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Sample GSM853943 Query DataSets for GSM853943
Status Public on Sep 20, 2019
Title AML with 11q23 AML6_11q23
Sample type RNA
 
Source name peripheral blood
Organism Homo sapiens
Characteristics genotype: 11q23
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 11q23
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 17.629095
100003 7.156537
100027 8.288884
100036 12.897648
100037 14.432278
100039 13.744145
100043 7.639664
100044 7.41012
100045 7.97882
100051 7.762247
100052 8.604753
100057 11.020914
100058 16.002362
100060 10.093836
100062 10.523348
100064 9.177607
100079 16.87975
100089 10.358003
100093 7.734788
100095 8.055353

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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