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Sample GSM603713 Query DataSets for GSM603713
Status Public on Dec 03, 2010
Title AML_GE_310
Sample type RNA
 
Source name AML blast cells
Organism Homo sapiens
Characteristics sex (male.1_female.2): 1
bm_%blasts: 50
hemoglobin: 9.1
pb_%blasts: 16
platelets: 58
white_blood_cells: 12.4
age: 47
tet2: WT
idh1.idh2: WT
Extracted molecule total RNA
Extraction protocol Total RNA extracted with Qiagen's Rneasy Plus Mini kit per manufacturer's instructions. cDNA synthesis carried out as previously described (Figueroa et al. PLoS One, 2008)
Label Cy5
Label protocol Random priming with 7-mers pre-labeled with either Cy3 or Cy5 according to manufacturer's instructions using the NimbleGen Dual-Color DNA Labeling Kit (cat # 05223547001)
 
Hybridization protocol See Roche NimbleGen website and Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319. for details
Scan protocol Scanning was performed using a GenePix 4000B scanner (Axon Instruments) as previously described in Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.
Description Sample name: 19762
Data processing RMA normalization using the RMA algorithm found in the oligo package (version 1.8.3)(Carvalho et al.) in BioConductor
 
Submission date Oct 04, 2010
Last update date May 08, 2012
Contact name Maria Eugenia Figueroa
E-mail(s) mef162@miami.edu
Organization name University of Miiami
Department Human Genetics
Lab Maria Figueroa
Street address 1501 NW 10th Ave, BRB 709A, Locator code C227
City Miami
State/province FL
ZIP/Postal code 33136
Country USA
 
Platform ID GPL6602
Series (1)
GSE24505 Leukemic IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiation

Data table header descriptions
ID_REF
VALUE log2 RMA intensity

Data table
ID_REF VALUE
HSAP0406S00000001 14.53222288
HSAP0406S00000002 12.88871578
HSAP0406S00000003 13.19963392
HSAP0406S00000004 12.75792727
HSAP0406S00000005 14.03806925
HSAP0406S00000006 9.929659565
HSAP0406S00000007 12.1045761
HSAP0406S00000008 12.97267235
HSAP0406S00000009 8.244623539
HSAP0406S00000010 11.23295433
HSAP0406S00000011 9.551058037
HSAP0406S00000012 13.10766866
HSAP0406S00000013 10.47718565
HSAP0406S00000014 10.03106281
HSAP0406S00000015 10.40572546
HSAP0406S00000016 12.74531017
HSAP0406S00000017 8.007858274
HSAP0406S00000018 9.735982848
HSAP0406S00000019 8.574181262
HSAP0406S00000020 8.048566046

Total number of rows: 36846

Table truncated, full table size 1075 Kbytes.




Supplementary file Size Download File type/resource
GSM603713.pair.gz 6.2 Mb (ftp)(http) PAIR
Processed data included within Sample table

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