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
lin- fetal liver cells transduced with N1dE
strain
C57BL/6
tissue
fetal liver (lin-)
age
14.5 embryonic days
antibody
none
genotype/variation
transduced with N1dE lentivirus

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were lysed in non-ionic detergents and protease inhibitor cocktail. Cells were digested by Micrococcal nuclease (MNase) at room temperature for 5 minutes and 0.25mM EDTA was used to stop the reaction. H3K27me3 antibody was incubated with anti-IgA magnetic beads for 2 hours. Digested chromatin was incubated with magnetic beads alone for 1.5 hours. Digested chromatin was separated from beads and incubated with antibody-bead complex overnight in IP buffer. IPs were washed twice and eluted for 1.5 hours. Histones were digested by Protease for 30min and DNA fragments were purified using Sera Mag magnetic beads in 30% PEG. The PCR program included an initial denaturation step at 98C for 30 sec, followed by 8 cycles at 98C for 15 sec, 65C for 30 sec, and 72C for 30 sec, and ending with a final step at 72C for 5 min. We performed native chromatin immunoprecipitation (ChIP) as described previously (Lorzadeh et al., 2016) using a validated anti-H3K27me3 antibody (cat #pAB-195-050,Diagenode). Libraries were constructed using an Agilent Bravo automated liquid handling platform. Illumina sequencing libraries were generated by end repair, 3' A-addition, and Illumina sequencing adaptor ligation.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
37490538
Reads aligned (%)
88.3
Duplicates removed (%)
7.8
Number of peaks
245 (qval < 1E-05)

mm9

Number of total reads
37490538
Reads aligned (%)
88.1
Duplicates removed (%)
8.0
Number of peaks
205 (qval < 1E-05)

Base call quality data from DBCLS SRA