GEO DataSets

(Submitter supplied) Transcriptome changes of Douglas-fir seedlings were analyzed to investigate molecular impacts of exposure to airborne emissions released from combustion of diesel fuel containing engineered cerium dioxide (CeO2) nanoparticle catalysts (DECe). We analyzed mRNA-sequencing data from exposed one-year-old needles. Our hypothesis is that 2-week chamber exposure to DECe would induce certain distinct transcriptome changes in the needles compared with responses to conventional diesel exhaust (DE) or filtered DECe Gas Phase. more...

Organism:

Pseudotsuga menziesii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24367

26 Samples

Download data: TXT

(Submitter supplied) Seasonal cycles of light, temperature and precipitation provide signals that set the timing of gene expression and growth for trees. Conifers possess evergreen needles to sense and respond to year-round external signals. We monitored gene activity in Douglas-fir needles for one year and found that gene expression is dependent on light at daily and annual scales. The majority of rhythmic genes achieve maximum activity +/- 2 hours from sunrise and sunset, and +/- 20 days from the winter and summer solstices. more...

Organism:

Pseudotsuga menziesii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16590

66 Samples

Download data: TXT

(Submitter supplied) Seasonal cycles of light, temperature and precipitation provide signals that set the timing of gene expression and growth for trees. Conifers possess evergreen needles to sense and respond to year-round external signals. We monitored gene activity in Douglas-fir needles for one year and found that gene expression is dependent on light at daily and annual scales. The majority of rhythmic genes achieve maximum activity +/- 2 hours from sunrise and sunset, and +/- 20 days from the winter and summer solstices. more...

Organism:

Pseudotsuga menziesii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16590

72 Samples

Download data: TXT

(Submitter supplied) Local adaptation and phenotypic plasticity are important components of plant responses to variations in environmental conditions. While local adaptation has been widely studied in trees, little is known about plasticity of gene expression in adult trees in response to ever-changing environmental conditions in natural habitats. Here we investigate plasticity of gene expression in needle tissue between two douglas-fir provenances represented by 25 adult trees using deep RNA sequencing (RNA-Seq). more...

Organism:

Pseudotsuga menziesii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16590

75 Samples

Download data: FASTA, TXT

(Submitter supplied) We developed a transcriptome resource for Douglas-fir covering key developmental stages of megagametophytes over time: prefertilization, fertilization, embryogenesis, and early, unfertilized abortion. Extracted RNA was sequenced using large-scale sequencing and reads were assembled to generate a de novo reference transcriptome of 105,505 predicted high-confidence transcripts. Expression levels were estimated based on alignment of the original reads to the reference.

Organism:

Pseudotsuga menziesii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16590

10 Samples

Download data: TXT

(Submitter supplied) This study characterizes the transcriptomic alterations of Laccaria bicolor S238N during interaction with Pseudotsuga menziesii. Three time-points were analyzed, two weeks, four weeks and six weeks after inoculation and compared to the transcriptome of free-living mycelium from Laccaria bicolor S238N.

Organism:

Laccaria bicolor S238N-H82; Pseudotsuga menziesii; Laccaria bicolor

Type:

Expression profiling by array

Platform:

GPL14641

12 Samples

Download data: PAIR

(Submitter supplied) We report sequencing the transcriptome of Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) during spring bud burst.

Organism:

Pseudotsuga menziesii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16590

83 Samples

Download data: CSV, FASTA

(Submitter supplied) Laccaria bicolor transcript profiles of different tissues and mycorrhizal root tips from different host trees were analyzed. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, department of energy) Laccaria bicolor genome sequence version 1. One goal was to compare gene expression profiles from ectomycorrhizal root tips with different host plants.

Organism:

Laccaria bicolor S238N-H82; Populus trichocarpa; Pseudotsuga menziesii; Populus deltoides

Type:

Expression profiling by array

Platform:

GPL14641

12 Samples

Download data: PAIR

(Submitter supplied) The Transcriptome of different tissues and developmental stages of Laccaria bicolor S238N was analyzed. The array probes were designed from gene models taken from the Joint Genome institute Laccaria bicolor genome sequence version1. One aim of this study was to verify the expression of the automatically annotated gene models in various tissues and to use this transcriptional information to confirm, to correct or to reject gene models. more...

Organism:

Populus trichocarpa; Laccaria bicolor; Laccaria bicolor S238N-H82; Pseudotsuga menziesii; Populus tremula x Populus alba

Type:

Expression profiling by array

Platform:

GPL6192

11 Samples

Download data: TXT