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Sample GSM1063580 Query DataSets for GSM1063580
Status Public on Jun 05, 2013
Title NF-3 DNA
Sample type genomic
 
Channel 1
Source name Methylated Genomic DNA from NF sample
Organism Homo sapiens
Characteristics tissue: heart left ventricle
dna type: Methylaed Genomic DNA
Extracted molecule genomic DNA
Extraction protocol DNA was extracted using a MagNAPure DNA Extraction System (Roche), quantiated, sonicated and enriched using the MethylCollector Ultra Kit (Active Motif) following the manufacturer's protocol. Both methylated and input DNA was amplified using whole genome amplification (Sigma-Aldrich).
Label Cy5
Label protocol DNA labeling was completed using NimbleGen Dual-Color DNA labeling Kit (Cat # 06370250001) following their standard operating protocol.
 
Channel 2
Source name Total Genomic DNA from NF Sample
Organism Homo sapiens
Characteristics tissue: heart left ventricle
dna type: total Genomic DNA
Extracted molecule genomic DNA
Extraction protocol DNA was extracted using a MagNAPure DNA Extraction System (Roche), quantiated, sonicated and enriched using the MethylCollector Ultra Kit (Active Motif) following the manufacturer's protocol. Both methylated and input DNA was amplified using whole genome amplification (Sigma-Aldrich).
Label Cy3
Label protocol DNA labeling was completed using NimbleGen Dual-Color DNA labeling Kit (Cat # 06370250001) following their standard operating protocol.
 
 
Hybridization protocol Hybridization was completed using NimbleGen Hybridization Kit (Cat # 05583683001)following their standard operating protocol.
Scan protocol Scanning was performed using Roche NimbleGen MS200 Microarray Scanner following the manufacturer's standard protocol
Data processing Each sample was processed utilizing NimbleScan software default values, including analysis of the 635/532 ratio utilizing a 500bp sliding window KS test according to manufacturer instructions.
 
Submission date Jan 14, 2013
Last update date Jun 05, 2013
Contact name William Lewis
Organization name Emory University
Department Pathology
Lab Lewis Lab
Street address 101 Woodruff Circle
City Atlanta
State/province Georgia
ZIP/Postal code 30322
Country USA
 
Platform ID GPL16284
Series (1)
GSE43435 Thymidine Kinase and mtDNA Depletion in Human Cardiomyopathy: Epigentic and Translational Evidence for Energy Starvation

Data table header descriptions
ID_REF
VALUE scaled log2 ratio 635/532

Data table
ID_REF VALUE
CHR10FS100027443_chr10:100025007-100036007 -0.11
CHR10FS100026308_chr10:100025007-100036007 -0.29
CHR10FS100033258_chr10:100025007-100036007 0.35
CHR10FS100033870_chr10:100025007-100036007 0.21
CHR10FS100032365_chr10:100025007-100036007 0.01
CHR10FS100035595_chr10:100025007-100036007 0.32
CHR10FS100034305_chr10:100025007-100036007 0.38
CHR10FS100033782_chr10:100025007-100036007 0.19
CHR10FS100025932_chr10:100025007-100036007 0.13
CHR10FS100026010_chr10:100025007-100036007 0.22
CHR10FS100032872_chr10:100025007-100036007 -0.58
CHR10FS100035389_chr10:100025007-100036007 0.23
CHR10FS100027247_chr10:100025007-100036007 0.01
CHR10FS100027933_chr10:100025007-100036007 -0.17
CHR10FS100034887_chr10:100025007-100036007 -0.23
CHR10FS100025432_chr10:100025007-100036007 0.35
CHR10FS100034395_chr10:100025007-100036007 0.07
CHR10FS100026630_chr10:100025007-100036007 -0.26
CHR10FS100025530_chr10:100025007-100036007 -0.03
CHR10FS100033172_chr10:100025007-100036007 -0.41

Total number of rows: 2081759

Table truncated, full table size 94413 Kbytes.




Supplementary file Size Download File type/resource
GSM1063580_511651_2011-11-09_10-03_Area1_532.pair.gz 42.7 Mb (ftp)(http) PAIR
GSM1063580_511651_2011-11-09_10-03_Area1_635.pair.gz 42.6 Mb (ftp)(http) PAIR
GSM1063580_511651_2011-11-09_10-03_Area1_ratio.gff.gz 28.3 Mb (ftp)(http) GFF
GSM1063580_511651_2011-11-09_10-03_Area1_ratio_peak_pvalues_mapToFeatures.txt.gz 100 b (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file
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