Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Breast
Cell type
HCC1954
Primary Tissue
Breast
Site of Extraction
Soft Tissue
Tissue Diagnosis
Adenocarcinoma Ductal

Attributes by original data submitter

Sample

source_name
HCC1954 cells, input
cell line
HCC1954
cell type
Breast cancer cell line
treatment
Control
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. ChIP-seq libraries were prepared for sequencing using standard Illumina protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
55417882
Reads aligned (%)
95.4
Duplicates removed (%)
2.1
Number of peaks
1020 (qval < 1E-05)

hg19

Number of total reads
55417882
Reads aligned (%)
94.6
Duplicates removed (%)
3.4
Number of peaks
1170 (qval < 1E-05)

Base call quality data from DBCLS SRA