NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1138088 Query DataSets for GSM1138088
Status Public on May 22, 2014
Title MLL#29
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 0.001528 BB 613.838440 2149.666748
SNP_A-1967418 BB 0.025035 BB 376.861542 1338.598877
SNP_A-1969580 BB 0.002524 BB 1287.188110 3861.116943
SNP_A-4263484 BB 0.007952 BB 645.127747 1591.650391
SNP_A-1978185 AA 0.022026 AA 838.642883 502.956665
SNP_A-4264431 AA 0.003861 AA 1909.083008 376.861542
SNP_A-1980898 AB 0.076624 AB 371.028351 788.679199
SNP_A-1983139 AA 0.005913 AA 1360.763062 641.146606
SNP_A-4265735 BB 0.004596 BB 519.866699 1282.692505
SNP_A-1995832 AB 0.024267 AB 1031.511108 1037.371948
SNP_A-1995893 BB 0.014206 BB 910.975403 2939.652344
SNP_A-1997689 BB 0.027408 BB 932.666565 1936.505859
SNP_A-1997709 AA 0.013563 AA 978.095825 359.548889
SNP_A-1997896 BB 0.005704 BB 1009.731262 3054.752930
SNP_A-1997922 AA 0.080380 AA 1164.110962 588.708069
SNP_A-2000230 AA 0.005549 AA 2817.276611 1570.733398
SNP_A-2000332 AB 0.009037 AB 2792.742920 2142.986328
SNP_A-2000337 AA 0.003360 AA 1072.245483 448.060883
SNP_A-2000342 AA 0.031397 AA 1725.927612 516.170898
SNP_A-4268173 AA 0.010683 AA 1072.245483 342.869293

Total number of rows: 909622

Table truncated, full table size 46157 Kbytes.




Supplementary file Size Download File type/resource
GSM1138088_MLL29.CEL.gz 24.0 Mb (ftp)(http) CEL
GSM1138088_MLL29.chp.gz 12.7 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap