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
CLK_Input_Sonicated_WT30_ZT06
strain
C57BL/6
tissue
Liver
age
Adult (3-6months)
antibodies
none, input

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Adult mouse liver were collected at 6 different time of the day (mouse held under LD12:12, time points every 4hrs starting at ZT2) Mouse liver were crosslinked with 1% formaldehyde for 10min, and nuclei were purified using standard sucrose cushion protocol. Nuclei were resuspended, flash frozen in liquid nitrogen and stored at -80C. Nuclei were thawed on ice, pelleted down and chromatin either was digested with micrococcal nuclease or sonicated using Bioruptor. Mnase digestion was performed for 15min using 30,000 gel unit per reaction Following chromatin shearing, chromatin was imunoprecipitated using an anti-CLK antibody. Immunoprecipitated chromatin and inpur fraction was purified and used for generating illumina libraries Illumina libraries were generated using standard protocol: end repair, add A, adapter ligation, amplification, gel purification.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
15627762
Reads aligned (%)
98.0
Duplicates removed (%)
13.9
Number of peaks
353 (qval < 1E-05)

mm9

Number of total reads
15627762
Reads aligned (%)
97.7
Duplicates removed (%)
14.0
Number of peaks
381 (qval < 1E-05)

Base call quality data from DBCLS SRA