Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Neural
Cell type
Hippocampal neurons
NA
NA

Attributes by original data submitter

Sample

source_name
FACS-sorted neuronal (NeuN+) nuclei
strain
C57BL/6
tissue
ventral hippocampus
age
11 weeks
Sex
female
estrous cycle stage
proestrus

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Ventral hippocampus was dissected from the brain, snap frozen in liquid nitrogen, and total nuclei were extracted using sucrose gradient centrifugation. Neuronal (NeuN+) nuclei were isolated by fluorescence-activated nuclei sorting with anti-NeuN antibody conjugated to AlexaFluor 488 on a FACSAria instrument. Detailed protocol for total nuclei isolation and purification of neuronal nuclei is provided in Kundakovic et al, 2017 (PMID:27113501). ATAC-seq libraries were prepared according to Buenrostro et al. 2013 (PMID:24097267) with some modifications. Illumina Nextera DNA Library Prep kit (FC-121-1030) and Nextera Index kit (FC 121-1011) were used to prepare the libraries.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
58672304
Reads aligned (%)
95.3
Duplicates removed (%)
1.4
Number of peaks
27538 (qval < 1E-05)

mm9

Number of total reads
58672304
Reads aligned (%)
95.2
Duplicates removed (%)
1.4
Number of peaks
27742 (qval < 1E-05)

Base call quality data from DBCLS SRA