Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ZBTB48

Cell type

Cell type Class
Uterus
Cell type
HeLa
Primary Tissue
Cervix
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
HeLa cell line, ZBTB48 KO, ZBTB48 ChIP
cell line
HeLa
genotype/variation
ZBTB48 KO
chip antibody
ZBTB48 (ab1)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Subconfluent HeLa and U2OS cells were washed twice with cold PBS and double cross-linked first with 2 mM DSG (Pierce, predissolved in DMSO) in PBS for 45 min at RT, intermitted by a wash with cold PBS and secondly with 1% formaldehyde in DMEM for 20 min at RT. The formaldehyde was quenched with glycine (0.125 M final concentration) for 5 min at RT, cells were scraped with a plastic scraper and washed once in PBS. For lysis, cells were resuspended in buffer 1 (50 mM Tris-HCl pH 8.0, 250 mM sucrose, 140 mM NaCl, 1 mM EDTA pH 8.0, 10% glycerol, 0.5% IGEPAL-630 (Sigma-Aldrich), 0.25% Triton X-100, 0.25% Tween20) for 15 min, pelleted and subsequently resuspended in buffer 2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0) for 10 min both at 4 ºC. Sonication was performed in 1.5 ml sonication buffer (1% SDS, 10 mM EDTA pH 8.0, 50 mM Tris-HCl pH 8.0) with a Branson Digital Sonifier S-450D for 7.5 min (30% amplitude, 10 sec on, 20 sec off). Library preparation was performed with the NuGEN Ovation Ultralow Library System V2 1-96. Libraries were prepared with a starting amount of 124-6869pg of ChIP DNA and 10-145ng of input DNA were amplified in 13-18 PCR cycles, depending of the starting material used. Libraries were profiled on a 2100 Bioanalyzer (Agilent) and quantified using the Qubit dsDNA HS Assay Kit on a Qubit 2.0 Fluorometer (Thermo Fisher). Size selection was performed with Lab ChIP XT with XT DNA 700 chips (Perkin Elmer) for the 300-500 bp fragment range according to the manufacturer's instructions. Libraries were pooled in equimolar ratio and sequenced on a HiSeq (Illumina), 50bp SR in high-output mode plus 7 cycles for the index read.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
38518453
Reads aligned (%)
22.6
Duplicates removed (%)
70.3
Number of peaks
7049 (qval < 1E-05)

hg38

Number of total reads
38518453
Reads aligned (%)
23.1
Duplicates removed (%)
69.8
Number of peaks
5929 (qval < 1E-05)

Base call quality data from DBCLS SRA