Transcriptomes of Wild Type tomato and slszp1 under +Al treatment
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ABSTRACT:
PROVIDER: PRJNA828447 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18831527_1.fastq.gz | Fastqsanger.gz | |||
| SRR18831527_2.fastq.gz | Fastqsanger.gz | |||
| SRR18831528_1.fastq.gz | Fastqsanger.gz | |||
| SRR18831528_2.fastq.gz | Fastqsanger.gz | |||
| SRR18831529_1.fastq.gz | Fastqsanger.gz |
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Project description:Transcriptomes of Wild Type tomato and slstop1 under -Al/+Al treatment
| PRJNA707414 | ENA
Project description:Purpose: Find SlSTOP1 regulated genes Methods: Total RNA was extracted from 20 days old wild-type tomato and slstop1 mutant plants treated with 0 and 60 μM Al solutions (pH 4.7). Three biological replicated samples were collected form each treatment and sequenced. Results:A total of 83.7 GB clean data was obtained by transcriptome sequencing. The clean data of each sample was more than 6.30 GB, and the percentage of q30 base was more than 93.82%. Conclusions: By RNA-seq analysis, we find potential SlSTOP1-regulated genes
2023-08-07 | GSE168433 | GEO
Project description:Purpose: Find SlSZP1 regulated genes Methods: Total RNA was extracted from 20 days old wild-type tomato and slszp1 mutant plants treated with 60 μM Al solutions (pH 4.7). Three biological replicated samples were collected form each treatment and sequenced. Results:A total of 40 GB clean data was obtained by transcriptome sequencing. The clean data of each sample was more than 6.11 GB, and the percentage of q30 base was more than 90.98%. Conclusions: By RNA-seq analysis, we find potential SlSZP1-regulated genes
2025-04-20 | GSE201111 | GEO
Project description:cDNA microarrays (Tom 1) were used to analyze changes in transcript accumulation in tomato (Solanum lycopersicum cv Money Maker) root cultures under Al-stress (20uM AlK(SO4)2). Out of the 1,362 genes that had significant changes in transcript accumulation (FDR<0.05), 569 were reduced and 793 were induced. The down-regulated genes included those found in the cell cycle (p34cdc2 protein kinase, cyclin, histone), putriscine synthesis, ABC transporter, germin-like protein. Al-induced genes included glutamate synthase, pectin modification, histidine synthesis, proline synthesis, metallothionein-like protein, multidrug efflux proteins (MATE), ethylene biosynthesis and detoxification proteins. Different isoforms in the multiple gene families of V-ATPase, glutathione transferases and others were either induced or repressed. A wide array of genes for regulating transcription and translation activities, and signal transduction were also affected.
2009-06-16 | GSE11816 | GEO
Project description:In order to find the gene which were regulated by SlLBD40, the fruits of WT and SlLBD40-KO-5 line were collected at 25 DDA to do the RNA-Seq. Total RNA was extracted from above tomato fruits by TRIzol reagent and three biological replicates were taken. The clean data were aligned to the tomato reference genome release SL2.50. According to the RNA-Seq data, many development-related genes were down-regulated in SlLBD40-KO-5 fruit. We find the potential SlLBD40-regulated genes.
2024-12-01 | GSE190128 | GEO
Project description:A self-designed Trichoderma high density oligonuclotide (HDO) microarray (Roche-NimbleGen, Inc., Madison, WI, USA) was constructed in a similar way than a previous Trichoderma HDO microarray (Samolski et al., 2009). The microarray was composed of 392,779 60-mer probes designed against 14,081 EST-derived transcripts (Trichochip-1) and the genomes of T. reesei (9,129 genes) and T. virens (11,643 genes). The Trichochip-1 ESTs were obtained from 28 cDNA libraries from eight different species (representing the biodiversity of this genus: T. harzianum, T. atroviride, T. asperellum, T. viride, T. longibrachiatum, T. virens, T. stromaticum and T. aggresivum), under a wide range of growth conditions, including biocontrol-related conditions and different nutritional situations (VizcaM-CM--no et al., 2006). This HDO microarray was used to analyze Trichoderma spp. transcriptomes after 20 h incubation in the presence of tomato plants. The Trichochip1 EST database was generated in the TrichoEST project funded by the EU (QLK3-CT-2002-02032). Eight samples were analyzed as follows: Strain T. reesei T6 grown in the presence or not of tomato plants, strain T. hamatum T7 grown in the presence or not of tomato plants, strain T. harzianum T34 grown in the presence or not of tomato plants and strain T. virens T87 grown in the presence or not of tomato plants. Three replicates for each samples were performed.
2012-02-27 | E-GEOD-29171 | biostudies-arrayexpress
Project description:Excess levels of Al3+ become highly harmful to plant roots as the toxic ions bind to the surface of root-tips. Plants can acquire tolerance to stress after multiple generations of exposure to stress conditions. After four consecutive generations of Al treatments (G4Al+ seeds), tomato plants appeared more tolerant to the stress condition. This project used laser capture microdissection (LCM) technology to isolate the Al-sensitive epidermal and outer cortical cells of root-tips. Tandem mass tag (TMT) proteomics analysis was conducted to identify proteomics changes related to the physiological properties in root growth under Al treated conditions.
2022-02-14 | PXD018234 | Pride
Project description:Transcriptomes of Wild Type tomato and sllbd40 fruit on different fruit stages
| PRJNA785967 | ENA
Project description:Purpose: Understanding the mechanism of malate accumulation in plants is beneficial for both plant nutrient and human health. However, little is known regarding regulation of malate accumulation in horticulture plants such as tomato. The goals of this study are to investigate potential regulation network of Al-Activated Malate Transporter 9 (ALMT9) which is the major locus responsible for the variation in fruit malate concentration observed in cultivared tomato. Methods: The transcriptomes of fruit at ripening stage from CK and SlALMT9 overexpressing line1 were evaluated using single-ended sequencing of Illumina HiSeq 2500. Raw sequences were filtered and the resulting sets of clean reads were used for the following analysis by tophat and edgeR software. Results: Among 1,887 differentially expressed genes, some structural genes involved in sugar and organic acid metabolism were differently expressed in SlALMT9 overexpressing line, which partially coincide with changes of sugar and organic acid concentration. PR genes was also altered in the OX lines, in agreement with previous study that tomato fruit malate is involved in pathogen infection. Three members of malate transporters, MATE (multidrug and toxin efflux), were up-regulated (SlMATE5 and 6) or down-regulated (SlMATE9) . Besides, three sugar transport proteins and four vacuole membrane or plasma membrane proteins were up-regulated in OX line Conclusions: Using RNA-seq analysis, 1,887 differentially expressed genes was revealed. Among them, several genes related to sugar and organic acid metabolism and transport, pathogen resistances were identified. This transcriptome study provides insight into the regulatory mechanism of fruit malate accumulation and the effect of the SlALMT9 to primary metabolism.
2018-02-16 | GSE89772 | GEO
Project description:Background: Fruit color is an important quality trait for nutrition value in tomato (Solanum lycopersicum) and has attracted huge attention for a long time. In order to dissect the yellow-fruit color of a novel tomato mutant n3122, we compared the dynamic transcriptome of the fruit pericarps from the mutant n3122 and its wild type red-fruited tomato cultivar M82. Results: The transcriptomes of fruits from M82 35 DPA (Days Post Anthesis), M82 47 DPA, M82 54 DPA, n3122 35 DPA, n3122 47 DPA, n3122 54 DPA and n3122 60 DPA were sequenced using an Illumina Hiseq 2000 sequencing platform. A total of 5568 differentially expressed genes (DEGs) were commonly identified in the four pairwise comparisons of M82_35 DPA vs n3122_35 DPA, M82_47 DPA vs n3122_47 DPA, M82_54 DPA vs n3122_54 DPA and M82_47 DPA vs n3122_60 DPA. Further Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed that carotenoids biosynthesis, ethylene biosynthesis and signaling transduction, and transcription factors associated fruit ripening were different between M82 and n3122 which might be the underlying mechanisms for the yellow-fruit color of tomato. Conclusions: This research provided a global data set of dynamic transcriptomic changes during fruit development and ripening for the wild type red-fruited tomato cultivar M82 and its yellow-fruited mutant n3122, and offered a base for elucidating the molecular mechanisms underlying tomato red/yellow fruit color mutation.
2017-04-10 | GSE73908 | GEO