Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SUPT5H

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
U2OS
treatment
None
sirna
siCTR
antibody
Spt5 D3 X scbt; Lot:B1310

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were treated with 1% formaldehyde for 10 min at 37 °C. After cell lysis, nuclei were re-suspended in RIPA buffer (10 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% NP40, 1% deoxycholic acid (DOC), 0.1% SDS, 1 mM EDTA) and DNA was fragmented to a size <300 bp using a Branson sonifier. Chromatin was immunoprecipitated with 15 µg of corresponding antibody for 6 hours. Chromatin was eluted with 1% SDS and crosslinking was reverted overnight. For purification, chloroform/phenol extraction was used. NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina®. Purified DNA was end-repaired, A-tailed, ligated to Illumina adaptors, size-selected (200 bp) and purified with Qiagen gel extraction kit. DNA fragments were amplified by 16 and 17 cycles of PCR and library size was tested with the Fragment Analyzer (Advanced Analytical). The amount of library DNA was quantified using a picogreen assay

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
33992312
Reads aligned (%)
99.6
Duplicates removed (%)
84.0
Number of peaks
7291 (qval < 1E-05)

hg38

Number of total reads
33992312
Reads aligned (%)
99.7
Duplicates removed (%)
83.2
Number of peaks
7298 (qval < 1E-05)

Base call quality data from DBCLS SRA