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| Status |
Public on Dec 21, 2015 |
| Title |
HypMac3 |
| Sample type |
SRA |
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| Source name |
Gastrocnemius muscle
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| Organism |
Mus musculus |
| Characteristics |
genotype/variation: LDLR-/-ApoB100/100
strain: C57BL/6J background
cell type: macrophages
condition: Hyperlipidemic
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| Treatment protocol |
Unilateral hindlimb ischemia was induced by ligating femoral artery proximal to the bifurcation of superficial and deep femoral artery in control, hyperlipidemic and type 2 diabetic mice. Ishcemic muscle macrophages and endothelial cells were FACS sorted at 1 week time point after femoral artery ligation
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from FACS sorted macrophages and endothelial cells using AllPrep DNA/RNA/Protein Mini Kit (Qiagen Finland, Helsinki, Finland) according to manufacturer's instructions.
Reduced representation bisulfite sequencing (RRBS) library was generated as described previously (Boyle P, Clement K, Gu H, Smith ZD, Ziller M, Fostel JL, Holmes L, Meldrim J, Kelley F, Gnirke A, Meissner A: Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling. Genome Biol 2012, 13(10):R92).
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
bismark 0.10.0 (relying on bowtie 2-2.0.5) for read alignment to mm10 genome (derived from UCSC)
methylKit 0.9.2 R package for differential methylation calling (R version 3.0.1). Prefiltering using function filterByCoverage with parameters lo.count=10 and hi.perc=99.0, differential methylation calculated using function calculateDiffMeth.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text files. <comparison>_Diff-all-promoter.txt files contain differential methylation results for proximal promoter regions (-1kb upstream and +500 bp downstream of the transcription start site (TSS)). Columns: row number, chromosome, start coordinate, end coordinate, strand, pvalue, qvalue, methylation difference.
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| Submission date |
Feb 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Mohan Babu |
| E-mail(s) |
babu.mohan@uef.fi
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| Phone |
+358403553685
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| Organization name |
A.I.Virtanen Institute, University of Eastern Finland
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| Department |
Biotechnology and Molecular Medicine
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| Lab |
Molecular Medicine
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| Street address |
Neulaniementie 2
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| City |
Kuopio |
| ZIP/Postal code |
70211 |
| Country |
Finland |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE65759 |
Genome wide promoter methylation analysis of mouse macrophages and endothelial cells isolated from ischemic hindlimbs using RRBS sequencing |
| GSE65803 |
Differential promoter methylation of macrophage genes correlates with impaired vascular growth in ischemic muscles of hyperlipidemic and type 2 diabetic mice |
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| Relations |
| BioSample |
SAMN03333590 |
| SRA |
SRX869437 |
| 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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