|
| Status |
Public on Dec 23, 2016 |
| Title |
Data 148 Area4 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Embryo_Ctl
|
| Organism |
Sus scrofa |
| Characteristics |
developmental stage: expanded_blastocyst
compound added: None
number per pool: 10
|
| Treatment protocol |
Porcine zygotes were exposed to 0.2% ethanol in PZM3 medium for 7 days. Embryos developped in thilghly sealed glass vials.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction using the PicoPure RNA Isolation Kit from Molecular Devices. The PicoPure RNA Isolation Kit enables to recover total cellular RNA from pico-scale samples. Researchers can obtain high recoveries of total cellular RNA from as little as a single cell to samples with up to 100 ug of RNA. RNA extraction from larger samples should be done using another kit or technique.
|
| Label |
Cy5
|
| Label protocol |
This procedure describes the amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Molecular devices). This procedure may be required for microarray experiments with extremely limited amounts of starting material. The RiboAmpb HSPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from picogram quantities of total cellular RNA. The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.
The labelling aRNA was done using the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.
|
| |
|
| Channel 2 |
| Source name |
Embryo_EtOH
|
| Organism |
Sus scrofa |
| Characteristics |
developmental stage: expanded_blastocyst
compound added: Ethanol
number per pool: 10
|
| Treatment protocol |
Porcine zygotes were exposed to 0.2% ethanol in PZM3 medium for 7 days. Embryos developped in thilghly sealed glass vials.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction using the PicoPure RNA Isolation Kit from Molecular Devices. The PicoPure RNA Isolation Kit enables to recover total cellular RNA from pico-scale samples. Researchers can obtain high recoveries of total cellular RNA from as little as a single cell to samples with up to 100 ug of RNA. RNA extraction from larger samples should be done using another kit or technique.
|
| Label |
Cy3
|
| Label protocol |
This procedure describes the amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Molecular devices). This procedure may be required for microarray experiments with extremely limited amounts of starting material. The RiboAmpb HSPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from picogram quantities of total cellular RNA. The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.
The labelling aRNA was done using the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.
|
| |
|
| |
| Hybridization protocol |
The hybridization of microarray slides 4x44K printed with oligonucleotides by Agilent for all EmbryoGENE related projects using the expression array protocol.
|
| Scan protocol |
Scan on a PowerScanner (Tecan) using the autogain function. Images were quantified using ArrayPro version 6.3 (MediaCybernetics)
|
| Data processing |
Background subtracted, Loess and Quantile normalized data obtained from log2 of processed Red signal/processed Green signal. Flexarray software used.
|
| |
|
| Submission date |
Dec 20, 2016 |
| Last update date |
Dec 23, 2016 |
| Contact name |
Florence Pagé-Larivière |
| E-mail(s) |
florence.page-lariviere.1@ulaval.ca
|
| Organization name |
Laval University
|
| Street address |
2440, boulevard Hochelaga
|
| City |
Québec |
| State/province |
Québec |
| ZIP/Postal code |
G1V 0A6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL17779 |
| Series (1) |
| GSE92609 |
Mechanisms involved in porcine early embryo survival following ethanol exposure |
|
