Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ZBTB48

Cell type

Cell type Class
Bone
Cell type
U2OS
Tissue
bone
Lineage
mesoderm
Description
osteosarcoma from the tibia of a 15 year old, J. Ponten and E. Saksela derived this line (originally 2T) in 1964 from a moderately differentiated sarcoma, viruses were not detected during co-cultivation with WI-38 cells or in CF tests against SV40, RSV or adenoviruses, mycoplasma contamination was detected and eliminated in 1972, (PMID: 6081590)

Attributes by original data submitter

Sample

source_name
U2OS cell line, WT, ZBTB48 ChIP
cell line
U2OS
genotype/variation
WT
chip antibody
ZBTB48 (ab2)

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
44951500
Reads aligned (%)
88.0
Duplicates removed (%)
68.4
Number of peaks
19268 (qval < 1E-05)

hg38

Number of total reads
44951500
Reads aligned (%)
88.6
Duplicates removed (%)
67.4
Number of peaks
19509 (qval < 1E-05)

Base call quality data from DBCLS SRA