Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ESR1

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

source_name
MCF7
tissue
mammary gland
cell line
MCF7
chip antibody
F3A6 (to ERalpha, Gronemeyer)
treatment
10min

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_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.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg19

Number of total reads
32986622
Reads aligned (%)
78.3
Duplicates removed (%)
17.4
Number of peaks
29976 (qval < 1E-05)

hg38

Number of total reads
32986622
Reads aligned (%)
79.7
Duplicates removed (%)
16.6
Number of peaks
29915 (qval < 1E-05)

Base call quality data from DBCLS SRA