Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Unclassified
Cell type
Unclassified
NA
NA

Attributes by original data submitter

Sample

source_name
ATAC-seq using nuclei from specific cell types
strain
C57BL6J
brain region
cerebellum

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Cerebellum was dissected and nuclei were isolated. ATAC-seq libraries were prepared as described previously (Buenrostro et al., 2013; 2015) with the following modifications: nuclei were resuspended in ice-cold lysis buffer, omitting incubation step on ice and centrifuged. Transposition reaction was performed for 30 min at 37°C using Tn5 transposase from Nextera. DNA fragments were purified and size selected using AMPure XP beads to yield 100-700bp fragments. Libraries were generated using the Nextera DNA Library Preparation Kit. ATAC-seq libraries were sequenced on Illumina NextSeq 500 to obtain 75bp paired-ended reads.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
54045728
Reads aligned (%)
93.1
Duplicates removed (%)
32.6
Number of peaks
5912 (qval < 1E-05)

mm9

Number of total reads
54045728
Reads aligned (%)
93.0
Duplicates removed (%)
32.7
Number of peaks
5895 (qval < 1E-05)

Base call quality data from DBCLS SRA