|
| Status |
Public on Dec 31, 2022 |
| Title |
Fertilized Egg Cell (~1 hap), biological rep 3 |
| Sample type |
RNA |
| |
|
| Source name |
Greenhouse grown rice, cv Katy
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
subspecies: japonica
cultivar: Katy
genotype: Wild type
developmental stage: Fertilized Egg Cell (~1 hap)
|
| Treatment protocol |
Egg cells (unfertilized), egg cells (fertilized) and zygotes were collected from anthesis florets, ovaries isolated and ovules excised to remove egg and zygote cells from the micropylar female gametophyte using non-enzymatic method described in Zhang et al (2010) for isolation of rice female gametophyte cells. Each biological technical replicate represents ~100 cells.
|
| Growth protocol |
Oryza sativa ssp. japonica, cultivar Katy were grown in greenhouses of the University of Oklahoma, under long-day, disease free conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified using the RNeasy plant mini kit according to manufacturer’s instructions (Qiagen). Yield per egg cell or zygote cell is estimated at 25 picogram (by Ohnishi et al., 2011, and our own estimates), so the total collection may represent ~2.5 ng Total RNA
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNAs were prepared with the Affymetrix GeneChip Two-Cycle cDNA Synthesis Kit for target preparation with signal amplification according to the standard Affymetrix protocol from total RNA of three replicates each of 100 unfertilized egg cells, 100 fertilized egg cells and 100 zygotes, respectively. According to estimate of Onishi et al. 2010 (PMID: 21106719) each egg cell is estimated to contain 25 pg and zygote slightly more (with paternal contribution); total RNA is estimated to be 2.5 ng for each 100 cell collection.
|
| |
|
| Hybridization protocol |
Fifteen ug of fragmented cRNA were hybridized for 16 hr at 45ºC on Affymetrix GeneChip Rice Genome oligonucleotide array. Subsequent GeneChip washing and staining steps were performed on a GeneChip Fluidics Station 450.
|
| Scan protocol |
The GeneChips were scanned using the GeneChip Scanner 3000.
|
| Description |
Gene expression data from pollen at anthesis
|
| Data processing |
Affymetrix MAS 5.0 processing, with all chips scaled to the same target value of 500.
|
| |
|
| Submission date |
Feb 17, 2011 |
| Last update date |
Dec 31, 2022 |
| Contact name |
Scott D Russell |
| E-mail(s) |
srussell@ou.edu
|
| Phone |
405 210-8935
|
| Organization name |
University of Oklahoma
|
| Department |
Dept of Microbiology and Plant Biology
|
| Street address |
770 Van Vleet Oval
|
| City |
Norman |
| State/province |
OK |
| ZIP/Postal code |
73019 |
| Country |
USA |
| |
|
| Platform ID |
GPL2025 |
| Series (1) |
| GSE27400 |
Comparative gene expression in mature egg cell, fertilized egg cell (1-1.5 hap) and fertilized zygote (2.5-3 hap) |
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