|
| Status |
Public on Sep 16, 2015 |
| Title |
SCM2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
SCM2
|
| Organism |
Sus scrofa |
| Characteristics |
developmental stage: Day 30 embryo
Sex: male
treatment group: Control
|
| Treatment protocol |
Sows were euthanized at day 30 of gestation and embryos were recovered for DNA and RNA extraction.
Embryos were collected at Day 30 post-ovulation from sows submitted to three different treatment groups such as C group; n= 6, FE group ; n=3 and SE group; n=3 group. Three males and three females D30E were pooled separately from each sow in each treatment group ending up with 24 distinct biological replicates.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Direct-zol™ RNA MiniPrep kit (Zymo Research Corporation, Irvine, CA, USA) was used for RNA extraction with in-column DNase treatment to remove DNA.
|
| Label |
Cy5
|
| Label protocol |
200ng of total RNA with adding of external RNA spike-in was used for aRNA synthesis according to the manual provided by Low Input Quick Amp Labeling Kit (Agilent Technologies, Inc., Santa Clara, CA, USA) for two-color processing. Antisense RNA (aRNA) labelling with Cy3 and Cy5 was performed according to the kit under ozone free environmental chamber.
|
| |
|
| Channel 2 |
| Source name |
SCM2
|
| Organism |
Sus scrofa |
| Characteristics |
developmental stage: Day 30 embryo
Sex: male
treatment group: IS21SE
|
| Treatment protocol |
Sows were euthanized at day 30 of gestation and embryos were recovered for DNA and RNA extraction.
Embryos were collected at Day 30 post-ovulation from sows submitted to three different treatment groups such as C group; n= 6, FE group ; n=3 and SE group; n=3 group. Three males and three females D30E were pooled separately from each sow in each treatment group ending up with 24 distinct biological replicates.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Direct-zol™ RNA MiniPrep kit (Zymo Research Corporation, Irvine, CA, USA) was used for RNA extraction with in-column DNase treatment to remove DNA.
|
| Label |
Cy3
|
| Label protocol |
200ng of total RNA with adding of external RNA spike-in was used for aRNA synthesis according to the manual provided by Low Input Quick Amp Labeling Kit (Agilent Technologies, Inc., Santa Clara, CA, USA) for two-color processing. Antisense RNA (aRNA) labelling with Cy3 and Cy5 was performed according to the kit under ozone free environmental chamber.
|
| |
|
| |
| Hybridization protocol |
Hybridization mixture and washing procedure were prepared and performed according to Agilent Gene Expression Hybridization Kit 60-mer oligo microarray protocol version 4.0.
|
| Scan protocol |
Array slides were immediately scanned at 5 μm resolution using an Axon 4200AL scanner (635 nm for Cy5 and at 532 nm for Cy3) with the autoscan feature from the default setting. TIFF images were analysed by software Gene Pix Pro 6.0.
|
| Description |
Dye-swap replicate of biological replicate 2
|
| Data processing |
FlexArray software version 1.6.3 (http://genomequebec.mcgill.ca/) was used for data normalization following first with simple background subtraction, LOWESS normalization within and between arrays.
|
| |
|
| Submission date |
Sep 15, 2015 |
| Last update date |
Sep 16, 2015 |
| Contact name |
Stephen Tsoi |
| E-mail(s) |
scmtsoi@gmail.com
|
| Phone |
780248-1567
|
| Organization name |
University of Alberta
|
| Department |
AFNS
|
| Lab |
Porcine Functional Genomics
|
| Street address |
4-32G Agriculture/Forestry Cen
|
| City |
Edmonton |
| State/province |
Alberta |
| ZIP/Postal code |
T6G 2P5 |
| Country |
Canada |
| |
|
| Platform ID |
GPL17779 |
| Series (1) |
| GSE73020 |
Detection of differentially expressed genes in Day 30 embryos during gestation in primiparous (PP) sow with different intermittent suckling and breeding strategies |
|
