|
| Status |
Public on Aug 01, 2017 |
| Title |
Wheat_rachis |
| Sample type |
RNA |
| |
|
| Source name |
Healthy_wheat_rachis
|
| Organism |
Fusarium graminearum |
| Characteristics |
infection status: non-infected
wheat tissue: Rachis
|
| Treatment protocol |
200 Fusarium graminearum PH-1 conidia were incoluated into the floral caity of the two florets, of the two spikelets, in the middle of the wheat head at anthesis. Wheat plants were kept at high humidity for the first 3 days, of which the first 24 hours was in the dark. At 7 days post infection the incoluted spikelets and the 7 sequential rachis internodes below the inoculated spikelet were collected and immediately frozen in liquid nitrogen. The individual wheat tissues were pooled for ten wheat heads to form a single biological replicate. Non-infected wheat spikelets and rachis was collected as a negative control. Three biological replicate were collected per treatment.
|
| Growth protocol |
Wheat plants were grown in a controlled environment with standard light, at 22 degrees and at ambient humidity
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Freeze dried samples were ground in liquid nitrogen with a pestle and mortar. Total RNA was extracted using the TRIzol® reagent (Invitrogen) with minor modifications to manufacturer’s instructions. Total RNA was precipitated at -20oC for 16 hours with 8 M lithium chloride.
|
| Label |
biotin
|
| Label protocol |
Purified total RNA (> 10 µg) was in vitro transcribed, labelled using the BioArray high yield RNA transcript labelling kit (T7) according to manufacturer’s instructions (Enzo Life Science)
|
| |
|
| Hybridization protocol |
Fragmented using 200 mM tris-acetate, pH 8.2, 500 mM MgOAc and mixed with the BioArray Eurkaryotic hydridization controls (Enzo Life Science) that included 3 nM control oligo B2, 20x control cRNA cocktail, herring sperma (10 mg / ml), acetylated BSA (50 mg / ml) 2x MES hybridization buffer and water. A final aRNA concentration of 10 µg in 200 µl was hybridized to the F. graminearum Affymetrix array
|
| Scan protocol |
GeneChips were scanned using the GeneArray Scanner
|
| Data processing |
Gene expression data from infecting hyphae within wheat floral tissue. The data was exported and RMA normalised using the Affymetrix Expression Console. Downstream analyses were performed with software R
|
| |
|
| Submission date |
Apr 02, 2016 |
| Last update date |
Aug 01, 2017 |
| Contact name |
Neil Brown |
| Organization name |
USP
|
| Street address |
Av. do Cafe
|
| City |
Ribeirao Preto |
| ZIP/Postal code |
14040903 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL18136 |
| Series (1) |
| GSE79853 |
The biphasic Fusarium graminearum transcriptome during symptomless and symptomatic wheat infection |
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