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Sample GSM1138076 Query DataSets for GSM1138076
Status Public on May 22, 2014
Title MLL#18
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 0.031854 BB 832.395691 1959.702393
SNP_A-1967418 NC 0.288543 BB 386.578064 508.214081
SNP_A-1969580 BB 0.003462 BB 1181.198608 3263.515137
SNP_A-4263484 AB 0.016397 AB 1127.162842 825.449829
SNP_A-1978185 AA 0.013130 AA 2107.808838 853.182312
SNP_A-4264431 AA 0.003616 AA 2010.215576 508.214081
SNP_A-1980898 BB 0.016881 BB 611.349365 1947.089478
SNP_A-1983139 AA 0.004292 AA 1562.993408 508.214081
SNP_A-4265735 AA 0.008890 AA 1487.312134 716.658875
SNP_A-1995832 BB 0.006366 BB 720.763489 1366.128784
SNP_A-1995893 BB 0.002699 BB 513.554871 2293.207764
SNP_A-1997689 BB 0.012162 BB 1001.630615 2529.510986
SNP_A-1997709 NC 0.329661 AA 892.213440 465.466370
SNP_A-1997896 AB 0.005035 AB 1123.457397 1950.265381
SNP_A-1997922 AB 0.002899 AB 700.184937 704.342041
SNP_A-2000230 AA 0.013481 AA 3023.281250 1793.742554
SNP_A-2000332 AB 0.009683 AB 2534.377441 1911.774536
SNP_A-2000337 AA 0.003640 AA 1099.374390 456.384369
SNP_A-2000342 AA 0.004645 AA 3248.880859 1189.996216
SNP_A-4268173 AB 0.002057 AB 1225.783569 919.191162

Total number of rows: 909622

Table truncated, full table size 46148 Kbytes.




Supplementary file Size Download File type/resource
GSM1138076_MLL18.CEL.gz 25.2 Mb (ftp)(http) CEL
GSM1138076_MLL18.chp.gz 12.8 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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