Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
USP7

Cell type

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

Attributes by original data submitter

Sample

source_name
293T-Rex
cell line
293T-Rex
chip antibody
anti-USP7 (Bethyl, catalog# A300-033A)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed in DMEM containing 10 mM Hepes, pH 7.6, 1% formaldehyde, 15 mM NaCl, 0.15 mM EDTA and 0.075 mM EGTA, for 10 min at room temperature. The reaction was quenched with 0.125 M glycine for 5 min at room temperature, cells were washed with PBS and lysed in 50 mM Hepes, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% Igepal CA630 and 0.25% Triton X-100. After centrifugation, isolated nuclei were washed once in 10 mM Tris pH 8.0, 200 mM NaCl, 1 mM EDTA and 0.5 mM EGTA, then resuspended in 10 mM Tris, pH 8.0, 1 mM EDTA, 0.5 mM EGTA and 0.5% N-Lauryl Sarcosine, and sonicated using a Diagenode Bioruptor to an average chromatin size of 200 bp. Libraries were prepared according to manufacturer’s instructions (Illumina). Immunoprecipitated DNA was first end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), and ligated to custom adapters with LigaFast (Promega, city, state #M8225). Fragments of 300±50 bp were size-selected and subjected to ligation-mediated PCR amplification (LM-PCR), using Phusion DNA polymerase (NEB M0530).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
71375576
Reads aligned (%)
59.9
Duplicates removed (%)
35.8
Number of peaks
1294 (qval < 1E-05)

hg38

Number of total reads
71375576
Reads aligned (%)
61.5
Duplicates removed (%)
34.4
Number of peaks
1226 (qval < 1E-05)

Base call quality data from DBCLS SRA