Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
NUTM1

Cell type

Cell type Class
Others
Cell type
TC-797
NA
NA

Attributes by original data submitter

Sample

source_name
TC-797 cultured cells
cell type
NUT carcinoma
cell line
TC-797
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
37760328
Reads aligned (%)
88.7
Duplicates removed (%)
6.5
Number of peaks
1005 (qval < 1E-05)

hg38

Number of total reads
37760328
Reads aligned (%)
90.7
Duplicates removed (%)
5.2
Number of peaks
968 (qval < 1E-05)

Base call quality data from DBCLS SRA