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Sample GSM656418 Query DataSets for GSM656418
Status Public on Jul 19, 2011
Title Maffucci Enchondroma
Sample type genomic
 
Source name Maffucci Enchondroma
Organism Homo sapiens
Characteristics disease: Maffucci
tumor: enchondroma (L2101)
Extracted molecule genomic DNA
Extraction protocol DNA from fresh frozen tissue was isolated using the wizard genomic DNA purification kit (Promega, Madison, WI), according to the manufacturer instructions.
Label biotin
Label protocol According to Affymetrix SNP 6.0 standard protocol
 
Hybridization protocol According to Affymetrix SNP 6.0 standard protocol
Scan protocol According to Affymetrix SNP 6.0 standard protocol
Data processing Genotyping was performed using the CRLMM algorithm in the Oligo package (Lin, 2008), copy number analysis using the aroma affymetrix package (Bengtsson, 2009), and we constructed LAIR plots to visualize regions of LOH and allelic imbalance (Corver, 2008) in R software (version 2.8). We have used CNCHP log ratio file as an input in Nexus (BioDiscovery, USA) software (version 4.1) and performed HMM based SNP-FASST segmentation for copy number analysis.
 
Submission date Jan 18, 2011
Last update date Jul 19, 2011
Contact name Twinkal Chandubhai Pansuriya
E-mail(s) t.c.pansuriya@lumc.nl
Phone 0031715266528
Organization name LUMC
Department Pathology
Street address Albinusdreef 2
City Leiden
State/province Zuid-Holland
ZIP/Postal code 2333ZA
Country Netherlands
 
Platform ID GPL6801
Series (2)
GSE26674 SNP array analysis on Maffucci tumours
GSE26675 Maffucci tumours

Data table header descriptions
ID_REF PROBE SET NAME
VALUE Genotype call
CONFIDENCE
FORCED CALL
SIGNAL A
SIGNAL B

Data table
ID_REF VALUE CONFIDENCE FORCED CALL SIGNAL A SIGNAL B
SNP_A-2131660 BB 0.003860 BB 1139.744629 5145.143066
SNP_A-1967418 AA 0.004559 AA 1097.117676 269.790344
SNP_A-1969580 BB 0.006561 BB 1593.095093 3911.542480
SNP_A-4263484 BB 0.007082 BB 753.835388 2566.433594
SNP_A-1978185 AA 0.001271 AA 1465.525146 415.896515
SNP_A-4264431 AB 0.008516 AB 1573.259155 1264.002808
SNP_A-1980898 AB 0.001210 AB 632.520935 568.050049
SNP_A-1983139 AA 0.001213 AA 3621.391357 1153.486572
SNP_A-4265735 AA 0.003972 AA 1750.464600 564.893066
SNP_A-1995832 AB 0.004184 AB 1807.798340 1261.022339
SNP_A-1995893 AB 0.032090 AB 1755.869995 2691.589355
SNP_A-1997689 BB 0.005155 BB 957.205444 3802.278320
SNP_A-1997709 AA 0.002069 AA 1986.683838 334.831085
SNP_A-1997896 AA 0.004088 AA 1442.588257 566.492554
SNP_A-1997922 AB 0.007801 AB 785.598572 679.037292
SNP_A-2000230 AA 0.007686 AA 2100.392334 1174.886108
SNP_A-2000332 AB 0.002083 AB 2373.705811 2397.700195
SNP_A-2000337 AA 0.010729 AA 1791.648315 363.844086
SNP_A-2000342 AA 0.008631 AA 4217.095703 1275.803467
SNP_A-4268173 AA 0.008379 AA 1123.981934 248.293091

Total number of rows: 909622

Table truncated, full table size 46140 Kbytes.




Supplementary file Size Download File type/resource
GSM656418_081112MJA_SNP6.0_100640_23_71.CEL.gz 30.4 Mb (ftp)(http) CEL
GSM656418_081112MJA_SNP6.0_100640_23_71.CN5.cnchp.gz 35.4 Mb (ftp)(http) CNCHP
GSM656418_081112MJA_SNP6.0_100640_23_71.birdseed_v2.chp.gz 13.2 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file
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