Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

Cell type Class
Breast
Cell type
HMLE
NA
NA

Attributes by original data submitter

Sample

source_name
HMLE-S4
cell line
HMLE-S4
treatment
DOX+
ip
H3K27ac

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was performed as described previously (PMID:23832113) using the following antibodies: 10μg of SOX4 antibody (CS-129-100, Diagenode), 5μg H3K4me3, H3K27ac, (ab8580, ab4729, Abcam), 5μg anti-RBP1 (PB-7C2, RNAPII) antibody (Euromedex), and 5μg H3K27me3 (39157, Active Motif). Truseq nano DNA sample preparation kit 10 (Illumina) was used for End-repair, A-tailing, and ligation of sequence adaptors. Samples were subsequently PCR amplified after which the libraries were size selected to remove adapter dimers and select fragments in the 200-500bp range. Barcoded libraries were sequenced on Illumina NextSeq500 sequencer (75bp, single-end, Utrecht DNA sequencing facility).

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
51837764
Reads aligned (%)
79.9
Duplicates removed (%)
14.8
Number of peaks
58792 (qval < 1E-05)

hg19

Number of total reads
51837764
Reads aligned (%)
79.7
Duplicates removed (%)
14.8
Number of peaks
58583 (qval < 1E-05)

Base call quality data from DBCLS SRA