Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Ar

Cell type

Cell type Class
Kidney
Cell type
Kidney
MeSH Description
Body organ that filters blood for the secretion of URINE and that regulates ion concentrations.

Attributes by original data submitter

Sample

source_name
AR_Cast1
strain
wild type ICR
tissue
kidney
age
8-12 weeks old
treatment
castrated+vehicle
chip antibody
AR (Sahu et al. 2011)

Sequenced DNA Library

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 20 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.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

mm10

Number of total reads
26769735
Reads aligned (%)
67.4
Duplicates removed (%)
12.0
Number of peaks
716 (qval < 1E-05)

mm9

Number of total reads
26769735
Reads aligned (%)
67.3
Duplicates removed (%)
12.1
Number of peaks
748 (qval < 1E-05)

Base call quality data from DBCLS SRA