Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H2A.XS139ph

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
normal breast cells
cell line
MCF10A
cell type
normal breast cells
chip antibody
gH2AX (ab81299, Abcam)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Genomic DNA from MCF10A cells or from growing MEFs was extracted by using Dneasy Blood&Tissue kit. Genomic DNA were sonicated and immunoprecipitated with antibodies anti 8-oxodG O/N. Eluted DNA was processed for library preparation. For ChIp_Seq anti gH2AX, lysates were clarified from sonicasted nuclei and histone-DNA complexes were isolated with specific antibody. Libraries were prepared according to Illumina's instructions

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
35846224
Reads aligned (%)
98.2
Duplicates removed (%)
10.2
Number of peaks
1114 (qval < 1E-05)

hg19

Number of total reads
35846224
Reads aligned (%)
97.1
Duplicates removed (%)
12.4
Number of peaks
1469 (qval < 1E-05)

Base call quality data from DBCLS SRA