Sample information curated by ChIP-Atlas

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.

Attributes by original data submitter

Sample

source_name
WCE CKp25 2wk_hippocampus
genotype/variation
CK-p25
age
3.5 months
time since treatment
2 weeks
tissue
Hippocampus
cross correlation
0.00952923135951132
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Mouse hippocampus was harvested immediately after euthanasia. Upon dissection tissue was flash-frozen in liquid nitrogen. The tissue was minced and crosslinked with 1% formaldehyde at room temperature for 15mins and quenched with 0.125M Glycine. The tissue was then homogenized in cell lysis buffer using the Tissue Lyser and a 5mm stainless steel bead. Then the nuclei were lysed in cell lysis buffer and chromatin was sheared by sonication. Chromatin was incubated overnight at 4C with the H3K9Ac antibody. Immune complexes were captured with Protein A-sepharose beads, washed and eluted. Enriched chromatin was then subjected to crosslink reversal and proteinase K digestion at 65C, phenol-chloroform extraction and ethanol precipitation. Sequencing libraries were prepared from ~1-5 ng ChIP (or input) DNA. Gel electrophoresis was used to retain library fragments between 300 and 600 bp. Prior to sequencing, libraries were quantified using Qubit (Invitrogen) and quality-controlled using Agilent’s Bioanalyzer. Single end sequencing was performed using the Illumina HiSeq 2000 platform according to standard operating procedures.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
14690818
Reads aligned (%)
98.6
Duplicates removed (%)
20.4
Number of peaks
295 (qval < 1E-05)

mm9

Number of total reads
14690818
Reads aligned (%)
98.3
Duplicates removed (%)
20.5
Number of peaks
314 (qval < 1E-05)

Base call quality data from DBCLS SRA