Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RELA

Cell type

Cell type Class
Kidney
Cell type
Renal cell carcinoma
NA
NA

Attributes by original data submitter

Sample

source_name
ccRCC cell line
transcription factor
NFkB
chip antibody
NFĸB p65 (sc-372, Santa Cruz)
source
786-O (ATCC CRL1932)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For each transcription factor, ~3x107 cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and stopped by adding glycine to a final concentration of 0.2M. Chromatin was extracted and sonicated to ~500bp (Vibra cell, SONICS). The total volume of immunoprecipitation was 1.5 ml and the amount of antibody used was 15 µg. The input DNA was precleared with protein G Dynabeads (LifeTechnologies) for 2 hr at 4°C and then incubated with antibodies conjugated protein G beads overnight at 4°C. The beads were washed 6 times with wash buffer at room temperature. Amplified DNA was used with NEBNext ChIP-Seq library prep reagent set (NEB)

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
71012417
Reads aligned (%)
52.0
Duplicates removed (%)
39.2
Number of peaks
16327 (qval < 1E-05)

hg38

Number of total reads
71012417
Reads aligned (%)
52.8
Duplicates removed (%)
38.5
Number of peaks
16656 (qval < 1E-05)

Base call quality data from DBCLS SRA