Expression data of Defensin-like genes (DEFLs) from different parts and treatments of Medicago truncatula and Arabidopsis thaliana
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
SUBMITTER: Kevin Silverstein
PROVIDER: E-GEOD-34401 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Since most of the DEFLs were recently discovered and many are not well represented on standard microarrays, little is known about their expression pattterns. To address this gap, we have designed a custom Affymetrix microarray (AtMtDEFL array) with known and predicted Arabidopsis and Medicago DEFL genes and the closely related maternally expressed gene family. The custom array was utilized for hybridizations of mRNAs from a wide range of conditions and tissues from both plant species, enabling a comparative analysis in the two model plant species. The custom chip transcript analysis provided the first expression evidence for many of the computationally identified DEFLs previously lacking gene expression evidence, and indicated both common and unique patterns of DEFL gene expression between the two model plant species. The custom designed Affymetrix chip consisting of nearly all DEFLs from Medicago truncatula was used for transcript profiling study in a variety of plant organs, developmental stages, and during symbiotic and pathogenic associations totalling 13 different treatments. Each treatment was supported by three biological replicates giving a grand total of 39 samples.
2013-02-23 | E-GEOD-34311 | biostudies-arrayexpress
Project description:We have undertaken a detailed study to identify expression polymorphism of NCRs. We used a custom Affymetrix oligonucleotide microarray to examine the expression changes of 566 NCRs in four different accessions of Medicago truncatula. Each accession was inoculated with two different rhizobial strains to assess the NCR expression differences caused by host-symbiont specificity. The NCRs displayed significant expression differences among the ecotypes but had subtle differences in gene expression because of strain difference. We used a custom Affymetrix chip containing 684 probe sequences of Medicago DEFLs to explore the expression polymorphism of NCRs in nodules inoculated with Sinorhizobium meliloti 1021(Sm1021) and Sinorhizobium medicae (SmA321) totalling 8 different treatments. Each treatment was supported by three biological replicates giving a grand total of 24 samples.
2014-06-20 | E-GEOD-34804 | biostudies-arrayexpress
Project description:The aim of the project is to determine the expression profile of Arabidopsis DEFL during sexual reproduction, in particular seed development. To this aim, we generated a customised Affymetrics array that was hybridized with labeled cDNA synthetised from total RNA. Plant were grown in a control environment chamber and were pollinated manually to precisely generate different stages of seed development. Samples were collected in tripicates.
2014-04-10 | E-GEOD-36086 | biostudies-arrayexpress
Project description:We have undertaken a detailed study to identify mechanisms regulating expression of NCRs. We used a custom Affymetrix oligonucleotide microarray to examine the expression changes of 566 NCRs in different stages of nodule development. Additionally, rhizobial mutants were used to understand the importance of the rhizobial components in induction of NCRs. Early NCRs were detected during the initial infection of rhizobia in nodules and continue to be expressed into the late stages of nodule development. Late NCRs were induced concomittant with bacteroid development in the nodules. The induction of these groups of genes was correlated with the number and morphology of rhizobia in the nodule. We used a custom Affymetrix chip containing 684 probe sequences of Medicago DEFLs to explore the expression patterns of NCRs in nodules inoculated with Sinorhizobium meliloti 1021(Sm1021) at marked developmental stages and nodules inoculated with various mutants derived from Sm1021 totalling 14 different treatments. Each treatment was supported by three biological replicates giving a grand total of 42 samples.
2013-03-05 | E-GEOD-34803 | biostudies-arrayexpress
Project description:Since most of the DEFLs were recently discovered and many are not well represented on standard microarrays, little is known about their expression pattterns. To address this gap, we have designed a custom Affymetrix microarray (AtMtDEFL array) with known and predicted Arabidopsis and Medicago DEFL genes and the closely related maternally expressed gene family. The custom array was utilized for hybridizations of mRNAs from a wide range of conditions and tissues from both plant species, enabling a comparative analysis in the two model plant species. The custom chip transcript analysis provided the first expression evidence for many of the computationally identified DEFLs previously lacking gene expression evidence, and indicated both common and unique patterns of DEFL gene expression between the two model plant species. The custom designed Affymetrix chip consisting of nearly all DEFLs from Arabidopsis thaliana was used for transcript profiling study in a variety of plant organs, developmental stages, and pathogenic associations totalling 16 different treatments. Each treatment was supported by three biological replicates giving a grand total of 48 samples.
2013-02-23 | E-GEOD-34398 | biostudies-arrayexpress
Project description:Arabidopsis MPK11 is activated and plays a role in the flg22 sensing. Mitogen-activated protein kinases (MAPKs) mediate cellular signal transduction during stress responses, as well as diverse growth and developmental steps in eukaryotes. Pathogen infection or treatment with conserved pathogen-associated molecular patterns (PAMPs) such as the bacterial flagellin-derived flg22 peptide are known to activate three Arabidopsis thaliana MAPKs, MPK3, MPK4 and MPK6. Several stresses, including flg22 treatment, are known to increase MPK11 expression but activation of MPK11 has not been shown. Here, we show that MPK11 activity can indeed be increased through flg22 elicitation. Expression profiling using a small-scale microarray for defense-related genes revealed that cinnamyl alcohol dehyrogenase 5 (CAD5) requires MPK11 for full flg22-induced expression. An mpk11 mutant showed increased flg22-mediated growth inhibition but no altered susceptibility to Pseudomonas syringae, Botrytis cinerea or Alternaria brassicicola. A 24 DNA microarray study using toral RNA from an Arabidopsis mutant (mpk11 SALK049352) as well as wild type treated with water or flg22.
2012-05-02 | E-GEOD-33648 | biostudies-arrayexpress
Project description:After 24 h of acclimatisation Medicago sativa seedlings were treated with HgCl2 diluted on fresh MS to a final concentration of 3 uM during 3, 6 and 24 h.
2014-03-03 | E-MEXP-3876 | biostudies-arrayexpress
Project description:Investigation of gene expression level changes in Daphnia pulex MFP strain between in the presence or absence of Chaoborus kairomone. 12 samples (4 conditions x 3 replicates) in one 12-plex NimbleGen array GPL11278
2015-05-13 | E-GEOD-63275 | biostudies-arrayexpress
Project description:ER-dependent gene expression was investigated in the LY2 endocrine resistant cell line by treatment with ICI 182780. Cells were steroid depleted for 3 days prior to treatment with ICI for 6 hours. Four biological replicates were processed and analysed.
2014-09-18 | E-MTAB-1870 | biostudies-arrayexpress
Project description:Salt tolerance in grapevine is associated with the exclusion of chloride ions (ClM-bM-^@M-^S) from the shoot. The rate-limiting step for this process has been identified as the passage of ClM-bM-^@M-^S between the root symplast and the xylem apoplast through membrane integral proteins. To identify candidate genes for these proteins we used a custom microarray to compare the root transcriptomes of three grapevine varieties (Vitis spp.) that differ in their capacity to exclude ClM-bM-^@M-^S from shoots. When challenged with 50 mM ClM-bM-^@M-^S there were transcriptional responses that differed across the rootstocks 140 Ruggeri (a good ClM-bM-^@M-^S excluder) and K51-40 (a poor ClM-bM-^@M-^S excluder), and Cabernet Sauvignon (an intermediate ClM-bM-^@M-^S excluder and Vitis vinifera control). The magnitude of these salt-induced changes correlated with the amount of ClM-bM-^@M-^S accumulated in shoots. Abiotic-stress responsive transcripts (e.g. heat shock proteins) were induced in 140 Ruggeri. Respiratory transcripts were repressed in Cabernet Sauvignon. Expression of hypersensitive response and ROS scavenging transcripts were altered in the sensitive K51-40. Despite these differences, no obvious candidate ClM-bM-^@M-^S transporters were identified from the salt treatment. In contrast, under control conditions where differences in shoot ClM-bM-^@M-^S exclusion between rootstocks were still significant, we identified a number of genes encoding putative ion channels including VvSLAH3, VvALMT1, and possible regulators of these proteins such as VvSnRK2.6 and calcium dependent protein kinases (CDPK) as being differentially expressed between rootstocks. Members of the low affinity nitrate transporter (NRT1), and chloride channel (CLC) families were also identified. We propose these as useful candidates for further study within breeding programs aimed at improving plant salt tolerance in grapevine and other crops. Comparative: genotype versus genotype (control); and control (0 mM Cl) versus salt (50 mM Cl). Rooted leaves were grown as described by Gong et. al. (2010) (Journal of Experimental Botany). After 2 weeks of hydroponic growth, plants were exposed to 0 mM or 50 mM chloride stress for 4 days. Three biological replicates were used for 140 Ruggeri. Four biological replicates were used for Cabernet Sauvignon. Four biological replicates were used for K51-40. Each biological replicate consisted of total roots from four individual plants pooled together.
2014-09-30 | E-GEOD-57770 | biostudies-arrayexpress