Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
WDR5

Cell type

Cell type Class
Breast
Cell type
Breast cancer cells
NA
NA

Attributes by original data submitter

Sample

source_name
Human Breast Cancer (BC) cell line
cell type
original BC cell line
growth protocol
DMEM/F12 supplemented with 5% Horse Serum, 2mM L-Glutamine, 1% Pen/Strep, 10mM HEPES and 1.05mM CaCl2
antibody
Anti-WDR5 (Antibody from Diego Pasini Lab)
treatment
Cells were infected with pRSI-U6-shLuc-UbiC-TagRFP-2A-Puro vector and selectioned with 3µg/ml of Puromycin

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP lysates were generated from 10-15x10^6 cells. Briefly, after cross-linking (1% formaldehyde), cells were lysed in SDS buffer (100 mM NaCl, 50 mM Tris HCl pH 8.1, 5 mM EDTA pH 8, 0.5% SDS, and protease inhibitors) and sonicated in IP buffer (100 mM NaCl, 100 mM Tris-HCl pH 8.1, 5 mM EDTA pH 8, 0.3% SDS, 1.7% Triton X-100) prior to overnight incubation with antibodies against respective antibodies. DNA was eluted in TE containing 2% SDS and crosslinks reversed by incubation overnight at 65ºC. DNA was then purified by QIAquick columns (Qiagen) and quantified by using Qubit for dsDNA (Thermo Fisher Scientific). ChIP DNA was prepared for HiSeq 2000 Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, PCR with index primers and purification. A mixture of T4 DNA polymerase, DNA polymerase I and T4 kinase was used according to manufacturer's instruction. Library preparation is carried out on SPRIworks Fragment Library System.

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

hg19

Number of total reads
66314761
Reads aligned (%)
48.5
Duplicates removed (%)
47.0
Number of peaks
2379 (qval < 1E-05)

hg38

Number of total reads
66314761
Reads aligned (%)
50.4
Duplicates removed (%)
45.3
Number of peaks
2261 (qval < 1E-05)

Base call quality data from DBCLS SRA