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Sample GSM1231539 Query DataSets for GSM1231539
Status Public on Sep 14, 2013
Title genomic DNA from microdissected human kidney72
Sample type genomic
 
Source name kidney 72
Organism Homo sapiens
Characteristics tissue: kidney tubule
Extracted molecule genomic DNA
Extraction protocol 1mm x 1mm biopsy tissues were placed under an Olympus model SZX12 stereomicroscope using 90x magnification. The biopsy tissue was manually microdissected at 4°C in RNALater for glomerular and tubular compartments using fine tip forceps. The corresponding tubulointerstitial and vascular compartment was placed into RLT solution. For easier designation we called this component tubules. Dissected tissue was homogenized using a Powergen125 (Fisher) homogenizer and stored at -80°C. Genomic DNA was prepared using DNA extraction kit (Qiagen) according to manufacturer's instructions.
Label Cy5 and Cy3
Label protocol Standard Illumina Protocol
 
Hybridization protocol bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
Scan protocol Arrays were imaged using iScan Reader using standard recommended Illumina scanner setting
Data processing GenomeStudio V2011.1; methylation module 1.9.0
 
Submission date Sep 13, 2013
Last update date Sep 14, 2013
Contact name Yi-An Ko
E-mail(s) yian.kia.ko@gmail.com
Organization name UPeenn
Department Genetics & Gene Regulation
Lab Susztak
Street address 415 curie blvd
City Philadelphia
State/province Pennsylvania
ZIP/Postal code 19104
Country USA
 
Platform ID GPL13534
Series (1)
GSE50874 Methylation Profiling of Human Kidney Tubules

Data table header descriptions
ID_REF
VALUE Average Beta
6055424146_R06C02.Detection Pval

Data table
ID_REF VALUE 6055424146_R06C02.Detection Pval
cg00000029 0.4592684 0
cg00000108 0.9290629 0
cg00000109 0.8248848 0
cg00000165 0.1811371 0
cg00000236 0.8174323 0
cg00000289 0.5263158 0
cg00000292 0.5000805 0
cg00000321 0.4197034 0
cg00000363 0.2243469 0
cg00000622 0.01840877 0
cg00000658 0.8292326 0
cg00000714 0.1568417 0
cg00000721 0.8977901 0
cg00000734 0.07128549 0
cg00000769 0.03344063 0
cg00000807 0.601768 0
cg00000884 0.8386949 0
cg00000905 0.09577033 0
cg00000924 0.4725631 0
cg00000948 0.8801997 0

Total number of rows: 485577

Table truncated, full table size 10997 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
Processed data are available on Series record

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