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Sample GSM271355 Query DataSets for GSM271355
Status Public on Mar 07, 2008
Title MCFDCIS 8wk T2
Sample type genomic
 
Source name MCFDCIS 8wk T2 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 Affymetrix 11K XbaI SNP array
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 1.1023 R 1 1 AA 0.099123
SNP_A-1507323 1.53267 R 0.4271 0.51 AB 0.418462
SNP_A-1507325 0.76913 R -2 -2 NoCall 10
SNP_A-1507326 0.898504 R 0.6984 0.8762 NoCall 0.836169
SNP_A-1507327 0.669786 R 0.3151 0.8694 NoCall 0.972573
SNP_A-1507328 1.00559 R 0.8993 0.638 NoCall 0.902034
SNP_A-1507329 1.3854 R 0.3052 0.4453 AB 0.582657
SNP_A-1507330 2.48053 R 0.7654 0.8322 NoCall 0.937741
SNP_A-1507331 1.95946 R 0.016 0 BB 0.287416
SNP_A-1507332 1.31764 R 0.2842 0.3102 AB 0.515383
SNP_A-1507335 2.61984 R 0.4149 0.4134 NoCall 1.306
SNP_A-1507336 3.1723 R 0.5273 0.84 NoCall 0.88403
SNP_A-1507337 1.7776 R 0.6217 0.8079 AA 0.669732
SNP_A-1507338 1.23557 R 0.8189 0.9747 AA 0.473356
SNP_A-1507339 0.459509 R 0.1064 0.147 BB 0.538975
SNP_A-1507340 2.03765 R 0.1965 0.1725 NoCall 0.974673
SNP_A-1507341 1.29279 R 1 0.9695 AA 0.018816
SNP_A-1507342 1.29053 R 1 1 AA 0.077995
SNP_A-1507343 0.526197 R -2 -2 NoCall 10
SNP_A-1507344 1.11798 R 0 0 BB 0.007583

Total number of rows: 11205

Table truncated, full table size 507 Kbytes.




Supplementary file Size Download File type/resource
GSM271355.CEL.gz 3.6 Mb (ftp)(http) CEL
GSM271355.TXT.gz 351.3 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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