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Sample GSM656407 Query DataSets for GSM656407
Status Public on Jul 19, 2011
Title Maffucci chondrosarcoma
Sample type genomic
 
Source name Maffucci chondrosarcoma
Organism Homo sapiens
Characteristics disease: Maffucci
tumor: chondrosarcoma
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 AB 0.001416 AB 2375.883789 2640.978760
SNP_A-1967418 BB 0.010395 BB 340.780426 618.703125
SNP_A-1969580 BB 0.008451 BB 1556.740601 4707.720215
SNP_A-4263484 AB 0.005013 AB 1499.523438 1253.268433
SNP_A-1978185 AA 0.002499 AA 1218.933350 281.501770
SNP_A-4264431 AB 0.002393 AB 1105.617676 854.156128
SNP_A-1980898 BB 0.003062 BB 261.371826 715.700500
SNP_A-1983139 AA 0.010134 AA 3646.336426 836.408325
SNP_A-4265735 AB 0.001102 AB 1382.403809 1389.797363
SNP_A-1995832 BB 0.008731 BB 349.917755 2119.490723
SNP_A-1995893 BB 0.003563 BB 452.296783 2365.668457
SNP_A-1997689 BB 0.002765 BB 632.217651 3682.252930
SNP_A-1997709 AA 0.006339 AA 1564.656738 233.860428
SNP_A-1997896 AA 0.005363 AA 1269.086304 412.200500
SNP_A-1997922 NC 0.192836 BB 373.949219 766.273254
SNP_A-2000230 AA 0.008357 AA 1956.217041 795.891724
SNP_A-2000332 AA 0.003236 AA 3227.931885 766.345703
SNP_A-2000337 AA 0.002022 AA 1371.542236 270.433685
SNP_A-2000342 AA 0.003804 AA 3055.741211 860.184082
SNP_A-4268173 AB 0.000802 AB 975.928467 946.967468

Total number of rows: 909622

Table truncated, full table size 46146 Kbytes.




Supplementary file Size Download File type/resource
GSM656407_080711MJA_SNP6.0_100446_38.CEL.gz 28.5 Mb (ftp)(http) CEL
GSM656407_080711MJA_SNP6.0_100446_38.CN5.cnchp.gz 35.3 Mb (ftp)(http) CNCHP
GSM656407_080711MJA_SNP6.0_100446_38.birdseed_v2.chp.gz 12.8 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file
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