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Sample GSM3716992 Query DataSets for GSM3716992
Status Public on Feb 12, 2020
Title EAE-3 [S4]
Sample type SRA
 
Source name EAE_astrocytes
Organism Mus musculus
Characteristics strain: C57Bl/6
genotype/variation: wild type
Sex: male
age: P90
sample group: undergoing EAE transduced with non-targeting lentiviruses
cell type: Flow cytometry sorted astrocytes
Treatment protocol Induction of EAE in mice intracranially transduced with pLenti-U6-sgMafg-Gfap-Cas9-2A-EGFP-WPRE or pLenti-U6-sgScrmbl-Gfap-Cas9-2A-EGFP-WPRE or non-transduced naive mice. EAE was induced by injecting 25 µg of MOG35-55 diluted in 100 µL of PBS emulsified in 100 µL of CFA per mouse.
Extracted molecule genomic DNA
Extraction protocol Each CNS was isolated per mouse. A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, washed in PBS, and stained with primary antibodies for flow cytometry. Once cells were sorted, cells were pelleted, washed, and genomic DNA was isolated using the Qiagen DNeasy Blood & Tissue Kit kit (Qiagen, #69504).
Bisulfite converted DNA libraries were generated by using the Zymo Pico-Methyl DNA kit (Zymo Research, #D5455) according to the manufacturer's protocol.
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina NextSeq 500
 
Description LIB037963_GEN00140764_S4
Data processing Reads were trimmed using Cutadapt (v1.14) to remove adapters and low quality reads.
Trimmed reads were then aligned to GRCm38 genome using Bismark (v0.20.1) and Bowtie2 (v0.20.1) with default settings.
Duplicated reads were removed using paired end mode
Methylation counts and percentages were extracted using bismark_methylation_extractor
Percentage methylation were visualized using IGV (v2.3.59)
Genome_build: GRCm38
Supplementary_files_format_and_content: bedgraph file with percent methylation at each CpG position
 
Submission date Apr 10, 2019
Last update date Feb 13, 2020
Contact name Michael Wheeler
E-mail(s) mwheeler0@bwh.harvard.edu
Organization name Brigham and Women's Hospital
Department Neurology
Street address 60 Fenwood Rd.
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL19057
Series (2)
GSE129606 Genome-wide analysis of DNA methylation profile in astrocytes isolated from naïve mice or EAE mice transduced with astrocyte-specific Mafg-targeting or non-targeting lentiviruses [WGBS]
GSE130119 MAFG-driven astrocytes promote CNS inflammation
Relations
BioSample SAMN11391728
SRA SRX5664984

Supplementary file Size Download File type/resource
GSM3716992_4_bismark_bt2_pe.deduplicated.bedGraph.gz 13.6 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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