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Sample GSM853954 Query DataSets for GSM853954
Status Public on Sep 20, 2019
Title AML with other karyotype AML17_other
Sample type RNA
 
Source name peripheral blood
Organism Homo sapiens
Characteristics genotype: Other
tissue: peripheral blood
disease state: Acute Myeloid Leukaemia
Growth protocol Patients’ samples (peripheral blood or bone marrow) were stored in the tissue bank of the St Bartholomew’s Hospital after informed written consent was obtained.
Extracted molecule total RNA
Extraction protocol Total RNA of AML patient samples was extracted from a total of 10 - 20 x 106 thawed cells using Trizol (Gibco-BRL) purification method. RNA quality was evaluated on the 2100 Bioanalyzer (Agilent Technologies) and the concentration was measured using a NanoDrop spectrophotometer (NanoDrop Technologies).
Label digoxigenin (DIG)
Label protocol Labeling was done with the Applied Biosystems Chemiluminescent RT-IVT Labeling Kit (P/N 4340472) using 2 ug high quality total RNA
 
Hybridization protocol Fifteen ug mRNA was hybridized to the ABI Human Genome Survey Microarray v1
Scan protocol DIG-labeled targets hybridize to the probes on the arrays and anti-digoxigenin-alkaline phosphatase is added to bind digoxigenin in cDNA targets. The ABI 1700 Expression Array System (ABI, U.S) was used to scan the arrays for chemiluminescence
Description AML with other karyotype
Data processing Signal intensity, S/N ratio (signal to noise ratio), and flags values were extracted for each array. The S/N ratio value of 3.0 and flags value of 5000 were used to exclude false positives and/or missing data. For those probes that passed the filtering criterion, the signal values were log2 transformed and normalized across arrays with quantile normalization method after control probes were removed.
 
Submission date Dec 27, 2011
Last update date Sep 20, 2019
Contact name Jacek Dariusz Marzec
E-mail(s) j.marzec@qmul.ac.uk
Organization name Barts Cancer Institute
Department Centre for Haemato-Oncology
Lab Cancer Genomics
Street address Charterhouse Square
City London
ZIP/Postal code EC1M 6BQ
Country United Kingdom
 
Platform ID GPL9851
Series (1)
GSE37021 Gene expression profiling in Acute Myeloid Leukemia (AML)

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
100002 14.871557
100003 7.491416
100027 7.581573
100036 9.72709
100037 12.138334
100039 8.286597
100043 7.06766
100044 8.548901
100045 7.915781
100051 8.650003
100052 8.008403
100057 8.909487
100058 15.988609
100060 8.167429
100062 11.445145
100064 11.486671
100079 14.064488
100089 13.57559
100093 7.554834
100095 12.757943

Total number of rows: 33096

Table truncated, full table size 529 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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