Antigen

Antigen Class

Bisulfite-Seq

Antigen

Bisulfite-Seq

Cell type

Cell type Class

Neural

Cell type

Retina

MeSH Description

The ten-layered nervous tissue membrane of the eye. It is continuous with the OPTIC NERVE and receives images of external objects and transmits visual impulses to the brain. Its outer surface is in contact with the CHOROID and the inner surface with the VITREOUS BODY. The outer-most layer is pigmented, whereas the inner nine layers are transparent.

Sample

source_name

Glast+ cells from P28 retinas

tissue

retina

strain

C57BL/6

developmental stage

Postnatal Day 28 (P28)

cell type

Glast+ cells

Sequenced DNA Library

library_strategy

Bisulfite-Seq

library_source

GENOMIC

library_selection

RANDOM

library_construction_protocol

Genomic DNA was purified from samples using the DNeasy Blood & Tissue Kit (QIAGEN #69504). DNA concentration of the samples was measured using the Qubit® dsDNA BR Assay Kit (Thermo Fisher Scientific). DNA quality of the samples was assessed with the Fragment AnalyzerTM and the DNF-487 Standard Sensitivity genomic DNA Analysis Kit (Advanced Analytical). Genomic DNA was sheared using Bioruptor® Pico sonication device (Diagenode Cat# B01060001). 1μl of this sample was used to assess the size of the DNA fragments obtained by High Sensitivity DNA chip for 2100 Bioanalyzer (Agilent). DNA concentration of the sample was measured after shearing using the Qubit® dsDNA BR Assay Kit (Thermo Fisher Scientific). WGBS libraries were prepared using the Whole Genome Bisulfite Sequencing (RRBS) Kit (Diagenode Cat# C02030034) following the kit manual. 1μg of sheared genomic DNA was used to start library preparation for each sample. Following library preparation, samples were bisulfite converted and amplified by PCR using 9 amplification cycles. Final PCR clean-up was performed twice using a 1.1x beads:sample ratio of Agencourt® AMPure® XP (Beckman Coulter). DNA concentration of the libraries was measured using the Qubit® dsDNA HS Assay Kit (Thermo Fisher Scientific). The library profiles were checked using the High Sensitivity DNA chip for 2100 Bioanalyzer (Agilent). WGBS libraries were sequenced on a HiSeq3000 (Illumina) using 150 bp single-end sequencing.

Sequencing Platform

instrument_model

Illumina HiSeq 3000

mm10

Number of total reads

624509154

Reads aligned (%)

87.9

Coverage rate (×)

10.4

Number of hyper MRs

275861 (qval < 1E-05)

mm9

Number of total reads

624509154

Reads aligned (%)

89.9

Coverage rate (×)

10.2

Number of hyper MRs

275169 (qval < 1E-05)