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22 results for “expressed sequence tag”
Fig. 4 in Expressed sequence tags in venomous tissue of Scorpaena plumieri (Scorpaeniformes: Scorpaenidae)
Fig. 4. Sequence alignment of putative lectin from Scorpaena plumieri. Alignment of a lectin-like EST in silico translated sequence from S. plumieri (ClustalW2 EBI) with fish-egg lectin from Oplegnathus fasciatus (BAL618145), Dicentrarchus labrax (CBK52298), Maylandia zebra (XP_004574029), and Oreochromis niloticus (XP003443389). The recombinant clone was isolated with antibody fraction derived from S. plumieri venom. * identifies and identical residue;: identifies a conserved residue. Underlined residues represent invariable sites, underlined IRLS = N-acetylation site.
Fig. 3 in Expressed sequence tags in venomous tissue of Scorpaena plumieri (Scorpaeniformes: Scorpaenidae)
Fig. 3. The classification of EST from Scorpaena plumieri based on their putative fractions. Three-hundred fifty-six EST edited sequences were initially analyzed with Blast and Swiss protein databanks. The consensus sequence was attributed a function based on the strongest match.
Fig. 2 in Expressed sequence tags in venomous tissue of Scorpaena plumieri (Scorpaeniformes: Scorpaenidae)
Fig. 2. Agarose gel electrophoresis of DNA isolated from clones. White colonies containing insert were grown and the plasmidial DNA isolated and digested with EcoRI enzyme. An aliquot from each clone (1-27) was electrophoresed on 1% Agarose gel and stained with ethidium bromide.
Fig. 1 in Expressed sequence tags in venomous tissue of Scorpaena plumieri (Scorpaeniformes: Scorpaenidae)
Fig. 1. Agarose- formaldehyde electrophoresis of RNA from Scorpaena plumieri. A) 1) 2 µg of E. coli tRNA; 2) 2 µg de rRNA de Rattus norvegicus; 3) and 4) 2 µg total RNA from S. plumieri spine gland. B) 1) 2 µg de total RNA from S. plumieri; 2) the same sample incubated 2 h a 37ºC before electrophoresis.
Data from: Exploitation of a turbot (Scophthalmus maximus L.) immune-related expressed sequence tag (EST) database for microsatellite screening and validation
In this study, we identified and characterized 160 microsatellite loci from an expressed sequence tag (EST) database generated from immune-related organs of turbot (Scophthalmus maximus). A final set of 83 new polymorphic microsatellites were validated after the analysis of 40 individuals from Atlantic origin including both wild and farmed individuals. The allele number and the expected heterozygosity ranged from 2 to 18 and from 0.021 to 0.951, respectively. Evidences of null alleles at moderate-high frequencies were detected at six loci using population data. None of the analyzed loci showed deviations from Mendelian segregation after analysis of five full-sib families including ~92 individuals/family. The markers are used to consolidate the turbot genetic map and, since they are mostly EST-derived, they will be very useful for comparative genomic studies within flatfishes and with model fish species. Using an in silico approach, we detected significant homologies of microsatellite sequences with the EST databases of the flatfish species with highest genomic resources (Senegalese sole, Atlantic halibut, bastard halibut) at 31% of these turbot markers. The conservation of these microsatellites within Pleuronectiformes will pave the way for anchoring genetic maps of different species and identifying genomic regions related to productive traits.
Data from: Exploitation of a turbot (Scophthalmus maximus L.) immune-related expressed sequence tag (EST) database for microsatellite screening and validation
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Data from: Mining microsatellite markers from public expressed sequence tags databases for the study of threatened plants
Background: Simple Sequence Repeats (SSRs) are widely used in population genetic studies but their classical development is costly and time-consuming. The ever-increasing available DNA datasets generated by high-throughput techniques offer an inexpensive alternative for SSRs discovery. Expressed Sequence Tags (ESTs) have been widely used as SSR source for plants of economic relevance but their application to non-model species is still modest. Methods: Here, we explored the use of publicly available ESTs (GenBank at the National Center for Biotechnology Information-NCBI) for SSRs development in non-model plants, focusing on genera listed by the International Union for the Conservation of Nature (IUCN). We also search two model genera with fully annotated genomes for EST-SSRs, Arabidopsis and Oryza, and used them as controls for genome distribution analyses. Overall, we downloaded 16 031 555 sequences for 258 plant genera which were mined for SSRsand their primers with the help of QDD1. Genome distribution analyses in Oryza and Arabidopsis were done by blasting the sequences with SSR against the Oryza sativa and Arabidopsis thaliana reference genomes implemented in the Basal Local Alignment Tool (BLAST) of the NCBI website. Finally, we performed an empirical test to determine the performance of our EST-SSRs in a few individuals from four species of two eudicot genera, Trifolium and Centaurea. Results: We explored a total of 14 498 726 EST sequences from the dbEST database (NCBI) in 257 plant genera from the IUCN Red List. We identify a very large number (17 102) of ready-to-test EST-SSRs in most plant genera (193) at no cost. Overall, dinucleotide and trinucleotide repeats were the prevalent types but the abundance of the various types of repeat differed between taxonomic groups. Control genomes revealed that trinucleotide repeats were mostly located in coding regions while dinucleotide repeats were largely associated with untranslated regions. Our results from the empirical test revealed considerable amplification success and transferability between congenerics. Conclusions: The present work represents the first large-scale study developing SSRs by utilizing publicly accessible EST databases in threatened plants. Here we provide a very large number of ready-to-test EST-SSR (17 102) for 193 genera. The cross-species transferability suggests that the number of possible target species would be large. Since trinucleotide repeats are abundant and mainly linked to exons they might be useful in evolutionary and conservation studies. Altogether, our study highly supports the use of EST databases as an extremely affordable and fast alternative for SSR developing in threatened plants.
Data from: Mining for single nucleotide polymorphisms and insertions / deletions in expressed sequence tag libraries of oil palm
The oil palm is a tropical oil bearing tree. Recently EST-derived SNPs and SSRs are a free by-product of the currently expanding EST (Expressed Sequence Tag) data bases. The development of high-throughput methods for the detection of SNPs (Single Nucleotide Polymorphism) and small indels (insertion / deletion) has led to a revolution in their use as molecular markers. Available (5452) Oil palm EST sequences were mined from dbEST of NCBI. CAP3 program was used to assemble EST sequences into contigs. Candidate SNPs and Indel polymorphisms were detected using the perl script auto_snip version 1.0 which has used 576 ESTs for detecting SNPs and Indel sites. We found 1180 SNP sites and 137 indel polymorphisms with frequency 1.36 SNPs / 100 bp. Among the six tissues from which the EST libraries had been generated, mesocarp had high frequency of 2.91 SNPs and indels per 100 bp whereas the zygotic embryos had lowest frequency of 0.15 per 100 bp. We also used the Shannon index to analyze the proportion of ten possible types of SNP/indels. ESTs from tissues of normal apex showed highest values of Shannon index (0.60) whereas abnormal apex had least value (0.02). The present report deals the use of Shannon index for comparing SNP/ indel frequencies mined from ESTlibraries and also confirm that the frequency of SNP occurrence in oil palm to use them as markers for genetic studies.
Data from: Mining of expressed sequence tag libraries of cacao for microsatellite markes using five computational tools
Expressed Sequence Tags (ESTs) provide researchers with a quick and inexpensive route for discovering new genes, and data on gene expression and regulation and provide genic markers that help in constructing genome maps. Cacao is an important perennial crop of humid tropics. Cacao EST sequences as available in public domain were downloaded and made into contigs. A total of 769 contigs were made using contigs assembly program pharp. Puative information of contigs were identified using NCBI and ExPASy tools such as BlastX, tblastn.
Data from: Analysis of expressed sequence tags from the placenta of the live-bearing fish Poeciliopsis (Poeciliidae)
Matrotrophic fish in the genus Poeciliopsis (Poeciliidae) have a placenta-like structure used in post-fertilization maternal provisioning of the developing embryo. To understand better the structure and function of the Poeciliopsis placenta we derived cDNA libraries from the maternal follicular placenta of two matrotrophic Poeciliopsis sister species, P. turneri and P. presidionis. These species inherited their placenta from a common ancestor and represent one of three independent origins of placentas in Poeciliopsis. Expressed sequence tags were generated and putative function was determined using BLASTX homology searches and Gene Ontology annotation. Reverse transcriptase-PCR was used to verify placenta tissue expression of a putative candidate gene, alpha-2 macroglobulin. 1956 (71.5% of the total submitted ESTs) and 924 (71.0% of the total submitted ESTs) unique transcripts were identified for the P. turneri and P. presidionis placenta, respectively. Homology search and Gene Ontology annotation revealed putative genes whose products may be involved in specific transport functions of the maternal follicle. These putative genes are excellent candidates for future research on the evolution of the placenta. We discuss our results in light of the parent-offspring conflict theory of placental evolution and in terms of the Poeciliid placenta structure and function.
Data from: "NGS based generation of expressed sequence tags for Lymantria dispar and Lymantria monacha, two closely related lepidopteran species with different responses to parasitism by Glyptapanteles liparidis" in Genomic Resources Notes accepted 1 December 2013 to 31 January 2014
Introduction: The gypsy moth, Lymantria dispar, and the nun moth, Lymantria monacha, are closely related species (Lepidoptera, Lymantriidae), co-seasonal and economically important forest pests on broadleaf and coniferous trees. In Central Europe, gypsy moth larvae are frequently parasitized by the gregarious, endoparasitic wasp Glyptapanteles liparidis (Hymenoptera, Braconidae). At oviposition, the female wasp injects between 10 and up to 100 eggs into the hemocoel of a single host larva, together with venom and calyx fluid containing polydnavirus (PDV) particles that subsequently play a critical role in suppressing the host immune response so that successful development of the parasitoid can proceed (Schopf 2007). These viruses, which are integrated in the genomic DNA of the wasp and undergo replication only in the female's ovary, rapidly enter host hemocytes, fat body, and nervous system following parasitization, and viral genes are expressed. In L. dispar larvae parasitized by G. liparidis, the host's hemocytes alter their behavior, fail to spread properly (thereby inhibiting the encapsulation response) and partly undergo programmed cell death (apoptosis), resulting in a dramatic drop in the host's total hemocyte number (Schafellner and Schläger 2009).
Data from: Mining for single nucleotide polymorphisms and insertions / deletions in expressed sequence tag libraries of oil palm
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Data from: Mining of expressed sequence tag libraries of cacao for microsatellite markes using five computational tools
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Data from: "NGS based generation of expressed sequence tags for Lymantria dispar and Lymantria monacha, two closely related lepidopteran species with different responses to parasitism by Glyptapanteles liparidis" in Genomic Resources Notes accepted 1 December 2013 to 31 January 2014
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Data from: Mining microsatellite markers from public expressed sequence tags databases for the study of threatened plants
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Data from: Analysis of expressed sequence tags from the placenta of the live-bearing fish Poeciliopsis (Poeciliidae)
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Sequences tags expressed in ovules of Arabidopsis thaliana using Massively Parallel Signature Sequencing (MPSS)
GEO Series GSE50020. Arabidopsis thaliana. 2 samples. Type: Expression profiling by MPSS.
Dataset of Expressed Sequence Tags for Arabian Camel
<p>The dataset consists of 23,602 expressed sequence tags (ESTs) from the Arabian camel. This dataset was made available as part of an effort to undertake a comprehensive re-annotation by leveraging the latest genomic databases and advanced bioinformatics tools. Our primary aim is to uncover potentially novel sequences to gain fresh genetic insights and expand our understanding of camel genetics. This research underscores the importance of revisiting genomic data and demonstrates how advancements in science and technology can significantly contribute to the fields of evolutionary biology and genomics. Through this reevaluation, we identified 2,648 potential novel ESTs, thereby enriching the genetic framework of the Arabian camel and offering new perspectives on its evolutionary characteristics.</p>
Rapid evolution in fungal reproductive genes as revealed by evolutionary analyses of expressed sequence tags in Neurospora
GEO Series GSE37034. Neurospora intermedia; Neurospora crassa. 4 samples. Type: Expression profiling by array.
ChIP-sequencing (ChIP-seq) experiments on female ESCs expressing V5-tagged REX1 and control wild-type Embryonic stem cells (ESCs)
GEO Series GSE36417. Mus musculus. 2 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.