protein A and G Dynabeads. Chromatin-immunoprecipitation was performed using an anti-ZEB1 antibody (Santa Cruz, SC-H102-X). Immuncomplexes were captured using Dnyabeads and DNA was extracted by QIAquick columns (MinElute). Several IPs were pooled for sequencing. Library preparation was performed with the NEBNext® Ultra DNA Library Prep Kit according to the manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
38200282
Reads aligned (%)
125.9
Duplicates removed (%)
16.3
Number of peaks
3326 (qval < 1E-05)

hg38

Number of total reads
38200282
Reads aligned (%)
127.2
Duplicates removed (%)
16.0
Number of peaks
3575 (qval < 1E-05)

Base call quality data from DBCLS SRA