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Sample GSM567060 Query DataSets for GSM567060
Status Public on Jul 19, 2011
Title L2195N
Sample type genomic
Source name Maffucci patient normal (fresh frozen)
Organism Homo sapiens
Characteristics disease: Maffucci
tissue: fresh frozen normal
sample type: control
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 GeneChip GSC3000 7G Whole-Genome Association System. According to Affymetrix SNP 6.0 standard protocol.
Description 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. Copy number inferred after correction with the 5 closest normals.
Submission date Jul 16, 2010
Last update date Jul 19, 2011
Contact name Twinkal Chandubhai Pansuriya
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 (4)
GSE22965 Genome-wide analysis of Ollier disease: Is it all in the genes?
GSE22984 Affymetrix SNP6.0 on Ollier disease-related tumors
GSE26674 SNP array analysis on Maffucci tumours

Data table header descriptions
ID_REF ProbeSet name
VALUE Genotype call

Data table
SNP_A-2131660 AB 0.002959 AB 2717.300293 3272.329346
SNP_A-1967418 BB 0.000547 BB 283.485687 742.465881
SNP_A-1969580 BB 0.000368 BB 1150.409668 3624.320312
SNP_A-4263484 AB 0.017492 AB 1664.286011 1562.571167
SNP_A-1978185 AA 0.003146 AA 1213.548950 379.754181
SNP_A-4264431 AB 0.004790 AB 1038.782227 762.530151
SNP_A-1980898 BB 0.002928 BB 235.507080 677.257019
SNP_A-1983139 AA 0.000900 AA 3069.562256 946.503113
SNP_A-4265735 AB 0.002654 AB 1726.923462 1639.880981
SNP_A-1995832 BB 0.001179 BB 481.848450 1905.584106
SNP_A-1995893 BB 0.001738 BB 611.385315 2633.151855
SNP_A-1997689 BB 0.000892 BB 729.508118 3643.386230
SNP_A-1997709 AA 0.011387 AA 1482.738525 353.075165
SNP_A-1997896 AA 0.001369 AA 1475.006226 479.039825
SNP_A-1997922 NC 0.245702 BB 428.914124 810.714722
SNP_A-2000230 AA 0.001222 AA 2317.954346 1029.626953
SNP_A-2000332 AA 0.009506 AA 2657.235840 704.095337
SNP_A-2000337 AA 0.001665 AA 1311.543457 282.690552
SNP_A-2000342 AA 0.001093 AA 3228.270752 1008.724670
SNP_A-4268173 AB 0.001808 AB 801.311157 689.586365

Total number of rows: 909622

Table truncated, full table size 46118 Kbytes.

Supplementary file Size Download File type/resource
GSM567060.CEL.gz 31.1 Mb (ftp)(http) CEL
GSM567060.CNCHP.gz 34.8 Mb (ftp)(http) CNCHP
GSM567060.chp.gz 13.0 Mb (ftp)(http) CHP
GSM567060.gqc.gz 1.0 Kb (ftp)(http) GQC
Processed data included within Sample table
Processed data provided as supplementary file

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