|
| Status |
Public on Apr 03, 2012 |
| Title |
AML with normal karyotype (NK) AML69_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 |
Apr 03, 2012 |
| 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 (3) |
| GSE34722 |
Gene expression profiling of Acute Myeloid Leukemia (AML) samples |
| GSE37021 |
Gene expression profiling in Acute Myeloid Leukemia (AML) |
| GSE37022 |
Genome-Wide Analysis of Acute Myeloid Leukemia Reveals Leukemia-Specific Methylome and Subtype-Specific Hypomethylation of Repeats |
|
