Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

Cell type

Cell type Class
Breast
Cell type
MCF-7
Primary Tissue
Breast
Site of Extraction
Pleura
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

ENA first public
2010-06-12
ENA last update
2018-03-08
External Id
SAMEA717119
INSDC center alias
CRUK-CRI
INSDC center name
CRUK-CRI
INSDC first public
2010-06-12T00:00:34Z
INSDC last update
2018-03-08T15:25:00Z
INSDC status
public
Submitter Id
E-TABM-828:SA1_breast_ab4457_hsa_CTCF_kd 1
broker name
ArrayExpress
cell line
MCF7
common name
human
organism part
breast
sample name
E-TABM-828:SA1_breast_ab4457_hsa_CTCF_kd 1
sex
female

Sequenced DNA Library

library_name
SA1_breast_ab4457_hsa_CTCF_kd 1
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were grown in phenol red-free DMEM supplemented with 5% charcoal dextran treated serum for at least three days (cell cycle analysis) or in full media (RNAi-ChIP-seq). Cells were transfected with siRNA for 48 hours using Lipofectamine2000 (Invitrogen, CA, USA). AllStars Negative Control siRNA (Qiagen) was used as negative (mock) controls. CTCF RNAi (Invitrogen Stealth, sense: GCGCUCUAA-GAAAGAAGAUUCCUCU, antisense: AGAGGAAUCUUCUUUCUUAGAGCGC). RAD21#1 (Invitrogen Stealth; sense: CAGCUUGAAUCAGAGUAGAGUGGAA, antisense: UUCCACUCUACUCUGAUUCAAGCUG) RAD21#2 (ON-TARGETplus SMARTpool L-006832) ChIP experiments were performed with well-characterized antibodies against CTCF (Millipore, 07-729), STAG1 (abcam, ab4457), RAD21 (abcam, ab992), ERa (santa cruz, sc-543), CEBPa (santa cruz, sc-9314) and MED12 (abcam, ab70842). ChIP-seq experiments were performed as recently described (Schmidt et al. 2009)

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg38

Number of total reads
31204432
Reads aligned (%)
96.2
Duplicates removed (%)
13.5
Number of peaks
41102 (qval < 1E-05)

hg19

Number of total reads
31204432
Reads aligned (%)
95.6
Duplicates removed (%)
14.5
Number of peaks
40864 (qval < 1E-05)

Base call quality data from DBCLS SRA