|
| Status |
Public on Jul 29, 2013 |
| Title |
Dye swap Mid-sporophyte sample 3 (Cy3) vs.Gametophyte sample 6 (Cy5) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Mid-sporophytic tissue of Physcomitrella patens sample 3
|
| Organism |
Physcomitrium patens |
| Characteristics |
ecotype: Villesexel
tissue: Mid-sporophytic tissue (defined as ovoid to near-spherical translucent green capsules with the foot, calyptras and calyptral remnants removed)
|
| Biomaterial provider |
Caspar Chater
|
| Treatment protocol |
Gametogenesis was initiated by transferring cultures to 15°C growth cabinet for three weeks with a 16-hour photoperiod (140 µmol m 2), after which they were flooded with sterile deionised water to promote fertilization of archegonia for about 2 hours. Subsequently the cultures were returned to gametophyte growth conditions for further development of the sporophytes.
|
| Growth protocol |
Plants were grown in Sanyo MLR incubators with a 16-hour photoperiod (140 µmol m 2), 22°C day temperature and 16°C night temperature. Protonema and gametophores were grown on organic-nitrogen-supplemented BCD medium in sterile petri dishes overlaid with sterile cellophane discs and sealed with micropore tape, as described (Knight et al, 2002). Gametophore production was initiated by sub-culturing protonemal fragments onto agar lacking cellophane discs and culturing these for longer than 14 days. Gametogenesis was initiated by transferring cultures to 15°C growth cabinet for three weeks with a 16-hour photoperiod (140 µmol m 2), after which they were flooded with sterile deionised water to promote fertilization of archegonia for about 2 hours. Subsequently the cultures were returned to gametophyte growth conditions for further development of the sporophytes.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from all plant tissues using the Spectrum Total Plant RNA extraction kit (Sigma, STRN250) following manufacturer’s recommendations. Approximately 100mg of tissue was harvested directly into liquid nitrogen in microcentrifuge tubes and ground to a powder. RNA integrity and concentration were analysed by agarose gel electrophoresis and an Agilent Bioanalyzer. Gametophyte RNA was extracted from seven day old protomenal tissue.
|
| Label |
Cy3
|
| Label protocol |
Samples were co-hybridised as total RNA with Cyanine (Cy-3) fluorescent ULS labels MOgene LC, an Agilent certified facility based in St Louis, MO, USA (www.mogene.com, MOGene LC, St. Louis)
|
| |
|
| Channel 2 |
| Source name |
Gametophytic protonemal tissue of Physcomitrella patens sample 6
|
| Organism |
Physcomitrium patens |
| Characteristics |
ecotype: Villesexel
tissue: 7 day old protonemal tissue
|
| Biomaterial provider |
Caspar Chater
|
| Treatment protocol |
No treatment was used
|
| Growth protocol |
Plants were grown in Sanyo MLR incubators with a 16-hour photoperiod (140 µmol m 2), 22°C day temperature and 16°C night temperature. Protonema and gametophores were grown on organic-nitrogen-supplemented BCD medium in sterile petri dishes overlaid with sterile cellophane discs and sealed with micropore tape, as described (Knight et al, 2002).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from all plant tissues using the Spectrum Total Plant RNA extraction kit (Sigma, STRN250) following manufacturer’s recommendations. Approximately 100mg of tissue was harvested directly into liquid nitrogen in microcentrifuge tubes and ground to a powder. RNA integrity and concentration were analysed by agarose gel electrophoresis and an Agilent Bioanalyzer.
|
| Label |
Cy5
|
| Label protocol |
Samples were co-hybridised as total RNA with Cyanine (Cy-5) fluorescent ULS labels MOgene LC, an Agilent certified facility based in St Louis, MO, USA (www.mogene.com, MOGene LC, St. Louis)
|
| |
|
| |
| Hybridization protocol |
Samples were hybridized to microarrays by MOgene LC, an Agilent certified facility based in St Louis, MO, USA (www.mogene.com, MOGene LC, St. Louis following Agilent protocols.
|
| Scan protocol |
Microarrays were scanned by MOgene LC.
|
| Data processing |
Image processing was carried out by MOgebe LC.
|
| |
|
| Submission date |
Oct 11, 2011 |
| Last update date |
Jul 29, 2013 |
| Contact name |
Martin-Timothy O'Donoghue |
| Organization name |
University of Sheffield
|
| Department |
Department of Animal and Plant Sciences
|
| Street address |
Western Bank
|
| City |
Sheffield |
| ZIP/Postal code |
S10 2TN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL14653 |
| Series (1) |
| GSE32928 |
Genome-wide transcriptomic analysis of the sporophyte of the moss Physcomitrella patens |
|
| Data table header descriptions |
| ID_REF |
|
| VALUE |
The log ratio |
| PValueLogRatio |
The p-value of the log ratio |
| gMeanSignal |
The mean of the Cy3 (green) signal (Mid-sporophyte 3) |
| rMeanSignal |
The mean of the Cy5 (red) signal (gametophyte 6) |
| gMedianSignal |
The median of the Cy3 (green) signal (Mid-sporophyte 3) |
| rMedianSignal |
The median of the Cy5 (red) signal (gametophyte 6) |
| gBGMeanSignal |
The mean of the background of the Cy3 (green) signal (Mid-sporophyte 3) |
| rBGMeanSignal |
The mean of the background of the Cy5 (red) signal (gametophyte 6) |
| gBGMedianSignal |
The median of the background of the Cy3 (green) signal (Mid-sporophyte 3) |
| rBGMedianSignal |
The median of the background of the Cy5 (red) signal (gametophyte 6) |
