Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Breast
Cell type
HC11 Mammary Epithelium
Tissue
Mammary
Cell Type
Epithelium (Immortalized And Nontransformed)

Attributes by original data submitter

Sample

source_name
HC11
cell type
Mammary epithelial cells
passage
4 to 7 (<10)
chip antibody
control IgG
strain
BALB/c

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were scraped and sonicated utilizing Diagenode Bioruptor at High setting and cycling 30 seconds ON, 30 seconds OFF. Ovol2-DNA complexes were isolated with lab generated anti-Ovol2 antibody specific against mouse. Libraries were prepared according to instructions for BiooScientific NEXTflex ChIP-Seq Library Systems. Specifically, DNA quality and fragment size was assessed by Qubit Sensitivity DNA assay, and the following library preparation steps were achieved with the following mixes: End repair of immunoprecipitated DNA with NEXTflex ChIP End Repair, 3' adenylation NEXTflex ChIP Adenylation mix, Adapter ligation with NEXTflex ChIP-Seq barcode kit containing barcodes to be used. PCR amplification used NEXTflex ChIP Primer Mix supplied in Bioo Scientific NEXTflex ChIP-Seq Barcode kit and amplified for the following program: 2min @ 98C, 30sec @ 98C, 30 sec @ 65C (repeated 16 cycles), 1min @ 72C, 4min @ 72C. Quality of libraries again assesses by Qubit DNA high Sensitivity.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
73890258
Reads aligned (%)
84.5
Duplicates removed (%)
73.2
Number of peaks
967 (qval < 1E-05)

mm9

Number of total reads
73890258
Reads aligned (%)
84.2
Duplicates removed (%)
73.2
Number of peaks
1088 (qval < 1E-05)

Base call quality data from DBCLS SRA