|
| Status |
Public on Dec 17, 2013 |
| Title |
THP-1 treated with PBS |
| Sample type |
RNA |
| |
|
| Source name |
THP-1, PBS treated 60 min
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: THP-1
treatment: PBS treated 60 min
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were dissoluved in TRIZOL, and total RNA were extracted with standerd protcol. RNA was further purified with Rnasy kit.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
0.60 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene Expression Microarray 8x60K Ver.2.0 for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
|
| |
|
| Submission date |
Feb 21, 2013 |
| Last update date |
Dec 17, 2013 |
| Contact name |
Kosuke Tanegashima |
| E-mail(s) |
tanegashima-ks@igakuken.or.jp
|
| Phone |
+81-3-5316-3130
|
| Organization name |
Tokyo Metropolitan Institute of Medical Science
|
| Lab |
Stem cell project
|
| Street address |
2-1-6 Kamikitazawa
|
| City |
Setagaya-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
156-8506 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17077 |
| Series (1) |
| GSE44550 |
THP-1 cells treated with CXCL14 |
|
