Curated Sample Data


Genome
hg19
Antigen Class
TFs and others
Antigen
HOXB7
Cell type Class
Breast
Cell type
BT-474

Cell type information


Primary Tissue
Breast
Site of Extraction
Soft Tissue
Tissue Diagnosis
Adenocarcinoma Ductal

Attributes by Original Data Submitter


source_name
BT-474 cells
cell type
Breast cancer cells derived from ductal carcinoma
passages
13-23
chip antibody
HOXB7 (H0291, Sigma-Aldrich)

Metadata from Sequence Read Archive

Library Description


library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and DNA-protein complexes were isolated with respective antibodies. Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

Platform Information


instrument_model
Illumina Genome Analyzer IIx

External Database Query

Logs in read processing pipeline


Number of total reads
31884248
Reads aligned (%)
94.7
Duplicates removed (%)
5.5
Number of peaks
941 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA