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Sample GSM1138090 Query DataSets for GSM1138090
Status Public on May 22, 2014
Title MLL#31
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 0.003773 BB 569.847351 1471.023804
SNP_A-1967418 BB 0.002278 BB 384.997681 781.930481
SNP_A-1969580 BB 0.002902 BB 949.767822 3457.951172
SNP_A-4263484 AB 0.002413 AB 1861.356689 1240.274902
SNP_A-1978185 AA 0.001156 AA 1753.586670 517.896912
SNP_A-4264431 AA 0.001108 AA 2419.786621 515.575989
SNP_A-1980898 BB 0.006150 BB 429.713684 1178.490723
SNP_A-1983139 AA 0.022963 AA 1192.455933 710.850159
SNP_A-4265735 AB 0.048022 AB 344.580841 723.065308
SNP_A-1995832 AA 0.000407 AA 2256.293701 566.015991
SNP_A-1995893 AA 0.002249 AA 2325.661133 1181.503296
SNP_A-1997689 BB 0.001797 BB 728.672729 3192.997803
SNP_A-1997709 AA 0.001564 AA 1600.516968 382.626373
SNP_A-1997896 AA 0.004342 AA 1492.680420 602.600342
SNP_A-1997922 AA 0.003258 AA 992.651062 368.633881
SNP_A-2000230 AA 0.005464 AA 1823.818115 1064.338135
SNP_A-2000332 AA 0.002344 AA 3061.832520 993.458618
SNP_A-2000337 AA 0.001433 AA 1085.683472 411.769257
SNP_A-2000342 AA 0.000813 AA 3485.950928 1038.073975
SNP_A-4268173 AA 0.004962 AA 1263.903564 350.063202

Total number of rows: 909622

Table truncated, full table size 46154 Kbytes.




Supplementary file Size Download File type/resource
GSM1138090_MLL31.CEL.gz 26.2 Mb (ftp)(http) CEL
GSM1138090_MLL31.chp.gz 12.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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