Identification of MOL1-dependent genes
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE61291 | GEO | 2016/03/24
SECONDARY ACCESSION(S): PRJNA260678
REPOSITORIES: GEO
Similar Datasets
Project description:We used RNA-seq to generate the transcriptional profile of WT and mol1-1 mutants in the second internode of the infloresence stem of 15 to 20 cm tall Arabidopsis. We then used stastical analysis to identify differentially expressed genes that potentially contribute to the mol1-1 mutant phenotype.
2016-03-24 | GSE71451 | GEO
Project description:We used RNA-seq to generate the transcriptional profile of wild type and mol1-1 mutants in the second internode of the inflorescence stem of 15 to 20 cm tall Arabidopsis. We then used statistical analysis to identify differentially expressed genes that potentially contribute to the mol1-1 mutant phenotype. RNA from three replicates each of WT and mol1-1 mutants were sequenced and differentially expressed genes were identified.
2016-03-24 | E-GEOD-71451 | biostudies-arrayexpress
Project description:15-20 cm tall PXY:GR-MPΔIII/IV plants were dipped headfirst in 15 µM dexamethasone or mock solution and after three hours of incubation second internodes were harvested and snap frozen in liquid nitrogen. Frozen plant material was pulverized with pestle and mortar and RNA was isolated by phenol/chlorophorm extraction as described previously (Mallory & Vaucheret 2010, PlantCell) with the modification of two additional concluding 70% EtOH washes
2017-05-29 | GSE97449 | GEO
Project description:15-20 cm tall 35S::Myc-GR-bdl plants were dipped headfirst in 15 µM dexamethasone or mock solution and after three hours of incubation second internodes were harvested and snap frozen in liquid nitrogen. Frozen plant material was pulverized with pestle and mortar and RNA was isolated by phenol/chlorophorm extraction as described previously (Mallory & Vaucheret 2010, PlantCell) with the modification of two additional concluding 70% EtOH washes
2017-05-29 | GSE97446 | GEO
Project description:Subsequently to primary growth, most dicotyledonous plants undergo secondary growth leading to an increased diameter of growth axes. During secondary growth initiation in shoots, a cylindrical meristem, the vascular cambium, is established by the initiation of meristematic activity in interfascicular regions, a process that ultimately leads to the formation of a continuous cylinder of vascular tissue along the shoot axis. In Arabidopsis this happens in a reduced area at the very base of the stem. In this study, a transcriptional comparison between the base and the first internode has been performed in order to asses the physiological state of both sample types and search for potential key regulators of the process. Total RNA was extracted from the base and the first internode from stems of 15cm tall Arabidopsis plants (ecotype Col-0). After RNA amplification, Cy3 or Cy5 targets were produced. Three independent biological replicates were used for each type of sample. Three hybridizations were performed, representing the three independent biological replicates, being one of them a dye swap.
2010-06-05 | E-GEOD-15446 | biostudies-arrayexpress
Project description:30 collars were taken from wild type plants or antiOsLIC transgenic plants respectively. One collar from one plant only. The leaves are just sprout 2-3 cm (about 1-2 days) from the stem. For measuring the genes expression level, Wild type plants were taken as control. The developing collar from both line2 of OsLIC antisense transgenic plants and wild type were harvested at the heading stage. The position of the collar was about 1cm above the last developed collar. Total RNA was extracted from the collars using TRIzol regeant (Invitrogen, P/N 15596-018, USA) and purified by using Qiagen RNeasy columns (QIAGEN, Cat. NO. 74104). All the processes for cDNA and cRNA synthesis, cRNA fragmentation, hybridization, washing and staining, and scanning, were conducted according to the GeneChip Standard Protocol (Eukaryotic Target Preparation, Affymetrix). Poly-A RNA Control Kit and the One-Cycle cDNA Synthesis kit were used in this experiment as described in the website: http://www.affymetrix.com/products/arrays/specific/rice.affx.
2008-12-22 | GSE12097 | GEO
Project description:The receptor-like protein kinases encoded by HAESA (HAE) and HAESA-LIKE 2 (HSL2) are essential for floral organ abscission in Arabidopsis thaliana and the double hae hsl2 mutant fails to abscise. Expression of HAE and HSL2 is specific to Abscission Zone (AZ) cells and is higher in stage 15 flowers than in earlier developmental stages. By stage 16 floral organs have begun to abscise, suggesting that HAE HSL2 are most active in stage 15 flowers. Samples were enriched for AZ RNA by isolating RNA from flower receptacles, the region from the base of the flower to slightly above the base of attachment of the sepals, petals, and stamen. RNA-seq was then used to analyze and compare the transcriptomes of wild type and hae-3 hsl2-3 mutants. 2034 genes were differentially expressed with a False Discovery Rate adjusted p < 0.05, of which 349 genes 2 fold or greater change. Of these 349, 277 were lower in the mutant and 72 were higher. Differentially expressed genes with lower expression were enriched for hydrolytic enzymes, cell-wall modifying enzymes, and defense related genes. This suggests that HAE HSL2 signaling regulates gene expression of enzymes necessary for abscission.
2013-01-14 | GSE35288 | GEO
Project description:The closely related Coffea arabica cultivars ‘Tall Mokka’ and ‘Typica’, with excellent flavor, but differing distinctively in the size of aerial organs, branching pattern and branch numbers. Differential gene expression analysis of shoot tips of arabica coffee cultivars 'Tall Mokka' and 'Typica' were done using Potato cDNA microarray as cross-species platform. Using cross-species microarray hybridization, we identified a prolyl oligopeptidase (CaPOP) gene as differentially expressed between the shoot tips of ‘Tall Mokka’ and ‘Typica’. Isolation and sequencing of POP genes from coffee identified three paralogs, CaPOP1, CaPOP2 and CaPOP3. All three genes were present in both cultivars, which suggest that differences in the expression of CaPOP are caused by factor(s) regulating the transcription of CaPOPs. CaPOP1 differs in sequence from CaPOP2 primarily in having two large deletions in the promoter region. CaPOP genes are homologous to arabidopsis At1g20380, encoding a post-proline cleaving enzyme that acts on substrates shorter than 30 amino acids. Ectopic expression of CaPOP1 under its native promoter in transgenic arabidopsis resulted in more secondary branches than in the wild type. This is the first study to successfully isolate CaPOP genes and characterize their expression in the developing tissues of coffee. This study also identified a novel role for prolyl oligopeptidase in control of branching. Eight coffee trees of 'Typica' ('K') and six trees of 'Tall Mokka' ('M') cultivar were used in this study. The trees were equally divided into two groups 'A' and 'B' for each cultivar ('MA','MB', 'KA' and 'KB') and treated as biological replicates. Eight two channel microarray hybridizations were done in following pairs: MA x KA, MA x KB, MB x KA, MB x KB and dye swap replicate of each pair. Summary: Two-sample experiment: Tall Mokka vs. Typica . 8 Hybridizations. 2 Biological replicates per sample. 1 Dye swap per array.
2011-08-03 | E-GEOD-31179 | biostudies-arrayexpress
Project description:Roswell Park Human 19K Array CGH<br><br>the format of the data is:<br> <br>Reporter Identifier<br>Band<br>Count - number of replicate spots the data represents (some spots are excluded in image analysis, usually because they are too dim to be reliable)<br>chr - Chromosome<br>Start - Start location in base pairs<br>Stop - Stop Location in Base pairs<br>Center - Center in base pairs<br>g_loc - graphing location this is the location of the center in base pairs if the chromosomes were laid end to end<br>Log2 ratio - log2 ratio (test/control)<br>Ratio - linear version of the ratio above <br>A - Measure of brightness A=(log2 cy3 + log2 cy5)/2 <br>Flag - Used to color code spots<br> 3 - red probably mismapped<br> 4 - green potentially polymorphic<br> 5 - light blue Shows a high degree of duplication with other area in the genome (see UCSC genome browser) <br>reference - Reference for why the clone was flagged <br>Pub Med link - Pub Med ID for why clone was flagged
2009-06-01 | E-MEXP-2141 | biostudies-arrayexpress
Project description:To gain insights into the molecular mechanisms controlling bamboo growth, mRNA differential display was used to clone genes that are differentially expressed in various tissues of shoots at different growth stages, and their expression patterns were further validated by cDNA microarray. A number of genes and signaling pathways are proposed to have significant roles in controlling the elongation of the bamboo culm. Etiolated shoots (average height: 15 cm) that had not yet emerged from the ground and green shoots (average height: 100 cm) of Bambusa oldhamii were collected. The shoots were divided into three parts, the culm base, the middle and the top regions for RNA extraction and processing. The RNA from the middle region of the etiolated shoots was used as a reference in microarray comparisons.
2012-12-31 | E-GEOD-40095 | biostudies-arrayexpress