Antigen

Antigen Class

Bisulfite-Seq

Antigen

Bisulfite-Seq

Cell type

Cell type Class

Neural

Cell type

Brain

MeSH Description

The part of CENTRAL NERVOUS SYSTEM that is contained within the skull (CRANIUM). Arising from the NEURAL TUBE, the embryonic brain is comprised of three major parts including PROSENCEPHALON (the forebrain); MESENCEPHALON (the midbrain); and RHOMBENCEPHALON (the hindbrain). The developed brain consists of CEREBRUM; CEREBELLUM; and other structures in the BRAIN STEM.

Sample

source_name

Brain

strain

C57BL/6

tissue

brain

age

8 weeks

treatment

left hemisphere of experimental stroke model (Control)

Sequenced DNA Library

library_strategy

Bisulfite-Seq

library_source

GENOMIC

library_selection

RANDOM

library_construction_protocol

After the middle cerebral artery occlusion, animal brains were removed, and the ipsilateral (IPC treatment) and contralateral cortices (serve as control) of the same brain were collected. Total RNA was isolated from three mouse brains using Trizol reagent. A total of two micrograms of RNA per sample was used as input material for library construction. Genomic DNA was isolated from three mouse brains using a DNeasy Blood & Tissue Kit according to the manufacturer's instructions. A total of 500 ng of DNA spiked with 5 ng of lambda DNA (Promega, Madison, WI) per sample was used as input material for library construction. Ribosomal RNA (rRNA) was removed by an Epicentre Ribo-zero rRNA Removal Kit (Epicentre, USA) according to the manufacturer's instructions. Subsequently, strand-specific sequencing libraries were generated with the dUTP method using the resulting RNA by an NEB Next Ultra Directional RNA Library Prep Kit for Illumina (NEB, USA) following the manufacturer's recommendations. For WGBS, a total of 500 ng of DNA spiked with 5 ng of lambda DNA (Promega, Madison, WI) per sample was fragmented to 250-350 bp by sonication with a Covaris M220, followed by end repair and methylated adaptor ligation. These DNA fragments were treated with bisulfite using an EZ DNA Methylation-Gold TM Kit. The obtained single-strand DNA fragments were amplified by PCR using KAPA HiFi HotStart Uracil + ReadyMix (2x) followed by purification by AMPure XP magnetic beads. The library concentration was quantified by a Qubit 2.0 Fluorometer, and the insert size was assessed on an Agilent Bioanalyzer 2100 system. RNA-Seq, WGBS

Sequencing Platform

instrument_model

Illumina Genome Analyzer

mm10

Number of total reads

118390606

Reads aligned (%)

92.4

Coverage rate (×)

4.9

Number of hyper MRs

241512 (qval < 1E-05)

mm9

Number of total reads

118390606

Reads aligned (%)

92.9

Coverage rate (×)

4.9

Number of hyper MRs

240886 (qval < 1E-05)