Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Liver
Cell type
Liver
MeSH Description
A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.

Attributes by original data submitter

Sample

source_name
frozen liver tumor tissue
stain
FVB
tissue
liver tumor
age
about 70 days-old
genotyping
LAP-tta-Arid1afl/+;Alb-cre;TRE-MYC
chip antibody
NA

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Frozen liver tumor tissues were minced quickly with a razorblade into small pieces which less than 0.5 cm3. Crosslink tissue in 1% formaldehyde for 20 min at room temperature.Dounce tissue in ice-cold PBS first with the loose and later with the tight pestle. Rinse tissue with PBS. genomic DNA were isolated and performed for ChIP-seq. ChIP-seq libraries were prepared using NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina Kit, and sequenced on Illumina NEXTseq 500 using High Output kit v2 reagents at CRI Sequencing Facility at UT Southwestern.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
9063851
Reads aligned (%)
95.0
Duplicates removed (%)
16.4
Number of peaks
210 (qval < 1E-05)

mm9

Number of total reads
9063851
Reads aligned (%)
94.8
Duplicates removed (%)
16.6
Number of peaks
204 (qval < 1E-05)

Base call quality data from DBCLS SRA