Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Neural
Cell type
Somatostatin positive neurons
NA
NA

Attributes by original data submitter

Sample

source_name
Brain
strain
C57BL/6J
tissue
CeA
cell type
Somatostatin positive (SOM+) neurons
genotype
WT
treatment
Control
Sex
male
age
2-3 months

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Brains were dissected and sectioned at 500 μm on ice in a stainless steel brain matrix (EMS 69090-C). PFC or CeA was microdissected in ice-cold PBS with 1x protease inhibitors (Roche) under a stereomicroscope. The tissue was resuspended in 500µl homogenization buffer containing 300mM sucrose, 60mM KCl, 15mM NaCl, 15mM Tris-HCl, 5mM MgCl2, 0.1mM EGTA, 1 mM DTT, 0.1mM PMSF and 1x protease inhibitors, EDTA-free (Roche), and disrupted using a cordless pestle motor homogenize tissue with 4 bursts of 5 seconds. Nuclei were prepared by a seven minute detergent lysis with the addition of IGEPAL CA-630 (Sigma) to a final concentration of 0.2%, followed by pelleting at 1500rcf and gentle resuspension in PBS containing 2% FBS for FACS sorting. Nuclei were filtered through 40 μm cell strainers and NucBlue was added to SOMErbb4-KO nuclei, while SOMH2B-GFP were gated on GFP. Nuclei were sorted into technical replicates of 50,000 nuclei and immediately proceeded to the ATAC-seq transposition reaction. For each library, 50,000 sorted nuclei were resuspended in Transposition Reaction Mix then incubated at 37° C. Using Qiagen MinElute Kit we purified 50uL reaction volume. Transposed DNA were stored at -20C. We used the primers in Buenrostro et al (2013) for library construction. ATAC-seq library quality was assessed on an agarose gel with 1X SYBR Gold to view banding. Libraries were quantified by both Bioanalyzer High Sensitivity Chips and the KAPA Illumina Library Quantification kit.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
68594004
Reads aligned (%)
91.2
Duplicates removed (%)
29.3
Number of peaks
34815 (qval < 1E-05)

mm9

Number of total reads
68594004
Reads aligned (%)
91.0
Duplicates removed (%)
29.5
Number of peaks
34808 (qval < 1E-05)

Base call quality data from DBCLS SRA