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Sample GSM1138091 Query DataSets for GSM1138091
Status Public on May 22, 2014
Title MLL#32
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 0.010928 BB 628.258362 2811.971191
SNP_A-1967418 BB 0.004178 BB 305.786072 769.801025
SNP_A-1969580 BB 0.007639 BB 844.071228 3625.912842
SNP_A-4263484 BB 0.001335 BB 613.322388 1983.198120
SNP_A-1978185 AA 0.003578 AA 1575.202271 441.177063
SNP_A-4264431 AA 0.004704 AA 2635.827881 470.359924
SNP_A-1980898 BB 0.012095 BB 391.550171 1107.435303
SNP_A-1983139 AA 0.001988 AA 1238.995605 512.322998
SNP_A-4265735 AA 0.004440 AA 1606.163574 482.259369
SNP_A-1995832 BB 0.015895 BB 540.266235 1005.493835
SNP_A-1995893 BB 0.003793 BB 461.738464 2351.813232
SNP_A-1997689 BB 0.001690 BB 692.899658 3101.387695
SNP_A-1997709 AA 0.000973 AA 1461.036133 382.118591
SNP_A-1997896 AA 0.002982 AA 1583.865723 582.161987
SNP_A-1997922 BB 0.001494 BB 553.539795 1204.784180
SNP_A-2000230 AA 0.008935 AA 3290.176270 1219.645020
SNP_A-2000332 AB 0.005053 AB 2382.434082 2766.296387
SNP_A-2000337 AA 0.004688 AA 1381.660156 399.154114
SNP_A-2000342 AA 0.015749 AA 4023.511230 714.209900
SNP_A-4268173 AA 0.015131 AA 2874.480469 449.731506

Total number of rows: 909622

Table truncated, full table size 46143 Kbytes.




Supplementary file Size Download File type/resource
GSM1138091_MLL32.CEL.gz 25.6 Mb (ftp)(http) CEL
GSM1138091_MLL32.chp.gz 12.8 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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