Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RELA

Cell type

Cell type Class
Kidney
Cell type
293
Primary Tissue
Kidney
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
p65-ChIP-TNF-12h
strain background
Human embryonic kidney
cell line
HEK 293 transfected with reporter construct
cell type
somatic cell
genotype/variation
TNF-a-treatment-12h
tissue
embryonic kidney
developmental stage
embryos
library strategy
ChIP
antibody
sc-372, Santa Cruz

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Total RNA of cells was isolated using RNeasy Mini Kit (Qiagen), and cDNA were sythesised using PrimeScript first strand cDNA synthesis kit (Takara) with oligo-dT. ChIP-seq were performed as previously described (Xiong et al, Molecular Cell 64, 913-925). P65 antibody (Cat# sc-372) was purchased from Santa Cruz. The ChIP-seq libraries were constructed using NEBNext DNA Sample Prep Master Mix (NEB).DNA libraries were subjected to size-selection using AMPure XP beads (Beckman Coulter) and PCR amplification (18-20 cycles for ChIP-seq DNA libraries). The RNA-seq libraries were constructed by BGI, Shenzhen, as the platform BGISEQ-500 instruction described.

Sequencing Platform

instrument_model
Illumina NovaSeq 6000

hg19

Number of total reads
22822275
Reads aligned (%)
106.2
Duplicates removed (%)
27.9
Number of peaks
716 (qval < 1E-05)

hg38

Number of total reads
22822275
Reads aligned (%)
107.3
Duplicates removed (%)
27.7
Number of peaks
862 (qval < 1E-05)

Base call quality data from DBCLS SRA