Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BRD4

Cell type

Cell type Class
Others
Cell type
TT
Primary Tissue
Thyroid
Tissue Diagnosis
Carcinoma Medullary

Attributes by original data submitter

Sample

source_name
TT medullary thyroid cancer cells
cell line
TT medullary thyroid cancer cells
chip antibody
BRD4 (Bethyl, cat: A301-985A100, lot: A301-985A50-6)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Lysates were sonicated with a microtip sonicator to shear the DNA. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. For each ChIP reaction, 30 ug of chromatin was precleared with protein A agarose beads (Invitrogen). ChIP reaction was set up using precleared chromatin and antibody and incubated overnight at 4 C. Protein A agarose beads were added and incubation at 4 C was continued for another 3 hr. Immune complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on HiSeq 2500/NextSeq 500.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
38740338
Reads aligned (%)
79.8
Duplicates removed (%)
16.7
Number of peaks
1540 (qval < 1E-05)

hg38

Number of total reads
38740338
Reads aligned (%)
82.1
Duplicates removed (%)
15.0
Number of peaks
1735 (qval < 1E-05)

Base call quality data from DBCLS SRA