Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
276
datasets available to search
ShareScore release 0.9.0
Dataset results
276 results for “plant transcriptomes”
Plant regeneration in leaf culture of Centaurium erythraea Rafn. Part 3: de novo transcriptome assembly and validation of housekeeping genes for studies of in vitro morphogenesis
<p>Six centaury transcriptomes (embryogenic calli, globular somatic embryos, cotyledonary somatic embryos, adventitious buds, leaves and roots of <em>in vitro</em> grown plants) were sequenced and <em>de novo</em> assembled using <a href="https://github.com/trinityrnaseq/trinityrnaseq/wiki">Trinity</a> .</p> <p><a href="https://zenodo.org/api/files/a0546879-e382-4cf9-8185-f188d1a0c5f0/CE_Assembly.tar.gz">CE_Assembly.tar.gz</a> - Centaury referent transcriptome comprises of 160.839 Trinity transcripts grouped in 105.726 Trinity genes.</p> <p><a href="https://zenodo.org/api/files/a0546879-e382-4cf9-8185-f188d1a0c5f0/CE_Assembly_fpkm.tar.gz">CE_Assembly_fpkm.tar.gz</a> - fpkm normalized read counts of the assembled transcripts in the six sequenced centaury tissues.</p> <p><a href="https://zenodo.org/api/files/a0546879-e382-4cf9-8185-f188d1a0c5f0/nt.db_CE_assembly.tar.gz">nt.db_CE_assembly.tar.gz</a> - annotation of assembled transcripts by mapping them against NCBI nucleotide (NT) database using BLASTn . The obtained results were filtered with E-value E ≤ 10<sup>-3</sup>.</p> <p><a href="https://zenodo.org/api/files/a0546879-e382-4cf9-8185-f188d1a0c5f0/swissprot.db_CE_assembly.tar.gz">swissprot.db_CE_assembly.tar.gz</a> - annotation of assembled transcripts by mapping them against NCBI nucleotide (<a href="https://zenodo.org/api/files/a0546879-e382-4cf9-8185-f188d1a0c5f0/swissprot.db_CE_assembly.tar.gz">s</a>wissprot) database using BLASTx . The obtained results were filtered with E-value E ≤ 10<sup>-3</sup>.</p> <p><a href="https://zenodo.org/api/files/a0546879-e382-4cf9-8185-f188d1a0c5f0/pfam30.db_CE_assembly.tar.gz">pfam30.db_CE_assembly.tar.gz</a> - annotation of assembled transcripts by mapping them against Pfam30 domain database using hmmer3. The obtained results were filtered with independent E-value E ≤ 10<sup>-3</sup>.</p>
Supplementary tables for publication "A reference-free algorithm discovers regulation in the plant transcriptome"
<p>Supplementary tables for publication "A reference-free algorithm discovers regulation in the plant transcriptome" (doi: https://doi.org/10.1101/2024.05.23.595613)</p> <p>Table A: complete list of significant anchors and associated genes from analysis of sorghum dataset</p> <p>Table B: complete list of significant anchors and associated genes from analysis of maize dataset</p> <p>Table C: complete list of significant anchors and associated genes from analysis of Arabidopsis P/Fe dataset</p> <p>Table D: complete list of significant anchors and associated genes from analysis of Arabidopsis FLOE1 dataset</p> <p>arabidopsis_floe1_ALL_anchors_satc_truncated.txt: data from the Arabidopsis FLOE1 dataset used to generate figures in the paper. Columns are sample ID, anchor, target, and counts of that anchor/target combination in that particular sample. </p> <p>arabidopsis_pfe_ALL_anchors_satc_truncated.txt: data from the Arabidopsis P/Fe dataset used to generate figures in the paper. Columns are sample ID, anchor, target, and counts of that anchor/target combination in that particular sample. </p> <p>maize_pollen_ALL_anchors_satc_truncated.txt: data from the maize dataset used to generate figures in the paper. Columns are sample ID, anchor, target, and counts of that anchor/target combination in that particular sample. </p> <p>sorghum_drought_ALL_anchors_satc_truncated.txt: data from the sorghum dataset used to generate figures in the paper. Columns are sample ID, anchor, target, and counts of that anchor/target combination in that particular sample.</p> <p>cryptic_splicing_anchors.tsv: list of anchors described in Supplementary Information section of the article that are examples of cryptic splicing. Columns are dataset name, gene name/ID, anchor sequence, target 1 sequence, and target 2 sequence. </p>
Comparative transcriptomics of tropical woody plants supports fast and furious strategy along the leaf economics spectrum in lianas
<p>Lianas, climbing woody plants, influence the structure and function of tropical forests. Climbing traits have evolved multiple times, including ancestral groups such as gymnosperms and pteridophytes, but the genetic basis of the liana strategy is largely unknown. Here, we use a comparative transcriptomic approach for 47 tropical plant species, including ten lianas of diverse taxonomic origins, to identify genes that are consistently expressed or downregulated only in lianas. Our comparative analysis of full-length transcripts enabled the identification of a core interactomic network common to lianas. Sets of transcripts identified from our analysis reveal features related to functional traits pertinent to leaf economics spectrum in lianas, including upregulation of genes controlling epidermal cuticular properties, cell wall remodeling, carbon concentrating mechanism, cell cycle progression, DNA repair and a large suit of downregulated transcription factors and enzymes involved in ABA-mediated stress response as well as lignin and suberin synthesis. Altogether, these genes are known to be significant in shaping plant morphologies through responses such as gravitropism, phyllotaxy and shade avoidance.</p>
Comparative transcriptomics of tropical woody plants supports fast and furious strategy along the leaf economics spectrum in lianas
Open the record for dataset details and reuse information.
Data from: One thousand plant transcriptomes and the phylogenomics of green plants
Open the record for dataset details and reuse information.
Full-length transcriptomes of 25 grassland plant species
Open the record for dataset details and reuse information.
Data from: Characterization of rhizome transcriptome and identification of a rhizomatous ER body in the clonal plant Cardamine leucantha
<p>The rhizome is a plant organ that develops from a shoot apical meristem but penetrates into belowground environments. To characterize the gene expression profile of rhizomes, we compared the rhizome transcriptome with those of the leaves, shoots and roots of a rhizomatous Brassicaceae plant, <i>Cardamine leucantha.</i> Overall, rhizome transcriptomes were characterized by the absence of genes that show rhizome-specific expression and expression profiles intermediate between those of shoots and roots. Our results suggest that both endogenous developmental factors and external environmental factors are important for controlling the rhizome transcriptome. Genes that showed relatively high expression in the rhizome compared to shoots and roots included those related to belowground defense, control of reactive oxygen species, and cell elongation under dark conditions. A comparison of transcriptomes further allowed us to identify the presence of an ER body, a defense-related belowground organelle, in epidermal cells of the <i>C. leucantha </i>rhizome, which is the first report of ER bodies in rhizome tissue.</p>
Leaf and shoot apical meristem transcriptomes of quinoa (Chenopodium quinoa Willd.) in response to photoperiod and plant development
<p>Our study focused on identifying key genes regulating flowering time and photoperiod response in quinoa. We examined the timing of photoperiod-induced floral transition and analyzed transcriptomes in photoperiod-sensitive and -insensitive quinoa accessions' leaf and shoot apical meristems. Histological analysis showed that floral transition in quinoa initiates two to three weeks after sowing. We found four groups of differentially expressed genes annotated in the QQ74-V2 reference genome that responded to plant development and floral transition, (i) 222 genes responsive to photoperiod in leaves, (ii) 1,812 genes differentially expressed between accessions under long-day conditions in leaves, (iii) 57 genes responding to developmental changes between weeks under short-day conditions in leaves, and (iv) 911 genes responding to floral transition within the shoot apical meristem. Interestingly, among numerous candidate genes, two<em> </em>putative <em>FT</em> orthologues and others (e.g., <em>SOC1</em>, <em>COL</em>, <em>AP1</em>) have been reported as key regulators of flowering time in other species. Additionally, we used co-expression networks to associate novel transcripts to a putative biological process based on the annotated genes within the same co-expression cluster. The candidate genes in this study would benefit quinoa breeding by identifying and integrating their beneficial haplotypes in crossing programs to develop adapted cultivars to diverse environmental conditions.</p> <p>We examined the timing of photoperiod-induced floral transition and analyzed transcriptomes in photoperiod-sensitive and -insensitive quinoa accessions' leaf and shoot apical meristems. Histological analysis revealed floral transition initiating two to three weeks after sowing. Differentially expressed genes were categorized in the QQ74-V2 reference genome, encompassing 222 genes responsive to photoperiod in leaves, 1,812 genes under long-day conditions, 57 genes during short-day conditions, and 911 genes during floral transition in shoot apical meristems. Notably, among numerous candidates, two putative FT orthologues and others (e.g., SOC1, COL, AP1) implicated in flowering time regulation in various species were identified. Co-expression networks associated novel transcripts with putative biological processes based on annotated genes in the same cluster. The candidate genes identified have potential applications in quinoa breeding, facilitating the incorporation of beneficial haplotypes in crossbreeding programs to develop cultivars adapted to diverse environmental conditions.</p>
Chromosome Numbers and Reproductive Life Cycles in Green Plants: A phylo-transcriptomic perspective
<p>The supplemental dataset for "Chromosome Numbers and Reproductive Life Cycles in Green Plants: A phylo-transcriptomic perspective."</p>
Alternative developmental and transcriptomic responses to host plant water limitation in a butterfly metapopulation
<p>The dataset is from a study examining the effects of host plant water stress on the developmental and transcriptomic responses of its specialist Lepidopteran herbivore. The study combines host plant metabolic profiling with development assays and full-transcriptome sequencing of herbivore larvae. First, we profiled metabolic differences between well-watered and water-limited ribwort plantain (<em>Plantago lanceolata</em>) using proton nuclear magnetic resonance spectroscopy (<sup>1</sup>H-NMR). Second, we tested how performance of developing Glanville fritillary (<em>Melitaea cinxia</em>) larvae was affected by host plant water limitation experienced at different larval developmental stages. Third, we examined larval gene regulatory responses to water limited host plants by sequencing full transcriptomes of 77 female larvae (RNA seq). Finally, to examine intrapopulation variation in the responses of the larvae, we compared the phenotypic and transcriptomic responses across full-sib families originating from different parts of the metapopulation. In this dataset, we provide data for the <em>P. lanceolata</em> metabolite responses to water limitation and developmental responses of the <em>M. cinxia</em> larvae to feeding on water limited <em>P. lanceolata</em>. The transcriptomic data are available from NCBI's Gene Expression Omnibus, with the accession number GSE159376.</p>
Data for: The relative impact of parental and current environment on plant transcriptomes depends on type of stress and genotype
<p>Through developmental plasticity, an individual organism integrates influences from its immediate environment with those due to the environment of its parents. While both effects on phenotypes are well documented, their relative impact has been little studied in natural systems, especially at the level of gene expression. We examined this issue in four genotypes of the annual plant <em>Persicaria maculosa</em> by varying two key resources light and soil moisture in both generations. Transcriptomic analyses showed that the relative effects of parent and offspring environment on gene expression (i.e., the number of differentially expressed transcripts, DETs) varied both for the two types of resource stress and among genotypes. For light, immediate environment induced more DETs than parental environment for all genotypes (although the precise proportion of parental versus immediate DETs varied among genotypes). By contrast, the relative effect of soil moisture varied dramatically among genotypes, from 8-fold more DETs due to parental than immediate conditions to 10-fold fewer. These findings provide evidence at the transcriptome level that the relative impacts of parental and immediate environment on the developing organism may depend on the environmental factor and vary strongly among genotypes, providing potential for the interplay of these developmental influences to evolve.</p>
Leaf and shoot apical meristem transcriptomes of quinoa (Chenopodium quinoa Willd.) in response to photoperiod and plant development
Open the record for dataset details and reuse information.
Data for: The relative impact of parental and current environment on plant transcriptomes depends on type of stress and genotype
Open the record for dataset details and reuse information.
Data from: Transcriptome response of the foundation plant Spartina alterniflora to the Deepwater Horizon oil spill
Open the record for dataset details and reuse information.
Data from: Enhanced competitive advantage of invasive plants by growth-defense trade-off: Evidence from phytohormone metabolism and transcriptomic analysis
Open the record for dataset details and reuse information.
Alternative developmental and transcriptomic responses to host plant water limitation in a butterfly metapopulation
Open the record for dataset details and reuse information.
Data from: Characterization of rhizome transcriptome and identification of a rhizomatous ER body in the clonal plant Cardamine leucantha
Open the record for dataset details and reuse information.
Transcriptomic findings light on mechanisms of marine and terrestrial evolutionary adaptation of Rhizophoraceae plants
Open the record for dataset details and reuse information.
Data from: Dissecting molecular evolution in the highly diverse plant clade Caryophyllales using transcriptome sequencing
Many phylogenomic studies based on transcriptomes have been limited to "single-copy" genes due to methodological challenges in homology and orthology inferences. Only a relatively small number of studies have explored analyses beyond reconstructing species relationships. We sampled 69 transcriptomes in the hyperdiverse plant clade Caryophyllales and 27 outgroups from annotated genomes across eudicots. Using a combined similarity- and phylogenetic tree-based approach, we recovered 10,960 homolog groups, where each was represented by at least eight ingroup taxa. By decomposing these homolog trees, and taking gene duplications into account, we obtained 17,273 ortholog groups, where each was represented by at least ten ingroup taxa. We reconstructed the species phylogeny using a 1,122-gene data set with a gene occupancy of 92.1%. From the homolog trees, we found that both synonymous and nonsynonymous substitution rates in herbaceous lineages are up to three times as fast as in their woody relatives. This is the first time such a pattern has been shown across thousands of nuclear genes with dense taxon sampling. We also pinpointed regions of the Caryophyllales tree that were characterized by relatively high frequencies of gene duplication, including three previously unrecognized whole-genome duplications. By further combining information from homolog tree topology and synonymous distance between paralog pairs, phylogenetic locations for 13 putative genome duplication events were identified. Genes that experienced the greatest gene family expansion were concentrated among those involved in signal transduction and oxidoreduction, including a cytochrome P450 gene that encodes a key enzyme in the betalain synthesis pathway. Our approach demonstrates a new approach for functional phylogenomic analysis in nonmodel species that is based on homolog groups in addition to inferred ortholog groups.
Data from: Transcriptomics of host-specific interactions in natural populations of the parasitic plant purple witchweed (Striga hermonthica)
Host-specific interactions can maintain genetic and phenotypic diversity in parasites that attack multiple host species. Host diversity, in turn, may promote parasite diversity by selection for genetic divergence or plastic responses to host type. The parasitic weed purple witchweed [Striga hermonthica (Delile) Benth.] causes devastating crop losses in sub-Saharan Africa and is capable of infesting a wide range of grass hosts. Despite some evidence for host adaptation and host-by-Striga genotype interactions, little is known about intraspecific Striga genomic diversity. Here we present a study of transcriptomic diversity in populations of S. hermonthica growing on different hosts (maize [Zea mays L.] vs. grain sorghum [Sorghum bicolor (L.) Moench]). We examined gene expression variation and differences in allelic frequency in expressed genes of aboveground tissues from populations in western Nigeria parasitizing each host. Despite low levels of host-based genome-wide differentiation, we identified a set of parasite transcripts specifically associated with each host. Parasite genes in several different functional categories implicated as important in host–parasite interactions differed in expression level and allele on different hosts, including genes involved in nutrient transport, defense and pathogenesis, and plant hormone response. Overall, we provide a set of candidate transcripts that demonstrate host-specific interactions in vegetative tissues of the emerged parasite S. hermonthica. Our study shows how signals of host-specific processes can be detected aboveground, expanding the focus of host–parasite interactions beyond the haustorial connection.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.