 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 15, 2009 |
| Title |
Uncovering the Arabidopsis thaliana nectary transcriptome: nectary and reference tissues |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by array
|
| Summary |
Many flowering plants attract pollinators by offering a reward of floral nectar. Remarkably, the molecular events involved in the development of nectaries, the organs that produce nectar, as well as the synthesis and secretion of nectar itself, are poorly understood. Indeed, to date, no genes have been shown to directly affect the de novo production or quality of floral nectar. To address this gap in knowledge, the ATH1 Affymetrix GeneChip array was used to systematically investigate the Arabidopsis nectary transcriptome to identify genes and pathways potentially involved in nectar production. In this study, we identified a large number of genes differentially expressed between secretory lateral nectaries and non-secretory median nectary tissues, as well as between mature lateral nectaries (post-anthessis) and immature lateral nectary tissue (pre-anthesis).
To identify genes that are specifically upregulated in nectary tissues, and therefore may contribute to nectar production, we compared individual nectary samples (ILN, MLN & MMN) with 51 non-nectary reference tissues (downloaded .cel files from other studies). 270 genes were identified as being significantly upregulated in nectaries. The expression patterns for multiple genes were also confirmed via RT-PCR.
The co-normalized RMA expression data (i.e., our own 8 nectary samples and 51 samples downloaded from GEO) are available as a supplementary file at the foot of this record.
|
| |
|
| Overall design |
Three different types of RNA samples were prepared from Arabidopsis thaliana ecotype Columbia-0 nectaries: mature lateral nectaries (MLN; Stage 14-15 flowers), immature lateral nectaries (ILN, Stage 11-12 flowers), and mature median nectaries (MMN, Stage 14-15 flowers) [developmental stages defined by (Smyth et al., 1990)]. MLN are secretory tissues, whereas, ILN and MMN are pre-secretory and nonsecretory tissues, respectively. All nectary tissues were separately dissected by hand from the flowers of primary inflorescences of ca. 30-35 day-old plants. All plants were grown in soil with a 16h light/8h dark light regimen. Due to the small size of nectaries, dissections took place over several days from 4-8 hours after dawn (h.a.d.).
The gene expression dataset obtained by our laboratory was enriched with third party expression data (i.e., 51 GEO Samples: GSM131510..GSM131660). The final gene expression dataset includes 59 hybridizations.
|
| |
|
| Contributor(s) |
Kram BW, Xu WW, Carter CJ |
| Citation(s) |
19604393 |
| |
| Submission date |
Apr 09, 2009 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Clay J Carter |
| E-mail(s) |
[email protected]
|
| Phone |
218-726-7347
|
| Organization name |
University of Minnesota Duluth
|
| Department |
Biology
|
| Street address |
1035 Kirby Dr
|
| City |
Duluth |
| State/province |
MN |
| ZIP/Postal code |
55812 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL198 |
[ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array |
|
| Samples (59)
|
|
| Relations |
| BioProject |
PRJNA116701 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE15617_59_ATH_samples_RMA.txt.gz |
7.5 Mb |
(ftp)(http) |
TXT |
| GSE15617_RAW.tar |
136.6 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
|
|
|
|
 |
Less...
More...