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Differential Gene Expression Datasets for "Identification of candidate repurposable drugs to combat COVID‑19 using a signature‑based approach"
<p>This dataset has the unfiltered transcriptome differential expression results used in the paper "Identification of candidate repurposable drugs to combat COVID‑19 using a signature‑based approach". </p>
Figure 7 in Identification of candidate genes involved with dicamba resistance in waterhemp (Amoronthus tuberculotus) via transcriptomics analyses
Figure 7. Temporal quantitative PCR results for (A) GST-nt, (B) ABC10, (C) PEROX12, and (D) GST-ct before and at multiple time points after dicamba treatment. Asterisks (*) indicate comparisons that were significant (t-test P-value <0.05), with error bars indicating variability across replicates.
Figure 4 in Identification of candidate genes involved with dicamba resistance in waterhemp (Amoronthus tuberculotus) via transcriptomics analyses
Figure 4. Genomic distribution in sliding 50-kb window plots of differentially expressed genes (DEs). The y-axis units refer to windows in mega base pairs (Mbp) Each plot represents one of the 16 pseudo-chromosomes of Amoronthus tuberculotus. Peaks represent clusters of DEs. Blue dashed lines represent previously identified hot-spot locations for 2,4-D resistance (Giacomini et al. 2020).
Figure 3 in Identification of candidate genes involved with dicamba resistance in waterhemp (Amoronthus tuberculotus) via transcriptomics analyses
Figure 3. Biological process GO-term enrichment analysis. Circle size represents the significance of overrepresented enrichment, and color gradient represents the significance of conditional enrichment. The x axis represents the number of genes annotated with each GO-term in the y axis.
Figure 2 in Identification of candidate genes involved with dicamba resistance in waterhemp (Amoronthus tuberculotus) via transcriptomics analyses
Figure 2. Volcano plot of all genes with key differentially expressed genes highlighted. Major genes with potential involvement in dicamba resistance are labeled according to their homologous UniprotKB ID. Genes in red and blue were significantly up- and downregulated, respectively, in dicamba-resistant relative to sensitive plants. The y axis refers to −log10 false discovery rate (FDR), and the x axis refers to the log2 expression fold change (FC).
Figure 8 in Identification of candidate genes involved with dicamba resistance in waterhemp (Amoronthus tuberculotus) via transcriptomics analyses
Figure 8. Proposed dicamba resistance mechanisms in the CHR population. Currently, knowledge about the synthetic auxin effect on plants indicates an overproduction of abscisic acid (ABA), leading to a large production of reactive oxygen species (ROS) and plant death (Christoffoleti et al. 2015; Gaines 2020). The proposed resistance mechanism is that enhanced response to oxidative stress via peroxidases and glutathione S-transferases alleviates dicamba toxicity. Other putative resistance mechanisms, such as glycosylation of dicamba and ABA, are also proposed with transport via ATP-binding cassette (ABC) transporters for further degradation. Overproduction of salicylic acid is also proposed as a potential tool for alleviating oxidative stress. Created with BioRender.com.
Figure 5 in Identification of candidate genes involved with dicamba resistance in waterhemp (Amoronthus tuberculotus) via transcriptomics analyses
Figure 5. Weighted co-expression network analysis results. (A) Gene expression dendrogram for module assignment where a total of 33 modules were identified. (B) Traitmodule correlation plot with values outside parentheses representing Pearson correlation and values inside parentheses representing the significance correlation P-values. Correlation values range from −1 to 1, with red values indicating a positive association and blue values indicating a negative association with dicamba resistance. ME refers to modules followed by their color code.
Figure 1 in Identification of candidate genes involved with dicamba resistance in waterhemp (Amoronthus tuberculotus) via transcriptomics analyses
Figure 1. Plant selection and phenotype classification for RNA-seq. Photos show the differences in phenotypes of some of the individuals selected for sequencing: (A) resistant plants and (B) sensitive plants. Selection was done based on visual damage estimation, biomass, and plant area measured via image analysis (Bobadilla et al. 2022). Photos were taken 14 d after treatment with dicamba at 560 g ai ha−1. The graph shows the relationship between biomass and plant area across resistant and sensitive individuals.
Selective sweeps identification in distinct groups of cultivated rye (Secale cereale L.) germplasm provides potential candidate genes for crop improvement
<p><strong>Background</strong></p> <p>During domestication and subsequent improvement, plants were subjected to intensive positive selection for desirable traits. Identification of selection targets is important with respect to the future targeted broadening of diversity in breeding programmes. Rye (<em>Secale</em> <em>cereale</em> L.) is a cereal that is closely related to wheat, and it is an important crop in Central, Eastern and Northern Europe. The aim of the study was (i) to identify diverse groups of rye accessions based on high-density, genome-wide analysis of genetic diversity within a set of 478 rye accessions, covering a full spectrum of diversity within the genus, from wild accessions to inbred lines used in hybrid breeding, and (ii) to identify selective sweeps in the established groups of cultivated rye germplasm and putative candidate genes targeted by selection. <strong> </strong></p> <p><strong>Results</strong></p> <p>Population structure and genetic diversity analyses based on high-quality SNP (DArTseq) markers revealed the presence of three complexes in the <em>Secale</em> genus: <em>S. sylvestre, S. strictum </em>and<em> S. cereale/vavilovii</em>, a relatively narrow diversity of <em>S. sylvestre</em>, very high diversity of <em>S. strictum</em>, and signatures of strong positive selection in <em>S. vavilovii</em>. Within cultivated ryes, we detected the presence of genetic clusters and the influence of improvement status on the clustering. Rye landraces represent a reservoir of variation for breeding, and especially a distinct group of landraces from Turkey should be of special interest as a source of untapped variation. Selective sweep detection in cultivated accessions identified 133 outlier positions within 13 sweep regions and 170 putative candidate genes related, among others, to response to various environmental stimuli (such as pathogens, drought, cold), plant fertility and reproduction (pollen sperm cell differentiation, pollen maturation, pollen tube growth), and plant growth and biomass production.</p> <p><strong>Conclusions</strong></p> <p>Our study provides valuable information for efficient management of rye germplasm collections, which can help to ensure proper safeguarding of their genetic potential and provides numerous novel candidate genes targeted by selection in cultivated rye for further functional characterisation and allelic diversity studies.</p>
Selective sweeps identification in distinct groups of cultivated rye (Secale cereale L.) germplasm provides potential candidate genes for crop improvement
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Identification of quantitative trait loci and associated candidate genes for pregnancy success in Angus – Brahman crossbred heifers
<p>Development of genomic tools to identify females with high genetic merit for reproductive function could increase the profitability and sustainability of beef production. Here, genome-wide association studies (GWAS) were performed on pregnancy outcome traits from a population of Angus – Brahman crossbred heifers. Furthermore, a validation GWAS was performed using data from another location. Heifers were genotyped with the Bovine GGP F250 array that contains ~250,000 SNPs. In the discovery population, heifers were bred in winter breeding seasons involving a single round of timed artificial insemination (AI) followed by natural mating for three months. Three phenotypes were analyzed: pregnancy outcome to first-service AI (PAI; n = 1481), pregnancy status at the end of the breeding season (PEBS; n = 1725), and pregnancy score (Pregscore where 1 = pregnant to first-service AI, 2 = pregnant to bull, 3 = not pregnant; n =1481). The heritability for PAI was estimated as 0.149. One large quantitative trait locus (QTL) that explained ~3% of the genetic variation for PAI was found on BTA7, in a region containing a cluster of γ-protocadherin genes and SLC25A2. Other QTLs explaining between 0.5-1% of the genetic variation were found on BTA12 and 25. The heritability of PEBS was estimated at 0.122. A large QTL on BTA7 was synonymous with the QTL for PAI, with minor QTL located on BTA5, 9, 10, 11, 19, and 20. Estimated heritability for Pregscore was 0.189. There was a large QTL on BTA7 synonymous with the other two traits as well as smaller QTLs on BTA1, 10, 15, 18, 19, and 20. The validation population for pregnancy status at the end of the breeding season were Angus-Brahman crossbred heifers bred by natural mating. In concordance with the discovery population, the large QTL on BTA7 and QTL on BTA10, 12 and 18 were identified. In summary, QTL and candidate SNPs associated with pregnancy outcomes in beef heifers were identified, including a large QTL associated with a group of protocadherin genes. Confirmation of these associations with larger populations could lead to the development of genomic estimates of reproductive function in beef cattle.</p>
Identification of quantitative trait loci and associated candidate genes for pregnancy success in Angus – Brahman crossbred heifers
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Data from: Identification and analysis of novel salt responsive candidate gene based SSRs (cgSSRs) from rice (Oryza sativa L.)
Background: Majority of the Asian people depend on rice for nutritional energy. Rice cultivation and yield are severely affected by soil salinity stress worldwide. Marker assisted breeding is a rapid and efficient way to develop improved variety for salinity stress tolerance. Genomic microsatellite markers are an elite group of markers, but there is possible uncertainty of linkage with the important genes. In contrast, there are better possibilities of linkage detection with important genes if SSRs are developed from candidate genes. To the best of our knowledge, there is no such report on SSR markers development from candidate gene sequences in rice. So the present study was aimed to identify and analyse SSRs from salt responsive candidate genes of rice. Results: In the present study, based on the comprehensive literature survey, we selected 220 different salt responsive genes of rice. Out of them, 106 genes were found to contain 180 microsatellite loci with, tri-nucleotide motifs (56%) being most abundant, followed by di-(41%) and tetra nucleotide (2.8%) motifs. Maximum loci were found in the coding sequences (37.2%), followed by in 5′UTR (26%), intron (21.6%) and 3′UTR (15%). For validation, 19 primer sets were evaluated to detect polymorphism in diversity analysis among the two panels consisting of 17 salt tolerant and 17 susceptible rice genotypes. Except one, all primer sets exhibited polymorphic nature with an average of 21.8 alleles/primer and with a mean PIC value of 0.28. Calculated genetic similarity among genotypes was ranged from 19%-89%. The generated dendrogram showed 3 clusters of which one contained entire 17 susceptible genotypes and another two clusters contained all tolerant genotypes. Conclusion: The present study represents the potential of salt responsive candidate gene based SSR (cgSSR) markers to be utilized as novel and remarkable candidate for diversity analysis among rice genotypes differing in salinity response.
Identification of genetic loci and functional analysis of candidate gene, OsCycB1;5 associated with seed callus induction in rice (Oryza sativa L.)
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Identification of New Candidate Genes for Hereditary Predisposition to Uveal Melanoma
ClinicalTrials.gov study NCT06550674. IPD Sharing: NO. Countries: 1. Publications: 1.
Data from: Identification and analysis of novel salt responsive candidate gene based SSRs (cgSSRs) from rice (Oryza sativa L.)
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Data from: Identification of candidate risk factor genes for human idelalisib toxicity using a collaborative cross approach
Idelalisib is a phosphatidylinositol 3-kinase inhibitor highly selective for the delta isoform that has shown good efficacy in treating chronic lymphocytic leukemia and follicular lymphoma. In clinical trials, however, idelalisib was associated with rare, but potentially serious liver and lung toxicities. In this study, we used the Collaborative Cross (CC) mouse population to identify genetic factors associated with the drug response that may inform risk management strategies for idelalisib in humans. Eight (8) male mice (4 matched pairs) from 50 CC lines were treated once daily for 14 days by oral gavage with either vehicle or idelalisib at a dose selected to achieve clinically-relevant peak plasma concentrations (150 mg/kg/day). The drug was well tolerated across all CC lines, and there were no observations of overt liver injury. Differences across CC lines were seen in drug concentration in plasma samples collected at the approximate Tmax on study Days 1, 7, and 14. There were also small but statistically significant treatment-induced alterations in plasma total bile acids and microRNA-122, and these may indicate early hepatocellular stress required for immune-mediated hepatotoxicity in humans. Idelalisib treatment further induced significant elevations in the total cell count of terminal bronchoalveolar lavage fluid, which may be analogous to pneumonitis observed in the clinic. Genetic mapping identified loci associated with interim plasma idelalisib concentration and the other three treatment-related endpoints. Thirteen (13) priority candidate quantitative trait genes identified in CC mice may now guide interrogation of risk factors for adverse drug responses associated with idelalisib in humans.
Data from: Identification of candidate effector genes of Pratylenchus penetrans
Pratylenchus penetrans is one of the most important species among root lesion nematodes (RLNs) due to the detrimental and economic impact that it causes in a wide range of crops. Similar to other plant-parasitic nematodes (PPNs), P. penetrans harbors a significant number of secreted proteins that play key roles during parasitism. Here we combined spatially and temporally resolved next generation sequencing datasets of P. penetrans to select a list of candidate genes aimed at the identification of a panel of effector genes for this species. We determined the spatial expression of transcripts of 22 candidate effectors within the esophageal glands of P. penetrans by in situ hybridization. These comprised homologues of known effectors of other PPNs with diverse putative functions, as well as novel pioneer effectors specific to RLNs. It is noteworthy that five of the pioneer effectors encode extremely proline-rich proteins. We then combined in situ localization of effectors with available genomic data to identify a non-coding motif enriched in promoter regions of a subset of P. penetrans effectors, and thus a putative hallmark of spatial expression. Expression profiling analyses of a subset of candidate effectors confirmed their expression during plant infection. Our current results provide the most comprehensive panel of effectors found for RLNs. Considering the damage caused by P. penetrans, this information provides valuable data to elucidate the mode of parasitism of this nematode and offers useful suggestions regarding the potential use of P. penetrans-specific target effector genes to control this important pathogen. This article is protected by copyright. All rights reserved.
Figure 6 in Identification of candidate genes involved with dicamba resistance in waterhemp (Amoronthus tuberculotus) via transcriptomics analyses
Figure 6. Differentially expressed (DE) genes' regulatory prediction analysis results: (A) total number of transcription factors (TFs) enriched per family; (B) number of DE genes with motifs specific for each enriched TF family. TF family names in the x axis are according to the nomenclature in the Plant Transcription Factor Database (PlantTFDB).
Data from: Identification of candidate effector genes of Pratylenchus penetrans
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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.