Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
HIF1A

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

source_name
MDA-MB-231 cells
cell line
MDA-MB-231 cells
chip antibody
HIF-1alpha (Bethyl Laboratories, Cat.# A300-286A)
treatment
1% O2

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Total RNA was isolated using a RNeasy Mini kit and treated with DNase (Qiagen). Chromatin was isolated using a SimpleChIP Enzymatic Chromatin IP kit (Cell Signaling Technology), sonicated to 200-300 bp in length, and subjected to immunoprecipitation overnight with respective antibodies. The ChIP DNA was eluted, decrosslinked, and purified. mRNA-seq libraries were prepared with a TruSeq Stranded mRNA Library Prep kit (Illumina). ChIP-seq libraries were prepared with a KAPA Hyper Library Preparation kit.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
38064732
Reads aligned (%)
90.6
Duplicates removed (%)
7.4
Number of peaks
1255 (qval < 1E-05)

hg38

Number of total reads
38064732
Reads aligned (%)
92.7
Duplicates removed (%)
6.2
Number of peaks
1235 (qval < 1E-05)

Base call quality data from DBCLS SRA