|
| Status |
Public on Jun 01, 2023 |
| Title |
HAM3_PBMC |
| Sample type |
RNA |
| |
|
| Source name |
HAM PBMC
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: HAM PBMC
|
| 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-2000 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 100ng total RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions.
|
| |
|
| Hybridization protocol |
17 hours at 65°C 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 37°C.
|
| 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 was set to Green, and No extended dynamic range was selected).
|
| Description |
Gene expression in HAM PBMC
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol : GE1-107_Sep09 and Grid: 026652_D_F_20110325) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
May 25, 2023 |
| Last update date |
Jun 01, 2023 |
| Contact name |
Makoto Yamagishi |
| E-mail(s) |
myamagishi@edu.k.u-tokyo.ac.jp
|
| Organization name |
The University of Tokyo
|
| Department |
Graduate School of Frontier Sciences
|
| Street address |
4-6-1, Shirokanedai, Minato-ku
|
| City |
Tokyo |
| ZIP/Postal code |
108-8639 |
| Country |
Japan |
| |
|
| Platform ID |
GPL13497 |
| Series (1) |
| GSE233437 |
EZH1/2 dual inhibitors suppress HTLV-1-infected cell proliferation and hyperimmune response in HTLV-1-associated myelopathy |
|
