|
| Status |
Public on Nov 11, 2010 |
| Title |
Root, biological rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Whole root, 4th leaf growing stage
|
| Organism |
Oryza sativa |
| Characteristics |
cv. Nipponbare
|
| Treatment protocol |
Collected biological samples were frozen in liquid nitrogen and kept -80C until RNA extraction.
|
| Growth protocol |
Young leaves and roots were collected from plants grown in a green house. Calli were generated from seeds for three weeks on MS medium at 30C, transferred to regeration medium, cultured for indicated days and collected. Shoots were collected from plants grown at 30C in a growth chamber for four weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with RNeasy plant mini kit (Qiagen) according to manufacturer's protocol.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared from 500 ng total RNA using One-Cycle cDNA Synthesis Kit (Affymetrix) according to manufacturers protocol (hws_kit_manual).
|
| |
|
| Hybridization protocol |
3.3 ug of labeled and fragmented cRNA was hybridized to GeneChip Rice Genome Array using GeneChip Hybridization Oven 640 (Affymetrix). Wash and stain was performed by GeneChip Fluidics Station 450 (Affymetrix). All operations were performed with Hybridization, Stain and Wash Kit (Affymetrix) according to manufacturer's protocol (hws_kit_manual).
|
| Scan protocol |
GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix).
|
| Description |
Gene expression data from mature root.
|
| Data processing |
CEL files produced by GCOS 1.3 were analyzed using the statistical software R with bioconductor package “affy”. Signal intensities were extracted by expresso algorithm with parameters : bgcorrect.method = “mas”, normalize = “F”, pmcorrect.method = “pmonly”, summary.method = “mas”. Extracted signal intensities were introduced into GeneSpring 7.3.1 (Agilent) and scaled to 75th percentile per chip. Mas5calls algorithm in package “affy” was used for detection call.
|
| |
|
| Submission date |
Jan 06, 2009 |
| Last update date |
Nov 11, 2010 |
| Contact name |
Nori Kurata |
| E-mail(s) |
[email protected]
|
| Phone |
+81-55-981-6808
|
| Organization name |
National Institute of Genetics
|
| Lab |
Plant genetics Lab.
|
| Street address |
1111 Yata
|
| City |
Mishima |
| State/province |
Shizuoka |
| ZIP/Postal code |
411-8540 |
| Country |
Japan |
| |
|
| Platform ID |
GPL2025 |
| Series (2) |
| GSE14300 |
Rice expression atlas (4): Vegetative tissues |
| GSE14304 |
Rice expression atlas: Plant reproductive process |
|
