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
Hippocampal excitatory neurons
replicate
2
genotype
control (floxed)
strain
C57BL/6J
fans antibody
anti-NeuN (Millipore MAB377)
chip antibody
-
tissue
Adult Forebrain (hippocampus)
age
3-4 month
gender
male

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Hippocampi were micro-dissected after cervical dislocation, washed in ice-cold PBS and pooled together, when fixation was needed 1% FA was used. Nuclei were isolated using our improved FANS protocol for SUN1-GFP+ cells. Extensive description of protocols indicated in Supplemental Experimental Procedures. ATAC-seq experiments were conducted as the original protocol (Buenrostro et al., 2013), using anti-NeuN (Millipore MAB377) to select mature neurons. Libraries were prepared with TruSeq.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
87080708
Reads aligned (%)
89.5
Duplicates removed (%)
18.0
Number of peaks
73019 (qval < 1E-05)

mm9

Number of total reads
87080708
Reads aligned (%)
89.5
Duplicates removed (%)
18.0
Number of peaks
73165 (qval < 1E-05)

Base call quality data from DBCLS SRA