|
| Status |
Public on Nov 01, 2011 |
| Title |
root, wildtype, replicate 3 |
| Sample type |
RNA |
| |
|
| Source name |
root (meristem, elongation and differentiation zone)
|
| Organism |
Medicago truncatula |
| Characteristics |
genotype/variation: Wildtype (Jemalong A17)
age: 7 days old
tissue: root meristem
|
| Growth protocol |
Medicago plants used for gene expression analysis were grown vertically on Färhaeus medium plates without nitrate. RNA was isolated from the Nod factor susceptible zone of 7-day-old roots samples snap-frozen in liquid N2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted and purified from root Nod factor suspension zone using the Qiagen RNeasy plant mini kit (Qiagen, Venlo, The Netherlands). RNA integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies, Amsterdam, The Netherlands) with 6000 Nano Chips. RNA was judged as suitable only if samples showed intact bands of 18S and 25S ribosomal RNA subunits, displayed no chromosomal peaks or RNA degradation products, and had a RNA integrity number (RIN) above 9.0.
|
| Label |
biotin
|
| Label protocol |
The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 ug total RNA. The protocol was conducted using the reagents provided by Affymetrix, as the manufacturer's instructions.
|
| |
|
| Hybridization protocol |
Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).
|
| Scan protocol |
Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).
|
| Data processing |
Expression estimates were calculated using GCRMA (v2.15.3) in Bioconductor, applying the emperical Bayes (EB) model for background estimation.
|
| |
|
| Submission date |
Jan 11, 2011 |
| Last update date |
Nov 02, 2011 |
| Contact name |
Guido Hooiveld |
| E-mail(s) |
guido.hooiveld@wur.nl
|
| Organization name |
Wageningen University
|
| Department |
Div. Human Nutrition & Health
|
| Lab |
Nutrition, Metabolism & Genomics Group
|
| Street address |
HELIX, Stippeneng 4
|
| City |
Wageningen |
| ZIP/Postal code |
NL-6708WE |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL4652 |
| Series (1) |
| GSE26548 |
Strigolactone biosynthesis requires the symbiotic GRAS-type transcription factors NSP1 and NSP2 |
|
