Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Liver
Cell type
Liver tumor
NA
NA

Attributes by original data submitter

Sample

source_name
mouse Tumor intitating stem cells
strain
C57BL/6
cell type
Tumor inititating stem cells
cell marker
CD133-
tissue
liver tumor
chip antibody
Isotype antibody

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Four pairs of TICs and Nanog-/CD133-/CD49f+ control cells (~1x10^5 per mouse) were isolated from four independent mouse liver tumors. ChIP was performed with NANOG antibody using CD 133+ as well as CD133– cell lines following a standard protocol as suggested by manufacturer (Millipore). In parallel, isotype control antibody was used as a control. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired and blunt, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters. After adapter ligation DNA was PCR amplified with Illumina primers for 15 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 Illumina Hi-Seq following the manufacturer's protocols.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 HiSeq 2000

mm10

Number of total reads
22674150
Reads aligned (%)
82.2
Duplicates removed (%)
24.8
Number of peaks
358 (qval < 1E-05)

mm9

Number of total reads
22674150
Reads aligned (%)
82.0
Duplicates removed (%)
24.9
Number of peaks
372 (qval < 1E-05)

Base call quality data from DBCLS SRA