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Sample GSM1138067 Query DataSets for GSM1138067
Status Public on May 22, 2014
Title MLL#12
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 0.001618 AB 1235.809082 1078.945557
SNP_A-1967418 BB 0.015044 BB 423.462036 744.693054
SNP_A-1969580 BB 0.000192 BB 1105.401978 3533.311768
SNP_A-4263484 AB 0.000796 AB 1880.757446 1432.110840
SNP_A-1978185 AA 0.002928 AA 1518.494019 557.701599
SNP_A-4264431 AA 0.000410 AA 2320.520264 486.069763
SNP_A-1980898 BB 0.001728 BB 482.359039 1345.949585
SNP_A-1983139 AA 0.000931 AA 1517.503662 569.687622
SNP_A-4265735 AA 0.007621 AA 1851.843506 647.016235
SNP_A-1995832 AB 0.002068 AB 1523.002808 1287.438843
SNP_A-1995893 AB 0.003716 AB 1353.684448 2044.997803
SNP_A-1997689 BB 0.003979 BB 661.043213 3298.097168
SNP_A-1997709 AA 0.002067 AA 1602.446045 373.401093
SNP_A-1997896 AA 0.008931 AA 2442.966797 807.616516
SNP_A-1997922 AB 0.000370 AB 881.791138 805.458313
SNP_A-2000230 AA 0.003992 AA 2808.569824 1163.040161
SNP_A-2000332 AB 0.003966 AB 2481.969727 2148.477051
SNP_A-2000337 AA 0.000367 AA 1141.509644 392.579834
SNP_A-2000342 AA 0.006071 AA 3111.946777 1195.468628
SNP_A-4268173 AB 0.006398 AB 1414.035889 1379.981201

Total number of rows: 909622

Table truncated, full table size 46152 Kbytes.




Supplementary file Size Download File type/resource
GSM1138067_MLL12.CEL.gz 26.4 Mb (ftp)(http) CEL
GSM1138067_MLL12.chp.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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