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Sample GSM853942 Query DataSets for GSM853942
Status Public on Sep 20, 2019
Title AML with normal karyotype (NK) AML5_nk
Sample type RNA
 
Source name peripheral blood
Organism Homo sapiens
Characteristics genotype: Normal Karyotype (NK)
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 normal karyotype (NK)
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 17.305751
100003 7.695978
100027 7.121669
100036 11.804792
100037 14.383208
100039 12.801902
100043 7.18244
100044 7.506502
100045 7.673245
100051 7.535225
100052 9.150066
100057 10.141267
100058 15.507168
100060 9.917437
100062 10.556067
100064 13.184002
100079 16.593471
100089 12.287874
100093 7.607337
100095 8.924337

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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