Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Breast
Cell type
MCF-7
Primary Tissue
Breast
Site of Extraction
Pleura
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
Immortal cell line
cell line
MCF-7
antibody target
H3K4me3
primary antibody
mouse monoclonal anti-H3K4me3 (Kimura et al., Cell Struct Funct. 2008;33(1):61-73., CMA304)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Fixed cells were lysed and histone-DNA complexes were isolated with antibodies. Immunostaining half of the protocol includes cell dispensing, fixation, permeabilization, blocking, reaction to primary anti-body and the ChILT probe. The reactive probe are integrated into a proximal genomic region to where the primary antibody is bound upon Tn5 activation. The integrated ChILT DNA is used for the linear amplification of genomic sequences and the transcribed RNAs are utilized for library preparation for deep-sequencing. Fixed cells were lysed and histone-DNA complexes were isolated with antibodies. Libraries were prepared on the Illumina HiSeq1500 and 2500 platforms.

Sequencing Platform

instrument_model
Illumina HiSeq 1500

hg38

Number of total reads
24986945
Reads aligned (%)
89.4
Duplicates removed (%)
66.8
Number of peaks
16791 (qval < 1E-05)

hg19

Number of total reads
24986945
Reads aligned (%)
89.1
Duplicates removed (%)
67.4
Number of peaks
16833 (qval < 1E-05)

Base call quality data from DBCLS SRA