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| Status |
Public on Jun 01, 2023 |
| Title |
IRF8KO microglia - mCpG_rep1 |
| Sample type |
SRA |
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| Source name |
Microglia
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| Organism |
Mus musculus |
| Characteristics |
cell type: FACS-sorted microglia
strain: C57BL/6J
genotype: IRF8KO
age: 3-month-old
treatment: untreated
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| Treatment protocol |
N.A.
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| Growth protocol |
Microglia were non-enzymatically isolated from a 3-month-old WT and IRF8KO brain, and enriched by cell sorting.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from 40,000 microglia using Quick-DNA Microprep plus kit (Zymo Research) as the manufacturer’s protocol.
50ng DNA was bisulfite-converted and processed to the library using Pico Methyl-Seq Library Prep Kit (Zymo Research) with an 8-cycle PCR amplification
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
2x75 paired-end sequence reads
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| Data processing |
Based on the Bismark M-bias plot, the adapters, low-quality sequence, and additional 10bp of 5'-end and 2bp of 3'-end were trimmed from the sequencing data using TrimGalore.
The data were first aligned using Bismark with -q --score-min L,0,-0.4 --ignore-quals --no-mixed --no-discordant --dovetail --maxins options, and then unmapped sequences were aligned additionally with single-end mode.
Duplicated sequences were removed before methylation calling.
Two methylation calls from each replicate were merged into a single coverage file.
Differential analyses between WT and IRF8KO were performed using R/DSS package with FDR<0.05 for the differential methylated loci (DMLs) and p<0.001 for the regions (DMRs).
Assembly: mm10
Supplementary files format and content: A single coverage file (.cov file) consists of each CpG locus, %mCpG, methylated cytosine counts, and unmethylated cytosine counts.
Supplementary files format and content: A list of DMLs with stats; IRF8NaiveDML.txt
Supplementary files format and content: A list of DMRs with stats; IRF8Naive1e-03.txt, generated by R/DSS
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| Submission date |
May 01, 2023 |
| Last update date |
Jun 01, 2023 |
| Contact name |
Keita Saeki |
| E-mail(s) |
keita.saeki@nih.gov
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| Organization name |
NIH/NICHD
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| Street address |
6 Center Drive
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| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL21493 |
| Series (2) |
| GSE231404 |
Genome-wide methylated CpG status in WT and IRF8KO microglia [WGBS] |
| GSE231406 |
IRF8 configures enhancer landscape in postnatal microglia and directs microglia specific transcriptional programs |
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| Relations |
| BioSample |
SAMN34504041 |
| SRA |
SRX20174653 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7273561_CpG_KS005_merged.bismark.cov.gz |
217.5 Mb |
(ftp)(http) |
COV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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