Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Lung
Cell type
Lung tumors
NA
NA

Attributes by original data submitter

Sample

source_name
lung tumors
genotype
KrasG12D/+;Trp53-/-;GFPi-GFP-2A-rTA;Luc
sample type
non-immunoprecipitated DNA

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
1% Formaldheyde fixation followed by SDS buffer lysis Libraries were prepared according to Illumina's instructions. 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 (32 to 52 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, library fragments of ~230 bp (insert plus adaptor and PCR primer sequences) were selected from an agarose gel. The final size-selected lib. was amplified by 15 cycle of PCR followed by column purification of amplified DNA. The purified DNA was captured on an Illumina flow cell for cluster generation. ChIP was performed by cross-linking proteins to DNA using 2mM DSG and 1% formaldehyde solution (Gargiulo et al, 2009). Immunoprecipitated DNA (ChIP-seq) and Input DNA were Libraries were sequenced on the Genome Analyzer of HiSeeq2000 following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
28857200
Reads aligned (%)
98.3
Duplicates removed (%)
9.8
Number of peaks
439 (qval < 1E-05)

mm9

Number of total reads
28857200
Reads aligned (%)
98.0
Duplicates removed (%)
9.8
Number of peaks
515 (qval < 1E-05)

Base call quality data from DBCLS SRA