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
Hippocampus
genotype/variation
CK
time since treatment
2 weeks
tissue
brain (hippocampus)
measurement
WCE
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. Tissues were minced and crosslinked in 1% formaldehyde (Thermo Scientific) for 15 min at room temperature and quenched with glycine for 5 min (Sigma). The samples were homogenized in cell lysis buffer containing proteinase inhibitors (complete, Roche) and chromatin was then fragmented to a size range of ~200-500 bp using a Branson 250 digital sonifier. Solubilized chromatin was then diluted and incubated with ~1 μg antibody at 4C overnight. 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. Isolated ChIP DNA was resuspended and quantified using the Qubit assay (Invitrogen). 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. 36 bp 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
218784640
Reads aligned (%)
93.6
Duplicates removed (%)
18.8
Number of peaks
861 (qval < 1E-05)

mm9

Number of total reads
218784640
Reads aligned (%)
93.3
Duplicates removed (%)
18.7
Number of peaks
1055 (qval < 1E-05)

Base call quality data from DBCLS SRA