Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
FOXJ3

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

Alias
E-MTAB-3687:FOXJ3_IP
Broker name
ArrayExpress
Description
Protocols: The stable cell lines were grown in DMEM supplement with 10% foetal bovine serum. Media contained 100 micro-g/ml of Hygromycin. Cells were cross-linked with Formaldehyde for 10 minutes. Expression of FOXJ3 was induced by treating the cells for 48 hours with 1 ug/ml doxycycline (Sigma). 'After reverse cross-link and protein digestion with Proteinase K (Roche), DNA was purified using Qiaquick, PCR purification kit (Qiagen) following the manufacturer''s instructions.' ChIP-seq was performed as described in Schmidt et al., 2009, using 60 x 10^6. Immuno-precipitation was performed overnight at 4 degrees C by incubating the shared DNA-protein complex with 6 ug of anti-Flag (Sigma) antibody previously coupled to Dynabeads protein G (Invitrogen). Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT. (2009) ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods 48: 240-248.
ENA checklist
ERC000011
INSDC center alias
University of Manchester
INSDC center name
University of Manchester
INSDC first public
2015-12-03T17:01:21Z
INSDC last update
2018-03-09T02:18:39Z
INSDC status
public
SRA accession
ERS781761
Sample Name
ERS781761
Title
FOXJ3_IP
cell line
U2OS
cell type
osteosarcoma
organism
Homo sapiens
sex
female

Sequenced DNA Library

library_name
FOXJ3_IP
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The stable cell lines were grown in DMEM supplement with 10% foetal bovine serum. Media contained 100 micro-g/ml of Hygromycin. Cells were cross-linked with Formaldehyde for 10 minutes. Expression of FOXJ3 was induced by treating the cells for 48 hours with 1 ug/ml doxycycline (Sigma). 'After reverse cross-link and protein digestion with Proteinase K (Roche), DNA was purified using Qiaquick, PCR purification kit (Qiagen) following the manufacturer''s instructions.' ChIP-seq was performed as described in Schmidt et al., 2009, using 60 x 10^6. Immuno-precipitation was performed overnight at 4 degrees C by incubating the shared DNA-protein complex with 6 ug of anti-Flag (Sigma) antibody previously coupled to Dynabeads protein G (Invitrogen). Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT. (2009) ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods 48: 240-248.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
40230573
Reads aligned (%)
98.0
Duplicates removed (%)
86.3
Number of peaks
739 (qval < 1E-05)

hg38

Number of total reads
40230573
Reads aligned (%)
98.9
Duplicates removed (%)
85.0
Number of peaks
1382 (qval < 1E-05)

Base call quality data from DBCLS SRA