|
| Status |
Public on Apr 02, 2020 |
| Title |
Paternal age effects (12vs16m) on blastocysts transcriptome-rep4 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
blastocysts
|
| Organism |
Bos taurus |
| Characteristics |
sample type: IVF with sperm from a 16 months old bull
|
| Growth protocol |
In vitro maturation, fertilization and culture of bovine embryos from slaughter ovaries. For more information, please refer to: Cagnone et al. 2012 Biol Reprod.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA and gDNA were extracted using the AllPrep DNA/RNA Micro Kit (Qiagen)
Amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Thermo Fisher).
|
| Label |
Cy5
|
| Label protocol |
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 |
blastocysts
|
| Organism |
Bos taurus |
| Characteristics |
sample type: IVF with sperm from a 12 months old bull
|
| Growth protocol |
In vitro maturation, fertilization and culture of bovine embryos from slaughter ovaries. For more information, please refer to: Cagnone et al. 2012 Biol Reprod.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA and gDNA were extracted using the AllPrep DNA/RNA Micro Kit (Qiagen)
Amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Thermo Fisher).
|
| Label |
Cy3
|
| Label protocol |
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)
|
| Description |
Biological replicates 4 of 4
|
| Data processing |
Signal intensity data files were normalized and analyzed using the FlexArray 1.6.1 software (Genome Quebec, URL: http://genomequebec.mcgill.ca/FlexArray). The first step in the data processing was to remove the background of intensity files using a simple background subtraction. Data were then normalized for dye bias using a within-array loess and a between-array « quantile » normalization to minimize array effects. To calculate fold changes of probe intensity, normalized data were assessed using the e Bayes moderated t-test (LIMMA) included in the FlexArray software. A False Discovery Rate algorithm (Benjamini-Hochberg) was also applied.
|
| |
|
| Submission date |
Mar 15, 2019 |
| Last update date |
Apr 03, 2020 |
| Contact name |
Marc-André Sirard |
| E-mail(s) |
[email protected]
|
| Organization name |
Université Laval
|
| Department |
Sciences Animales
|
| Street address |
Offfice 2732, 2440 Hochelaga Blvd.
|
| City |
Québec City |
| State/province |
Quebec |
| ZIP/Postal code |
G1V 0A6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL13226 |
| Series (2) |
| GSE128356 |
Transcriptomic analysis of blastocyst according to peripubertal age of bull (12 vs 16 months) |
| GSE128629 |
The age of the bull influences the transcriptome and epigenome of the blastocysts |
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