Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
WDR5

Cell type

Cell type Class
Blood
Cell type
MV-4-11
Primary Tissue
Blood
Tissue Diagnosis
Leukemia Acute Myelogenous

Attributes by original data submitter

Sample

source_name
MV4:11
cell line
MV4:11
treatment
2 µM C6nc for 4 hours
chip antibody
Cell Signaling WDR5 (D9E1I)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-Seq experiments, chromatin was clarified from sonicated cell lysates by centrifugation and incubated overnight with corresponding antibodies. For RNA-Seq, cells were washed in PBS then lysed in 500 uL Trizol and total RNA was isolated using the Zymo Research Direct-zol RNA MiniPrep kit (Zymo Research #R2050) with on-column DNase digestion following the manufacturers instructions. For PRO-Seq experiments, nuclei were extracted through hypotonic lysis with a low amount of non-ionic detergent. For ChIP-Seq experiments, indexed libraries were made from precipitated DNA using the DNA Ultra II Kit (NEB) per the manufacturer's protocol. For RNA-Seq, library preperation was completed by Genewiz using their standard methods. For PRO-Seq experiments, libraries were made using RNA that was made through a biotin-run on reaction. Biotin-RNA was base hydrolyzed, and extracted. 3'-adaptors were ligated to ends and 5'caps were removed, repaired, and then 5'-adaptors were ligated as well. Purified and intact biotin-RNA containing adaptors was used in a reverase transcriptase reaction to generate cDNA and cDNA was used to amplify full library using NEB High Fidelity Phusion polymerase.

Sequencing Platform

instrument_model
Illumina HiSeq 3000

hg19

Number of total reads
72706178
Reads aligned (%)
21.6
Duplicates removed (%)
75.9
Number of peaks
1391 (qval < 1E-05)

hg38

Number of total reads
72706178
Reads aligned (%)
23.4
Duplicates removed (%)
74.2
Number of peaks
1379 (qval < 1E-05)

Base call quality data from DBCLS SRA