NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1138060 Query DataSets for GSM1138060
Status Public on May 22, 2014
Title MLL#8
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 0.005779 BB 701.537231 1899.794189
SNP_A-1967418 BB 0.001766 BB 341.373810 754.247864
SNP_A-1969580 BB 0.001918 BB 1194.554443 3448.994629
SNP_A-4263484 AB 0.008255 AB 1490.760986 975.818909
SNP_A-1978185 AA 0.004799 AA 2095.157715 531.175903
SNP_A-4264431 AA 0.006900 AA 1522.079346 395.609650
SNP_A-1980898 AA 0.039321 AA 1041.204468 395.609650
SNP_A-1983139 AA 0.000733 AA 1410.565552 536.356079
SNP_A-4265735 NC 0.377072 AA 894.748413 493.206055
SNP_A-1995832 AA 0.003926 AA 2475.437500 720.676880
SNP_A-1995893 AA 0.001645 AA 2598.951904 1272.802002
SNP_A-1997689 BB 0.000670 BB 720.612976 2961.488037
SNP_A-1997709 AA 0.001927 AA 1628.935669 383.221985
SNP_A-1997896 AA 0.002469 AA 1634.428955 636.116577
SNP_A-1997922 AA 0.018877 AA 802.750549 309.457703
SNP_A-2000230 AA 0.008238 AA 1402.299072 1308.209106
SNP_A-2000332 AB 0.006420 AB 1966.992065 2089.008789
SNP_A-2000337 AA 0.001230 AA 1210.732788 376.424988
SNP_A-2000342 AA 0.003147 AA 2907.659424 973.270203
SNP_A-4268173 AA 0.006165 AA 1284.929565 407.956573

Total number of rows: 909622

Table truncated, full table size 46146 Kbytes.




Supplementary file Size Download File type/resource
GSM1138060_MLL8.CEL.gz 26.2 Mb (ftp)(http) CEL
GSM1138060_MLL8.chp.gz 12.9 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