Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Breast
Cell type
HMLE
NA
NA

Attributes by original data submitter

Sample

source_name
Mesenchymal derivatives of HMLE cells
cell type
NAMEC8
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was performed using the SimpleChIP® Plus Enzymatic Chromatin IP Kit (Magnetic Beads) (Cell Signaling Technology; #9005); PHF2 Antibody (Cell Signaling Technology, Catalog #3497 Lot#2) To make libraries, TruSeq ChIP protocol was followed as described in the kit (Illumina; Catalog # IP-202-1012) manual Libraries were pooled together and sequenced on the HiSeq 2500 sequencer using the Standard sequencing protocols. Images analysis and base calling was done using the Standard Illumina pipeline, and then demultiplexed into fastq files

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
40742433
Reads aligned (%)
90.3
Duplicates removed (%)
4.3
Number of peaks
1063 (qval < 1E-05)

hg19

Number of total reads
40742433
Reads aligned (%)
89.5
Duplicates removed (%)
5.7
Number of peaks
1276 (qval < 1E-05)

Base call quality data from DBCLS SRA