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Sample GSM1138077 Query DataSets for GSM1138077
Status Public on May 22, 2014
Title MLL#19
Sample type genomic
 
Source name Leukemic cells obtained from bone marrow or blood at diagnosis
Organism Homo sapiens
Characteristics disease: leukemia
cell type: t-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 0.004572 AB 1058.233032 908.453552
SNP_A-1967418 BB 0.004859 BB 411.753113 1044.540527
SNP_A-1969580 BB 0.037811 BB 1473.348999 3476.781250
SNP_A-4263484 AB 0.005782 AB 2365.653320 1579.317017
SNP_A-1978185 AA 0.008898 AA 2351.005859 584.442261
SNP_A-4264431 AA 0.013624 AA 2802.413574 701.225403
SNP_A-1980898 AA 0.007064 AA 2517.538086 431.704468
SNP_A-1983139 AA 0.004679 AA 1727.273438 646.385620
SNP_A-4265735 BB 0.002089 BB 613.744934 1538.733765
SNP_A-1995832 AB 0.003604 AB 1311.532837 1288.261108
SNP_A-1995893 AB 0.001903 AB 1403.037720 1992.972656
SNP_A-1997689 BB 0.003419 BB 684.242065 2609.325195
SNP_A-1997709 AA 0.011348 AA 1425.228760 493.790802
SNP_A-1997896 AA 0.003339 AA 2157.971680 738.565369
SNP_A-1997922 AB 0.009386 AB 1145.340698 1108.683350
SNP_A-2000230 AA 0.005353 AA 3026.769287 1240.639771
SNP_A-2000332 AB 0.001622 AB 2175.464844 2303.044434
SNP_A-2000337 AA 0.009082 AA 1486.741211 423.073303
SNP_A-2000342 AA 0.003625 AA 3752.887695 1168.689941
SNP_A-4268173 AA 0.006838 AA 2545.125000 626.979370

Total number of rows: 909622

Table truncated, full table size 46154 Kbytes.




Supplementary file Size Download File type/resource
GSM1138077_MLL19.CEL.gz 26.9 Mb (ftp)(http) CEL
GSM1138077_MLL19.chp.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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