Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RUNX1

Cell type

Cell type Class
Breast
Cell type
MCF 10A
Primary Tissue
Breast
Tissue Diagnosis
Fibrocystic Disease

Attributes by original data submitter

Sample

source_name
MCF10A breast epithelial cells
tissue
Breast epithelium
phenotype
normal-like
chip-antibody
Runx1 (CST 4336BF) - Lot #2
cell line
MCF10A

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Harvested lysates were fixed in 1% MeOH formaldehyde and sonicated. Following sonication, samples were incubated with RUNX1 ab for ChIP reaction. Ab-DNA complex isolated using Protein A/G beads and magnets. DNA was purified from solution and subject to library construction ChIP libraries were generated using Accel-NGS® 2S Plus DNA Library kit (Swift Biosciences, Ann Arbor, MI) following manufacturers protocol. Input and RUNX1 ChIP samples were normalized to 1ng prior to library generation. Libraries were amplified in an optional PCR step for 12 total cycles. Finalized libraries were double size selected using AMPure XP beads (0.8X and 0.2X volume ratios to sample), resulting in the majority fragments sized between 250-400bp.

Sequencing Platform

instrument_model
Illumina HiSeq 1500

hg19

Number of total reads
21934211
Reads aligned (%)
93.5
Duplicates removed (%)
4.0
Number of peaks
1127 (qval < 1E-05)

hg38

Number of total reads
21934211
Reads aligned (%)
95.4
Duplicates removed (%)
2.9
Number of peaks
1193 (qval < 1E-05)

Base call quality data from DBCLS SRA