Long-term transcriptional memory in rice plants submitted to salt shock
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ABSTRACT:
PROVIDER: PRJNA628609 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11614374_1.fastq.gz | Fastqsanger.gz | |||
| SRR11614374_2.fastq.gz | Fastqsanger.gz | |||
| SRR11614375_1.fastq.gz | Fastqsanger.gz | |||
| SRR11614375_2.fastq.gz | Fastqsanger.gz | |||
| SRR11614376_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: Soil salinity is one of the main environmental factors that negatively influences yield, especially for sensitive crops such as rice. Studies report that a disturbing event can prepare the plant for a subsequent event through memory acquisition, involving physiological and molecular processes. Therefore, genes that provide altered responses in subsequent events define a category known as "memory genes." In this work, the RNA-Sequencing (RNA-Seq) technique was used to analyse the transcriptional profile of rice plants subjected to different salt shock events and to characterise genes associated with long-term memory. Methods: The mRNA of rice plants cv. Ligeirinho was generated using deep sequencing, in duplicate, using Illumina Hi-Seq 2500, for the following treatments:I) control (C): plants received irrigation with water and nutrient solution throughout the experiment; II) vegetative (SV), plants were exposed to saline shock only at the vegetative stage; III) reproductive (SR) plants were exposed to saline shock only at the reproductive stage; and IV) vegetative + productive (SV+R), plants were exposed to saline shock at the vegetative stage (first shock event) and at the reproductive stage (recurrent event). The sequence reads that passed quality filters were analyzed at the transcript level using this method: Mapping using STAR and identification of differentially expressed genes (DEGs) was performed with the edgeR (false discovery rates - FDRs of <0.05). RT–qPCR validation was performed using SYBR Green assays. Results: Plants subjected to recurrent salt shock showed differences in differentially expressed genes (DEGs). Additionally, the mammalian target of rapamycin (mTOR) pathways, and carbohydrate and amino acid associated pathways were altered under all conditions. Memory genes can be classified according to their responses during the first event (+ or –) and the second shock event (+ or –), being possible to observe a larger number of transcripts for groups [+/–] and [–/+], genes characterised as "revised response." Conclusions: This is the first long-term transcriptional memory study in rice plants under salt shock, providing new insights into the process of plant memory acquisition.
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Project description:Long-term transcriptional memory in rice plants submitted to salt shock
| PRJNA628609 | ENA
Project description:We used a custom-designed microarray to characterize the transcriptional response that accompanies longt-term sensitization training in the marine mollusk Aplysia californica. We characterized transcription for a new memory (1 day after training), a forgotten memory (8 days after training) and for a long-term savings memory (8 days after training but 1 day after a reminder that re-instates the sensitization memory). All animals received a 1-day unilateral LTS training protocol (4 rounds of noxious shock at 30 min intervals, each shock 10s of 1/2s off 1/2on 90mA 60-hz biphasic square-wave shock). This produced robust sensitization in all animals (measured as an increase in T-SWR response from baseline to 24h after training). In the forgetting condition, animals received training on day 1, and post-tests on days 7 and 8 showed little-to-no evidence of recall (T-SWR responses on the trained side returned to close to baseline). In the savings condition, animals received training on day 1 that produced strong sensitization, showed forgetting on day 7, and then received a weak bilateral shock as a reminder (day 7), producing a long-term savings memory on day 8 (a re-instatement of the behavioral expression of sensitization on the previously trained side). In the new memory condition, animals received sham training on day 1, then real training on day 7, producing robust sensitization measured on day 8. Pleural ganglia were harvested on day 8. Samples from a left-trained and right-trained animal were combined to smooth out lateralized gene expression. The pleural ganglia contains the VC nociceptors, which are thought to play a primary role in expressing LTS memory.
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Project description:In this study, we have analyzed the expression profiles of rice genes under control and heat shock conditions using microarray technology to identify the genes differentially expressed. Keywords: Heat shock
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Project description:Potted Cabernet Sauvignon vines in the greenhouse were exposed to irrigated controls, non-irrigated water-deficits, and saline treatments for 16 days. Plant shoot tips were harvested every 4 days (0,4,8,12, and 16 days) to measure the progression of changes of global gene expression due to the stress. PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Grant Cramer. The equivalent experiment is VV2 at PLEXdb.
2011-08-26 | GSE31677 | GEO
Project description:Transcriptional differentiation in response to environmental stresses plays critical roles in adaptation. Mangroves are dominant in intertidal zones and form dense forest at the sea-land interface, but little is known about the impact of transcriptional phenotype on their adaptation to the saline environments. To address this issue, we prepared customized chips containing cDNA from the root cDNA library of a mangrove species, Ceriops tagal, and then monitored the time-course transcript profiles in the roots by conducting a series of microarray experiments. Five durations of salt shock with 500 mM NaCl, namely 2, 5, 10, 24 and 192 hours, were included. A total of 88 unigenes that were recognized to be up- or down-regulated by salt shock and both gene categories in relation to stresses-induced responses and transcription factor activity were over-predominant. The stresses-responsive genes were significantly overrepresented, some of which were regulated in differential manners from their homologues genes in Arabidopsis. Specific transcriptional regulations were employed by C. tagal to cope with salt shock, which could benefit the salt-tolerant lifestyle of this mangrove species and possibly contribute to establishment of adaptation to the saline environments.
2013-12-31 | GSE30909 | GEO
Project description:In this study, we have analyzed the expression profiles of rice genes under control and heat shock conditions using microarray technology to identify the genes differentially expressed. Experiment Overall Design: 14-day-old light-grown rice seedlings grown under controlled conditions and those subjected to heat shock were used for RNA extraction and hybridization on Affymetrix microarrays. Three technical replicates of each sample were used for microarray analysis. For heat shock treatment, the seedlings were kept in a chamber at 42 degree C. The seedlings kept at 28-30 degree C, served as control (Seedling).
2009-01-17 | E-GEOD-14275 | biostudies-arrayexpress
Project description:The WP3 strains was cultured at 20°C and salt shocked with 12% (w/v) NaCl for 90 min. The transcriptional profiles after and before salt shock were compared.
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Project description:The WP3 strains was cultured at 20°C and salt shocked with 12% (w/v) NaCl for 60 min. The transcriptional profiles after and before salt shock were compared.
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Project description:The WP3 strains was cultured at 20°C and salt shocked with 12% (w/v) NaCl for 30 min. The transcriptional profiles after and before salt shock were compared.
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