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Sample GSM1138058 Query DataSets for GSM1138058
Status Public on May 22, 2014
Title MLL#7
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 0.006609 BB 661.744812 2581.006592
SNP_A-1967418 BB 0.015118 BB 304.226959 542.653320
SNP_A-1969580 BB 0.003323 BB 1035.310791 3813.074707
SNP_A-4263484 AB 0.002478 AB 1697.615234 1207.699585
SNP_A-1978185 AA 0.007807 AA 2317.568359 737.952698
SNP_A-4264431 NC 0.124725 AB 927.943237 501.708374
SNP_A-1980898 AB 0.004089 AB 692.322388 694.859924
SNP_A-1983139 AA 0.008005 AA 1076.973755 416.116882
SNP_A-4265735 AB 0.002958 AB 635.994995 791.178406
SNP_A-1995832 AA 0.010582 AA 2896.193604 529.922119
SNP_A-1995893 AA 0.000305 AA 2485.486084 1277.122192
SNP_A-1997689 BB 0.001043 BB 792.752075 2876.247559
SNP_A-1997709 AA 0.007379 AA 1870.309692 381.820038
SNP_A-1997896 AA 0.004776 AA 1520.992065 646.654419
SNP_A-1997922 AA 0.008169 AA 999.144714 416.116882
SNP_A-2000230 AA 0.006858 AA 1530.095703 1389.266724
SNP_A-2000332 AA 0.000256 AA 2939.981201 1108.106567
SNP_A-2000337 AA 0.002599 AA 1090.778076 355.299408
SNP_A-2000342 AA 0.003533 AA 2918.830078 839.071289
SNP_A-4268173 AB 0.015147 AB 712.668823 570.749390

Total number of rows: 909622

Table truncated, full table size 46139 Kbytes.




Supplementary file Size Download File type/resource
GSM1138058_MLL7.CEL.gz 26.0 Mb (ftp)(http) CEL
GSM1138058_MLL7.chp.gz 12.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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