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Sample GSM271361 Query DataSets for GSM271361
Status Public on Mar 07, 2008
Title MCFDCIS+RASF T1 Exp2 35 days
Sample type genomic
 
Source name MCFDCIS+RASF T1 Exp2 xenograft
Organism Homo sapiens
Characteristics none
Growth protocol Cells were grown in the media recommended by the providers. MCFDCIS cells were injected subcutaneously into 6-9 week old female nude mice alone or together with 2-3 fold excess of HME, RASF, PBS, or PBTS cells in 50% Matrigel. Tumors were allowed to grow for 3-8 weeks.
Extracted molecule genomic DNA
Extraction protocol We use the guanidinium thiocyanate/cesium chloride centrifugation method to isolate RNA/DNA from large amounts of tissue/cells and the mMACS mRNA isolation kit for small amounts (less than 1 million cells). The DNA fraction was extracted with PC8, treated with proteinase K and isopropanol precipitated.
Label biotin
Label protocol standard Affymetrix protocol
 
Hybridization protocol SNP array hybridizations were performed by the Dana-Farber Microarray Core using Affymetrix 11K XbaI or 250K StyI SNP arrays and protocols recommended by Affymetrix
Scan protocol Arrays were scanned using a confocal laser scanner, and Affymetrix genotyping software (Affymetrix GeneChip 5.0) was used to make allele calls for all loci.
Description MCFDCIS+RASF T1 Exp2 35 days
Data processing Data were then analyzed using dChip or genepattern software.
 
Submission date Mar 06, 2008
Last update date Mar 06, 2008
Contact name Kornelia Polyak
E-mail(s) kornelia_polyak@dfci.harvard.edu
Phone 617-632-2106
Organization name Dana-Farber Cancer Institute
Department Medical Oncology
Lab Polyak
Street address 450 Brookline Ave
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
 
Platform ID GPL1266
Series (1)
GSE10747 Analysis of genetic changes in MCF10A series cells and MCFDCIS derived xenografts

Data table header descriptions
ID_REF
VALUE copy number (dChip)
LOH L - loss, R - retention, N - no call (dChip)
RAS 1 relative allele signal 1 (GCOS)
RAS 2 relative allele signal 2 (GCOS)
Call genotype (GCOS)
Call Zone call zone score (GCOS)

Data table
ID_REF VALUE LOH RAS 1 RAS 2 Call Call Zone
SNP_A-1507322 1.1973 R 1 0.9855 AA 0.048597
SNP_A-1507323 1.80708 R 0.442 0.516 AB 0.360953
SNP_A-1507325 1.54303 R 0.3576 0.3211 AB 0.279076
SNP_A-1507326 2.04233 R 0.7267 0.8681 NoCall 0.898557
SNP_A-1507327 1.12114 R 0.2844 0.6216 AB 0.208424
SNP_A-1507328 1.64497 R 0.7911 0.6356 AB 0.468222
SNP_A-1507329 2.05017 R 0.4333 0.4079 AB 0.235251
SNP_A-1507330 4.11393 R 0.6706 0.7676 AB 0.540948
SNP_A-1507331 2.89823 R 0.0325 0.0185 BB 0.179236
SNP_A-1507332 1.53777 R 0.3469 0.3374 AB 0.391194
SNP_A-1507335 2.39396 R 0.3694 0.2191 BB 0.530945
SNP_A-1507336 2.89767 R 0.759 0.9546 AA 0.087429
SNP_A-1507337 1.92916 R 0.7021 0.8279 AA 0.398272
SNP_A-1507338 1.25415 R 0.793 0.9508 AA 0.592486
SNP_A-1507339 1.27949 R 0.3405 0.4667 AB 0.182798
SNP_A-1507340 2.50275 R 0.2466 0.2137 AB 0.767662
SNP_A-1507341 2.13795 R 0.9973 0.9696 AA 0.022607
SNP_A-1507342 0.860679 R 1 1 AA 0.077995
SNP_A-1507343 1.06351 R -2 -2 NoCall 10
SNP_A-1507344 1.54263 R 0 0 BB 0.007583

Total number of rows: 11205

Table truncated, full table size 510 Kbytes.




Supplementary file Size Download File type/resource
GSM271361.CEL.gz 3.6 Mb (ftp)(http) CEL
GSM271361.TXT.gz 356.7 Kb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file
Processed data are available on Series record

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