Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Neural
Cell type
Dentate Gyrus
MeSH Description
A subsection of the hippocampal formation, described by Lorente de No, that composes the hilus of the DENTATE GYRUS.

Attributes by original data submitter

Sample

source_name
Dentate gyrus
tissue
dentate gyrus
strain
C57BL6
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody Samples that met the Illumina sample input guidelines were prepared according the TruSeq¨ ChIP Sample Preparation kit (Illumina Inc., San Diego, California, USA) with minor modifications. Libraries were size selected for an average size of 350 bp using SPRI-based bead selection. Quality and quantity of the finished libraries were assessed using an Agilent DNA1000 chip and Qubit¨ dsDNA HS Assay Kit, respectively. Libraries were standardized to 2_M. Cluster generation was performed using standard Cluster Kits (v3) and the Illumina Cluster Station. Single 100bp sequencing was performed, using standard SBS chemistry (v3) on an Illumina HiSeq2000 sequencer. Images were analyzed using the standard Illumina Pipeline, version 1.8.2.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
53318036
Reads aligned (%)
99.9
Duplicates removed (%)
12.1
Number of peaks
253 (qval < 1E-05)

mm9

Number of total reads
53318036
Reads aligned (%)
99.9
Duplicates removed (%)
12.1
Number of peaks
273 (qval < 1E-05)

Base call quality data from DBCLS SRA