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| Status |
Public on Dec 31, 2019 |
| Title |
JZ110 |
| Sample type |
SRA |
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| Source name |
Brain
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: brain
age: 8 weeks
treatment: left hemisphere of experimental stroke model (Control)
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| Extracted molecule |
genomic DNA |
| Extraction 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
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina Genome Analyzer |
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| Data processing |
RNA-seq data was aligned to mm10 genome using osa version 2.1.14 with default parameter
the gene counts were generated using htseq tool
differential expression genes were identified by deseq2 package
WGBS data was aligned to mm10 genome using Bsmooth pipeline to get depth of each CpG sites
differential methylated regions were identified using bsseq package
Genome_build: mm10
Supplementary_files_format_and_content: gene counts and CpG depth file were plain text formated
Supplementary_files_format_and_content: 1st column is the chromosome NO.
Supplementary_files_format_and_content: 2nd column is the coordinate of CpG cite on the chromosome (1-based)
Supplementary_files_format_and_content: 3rd column is the base type, i.e., if the base is C , the base type is 1 , G then 4. (the binucleotide arrangement is CG)
Supplementary_files_format_and_content: we average the CpG methylation profile on both the forward and backward strand by this trick.
Supplementary_files_format_and_content: 4th column is the number of methylated C at this CpG site
Supplementary_files_format_and_content: 5th column is the total number of CpG site
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| Submission date |
Nov 02, 2018 |
| Last update date |
Jan 01, 2020 |
| Contact name |
Yun Liu |
| E-mail(s) |
yliu39@fudan.edu.cn
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| Organization name |
Fudan University
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| Street address |
130 Dong An Road
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| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
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| Platform ID |
GPL9185 |
| Series (1) |
| GSE122107 |
Next Generation Sequencing Combined Analysis of DNA Methylome and Transcriptome Reveal Novel Candidate Genes of Neuroprotective with Response to Ischemic Preconditioning |
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| Relations |
| BioSample |
SAMN10365696 |
| SRA |
SRX4968742 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3455022_JZ110.cg.txt.gz |
175.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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