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Hordeum vulgare
168 Downloadable Samples
Affymetrix Barley Genome Array (barley1)
Description
Expression analysis was performed on total RNA from the Q21861 and SM89010 barley lines, and 75 derived doubled haploid progeny, with CI 16137 included as an internal Mla1 allele control. Samples were blocked by time-point and completely randomized within each block. For each sample, seven day old seedlings were inoculated with Blumeria graminis f. sp. hordei (Bgh) isolate 5874 (AVRa1, AVRa6, AVRa12), and first leaves were collected at 16 and 32 hours after inoculation (HAI). ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Roger Wise. The equivalent experiment is BB96 at PLEXdb.]
Publication Title
No associated publication
Sample Metadata Fields
Age, Specimen part, Time
View Samples
GSE66913- Vitis riparia, Vitis hybrid cultivar
- 167 Downloadable Samples
- Affymetrix Vitis vinifera (Grape) Genome Array (vitisvinifera)
Description
Bud endodormancy induction response of two genotypes (Seyval a hybrid white wine grape and V. riparia, PI588259 a native north american species) was compared under long and short photoperiod. Three separate replicates (5 plants/replicate) were treated in each of 2 separate years (2007 and 2008) to generate paradormant (LD) and same aged endodormancy-induced (SD) buds for transcriptomic, proteomic and metabolomic analysis. Potted, spur-pruned two to six-year-old vines were removed from cold storage (Seyval 3-19-07, 3/18/08; V. riparia 3/26/07, 3/24/08) and grown under a LD (15 h) at 25/20 + 3C day/night temperatures (D/N). When vines reached 12-15 nodes they were randomized into groups for differential photoperiod treatments. On 4/30/07 and 4/28/08 LD and SD (13 h) treatments were imposed with automated photoperiod system (VRE Greenhouse Systems). Temperatures were maintained at 25/20 + 3C D/N. Three replications (5 vines/replication) were harvested between 5/07-6/07 and then again in 5/08-6/08. At 1, 3, 7, 14, 21, 28 and 42 days of differential photoperiod treatment, buds were harvested from nodes 3 to 12 (from the base of the shoot) of each separate replicate, immediately frozen in liquid nitrogen, and placed at -80C for future RNA, protein and metabolite extraction. These time points encompass early reversible phases as well as key time points during transition to irreversible endodormancy development. After photoperiod treatments and bud harvests, all pruned vines were returned to LD and monitored for bud endodormancy. The endodormant vines were identified after 28 days and moved to cold storage. The nondormant vines were allowed to grow again and induced into dormancy at a later date. Acknowledgement:This study was funded by NSF Grant DBI0604755 and funds from the South Dakota Agriculture Experiment Station. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Anne Fennell. The equivalent experiment is VV18 at PLEXdb.]
Publication Title
Short day transcriptomic programming during induction of dormancy in grapevine.
Sample Metadata Fields
Age, Specimen part
View Samples- Hordeum vulgare
- 166 Downloadable Samples
- Affymetrix Barley Genome Array (barley1)
Description
The QxSM doubled-haploid mapping population was generated from a single Q21861 x SM89010 F1 plant (Borovkova et al. 1995; Steffenson et al. 1995). Four flats (each flat contained 75 DH lines + 4 replicates of each parent = 81 cones/flat) were grown in a completely randomized design at the ARS Cereal Disease Lab, University of Minnesota, St. Paul. The four flats were divided into two replicates of two flats each. Nine days after sowing, one flat of each replicate was inoculated (INOC) with TTKS urediniospores were suspended in Soltrol oil with an inoculum weight of 0.25 mg per flat and the other was mock-inoculated (MOCK). Each (MOCK and INOC) replicate was incubated in its own dew chamber overnight. After inoculation, replicates were placed in separate mist chambers for 16 hours in the dark, followed by lights for 5 hours, and then moved to the greenhouse for 2 hours. The growth stage of barley was first leaf unfolded (PO:0007094) and five seedlings were harvested and placed in liquid nitrogen for each line in the population within a 1.5 hour period at 24 hours after inoculation (hai). ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Roger P. Wise. The equivalent experiment is BB64 at PLEXdb.]
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Hordeum vulgare
- 144 Downloadable Samples
- Affymetrix Barley Genome Array (barley1)
Description
A split-split-plot design with 144 experimental units (3 replications x 4 genotypes x 6 time points x 2 treatment types) was used to profile barley plants containing variants of Mla1 and Mla6 powdery mildew resistance genes in response to inoculation with the Blumeria graminis f. sp. hordei (Bgh) isolates 5874 (AvrMla1, AvrMla6). Barley leaves were harvested from inoculated and non-inoculated plants at 6 time points (0,8,16,20,24 and 32 hrs) after Bgh inoculation. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Rico Caldo. The equivalent experiment is BB10 at PLEXdb.]
Publication Title
Blufensin1 negatively impacts basal defense in response to barley powdery mildew.
Sample Metadata Fields
Specimen part, Time
View Samples- Glycine max
- 117 Downloadable Samples
- Affymetrix Soybean Genome Array (soybean)
Description
Experimental design: 2 genotypes: PI230970 (resistant USDA Plant Introduction (PI) line containing SBR Rpp2 resistance gene) & Embrapa-48 (susceptible Brazilian cultivar) 2 treatments: Soybean rust challenge & mock infection 3 replications 10 time points: 6, 12, 18, 24, 36, 48, 72, 96, 120, 168hai TOTAL: 120 Affymetrix GeneChip(R) Soybean Genome Arrays ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Martijn van de Mortel. The equivalent experiment is GM2 at PLEXdb.]
Publication Title
Distinct biphasic mRNA changes in response to Asian soybean rust infection.
Sample Metadata Fields
Specimen part, Time
View Samples- Hordeum vulgare
- 108 Downloadable Samples
- Affymetrix Barley Genome Array (barley1)
Description
A large-scale parallel expression analysis was conducted to elucidate Mla-specified responses to powdery mildew infection using 22K Barley1 GeneChip probe arrays. Our goal was to identify genes differentially expressed in incompatible (resistant) vs. compatible (susceptible) and Mla-specified Rar1-dependent vs. -independent interactions. A split-split-plot design with 108 experimental units (3 replications x 2 isolates x 3 genotypes x 6 time points) was used to profile near-isogenic lines containing the Mla1, Mla6, and Mla13 resistance specificities in response to inoculation with the Blumeria graminis f. sp. hordei (Bgh) isolates 5874 (AvrMla1, AvrMla6) and K1 (AvrMla1, AvrMla13). ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Rico Caldo. The equivalent experiment is BB4 at PLEXdb.]
Publication Title
Interaction-dependent gene expression in Mla-specified response to barley powdery mildew.
Sample Metadata Fields
Specimen part, Time
View Samples- Hordeum vulgare
- 90 Downloadable Samples
- Affymetrix Barley Genome Array (barley1)
Description
Transcriptome comparison of 15 lines representing the University of Minnesota six-rowed malting breeding program at two time points of the malting process: 'out of steep' and '3 days of germination'. Three replicates of each genotype and time point were accomplished. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Maria Muoz-Amatriain. The equivalent experiment is BB91 at PLEXdb.]
Publication Title
Transcriptome analysis of a barley breeding program examines gene expression diversity and reveals target genes for malting quality improvement.
Sample Metadata Fields
Age, Specimen part
View Samples- Triticum aestivum
- 90 Downloadable Samples
- Affymetrix Wheat Genome Array (wheat)
Description
Resistance mechanisms of wheat to Fusarium graminearum are still poorly understood. Multiple reports have investigated transcriptomic differences between resistant and susceptible genotypes. To investigate the genetic determinants underlying the two major contributor QTL Fhb1 and Qfhs.ifa-5A, we generated a set of near-isogenic lines, that we have used for transcriptomic studies using the Affymetrix wheat GeneChip: 4 near-isogenic lines (BC5F2) derived from a cross of CM82036 and cv Remus (susceptible recurrent parent) and the resistant parent CM82036 have been inoculated with Fusarium spore suspension or water as control at anthesis. Samples have been taken at 3 timepoints 8, 24 and 72 hours after inoculation. Five wheat heads per condition were pooled into one sample, that has been used for RNA preparation. Including 3 replicates a total of 90 microarrays have been hybridized. Our results identify a wide variety of genes (631 transcripts) that are differentially regulated for Fusarium graminearum in all genotypes after 72 h and 339 genes that are upregulated only in lines without Qfhs.ifa.5A. Few genes were found differentially regulated for Fusarium and QTL. Many interesting candidates emerge from the set of QTL-specific genes that are constitutively expressed when comparing water-treated samples. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Wolfgang Schweiger. The equivalent experiment is TA41 at PLEXdb.]
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Treatment, Time
View Samples- Vitis riparia, Vitis hybrid cultivar
- 84 Downloadable Samples
- Affymetrix Vitis vinifera (Grape) Genome Array (vitisvinifera)
Description
Bud endodormancy induction response of two genotypes (Seyval a hybrid white wine grape and V. riparia, PI588259 a native north american species) was compared under long (15h) and short (13h) photoperiod. Three separate replicates (5 plants/replicate) were treated to generate paradormant (LD) and same aged endodormancy-induced (SD) buds for transcriptomic, proteomic and metabolomic analysis. Potted, spur-pruned two to six-year-old vines were removed from cold storage (Seyval 3-19-07; V. riparia 3/26/07) and grown under a LD (15 h) at 25/20 + 3C day/night temperatures (D/N). When vines reached 12-15 nodes (3-25-07) they were randomized into LD or SD treatments with 25/20 + 3C D/N in climate controlled greenhouses with automated photoperiod system (VRE Greenhouse Systems). Three replications (5 vines/replication) were harvested between 5/07-6/07 and then again in 5/08-6/08 for a total of six replications. All treatments are repeated at the same time every year and harvested at the same time of day each year to minimize biological noise. At 1, 3, 7, 14, 21, 28 and 42 days of LD and SD treatment, buds were harvested from nodes 3 to 12 of each separate replicate, immediately frozen in liquid nitrogen, and placed at -80C for future RNA, protein and metabolite extraction. These time points encompass early reversible phases as well as key time points during transition to irreversible endodormancy development. After photoperiod treatments and bud harvests, all pruned vines were returned to LD and monitored for bud endodormancy. The endodormant vines were identified after 28 days and moved to cold storage. The nondormant vines were allowed to grow again and induced into dormancy at a later date. Acknowledgement:This study was funded by NSF Grant DBI0604755 and funds from the South Dakota Agriculture Experiment Station. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Anne Fennell. The equivalent experiment is VV10 at PLEXdb.]
Publication Title
Differential floral development and gene expression in grapevines during long and short photoperiods suggests a role for floral genes in dormancy transitioning.
Sample Metadata Fields
Age, Specimen part
View Samples- Hordeum vulgare
- 72 Downloadable Samples
- Affymetrix Barley Genome Array (barley1)
Description
Time-course expression profiles of Bgh challenged barley cultivar C.I. 16151 (harboring the Mla6 powdery mildew resistance allele) and its fast-neutron-derived "Bgh-induced tip cell death1" mutant, bcd1, were compared using the 22K Barley1 GeneChip. Planting, stage of seedlings, harvesting, and experimental design were part of a larger experiment described by Caldo et al. (2004). PLEXdb BB4. Experiment Design: C.I. 16151 (wildtype) and bcd1 (mutant) were planted in separate 20 x 30-cm flats using sterilized potting soil. Each experimental flat consisted of six rows of 15 seedlings, with rows randomly assigned to one of six harvest time points (0, 8, 16, 20, 24, and 32 hai). Seedlings grown to the 1st leaf stage with 2nd leaf unfolded were inoculated with a high density of fresh conidiospores (84 +/- 19 spores/mm2). Groups of flats were placed at 18C (8-hour darkness, 16-hour light) in separate controlled growth chambers corresponding to the Bgh isolates. Rows of plants were harvested at each assigned time points and snap frozen in liquid nitrogen. The entire experiment was repeated three times in a standard split-split-plot design with 72 experimental units (2 genotypes x 2 pathogen isolates x 6 time points x 3 replications). Treatment Description: The samples constituted pairwise combinations of the the cultivar C.I. 16151(containing the Mla6 resistance allele), and its fast-neutron-derived "Bgh-induced tip cell death1" mutant, bcd1 with the two Bgh (Blumeria graminis f. sp. hordei) isolates, 5874 (AvrMla6, AvrMla1) and K1 (AvrMla13, AvrMla1). For each replication, individual genotypes were planted in separate 20 x 30 cm flats using sterilized potting soil. Each experimental flat consisted of six rows of 15 seedlings, with rows randomly assigned to one of six harvest times (0, 8, 16, 20, 24, and 32 hai). Seedlings were grown to the 2nd-leaf stage with 1st leaf unfolded, and inoculation was performed at 4 PM Central Standard Time by tipping the flats at 45oC and dusting the plants with a high density of fresh conidiospores [84 +/- 19 spores/mm2]. This procedure was repeated from the opposite angle to ensure that a high proportion of the cells are in contact with the fungus. This conidial density per unit leaf area routinely results in greater than 50% of epidermal cells that are successfully infected. Groups of flats were placed at 18oC (8 hours darkness, 16 hours light, 8 hours darkness) in separate controlled growth chambers corresponding to the Bgh isolate. Rows of plants were harvested at their assigned harvest times and flash-frozen in liquid nitrogen. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Roger P Wise. The equivalent experiment is BB46 at PLEXdb.]
Publication Title
Interaction-dependent gene expression in Mla-specified response to barley powdery mildew.
Sample Metadata Fields
Age, Specimen part, Time
View Samples