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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 20, 2023 |
| Title |
O DNA methylation replicate 4 |
| Sample type |
SRA |
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| Source name |
Skeletal muscle stem cells
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
Sex: Male
age: 22 months
cell type: Skeletal muscle stem cells
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
FACS-isolated MuSCs were snap-frozen. Genomic DNA was extracted using the QIAamp Micro DNA extraction kit (Qiagen).
DNA (150 ng) was sheared with a Bioruptor 300 (Diagenode) and then end-repaired and A-tailed with the NEBNext DNA Library Prep kit (NEB). Methylated Illumina adapters were ligated with LigaFast (Promega), and size selection was performed with AMPure XP beads (Beckman Coulter). Bisulfite conversion was performed with the EZ DNA Methylation Direct kit (Zymo) and amplified with 14 cycles with PfuTurbo Cx Hotstart DNA Polymerase (Agilent) followed by final size selection with the AMPure XP beads. Libraries underwent paired-end 101-bp sequencing at the Stanford Genome Sequencing Service Center with an Illumina HiSeq 2000 at low cluster density with PhiX spike-in to a depth of 115-200 million reads.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
processed data file: oldCpGmethylratios.bedGraph
processed data file: Aging_MuSC_WGBS.txt
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| Data processing |
Reads were adapter- and quality-trimmed with trim_galore (www.bioinformatics.babraham.ac.uk/projects/trim_galore) (quality cutoff 20, adapter stringency 1, final length filter 50) and then deduplicated, mapped to the mm10 version of the mouse genome, and called for methylation using Bismark (Krueger et al. 2011) (seedmms 1, maxins 1000, ignore_r2 2). Bisulfite conversion efficiency (as assessed by conversion of non-CpG cytosines) was >99.5%.
Genes lacking an Entrez ID and ERCC reads were filtered out. Raw count data were then normalized using edgeR with the TMM method (Robinson et al. 2010).
DSS (Wu et al. 2012) was used to estimate CpG methylation means, dispersions, and significance across the two age groups (default parameters).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Aging_MuSC_WGBS.txt: Tab-delimited text file containing CpGs profiled in both age groups, with genome (mm10) position (0-based coordinate) and methylation means, dispersions, p-values, and FDR (BH correction) values from DSS.
Supplementary_files_format_and_content: bedGraph files: bedGraph format for genome browsers of the mean methylation ratios of each CpG estimated by DSS, each age group in a separate bedGraph file.
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| Submission date |
Jun 18, 2020 |
| Last update date |
Mar 20, 2023 |
| Contact name |
Jamie O. Brett |
| E-mail(s) |
jamie.o.brett@gmail.com
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| Organization name |
Stanford University
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| Department |
Neurology and Neurological Sciences
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| Lab |
Thomas A. Rando
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| Street address |
3801 Miranda Avenue, Building 100, Room E4-216
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| City |
Palo Alto |
| State/province |
CA |
| ZIP/Postal code |
94304 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE152797 |
Multiomics profiling of young and old quiescent skeletal muscle stem cells [aging WGBS] |
| GSE152798 |
Multiomics profiling of young and old quiescent skeletal muscle stem cells |
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| Relations |
| BioSample |
SAMN15317611 |
| SRA |
SRX8575808 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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