Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
NUTM1

Cell type

Cell type Class
Lung
Cell type
24335
NA
NA

Attributes by original data submitter

Sample

source_name
24335
chip antibody
NUT (anti-NUT, 15 ul per IP; Cell Signaling, catalog no. 3625)
cell type
NMC
cell line
ZNF532-NUT 24335
agent
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The main steps of BioTAP-XL procedure: harvesting cells, formaldehyde cross-linking, chromatin preparation, affinity purification, input and IP protein recovery were performed as described (12, 36). Cross-linked chromatin for ChIP-seq experiments using antibodies against proteins and histone modifications was prepared from 5 × 10(8) 24335 (ZNF532-NUT) NMC cells as described (36). Nascent RNA was purified as described (3). Each RNA library was constructed from 50 ng of nascent RNA following the manufacturer’s instructions (NEBNext Ultra directional RNA library prep kit, New England BioLabs) ChIP-seq library preparation were performed as described (Alekseyenko et al. 2015). RNA library was constructed from 50 ng of nascent RNA following the manufacturer’s instructions (NEBNext Ultra directional RNA library prep kit, New England BioLabs)

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
36634797
Reads aligned (%)
193.0
Duplicates removed (%)
1.7
Number of peaks
638 (qval < 1E-05)

hg38

Number of total reads
36634797
Reads aligned (%)
194.5
Duplicates removed (%)
1.6
Number of peaks
768 (qval < 1E-05)

Base call quality data from DBCLS SRA