Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Breast
Cell type
Carcinoma, Ductal, Breast
MeSH Description
An invasive (infiltrating) CARCINOMA of the mammary ductal system (MAMMARY GLANDS) in the human BREAST.

Attributes by original data submitter

Sample

source_name
Mammary gland:Breast: derived from metastatic site. pleural effusion
disease
Ductal Carcinoma
morphology
epithelial
chip antibody
NA

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin extrated cell cell lysate was sonicated and shered to 300bp to 1kb fragments using a Sonifier Cell Disruptor (Branson Ultrasonics #101-063-588). To 0.5ml sheared chromatin (after clarification of debrie), we added 150µl ChIP mix (440mM NaCl, 0.44% sodium deoxycholate, 4.4% Triton X-100) and antibody-coupled beads for immunoprecipitation overnight at 4C. Precipitated DNA fragments were processed to ChIP-seq library using the ThruPLEX DNA-seq 12S kit (Takara #R400428) according to manufacturer's instructions. 75bp single end 10M depth

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
19113420
Reads aligned (%)
72.9
Duplicates removed (%)
5.6
Number of peaks
6348 (qval < 1E-05)

hg19

Number of total reads
19113420
Reads aligned (%)
70.6
Duplicates removed (%)
9.8
Number of peaks
5969 (qval < 1E-05)

Base call quality data from DBCLS SRA