|
| Status |
Public on Jun 20, 2019 |
| Title |
Mock 0hr Replicate 3 |
| Sample type |
RNA |
| |
|
| Source name |
18 day old A17 Medicago roots, mock-inoculated, 0hr sample
|
| Organism |
Medicago truncatula |
| Characteristics |
genotype: A17
tissue: root
|
| Treatment protocol |
At dawn on day 14 post inoculation (14 dpi) roots were treated with 2ml liquid MFM supplemented with 5mM NH4NO3 (nitrogen-replete treatment) or liquid MFM supplemented with 0.1mM NH4NO3 (nitrogen-deplete treatment) then sampled at 2hr, 6hr or samples were taken at the point of treatment 0hr.
|
| Growth protocol |
Seeds were germinated then grown for 4 days on 0.8% agar-modified nitrogen-free Fahräeus medium (MFM) plates before being mock- or rhizobia inoculated with 2mL of OD600=0.02 of Sinorhizobium meliloti 1021 overnight culture. Plants were grown for a further 14 days before treating. All plant growth was in long day (16hr light/8hr dark) constant 25 oC conditions in a Sanyo growth chamber (MLR251).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Root samples were harvested then total RNA extracted using the Qiagen plant RNeasy kit. Total RNA samples were then treated with the TURBO DNA-free kit (Life Technologies) to remove residual DNA.
|
| Label |
Cy3
|
| Label protocol |
cDNA was synthesised from RNA using the Ovation Pico WTA System (NuGEN Technologies Inc., San Carlos, CA, USA) and purified using Qiagen Qiaquick PCR purification kit. dscDNA was labelled with Cy3 using the Nimblegen one-color DNA labeling kit.
|
| |
|
| Hybridization protocol |
Following fragmentation, 4 ug of cRNA was hybridized for 16 hr at 42oC on a NimbleGen hybridization station.
|
| Scan protocol |
Slides were scanned using an MS 200 microarray scanner and associated NimbleGen software using only the 480 nm laser with gain calculated using the autogain feature of NimbleScan, based on a representative region of the slide (an area covering around half an array found to have average intensity based on a prescan at lower resolution), as per manufacturer’s instructions. Grids were aligned automatically to each microarray image and manually verified, ensuring reference spots in each corner and in the centre of the array were aligned to the grid and the alignment score minimised.
|
| Description |
NimbleGen gene expression array data for custom-design array based on the Medicago truncatula v3.5 genome
|
| Data processing |
Data were obtained using NimbleScan and normalised by robust multichip averaging (RMA) (quantile normalisation, taking into account outlier probes per gene) and summarised to gene level by median polish.
|
| |
|
| Submission date |
Jul 09, 2018 |
| Last update date |
Jun 20, 2019 |
| Contact name |
Miriam Gifford |
| E-mail(s) |
[email protected]
|
| Phone |
02476575268
|
| Organization name |
University of Warwick
|
| Department |
School of Life Sciences
|
| Lab |
Gifford lab
|
| Street address |
Gibbet Hill Road
|
| City |
Coventry |
| ZIP/Postal code |
CV4 7AL |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL25305 |
| Series (1) |
| GSE116789 |
Regulation of resource partitioning coordinates lateral root and nodule development in the legume Medicago truncatula |
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