|
| Status |
Public on Mar 10, 2021 |
| Title |
8-cell embryo spent media, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
8-cell embryo spent media (60-80 hours post fertilization)
|
| Organism |
Bos taurus |
| Characteristics |
source: spent media conditioned with group-cultured 8-cell bovine embryos
|
| Growth protocol |
Bovine embryos were in-vitro produced following standard laboratory procedures. Briefly, ovaries were obtained from the local abbotoir and oocytes were retrieved and matured for 24 hours prior to co-culture with bovine sperm for in-vitro fertilization. After 18 hours, presumptive zygotes were transferred to in-vitro culture media and grown in groups of 20 to the desired time stage of development. 2-cell, 8-cell, and blastocyst embryos were cultured for 18-30 hours, 60-80 hours, and 168-192 hours post fertilization. At each time point, embryos were remove from the in-vitro culture media and approximetely 25 µL of spent in-vitro culture media was extracted from each in-vitro culture drops. Spent media samples from each developmental stage was pooled together, flash frozen in liquid nitrogen, and stored at -80 ˚C until total RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiazol extraction for total RNA extract was performed as per manufacturer's instructions
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from ~50ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)
|
| |
|
| Hybridization protocol |
Following fragmentation, ~50ng of cRNA were heated to 99˚C for 5 minutes, then heated at 45˚C for 5 minutes, prior to hybridization via constant agitation at 60rpm for 16 hours at 48˚C on an Affymetrix 450 Fluidics Station.
|
| Scan protocol |
Genechips were scanned using the Affymetrix GCS 3,000 Scanner
|
| Data processing |
RMA algorithm. Data was processed with Affymetrix Genechip command console software and analyzed using Affymetric Transcriptome Analysis Concole whereby probesets were differentially expressed at a fold-change of ≤ -2 or ≥ 2, ≥ 50% of samples have a detectable ablove background value of < 0.05 and a false discovery rate of < 0.05.
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| |
|
| Submission date |
Mar 09, 2021 |
| Last update date |
Mar 10, 2021 |
| Contact name |
Paul Nico Del Rio |
| E-mail(s) |
pdelrio@uoguelph.ca
|
| Phone |
6476875620
|
| Organization name |
University of Guelph
|
| Department |
Reproductive and Biotechnology Laboratory
|
| Lab |
Paul Nico Del Rio
|
| Street address |
195 Kingswood Drive
|
| City |
Brampton |
| State/province |
ON |
| ZIP/Postal code |
L6V 3B2 |
| Country |
Canada |
| |
|
| Platform ID |
GPL21572 |
| Series (1) |
| GSE168551 |
miRNA expression data of spent in-vitro culture media condtioned with 2-cell, 8-cell, and blastocyst staged bovine embryos |
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