|
| Status |
Public on Feb 12, 2020 |
| Title |
KO-1 [Sample10] |
| Sample type |
SRA |
| |
|
| Source name |
KO_astrocytes
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6
genotype/variation: wild type
Sex: male
age: P90
sample group: undergoing EAE transduced with Mafg-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 HiSeq 4000 |
| |
|
| Description |
10_R*_001
|
| 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 |
GPL21103 |
| 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 |
SAMN11391727 |
| SRA |
SRX5664985 |
