|
| Status |
Public on Mar 25, 2010 |
| Title |
caryopses at T 7:00 AM, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Barley caryopses
|
| Organism |
Hordeum vulgare |
| Characteristics |
tissue: whole carypses from the mid region of the spike, awns removed
genotype: Hordeum vulgare cultivar 'Golden Promise'
age: 11 to 12 days after anthesis
|
| Growth protocol |
Barley plants were grown in the green house in 10 cm pots in soil with additional lighting from Xenon light bulbs (15h light [6:00 AM - 9:00 PM], 9h dark [9:00 PM - 6:00 AM]; ~24°C; 40% rel. Humidity, October 2006)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
100mg of pooled homogenized plant material was mixed with 900µl of sarcosyl buffer (1% sodium lauryl sarcosinate, 0.1M Tris-HCl pH 7.5, 0.1M NaCl, 20mM EDTA, 50mM beta-mercaptoethanol) and purification of nucleic acids was done by three steps of phenol-chloroform-isoamylalcohol (25:24:1) extractions. Precipitation of nucleic acids was performed with sodium acetate (pH 5.2) and 1 volume isopropanol. After centrifugation, sediment was washed with ethanol and purified RNA was dissolved in DEPC treated water. Incubation at 65°C for 5min, followed by centrifugation at 4°C was performed to remove residual high molecular weight polysaccharides. The obtained RNA solution was purified following the RNeasy (Quiagen) clean up protocol. RNA quantity and integrity were assessed using RNA 6000 Nano LabChip Kit and the BioAnalyzer software (Agilent).
|
| Label |
biotin
|
| Label protocol |
1µg of total RNA were used to synthesize amplified labeled cRNA (MessageAmp™ II aRNA Amplification Kit; Ambion).
|
| |
|
| Hybridization protocol |
After fragmentation of cRNA using the RNA Fragmentation Reagents (Ambion), 13.5µg of cRNA was hybridized to Affymetrix Barley1 GeneChips (GEO accsession GPL1340) according to manufacturers manual. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the protocol 'EukGE-WS2V4'.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip® scanner GS3000 7G according to manufacturers manual.
|
| Description |
Gene expression data from developing Barley caryopses 12 days after anthesis, at 7:00 AM; 10 h after start of experiment, 1 h after onset of light
|
| Data processing |
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 200.
|
| |
|
| Submission date |
Jan 25, 2010 |
| Last update date |
Mar 25, 2010 |
| Contact name |
Joachim Kilian |
| E-mail(s) |
joachim.kilian@zmbp.uni-tuebingen.de
|
| Phone |
+ 49 (0) 7071 29 73087
|
| Fax |
+ 49 (0) 7071 29 3287
|
| Organization name |
University of Tuebingen
|
| Department |
ZMBP Plant Physiology
|
| Lab |
AG Wanke
|
| Street address |
Auf der Morgenstelle 1
|
| City |
Tuebingen |
| ZIP/Postal code |
D-72076 |
| Country |
Germany |
| |
|
| Platform ID |
GPL1340 |
| Series (1) |
| GSE20034 |
Diurnal expression data from developing barley caryopses |
|
