Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

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
cell line
MCF7
oxygen state
hypoxia
timepoint
24 hours
oxygen concentration
0.02%
chip antibody
anti-H3K4me3 (Abcam, catalog# Ab8580, lot# 1054726)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
MCF7 cells were transferred to hypoxic culturing conditions for the indicated durations and immediately fixed to avoid reoxygenation. After 24 hours of hypoxia, cells were reoxygenated for 8 hours. Cells were disrupted by sonication, yielding genomic DNA fragments ranging from 200-1000 bp, with a bulk size of 200-500bp. For each immunoprecipitation 10-20 million cells were used. ChIPs were performed and analyzed using standard protocols (antibody: H3K4me3 and H3K27me3 (07-449; Upstate)). ChIP-seq libraries were prepared for sequencing using standard 36 bp paired-end protocol for the Illumina Genome Analyser IIx (GAIIx). Two lanes were used per sample for sufficient coverage.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg38

Number of total reads
16745685
Reads aligned (%)
87.0
Duplicates removed (%)
1.2
Number of peaks
11247 (qval < 1E-05)

hg19

Number of total reads
16745685
Reads aligned (%)
86.4
Duplicates removed (%)
1.3
Number of peaks
11235 (qval < 1E-05)

Base call quality data from DBCLS SRA