Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
HSF1

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
estrogen treated for 1hour (10nM)
cell line
MCF7
tumor
adenocarcinoma
Sex
female
age
69 years
tissue/cells
breast
chip antibody
HSF1 polyclonal antibody (Enzo, ADI-SPA-901)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
At the appointed experimental points culture medium was removed and fixation was performed using 1% formaldehyde in PBS for 12 min at RT with rotating. Formaldehyde fixation was quenched by glycine (125 mM final concentration) and then nuclei were isolated using buffers and protocol from iDeal ChIP-seq Kit for Transcription Factors (Diagenode). Chromatin of nuclei re-suspended in 200 µl was sheared using Bioruptor® PLUS combined with the Bioruptor® Water cooler & Single Cycle Valve (at HIGH power setting) with 20 cycles of 30 sec shearing followed by 30 sec of standby; chromatin fragments with approximate length 100-600 bp were obtained. Chromatin immunoprecipitation was carried out using the iDeal ChIP-seq Kit for Transcription Factors (Diagenode) with 30μg of chromatin and 3µl/sample of anti-HSF1 polyclonal antibody (ADI-SPA-901, Enzo) or without antibody (mock-IP), according to the manufacturer protocol. Immunoprecipitated DNA fragments from six ChIP replicates was pooled. ChIP samples and input DNA were sequenced using the HiSeq 1500 system with TruSeq workflow (Illumina)

Sequencing Platform

instrument_model
Illumina HiSeq 1500

hg19

Number of total reads
41907853
Reads aligned (%)
88.5
Duplicates removed (%)
7.2
Number of peaks
1878 (qval < 1E-05)

hg38

Number of total reads
41907853
Reads aligned (%)
90.4
Duplicates removed (%)
5.9
Number of peaks
1934 (qval < 1E-05)

Base call quality data from DBCLS SRA