Antigen

Antigen Class

Input control

Antigen

Input control

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/6J

genotype/variation

WT

antibody

WCE

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

For ChIPseq, frozen tissue was fixed with 2mM disuccinimidyl glutarate in PBS for 35 min, 1 % formaldehyde for 10 min, and quenched with 125 mM glycine. Fixed homogenate was washed twice, douce-homogenized, and resuspend in Lysis Buffer (1 mM EDTA, 0.5 mM EGTA, 10 mM Tris pH 8.0, 0.5 % sarcosyl) and chromatin sheared using a BioruptorPlus (Diagenode Inc, NJ) set to high for 40 cycles of 30 sec on, 30 sec off. About 3 µg chromatin was precleared and ChIP was performed using 5 µg HDAC3 antibody (Abcam, ab7030) overnight, followed by enrichment using protein A sepharose beads for 4 hours. Beads were washed 4 times with RIPA buffer and once with TE, then eluted and reverse-cross linked in TE plus 1 % SDS at 65oC. Chromatin was subjected to RNase and proteinase K treatment, followed by DNA purification by phenol chloroform extraction and ethanol precipitation. DNA pellets were resuspended in 10 mM Tris. For RNAseq, RNA wwas extracted from frozen tissue using Trizol according to manufacturers protocol (Invitrogen). RNA (3 µg) was DNase I treated (4 U, Worthington Biochemical Corporation), purified using RNA Clean and Concentrator-5 Kit (Zymo Research) according to manufacturers’ instructions and eluted with 14 µl DEPC-treated water. RNAseq libraries were prepared and sequenced as previously described (Gjorneska et al. Nature 2015). ChIPseq libraries were prepared and sequenced as previously described (Gjorneska et al. Nature 2015).

Sequencing Platform

instrument_model

Illumina HiSeq 2000

mm10

Number of total reads

41219783

Reads aligned (%)

98.2

Duplicates removed (%)

18.9

Number of peaks

556 (qval < 1E-05)

mm9

Number of total reads

41219783

Reads aligned (%)

98.0

Duplicates removed (%)

19.0

Number of peaks

606 (qval < 1E-05)