Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
HSF1

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
HSF1 ChIP DNA from cells heat shocked at 43°C for 10 minutes
cell line
U-2 OS
antibody
anti-HSF1
Sex
female
tissue/cells
bone/osteosarcoma
age
15 years

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed by adding of formaldehyde to a final concentration of 1% and incubated at room temperature for 10 minutes. Next 2.5 M glycine was added (1/20 volume) for 5 minutes. Cells were washed with ice-cold PBS and lysed following the manufacturer’s protocol. For analyses of HSF1 binding, the ChIP assay was carried out according to protocol for ChIP kit of Invitrogen (Dynabeads Protein A). For 40 µg of chromatin, sonicated to 100-500 bp fragments and 4 µg of rabbit anti-HSF1 (cat. no SPA-901, Enzo) polyclonal antibodies were used. Sequencing libraries were generated using ChIP-Seq Sample Prep Kit (Illumina). Template amplification and cluster generation were performed using the cBot and TruSeq SR Cluster Kit v2 cBot-GA for cBot, and 80 nucleotides were sequenced with Illumina Genome Analyzer IIx using TruSeq SBS Kit v5 sequencing kits.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg19

Number of total reads
41622402
Reads aligned (%)
84.8
Duplicates removed (%)
59.9
Number of peaks
11115 (qval < 1E-05)

hg38

Number of total reads
41622402
Reads aligned (%)
86.1
Duplicates removed (%)
58.1
Number of peaks
11569 (qval < 1E-05)

Base call quality data from DBCLS SRA