|
| Status |
Public on Sep 01, 2007 |
| Title |
2HA 10:4, biological rep 3 |
| Sample type |
RNA |
| |
|
| Source name |
Medicago truncatula 2HA leaf explants, 2 weeks on 10:4
|
| Organism |
Medicago truncatula |
| Characteristics |
2HA
|
| Treatment protocol |
Leaf explants were plated onto P4 medium containing 10 µM NAA and 4 µM BAP (P4 10:4) for 2 weeks
|
| Growth protocol |
Medicago truncatula cv Jemalong and a highly regenerable seed line 2HA (Nolan et al, Plant Cell Rep 8: 278–281), which was derived from cultivar Jemalong, were used for the plant growth explant tissue culture. The basal medium used for the culture was P4, which is based on Gamborg's B5 medium as described by Thomas et al (Plant Sci 69: 189–198). All cultures were grown in the dark.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted and purified from plant tissues using the Qiagen RNeasy plant mini kit (Qiagen).
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA was generated using the Enzo BioArray kit (Affymetrix), purified using RNeasy spin columns (Qiagen), according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Fifteen to 20 µg of each biotin-labeled fragmented cRNA sample was used to prepare 300 µL of hybridization mixture. Aliquots of each sample (100 µL) were hybridized for 16 hours at 45 degrees celcius onto Test3 arrays to check the quality of the samples prior to hybridization (200 µL) onto the Medicago GeneChip arrays
|
| Scan protocol |
GeneChips were scanned with the Agilent GeneArray Scanner (Affymetrix)
|
| Description |
Gene expression data from Medicago truncatula 2HA after 2 weeks 0f 10:4 treatment
|
| Data processing |
To remove certain systematic biases from microarray, the raw Affymetrix data (.cel files) were normalized with the GCRMA (GC content – Robust Multi-Array Average) algorithm (ver. 2.2.0) including quantile normalization and variance stabilisation, using the affy package of the bioconductor software. The normalized average of the replicates was then log transformed in base 2 to reduce the proportional relationship between random error and signal intensity. Differentially expressed genes were identified by evaluating the log2 ratio between the two conditions
|
| |
|
| Submission date |
Jun 14, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Peta Holmes |
| E-mail(s) |
peta.holmes@anu.edu.au
|
| Phone |
61261253087
|
| URL |
http://www.rsbs.anu.edu.au/ResearchGroups/GIG/
|
| Organization name |
Genomic Interactions Group
|
| Department |
Reseach School of Biological Sciences
|
| Street address |
Building 46, Australian National University
|
| City |
Canberra |
| State/province |
Australian Capital Territory |
| ZIP/Postal code |
0200 |
| Country |
Australia |
| |
|
| Platform ID |
GPL4652 |
| Series (1) |
| GSE8131 |
A transcript profile of Medicago truncatula 2HA and Jemmalong during somatic embryogenesis |
|
