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Sample GSM902418 Query DataSets for GSM902418
Status Public on Mar 28, 2012
Title MC0026_MCRxxx6_BM_CD138pos
Sample type genomic
 
Channel 1
Source name MC0026_MCRxxx6_BM_CD138pos DNA
Organism Homo sapiens
Characteristics cell type: CD138 Positive Myeloma Cells
sample order: 1
tc class: 4p16
cyto risk: high
17p13 deletion: monoallelic
ploidy: non-hyperdiploid
uams 70gene index: NA
copy number abnormalities: 76
time since sample1 months: 9.87
Treatment protocol CD138 positive tumor cells were isolated from bone marrow aspirates using magnetic sorting, both Miltenyi and Stemcell Technologies
Growth protocol Bone marrow aspirates were attained from patients after they signed informed consent documentation
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from cell lysates stored in TRIzol or using Puregene isolations from Dry Cell Pellets
Label Cy5
Label protocol genomic DNA was digested with DNaseI for 12 minutes, digested DNA was labeled using the Invitrogen BioPrime Labeling kit, Test tumor samples were labeled with Cy5 and control DNA were labeled with Cy3
 
Channel 2
Source name Promega Female DNA
Organism Homo sapiens
Characteristics reference: Promega Female DNA
Treatment protocol CD138 positive tumor cells were isolated from bone marrow aspirates using magnetic sorting, both Miltenyi and Stemcell Technologies
Growth protocol Bone marrow aspirates were attained from patients after they signed informed consent documentation
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from cell lysates stored in TRIzol or using Puregene isolations from Dry Cell Pellets
Label Cy3
Label protocol genomic DNA was digested with DNaseI for 12 minutes, digested DNA was labeled using the Invitrogen BioPrime Labeling kit, Test tumor samples were labeled with Cy5 and control DNA were labeled with Cy3
 
 
Hybridization protocol hybridizations were carried out as suggested in the Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Protocol Version 6.2 (October 2009)
Scan protocol scans were carried out as suggested in the Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Protocol Version 6.2 (October 2009) with both PMTs at 100%
Description Competitive Oligo CGH assay, MC0026_MCRxxx6_BM_CD138pos versus Promega Female DNA
Data processing Raw data was extracted from TIFF image files by Agilent Feature extraction using protocol CGH_107_Sep09 and grid 014693_D_F_20080627
 
Submission date Mar 26, 2012
Last update date Mar 28, 2012
Contact name Jonathan J Keats
E-mail(s) [email protected]
Phone 602-343-8690
Organization name Translational Genomics Research Institute (TGen)
Department Integrated Cancer Genomics
Lab Multiple Myeloma Research Lab - Keats Lab
Street address 445 N. Fifth Street
City Phoenix
State/province Arizona
ZIP/Postal code 85004
Country USA
 
Platform ID GPL4091
Series (2)
GSE36822 Clonal competition with alternating dominance in multiple myeloma [244kCGH]
GSE36825 Clonal competition with alternating dominance in multiple myeloma

Data table header descriptions
ID_REF
VALUE normalized log10 ratio Cy5/Cy3

Data table
ID_REF VALUE
1 -1.203996559e-002
2 -2.473804464e-001
3 0.000000000e+000
4 7.134757142e-002
5 -5.489907238e-002
6 -5.084166245e-003
7 5.644876367e-002
8 2.727218227e-002
9 -3.208869869e-002
10 -1.670035089e-001
11 -1.203702539e-002
12 1.990964636e-002
13 -9.443882917e-002
14 5.691728456e-002
15 1.358482284e-001
16 -5.335228436e-002
17 1.351842629e-001
18 -4.387419991e-001
19 3.615746299e-002
20 1.341536036e-001

Total number of rows: 243430

Table truncated, full table size 5709 Kbytes.




Supplementary file Size Download File type/resource
GSM902418_MC0026_MCRxxx6_BM_CD138pos_244A.txt.gz 23.4 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file
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