|
| Status |
Public on Jun 15, 2024 |
| Title |
pig ovary |
| Sample type |
RNA |
| |
|
| Source name |
PO-ovary-tissue
|
| Organism |
Sus scrofa |
| Characteristics |
breed: pig
tissue: Ovary
gender: Female
developmental stage: estrous cycle 15 days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
animal collection protocol: Ovarian tissue samples were harvested following the method of Kim et al. (2012). (PLoS One. 2012;7(10):e46194. doi: 10.1371/journal.pone.0046194.)
Total RNA was extracted from the pocine tissue using the TRI REAGENT (MRC, OH) according to the manufacturer’s instructions. The total RNA quality and quantity was assessed by Agilent bioanalyzer 2100 analysis.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS 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-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
1.65 ug of Cy3-labelled cRNA (specific activity >5.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Pocine Genome Oligo Microarrays (G2519F-026440) 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 Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
Differentially expression of genes in minipig ovary vs. pig ovary
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 026440_D_20100525) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Jun 12, 2024 |
| Last update date |
Jun 15, 2024 |
| Contact name |
SangHwan Kim |
| E-mail(s) |
[email protected]
|
| Phone |
+82316705127
|
| Organization name |
Hankyong National University
|
| Department |
School of Animal Life Convergence Science
|
| Lab |
Animal Developmantal Biotechnology
|
| Street address |
327, Jungang-ro
|
| City |
Ansung |
| State/province |
Gyeonggi-do |
| ZIP/Postal code |
17579 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL16571 |
| Series (1) |
| GSE269724 |
Porcine ovary tissues : Minipig ovary vs. Pig ovary |
|
