|
| Status |
Public on Aug 11, 2016 |
| Title |
Data Heifer #10994 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Blasto_heifer_14
|
| Organism |
Bos taurus |
| Characteristics |
sample type: in_vitro
developmental stage: early_blastocyst
breed (cattle): holstein
time of embryo collection: 168 hpf (hours post-in-vitro fertilization)
heifer age: 14 months
tissue or cell type: embryo
|
| Treatment protocol |
Ovarian stimulation: Each heifer was first treated with progesterone (CIDR) during the luteal phase. The dominant follicle was aspirated 36 hours prior to administration of hormones. The ovarian stimulation program consisted of 6 injections of 30mg FSH administered at 12h intervals. Ovum pick up was performed 43h after the last FSH injection. Using transvaginal ultrasonography, follicular diameters were then measured and cumulus-oocyte complexes were collected by transvaginal puncture, under epidural, with needle aspiration. COCs and granulosa cells were collected in warm HEPES-buffered Tyrode's medium containing Hepalean and transferred to laboratory for IVM.
Embryo production : In vitro maturation (IVM), in vitro fertilization (IVF), in vitro culture (IVC)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the pools using the AllPrep DNA/RNA micro kit, following the Parallel gDNA and total RNA extraction protocol. Total RNA integrity and concentration were evaluated on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) with the RNA PicoLab Chip (Agilent Technologies).
Amp protocol: To generate enough material for hybridization, the samples were linearly amplified. Antisense RNA (aRNA) was produced using the RiboAmp®HSPlus RNA Amplification kit (Thermo fisher Scientific). After two amplification rounds of 6 hr each, the aRNA output was quantified using the NanoDrop ND-1000 (Nano-Drop Technologies, Wilmington, DE).
|
| Label |
Cy5
|
| Label protocol |
For each sample, aRNA was labeled using the ULS Fluorescent Labeling Kit for Agilent arrays (Cy3/Cy5) (Kreatech Diagnostics, Amsterdam, Netherlands). The labeled product was then purified with the Pico-Pure RNA Isolation Kit.
|
| |
|
| Channel 2 |
| Source name |
Blasto_heifer_8
|
| Organism |
Bos taurus |
| Characteristics |
sample type: in_vitro
developmental stage: early_blastocyst
breed (cattle): holstein
time of embryo collection: 168 hpf (hours post-in-vitro fertilization)
heifer age: 8 months
tissue or cell type: embryo
|
| Treatment protocol |
Ovarian stimulation: Each heifer was first treated with progesterone (CIDR) during the luteal phase. The dominant follicle was aspirated 36 hours prior to administration of hormones. The ovarian stimulation program consisted of 6 injections of 30mg FSH administered at 12h intervals. Ovum pick up was performed 43h after the last FSH injection. Using transvaginal ultrasonography, follicular diameters were then measured and cumulus-oocyte complexes were collected by transvaginal puncture, under epidural, with needle aspiration. COCs and granulosa cells were collected in warm HEPES-buffered Tyrode's medium containing Hepalean and transferred to laboratory for IVM.
Embryo production : In vitro maturation (IVM), in vitro fertilization (IVF), in vitro culture (IVC)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the pools using the AllPrep DNA/RNA micro kit, following the Parallel gDNA and total RNA extraction protocol. Total RNA integrity and concentration were evaluated on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) with the RNA PicoLab Chip (Agilent Technologies).
Amp protocol: To generate enough material for hybridization, the samples were linearly amplified. Antisense RNA (aRNA) was produced using the RiboAmp®HSPlus RNA Amplification kit (Thermo fisher Scientific). After two amplification rounds of 6 hr each, the aRNA output was quantified using the NanoDrop ND-1000 (Nano-Drop Technologies, Wilmington, DE).
|
| Label |
Cy3
|
| Label protocol |
For each sample, aRNA was labeled using the ULS Fluorescent Labeling Kit for Agilent arrays (Cy3/Cy5) (Kreatech Diagnostics, Amsterdam, Netherlands). The labeled product was then purified with the Pico-Pure RNA Isolation Kit.
|
| |
|
| |
| 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 |
Rep 3 of 4
|
| Data processing |
Background subtracted, Loess and Quantile normalized data obtained from log2 of processed Red signal/processed Green signal. Flexarray software used.
|
| |
|
| Submission date |
Aug 10, 2016 |
| Last update date |
Aug 11, 2016 |
| Contact name |
Léonie Morin-Doré |
| Organization name |
Laval University
|
| Department |
Animal Sciences
|
| Street address |
2440, boulevard Hochelaga
|
| City |
Quebec |
| State/province |
Quebec |
| ZIP/Postal code |
G1V 0A6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL13226 |
| Series (2) |
| GSE85436 |
Transcriptomic evaluation of bovine embryo quality on blastocysts obtained from peri-pubertal oocyte donors [8 mo vs 14 mo] |
| GSE85438 |
Transcriptomic evaluation of bovine embryo quality on blastocysts obtained from peri-pubertal oocyte donors |
|
