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Sample GSM1138071 Query DataSets for GSM1138071
Status Public on May 22, 2014
Title MLL#15
Sample type genomic
 
Source name Leukemic cells obtained from bone marrow or blood at diagnosis
Organism Homo sapiens
Characteristics disease: leukemia
cell type: de novo AML
Treatment protocol None
Growth protocol DNA was extracted from cryopreserved mononuclear cell preparations of diagnostic bone marrow or peripheral blood from AML cases with t(9;11)
Extracted molecule genomic DNA
Extraction protocol AllPrep DNA/RNA Mini Kit (Qiagen)
Label biotin
Label protocol 250 nanograms of genomic DNA were digested to completion with NspI or StyI, ligated to adapaters and amplified by PCR. 200-270 micrograms of pooled amplified DNA were fragmented and end-labeled with a biotinylated nucleotide according to the Genome-Wide Human SNP Nsp/Sty 6.0 User Guide 702504 Rev 3, 2008, Affymetrix)
 
Hybridization protocol 200-270 micrograms of amplified and biotinylated DNA were hybridized for 16-18 hr at 50C on a GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the AffymetrixGeneChip Scanner 3000 7G.
Description DNA extracted from tumor cells obtained at diagnosis
Data processing Genotyping Console/birdseed-v2
 
Submission date May 08, 2013
Last update date May 22, 2014
Contact name Michael Kuehn
E-mail(s) michael.kuehn@uniklinik-ulm.de
Organization name University Hospital of Ulm
Street address Albert-Einstein-Allee 23
City Ulm
ZIP/Postal code 89081
Country Germany
 
Platform ID GPL6801
Series (1)
GSE46745 Genome-wide Genotyping of Acute Myeloid Leukemia with Translocation t(9;11)(p22;q23) Reveals Novel Recurrent Genomic Alterations

Data table header descriptions
ID_REF PROBE SET NAME
VALUE CALL
CONFIDENCE
FORCED CALL
SIGNAL A
SIGNAL B

Data table
ID_REF VALUE CONFIDENCE FORCED CALL SIGNAL A SIGNAL B
SNP_A-2131660 AB 0.004335 AB 1039.563232 973.012146
SNP_A-1967418 BB 0.005542 BB 420.956238 1057.067383
SNP_A-1969580 BB 0.002287 BB 978.485657 3472.215576
SNP_A-4263484 AA 0.000768 AA 2585.911377 504.830109
SNP_A-1978185 AA 0.005526 AA 1916.999268 733.888428
SNP_A-4264431 AA 0.004439 AA 2372.570557 416.400452
SNP_A-1980898 BB 0.001336 BB 338.844940 1399.140137
SNP_A-1983139 AA 0.004127 AA 1286.617065 603.893860
SNP_A-4265735 NC 0.117506 AB 930.327759 615.144897
SNP_A-1995832 AA 0.001805 AA 2274.648926 642.028564
SNP_A-1995893 AA 0.009795 AA 2470.398682 1573.282349
SNP_A-1997689 BB 0.007429 BB 529.567810 2578.449707
SNP_A-1997709 AA 0.005647 AA 1799.666382 376.691315
SNP_A-1997896 AA 0.002809 AA 1748.923706 563.323669
SNP_A-1997922 AA 0.001650 AA 1146.100830 345.977539
SNP_A-2000230 AA 0.002780 AA 2008.885376 1437.392456
SNP_A-2000332 AB 0.001107 AB 2308.803711 2512.583740
SNP_A-2000337 AA 0.030727 AA 1252.722900 567.673645
SNP_A-2000342 AA 0.004616 AA 3039.204102 763.158020
SNP_A-4268173 AA 0.001431 AA 1649.589966 439.424500

Total number of rows: 909622

Table truncated, full table size 46152 Kbytes.




Supplementary file Size Download File type/resource
GSM1138071_MLL15.CEL.gz 26.4 Mb (ftp)(http) CEL
GSM1138071_MLL15.chp.gz 12.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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