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Sample GSM1138050 Query DataSets for GSM1138050
Status Public on May 22, 2014
Title MLL#2
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 BB 0.002786 BB 657.229736 1870.573120
SNP_A-1967418 BB 0.002816 BB 333.509064 714.921448
SNP_A-1969580 BB 0.007490 BB 1018.132812 2762.096436
SNP_A-4263484 BB 0.003412 BB 708.230835 1809.191772
SNP_A-1978185 AA 0.007450 AA 2117.697510 773.460571
SNP_A-4264431 AA 0.009936 AA 1344.783813 375.090515
SNP_A-1980898 AB 0.006488 AB 745.099304 616.992981
SNP_A-1983139 AA 0.004422 AA 1377.254272 627.057495
SNP_A-4265735 AB 0.000847 AB 856.014465 824.222595
SNP_A-1995832 AB 0.010192 AB 1868.505127 1436.416748
SNP_A-1995893 AB 0.003338 AB 1442.782349 2188.893555
SNP_A-1997689 BB 0.004933 BB 796.427551 3498.293701
SNP_A-1997709 AA 0.000443 AA 1496.034058 406.303986
SNP_A-1997896 AA 0.000615 AA 1832.374146 628.971619
SNP_A-1997922 AB 0.002392 AB 820.168091 666.798645
SNP_A-2000230 AA 0.011100 AA 1586.531860 1649.771851
SNP_A-2000332 AB 0.002381 AB 2303.302734 2611.163086
SNP_A-2000337 AA 0.000464 AA 1170.535278 407.665497
SNP_A-2000342 AA 0.002461 AA 2978.839844 969.530884
SNP_A-4268173 AB 0.008624 AB 520.662720 672.815002

Total number of rows: 909622

Table truncated, full table size 46145 Kbytes.




Supplementary file Size Download File type/resource
GSM1138050_MLL2.CEL.gz 26.6 Mb (ftp)(http) CEL
GSM1138050_MLL2.chp.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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