Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MAX

Cell type

Cell type Class
Unclassified
Cell type
Unclassified
NA
NA

Attributes by original data submitter

Sample

source_name
COL0829
sirna
N/A
antibody
MAX

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were prepared from sonicated cells and TF-DNA complexes were isolated with antibody. An Illumina sequencing library was prepared from DNA using the NEBNext ChIP-seq library prep reagent set for Illumina (New England Biolabs) as per manufacturer's protocol with DNA purification using Qiaquick PCR purification or Minelute PCR purification kits and 2% agarose gel DNA size selection. The library was sequenced with an Illumina HiSeq 2500 (Rapid Run, single-end, 50 bp)

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
45866545
Reads aligned (%)
19.4
Duplicates removed (%)
80.0
Number of peaks
2450 (qval < 1E-05)

hg38

Number of total reads
45866545
Reads aligned (%)
20.4
Duplicates removed (%)
79.1
Number of peaks
2495 (qval < 1E-05)

Base call quality data from DBCLS SRA