|
| Status |
Public on Feb 23, 2012 |
| Title |
ATL #12 |
| Sample type |
RNA |
| |
|
| Source name |
ATL-#12
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Adult T-cell Leukemia (ATL) cells
atl subtype: Acute
age (y): 57
gender: M
disease state: Adult T-cell Leukemia (ATL)
|
| Treatment protocol |
Freshly drawn peripheral blood from ATL patients and healthy volunteers was subjected to PBMC isolation. Then PBMC from healthy donor was further subjected to isolation of CD4+ T-cells by negative isolation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TriZol (Invitrogen) following the manufacturer's recommendations. The protocol includes DNaseI treatment to eliminate any genomic DNA contamination. The extracted total RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 500ng total RNA using the Low RNA Linear Amplification Kit (Agilent) according to the manufacturer's instructions.
|
| |
|
| Hybridization protocol |
17 hours at 65C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) for 1min and with GE Wash buffer 2 (Agilent) for 1min at 37C.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44K microarray slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green, and Green PMT is set to XDR Hi 100% and XDR Lo 10%).
|
| Description |
mRNA expression in ATL
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol : GE1-v5_95_Feb07 and Grid: 014850_D_F_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Nov 10, 2011 |
| Last update date |
Feb 23, 2012 |
| Contact name |
Kazumi Nakano |
| Organization name |
The University of Tokyo
|
| Department |
Department of Medical Genome Sciences, Graduate School of Frontier Sciences
|
| Lab |
Laboratory of Tumor Cell Biology
|
| Street address |
4-6-1, Sirokanedai, Minatoku
|
| City |
Tokyo |
| ZIP/Postal code |
108-8639 |
| Country |
Japan |
| |
|
| Platform ID |
GPL4133 |
| Series (1) |
| GSE33615 |
Whole genome gene expression profiling in Adult T-cell Leukemia (ATL) cells and in Normal CD4+ T-cells |
|
