Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Kidney
Cell type
293
Primary Tissue
Kidney
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
HEK293 cells, IgG.shRECQL5-5
cell line
HEK293
chip antibody
Non-specific IgG control
treatment
RECQL5 shRNA 5

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were cross-linked with formaldehyde 1% final. Nuclei were extracted in low salt conditions and burst in high salt before shearing the DNA to reduce the size to 300-400 bp and performing ChIP with an RNA Pol II specific antibody. DNA libraries were prepared according to Illumina's instructions and run on a GAIIX sequencer

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg38

Number of total reads
37327970
Reads aligned (%)
85.7
Duplicates removed (%)
5.3
Number of peaks
996 (qval < 1E-05)

hg19

Number of total reads
37327970
Reads aligned (%)
84.9
Duplicates removed (%)
6.7
Number of peaks
1260 (qval < 1E-05)

Base call quality data from DBCLS SRA