Antigen

Antigen Class

Histone

Antigen

H3K9me3

Cell type

Cell type Class

Neural

Cell type

Hippocampus

MeSH Description

A curved elevation of GRAY MATTER extending the entire length of the floor of the TEMPORAL HORN of the LATERAL VENTRICLE (see also TEMPORAL LOBE). The hippocampus proper, subiculum, and DENTATE GYRUS constitute the hippocampal formation. Sometimes authors include the ENTORHINAL CORTEX in the hippocampal formation.

Sample

source_name

hippocampus

strain

C57BL/6

age

3 months old

tissue

hippocampus

chip-antibody

H3K9me3 (diagenode, Cat. C15410193)

genotype

WT

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Mouse was perfused with 4% PFA solution, and hippocampus was homogenized and fixed in 1% PFA for 10 minutes. Chromatin was fragmented by sonication to obtain fragments 100–1000 bp in length. For each ChIP assay, 2 ug of antibodies were coupled to 200 ul magnetic beads. Chromatin was reverse-crosslinked, purified and quantified with a Qubit fluorometer and quality-controlled using Agilent’s Bioanalyzer. DNA was end-repaired, adenylated, and ligated to TruSeq sequencing adaptors. DNA was purified by AMPure beads or DNA purification kit according to the DNA amount. Library DNA was amplified by Phusion HF (NEB, Cat. M0530L). The amplified DNA was size selected using 2% agarose gel for 100-300bp DNA fragments.

Sequencing Platform

instrument_model

Illumina HiSeq 2500

mm10

Number of total reads

32406690

Reads aligned (%)

87.5

Duplicates removed (%)

31.5

Number of peaks

571 (qval < 1E-05)

mm9

Number of total reads

32406690

Reads aligned (%)

86.8

Duplicates removed (%)

31.3

Number of peaks

698 (qval < 1E-05)