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Sample GSM1604120 Query DataSets for GSM1604120
Status Public on Dec 21, 2015
Title DiabEC2
Sample type SRA
 
Source name Gastrocnemius muscle
Organism Mus musculus
Characteristics genotype/variation: IGF-II/LDLR-/-ApoB100/100
strain: C57BL/6J background
cell type: Enodthelial cells
condition: type 2 diabetic
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
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).
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection Reduced Representation
Instrument model Illumina HiSeq 2500
 
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.
 
Submission date Feb 09, 2015
Last update date May 15, 2019
Contact name Mohan Babu
E-mail(s) babu.mohan@uef.fi
Phone +358403553685
Organization name A.I.Virtanen Institute, University of Eastern Finland
Department Biotechnology and Molecular Medicine
Lab Molecular Medicine
Street address Neulaniementie 2
City Kuopio
ZIP/Postal code 70211
Country Finland
 
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
Relations
BioSample SAMN03333587
SRA SRX869448

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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