Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Breast
Cell type
T-47D
Primary Tissue
Breast
Tissue Diagnosis
Adenocarcinoma Ductal

Attributes by original data submitter

Sample

source_name
T47D
cell line
T47D
genotype/variation
T47D Flp control cells
passages
<10
antibody
anti-H3K4me1 (abcam, ab8895)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were treated with a hypotonic buffer, and lysed with Tris-HCl pH 8.0 based buffer with appropriate concentration of SDS. Chromatin fragmentation was performed by sonication with Covaris. DNA was precipitated with antibody against each target protein. Libraries were prepared according to BIOO SCIENTIFIC instruction.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
47168218
Reads aligned (%)
97.6
Duplicates removed (%)
2.4
Number of peaks
3135 (qval < 1E-05)

hg19

Number of total reads
47168218
Reads aligned (%)
96.9
Duplicates removed (%)
2.4
Number of peaks
3044 (qval < 1E-05)

Base call quality data from DBCLS SRA