Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Liver
Cell type
Liver tumor cell line
NA
NA

Attributes by original data submitter

Sample

source_name
Liver tumor cell line, sgp53/Cas9, input
strain/background
C57BL/6
cell type
Liver tumor cell line
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
0.5 million liver tumor cells were crosslinked for 10 minutes using 1% formaldehyde, followed by quenching with 0.125M glycine for 10 minutes. To prepare chromatin from crosslinked cells, aliquots of cells were kept in individual eppendorf tubes for sonication to maximize the chromatin fragmentation efficiency. After purifying immunoprecipitated DNA, a TruSeq ChIP Sample Prep Kit (Illumina) was used to construct the ChIP-Seq library following the manufacturer's protocol except for amplifying the adaptor-ligated library for 15 cycles. ChIP-Seq libraries were sequenced using an Illumina HiSeq 2000 platform with single-end reads of 50 bases. Four libraries at equal molarity were pooled to aim for a sequencing depth of 20-40 million aligned reads per sample.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
57507041
Reads aligned (%)
93.8
Duplicates removed (%)
14.7
Number of peaks
670 (qval < 1E-05)

mm9

Number of total reads
57507041
Reads aligned (%)
93.5
Duplicates removed (%)
14.5
Number of peaks
761 (qval < 1E-05)

Base call quality data from DBCLS SRA