Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
HIF1A

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 cells
strain
ATCC HTB-96
tissue
bone
genotype
osteosacoma
chip antibody
hHIF1A active motif (cat # 39665).

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
total RNA was extracted using a RNeasy MinElute Cleanup Kit NEBNext DNA Library Prep Master Mix Set for Illumina for RNA-seq and NEXTflex ChIP-seq Kit, Bioo Scientific for chip-seq RNA-seq: total RNA was extracted using a RNeasy MinElute Cleanup Kit (QIAGEN, Catalog no. 74204). Double-stranded cDNA was synthesized according to the mRNA Sequencing Sample Preparation Guide (part#1004898 Rev.D, Illumina, San Diego, CA) and single-end libraries were prepared using the NEBNext DNA Library Prep Master Mix Set for Illumina (New England BioLabs, Catalog no.74204 E6040L). For RNA-seq of RNaseH treated MEF cells, the protocols were mainly adopted as previously described (Nat Methods 10: 623-629). For qRNA-seq of MEF cells, the GeneRead rRNA Depletion Kit (Qiagen) was used to remove ribosome RNA. Nascent RNA-seq of U2OS cells was performed as previously described (Science 322: 1845-1848), with the exception of not applying a strand specific method. ChIP-seq procedure as previously described (Cell. 2013 May 9;153(4):855-68). For the Bmal1 and IgG ChIP-seq, the RIPA buffer was diluted 1 to 10. For HIF1A CHIP-seq, protocols are used as described (ChIP-IT high sensitive kit (Cat# 53040, Active Motif)). The library was constructed using a commercially available kit (NEXTflex ChIP-seq Kit, Bioo Scientific). Samples were indexed using NEXTflex™ DNA Barcodes (Bioo Scientific). The library was qualified using an Agilent 2100 Bioanalyzer (Agilent) and quantified using KAPA Library Quantification Kits (Kappa Biosystems). Finally, the indexed libraries were sequenced using a HiSeq 2500 (Illumina).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
44345789
Reads aligned (%)
98.2
Duplicates removed (%)
5.8
Number of peaks
2227 (qval < 1E-05)

hg38

Number of total reads
44345789
Reads aligned (%)
99.0
Duplicates removed (%)
3.9
Number of peaks
2468 (qval < 1E-05)

Base call quality data from DBCLS SRA