Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RELA

Cell type

Cell type Class
Digestive tract
Cell type
SW 480
Primary Tissue
unresolved
Tissue Diagnosis
unresolved

Attributes by original data submitter

Sample

source_name
SW480_16 hr TNF-α p65 ChIP-seq
cell line
SW480
cell type
Human Colon Cancer Cell Line
chip antibody
12.5 ng ml-1 TNF-α for 16 hr
chip antibody
anti-p65 (sc372x)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For GRO-seq analyses, nuclei were prepared and used for run-on reactions using BrUTP. Following nascent RNA enrichment with anti-BrdU agarose beads (SCBT), RNA was extracted using TRIzol LS reagent and used for library preparation. For ChIP, lysates from sonicated nuclei were prepared and protein-DNA complexes were IP'd with corresponding antibodies. For RNA-seq, total RNA was extracted using TRIzol LS reagent and strand-specific libraries were prepared from 1 mg of RNA ChIP-seq libraries were prepared according to Illumina's ChIP Truseq protocol. RNA-seq libraries were prepared following the dUTP second strand cDNA method using NEXTflex barcodes. GRO-seq libraries were prepared similarly. Please refer to the methods section for detailed protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg19

Number of total reads
34528256
Reads aligned (%)
19.0
Duplicates removed (%)
80.6
Number of peaks
9406 (qval < 1E-05)

hg38

Number of total reads
34528256
Reads aligned (%)
20.0
Duplicates removed (%)
79.7
Number of peaks
9391 (qval < 1E-05)

Base call quality data from DBCLS SRA