Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Neural
Cell type
Retinal ganglion cells
NA
NA

Attributes by original data submitter

Sample

source_name
Retinal ganglion cells
strain
C57BL/6
tissue
Retina
age
8-10 weeks
genotype
Arid1a del/del

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
The dissected retinas were dissociated in EBSS containing papain and DNase (Worthington) for 20min at 37℃, with gentle shaking every 5min, then digestion was stopped by adding Ovomucoid/EBSS (Worthington). The dissociated retinal cells were incubated with FC block antibody (1:100, BD Biosciences 553141), and then stained with Thy1.2-PE antibody (1:100, Invitrogen 12-0902-82) and DAPI. FACS sorting was performed with a BD FACSAria IIIu instrument. ATAC-seq libraries were prepared from the purified RGCs using TruePrep DNA Library Prep Kit V2 for Illumina.

Sequencing Platform

instrument_model
HiSeq X Ten

mm10

Number of total reads
44169030
Reads aligned (%)
40.6
Duplicates removed (%)
30.6
Number of peaks
153 (qval < 1E-05)

mm9

Number of total reads
44169030
Reads aligned (%)
40.6
Duplicates removed (%)
30.6
Number of peaks
119 (qval < 1E-05)

Base call quality data from DBCLS SRA