Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
WDR5

Cell type

Cell type Class
Bone
Cell type
SKMNC
NA
NA

Attributes by original data submitter

Sample

source_name
SKMNC
cell line
Ewing sarcoma cell line SKMNC
chip antibody
WDR5 (Bethyl, A302-429A)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin from formaldehyde-fixed cells (3-10 x 10^6 cells per epitope) was fragmented to a size range of 200 - 700 bases with a Branson 250 Sonifier. Solubilized chromatin was immunoprecipitated with the indicated antibodies and Protein G-Dynabeads (Life Technologies). Immunoprecipitated DNA was extracted with the Mini-Elute PCR purification kit (Qiagen) after crosslink reversal, RNAse A and Proteinase K treatment. ChIP DNA samples were used to generate Illumina sequencing libraries following standard protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
15355904
Reads aligned (%)
99.5
Duplicates removed (%)
45.0
Number of peaks
3007 (qval < 1E-05)

hg38

Number of total reads
37726161
Reads aligned (%)
98.2
Duplicates removed (%)
43.5
Number of peaks
7992 (qval < 1E-05)

Base call quality data from DBCLS SRA