|
| Status |
Public on Aug 26, 2010 |
| Title |
2xX4x interploidy cross (Cy3-labelled) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Siliques
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
developmental stage: 5 days after pollination
maternal ecotype: C24
paternal ecotype: C24
maternal genetic modification: A9-barnase transgene
paternal genetic modification: none
|
| Treatment protocol |
none
|
| Growth protocol |
Plants were grown at 18hr day cycles at 60% humidity. Male sterile lines were pollinated by the appropriate pollen depending on the cross and siliques harvested in liquid nitrogen at 5 days after pollination (DAP).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
mRNA was extracted from whole siliques using the hot borate method for total RNA extraction and the Oligotex mRNA Midi Kit (Qiagen) to isolate poly-A+ mRNA.
|
| Label |
Cy3
|
| Label protocol |
Cy3- and Cy5-labelling were carried out using Agilent standard operating protocols.
|
| |
|
| Channel 2 |
| Source name |
Siliques
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
developmental stage: 5 days after pollination
maternal ecotype: C24
paternal ecotype: C24
maternal genetic modification: A9-barnase transgene
paternal genetic modification: none
|
| Treatment protocol |
none
|
| Growth protocol |
Plants were grown at 18hr day cycles at 60% humidity. Male sterile lines were pollinated by the appropriate pollen depending on the cross and siliques harvested in liquid nitrogen at 5 days after pollination (DAP).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
mRNA was extracted from whole siliques using the hot borate method for total RNA extraction and the Oligotex mRNA Midi Kit (Qiagen) to isolate poly-A+ mRNA.
|
| Label |
Cy5
|
| Label protocol |
Cy3- and Cy5-labelling were carried out using Agilent standard operating protocols.
|
| |
|
| |
| Hybridization protocol |
For each experimental cross (interploidy or fis1X2x), one array was hybridised using a Cy3-labelled sample together with a Cy5-labelled 2xX2x control cross sample using Agilent standard operating protocols. Then the dyes were swapped and the hybridisation was repeated with additional arrays.
|
| Scan protocol |
Agilent standard operating protocol.
|
| Description |
2xX4xCy3
|
| Data processing |
Quantitation, background correction and normalisation was performed for each array separately and independently using Agilent Feature Extraction Software (Apr 2002). Probes with negative signal values were excluded, creating missing values. Values for multiply spotted probes were averaged. For the fis1X2xCy3 and fis1X2xCy5 samples, probes with negative signal values and individual signal values for multiply spotted probes are included in the supplementary data files.
|
| |
|
| Submission date |
Jan 22, 2010 |
| Last update date |
Aug 26, 2010 |
| Contact name |
Reiner Schulz |
| E-mail(s) |
[email protected]
|
| Organization name |
King's College London
|
| Department |
Medical & Molecular Genetics
|
| Lab |
Epigenetics
|
| Street address |
8th floor Guy's Tower
|
| City |
London |
| ZIP/Postal code |
SE1 9RT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL9964 |
| Series (2) |
| GSE20006 |
Parent-of-origin effects in seeds of Arabidopsis thaliana: Agilent |
| GSE20007 |
Transcriptional profiles underlying parent-of-origin effects in seeds of Arabidopsis thaliana |
|
