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Sample GSM1138066 Query DataSets for GSM1138066
Status Public on May 22, 2014
Title MLL#11
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 BB 0.007125 BB 489.261200 1396.882568
SNP_A-1967418 AB 0.004903 AB 729.785645 647.817383
SNP_A-1969580 BB 0.001679 BB 1211.430908 3540.633057
SNP_A-4263484 BB 0.002746 BB 827.269775 2068.644287
SNP_A-1978185 AA 0.001536 AA 1718.134888 606.353210
SNP_A-4264431 AA 0.007147 AA 2287.428711 371.783844
SNP_A-1980898 BB 0.001023 BB 329.874237 1348.510254
SNP_A-1983139 AA 0.002185 AA 1212.847168 530.229980
SNP_A-4265735 NC 0.556858 AA 832.609253 459.390198
SNP_A-1995832 AB 0.006009 AB 1420.318604 1451.532837
SNP_A-1995893 AB 0.001956 AB 1624.921875 2062.434570
SNP_A-1997689 BB 0.000987 BB 714.911865 2880.223389
SNP_A-1997709 AA 0.000244 AA 1532.864624 404.114105
SNP_A-1997896 AA 0.004541 AA 2217.482666 676.185242
SNP_A-1997922 AB 0.003522 AB 676.185242 655.324951
SNP_A-2000230 AA 0.002814 AA 1927.957520 1382.935547
SNP_A-2000332 AA 0.005290 AA 2856.460449 1308.799316
SNP_A-2000337 AA 0.004670 AA 1073.273926 328.958466
SNP_A-2000342 AA 0.002081 AA 3018.004395 955.074097
SNP_A-4268173 AA 0.004040 AA 1430.072266 436.179382

Total number of rows: 909622

Table truncated, full table size 46159 Kbytes.




Supplementary file Size Download File type/resource
GSM1138066_MLL11.CEL.gz 26.8 Mb (ftp)(http) CEL
GSM1138066_MLL11.chp.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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