Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me1

Cell type

Cell type Class
Gonad
Cell type
IOE11
NA
NA

Attributes by original data submitter

Sample

source_name
ovarian epithelial cell line
cell line
IOE4
tissue
ovarian epithelial cells
antibody
H3K4me1 (Abcam ab8895)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For each cell line, four 15 cm culture dishes of approximately 90% confluent cells were cross-linked in 1% formaldehyde for 10 min at room temperature before lysing cells in SDS buffer and sonicating to shear genomic DNA to approximately 100-500 bp fragments. Insoluble cell debris was discarded, and the supernatant from pairs of dishes were combined to represent two biological replicates per cell line. The material was divided into aliquots for input, FAIRE and ChIP. Immunoprecipitations were performed overnight at 4°C using antibodies against H3K27ac (Abcam ab4729) and H3K4me1 (Abcam ab8895) followed by incubation with protein A/G agarose beads (Pierce). Following washing and elution from beads, the DNA was ethanol precipitated, and the pellet washed with 70% ethanol. Recovered DNA was re-suspended in water for sequencing. Purification and recovery of FAIRE material was performed as previously described in parallel with ChIP to ensure that annotation of open chromatin/nucleosome depletion was performed from the same cell lysate sample as annotation of histone acetylation and methylation marks.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
53391636
Reads aligned (%)
96.5
Duplicates removed (%)
3.2
Number of peaks
53730 (qval < 1E-05)

hg19

Number of total reads
53391636
Reads aligned (%)
96.1
Duplicates removed (%)
4.0
Number of peaks
54348 (qval < 1E-05)

Base call quality data from DBCLS SRA