|
| Status |
Public on Dec 31, 2022 |
| Title |
Synergid Cell, biological rep 3 |
| Sample type |
RNA |
| |
|
| Source name |
Greenhouse grown rice, cv Katy
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
cell type: Synergid Cell
genotype: Wild type
|
| Treatment protocol |
Synergids and antipodals were collected from anthesis florets. Ovaries were excised and ovules bisected to remove the selected cell types from the female gametophyte using a non-enzymatic method modified from Zhang et al (2010). Synergids were isolated from the micropylar female gametophyte and antipodals from the chalazal female gametopyte.
|
| 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).
|
| 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 25 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 synergids at anthesis
|
| Data processing |
GCOS 2.0. Affymetrix MAS 5.0 processing, with all chips scaled to the same target value of 500.
|
| |
|
| Submission date |
Mar 21, 2014 |
| 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) |
| GSE56108 |
Comparative gene expression in synergid cells and antipodal cells at anthesis |
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