|
| Status |
Public on Aug 23, 2017 |
| Title |
SVP[Pfs25]+SVP[R848] Pre-bleed [E11_11 prebleed] |
| Sample type |
RNA |
| |
|
| Source name |
SVP[Pfs25]+SVP[R848] Pre-bleed
|
| Organism |
Macaca mulatta |
| Characteristics |
tissue: Whole blood
|
| Treatment protocol |
Blood was collected directly into PAXgene® tubes prior to and 24 hours after immunization and stored at -20C until ready for analysis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using the PAXgene® Blood RNA Kit, PreAnalytiX, Qiagen following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2200 Tapestation (Agilent Technologies, Santa Clara, CA, USA).
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low Input One-Color Quick Amp Labeling Kit (Agilent Technologies) 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-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Rhesus Macaque Gene Expression Microarrays v2 (part number G2519F-026806) 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).
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44K array slides (Scan Area 61x21.6 mm, Scan resolution 3 µm, Dye channel is set to Green and Green PMT is set to 100%).
|
| Data processing |
Raw images were analyzed using the Agilent Feature Extraction software, and background corrected gProcessed signals were subjected to quantile normalization.
|
| |
|
| Submission date |
Aug 22, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
Elizabeth Anne Thompson |
| E-mail(s) |
elizabeth.thompson@ki.se
|
| Phone |
851776698
|
| Organization name |
Karolinska Institutet
|
| Department |
Department of Medicine, Solna
|
| Lab |
Loré
|
| Street address |
L2:04
|
| City |
Stockholm |
| ZIP/Postal code |
17176 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL16026 |
| Series (1) |
| GSE102909 |
Peripheral blood transcriptomics following immunization with TLR-adjuvanted nanoparticle vaccine in rhesus macaques |
|
