Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
NUTM1

Cell type

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

Attributes by original data submitter

Sample

source_name
293TRex-Flag-BRD4-NUT-HA cultured cells
cell type
Human embryonic kidney
cell line
293TRex-Flag-BRD4-NUT-HA
chip antibody
NUT (C52B1) Rabbit mAb (Cell Signaling Technology Signaling #3625S, lot 4 RRID: AB_2066833)
spike-in
Drosophila melanogaster Kc167 cells

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Human cells were mixed with Drosophila cells at a 2:1 ratio and then cells were cross-linked with 1% EM-grade paraformaldehyde. Cells were lysed with detergent and chromatin solubilized by shearing (for H3K27ac IP) or shearing and enzymatic digestion (for BRD4-NUT IP). An aliquot was removed as the input control and the samples then immunoprecipitated with the respective antibody. DNA-protein cross-links were reversed and the DNA then purified. DNA was prepared for next-generation sequencing using a NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs).

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
35274598
Reads aligned (%)
90.0
Duplicates removed (%)
6.2
Number of peaks
2534 (qval < 1E-05)

hg38

Number of total reads
35274598
Reads aligned (%)
92.0
Duplicates removed (%)
4.6
Number of peaks
2506 (qval < 1E-05)

Base call quality data from DBCLS SRA