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Sample GSM271345 Query DataSets for GSM271345
Status Public on Mar 07, 2008
Title MCFDCIS
Sample type genomic
 
Source name MCFDCIS cell line
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 2.58324 R 0.9916 0.9537 AA 0.069351
SNP_A-1507323 1.40821 R 0.6012 0.5542 AB 0.242647
SNP_A-1507325 2.70231 R 0.4807 0.4303 AB 0.360759
SNP_A-1507326 1.98654 R 0.7328 0.8053 NoCall 0.807247
SNP_A-1507327 1.42612 R 0.2534 0.5658 AB 0.316552
SNP_A-1507328 1.17628 R 0.5945 0.488 AB 0.5797
SNP_A-1507329 2.05337 R 0.3681 0.7858 NoCall 1.264809
SNP_A-1507330 3.04168 R 0.6412 0.7446 AB 0.361642
SNP_A-1507331 2.79538 R 0.0842 0 BB 0.148912
SNP_A-1507332 2.36104 R 0.5053 0.498 AB 0.651114
SNP_A-1507335 2.38104 R 0.1583 0.0859 BB 0.217331
SNP_A-1507336 2.78041 R 0.749 0.8478 AA 0.534663
SNP_A-1507337 1.49469 R 0.7736 0.9551 AA 0.39938
SNP_A-1507338 5.08183 R 1 1 AA 0.253029
SNP_A-1507339 1.61294 R 0.4605 0.5687 AB 0.336317
SNP_A-1507340 1.94586 R 0.2027 0.2157 NoCall 0.883462
SNP_A-1507341 2.31934 R 0.9973 0.9836 AA 0.080856
SNP_A-1507342 3.15006 R 0.9987 0.9969 AA 0.073443
SNP_A-1507343 2.60336 R 0.5387 0.456 AB 0.243343
SNP_A-1507344 1.99999 R 0 0.0675 BB 0.1865

Total number of rows: 11205

Table truncated, full table size 505 Kbytes.




Supplementary file Size Download File type/resource
GSM271345.CEL.gz 3.6 Mb (ftp)(http) CEL
GSM271345.TXT.gz 355.9 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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