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25,372 results for “Transcriptomics”
Orthology guided transcriptome assembly of Italian ryegrass and meadow fescue for single nucleotide polymorphisms discovery (data set)
<p>Transcriptome sequencing was performed on ten samples (corresponding to six genotypes) of <em>Festuca pratensis</em> and ten samples (corresponding to six genotypes) of <em>Lolium multiflorum</em> and fourteen samples of<em> Lolium perenne</em> (corresponding to fourteen genotypes). Using the OGA approach, 18,952 non-redundant <em>F. pratensis</em> transcripts were assembled by combining the contigs of all six genotypes based on orthology with the <em>Brachypodium distachyon </em>proteome. Similarly, <em>19,036</em> non-redundant<em> L. multiflorum</em> transcripts were assembled and annotated. In total, 17,455 orthologous transcripts were shared between the transcriptomes of the two species. Out of these, 16,613 orthologous transcripts overlap with the previously published<em> L. perenne</em> transcriptome containing 19,279 non-redundant transcripts(fasta files). We identified SNPs, the following criteria were used to classify it as one of following three classes (1) intraspecific SNPs (INTRA), (2) interspecific SNPs in two-way comparison (INTER-2W) and (3) interspecific SNPs in three-way comparison (INTER-3W) (GFF files).</p>
A survey of the sorghum transcriptome using single-molecule long reads
<p>Alternative splicing and alternative polyadenylation (APA) of pre-mRNAs greatly contribute to transcriptome diversity, coding capacity of a genome and gene regulatory mechanisms in eukaryotes. Second-generation sequencing technologies have been extensively used to analyze transcriptomes. However, a major limitation of short-read data is that it is difficult to accurately predict full-length splice isoforms. Here we sequenced the sorghum transcriptome using Pacific Biosciences single molecule real time long-read isoform sequencing and developed a pipeline called TAPIS (Transcriptome Analysis Pipeline for Isoform Sequencing) to identify full-length splice isoforms and APA sites. Our analysis reveals transcriptome-wide full-length isoforms at an unprecedented scale with over 11,000 novel splice isoforms. Additionally, we uncover APA of ~11,000 expressed genes and more than 2,100 novel genes. These results greatly enhance sorghum gene annotations and aid in studying gene regulation in this important bioenergy crop. The TAPIS pipeline will serve as a useful tool to analyze Iso-Seq data from any organism.</p>
Orthology guided transcriptome assembly of Italian ryegrass and meadow fescue (update data set)
<p>Transcriptome sequencing was performed on ten samples (corresponding to six genotypes) of <em>Festuca pratensis</em> and ten samples (corresponding to six genotypes) of <em>Lolium multiflorum</em> and fourteen samples of<em> Lolium perenne</em> (corresponding to fourteen genotypes). Using the OGA approach, 18,952 non-redundant <em>F. pratensis</em> transcripts were assembled by combining the contigs of all six genotypes based on orthology with the <em>Brachypodium distachyon </em>proteome. Similarly, <em>19,036</em> non-redundant<em> L. multiflorum</em> transcripts were assembled and annotated. In total, 17,455 orthologous transcripts were shared between the transcriptomes of the two species. Out of these, 16,613 orthologous transcripts overlap with the previously published<em> L. perenne</em> transcriptome containing 19,279 non-redundant transcripts(fasta files). We identified SNPs, the following criteria were used to classify it as one of following three classes (1) intraspecific SNPs (INTRA), (2) interspecific SNPs in two-way comparison (INTER-2W) and (3) interspecific SNPs in three-way comparison (INTER-3W) (GFF files).</p>
Figure 12. from: Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data - Biodiversity Data Journal 1: e1013 (28 October 2013) https://doi.org/10.3897/BDJ.1.e1013
Figure 12. - Map of Croatia showing the locality of Eupolybothrus cavernicolus Komerički & Stoev sp. n.
Figure 10a. from: Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data - Biodiversity Data Journal 1: e1013 (28 October 2013) https://doi.org/10.3897/BDJ.1.e1013
Figure 10a. - Eupolybothrus cavernicolus Komerički & Stoev sp. n., male paratype. Figure 10a. close up of the tip of prefemoral spine p Figure 10b. coxal pore pit, meso-ventral view <br> close up of the tip of prefemoral spine p
Figure 9b. from: Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data - Biodiversity Data Journal 1: e1013 (28 October 2013) https://doi.org/10.3897/BDJ.1.e1013
Figure 9b. - Eupolybothrus cavernicolus Komerički & Stoev sp. n., male paratype. Figure 9a. close up of the clusp of setae on male prefemur 15 Figure 9b. close up of the setose protuberance on male prefemur 15 <br> close up of the setose protuberance on male prefemur 15
Figure 8a. from: Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data - Biodiversity Data Journal 1: e1013 (28 October 2013) https://doi.org/10.3897/BDJ.1.e1013
Figure 8a. - Eupolybothrus cavernicolus Komerički & Stoev sp. n., male paratype. Figure 8a. prefemur 15, mesoventral view. Abbreviations: prefemoral knob (pk), circular setose protuberance (cp), cluster of setae (sc). Figure 8b. close up of the prefemoral knob, ventral view <br> prefemur 15, mesoventral view. Abbreviations: prefemoral knob (pk), circular setose protuberance (cp), cluster of setae (sc).
Figure 20a. from: Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data - Biodiversity Data Journal 1: e1013 (28 October 2013) https://doi.org/10.3897/BDJ.1.e1013
Figure 20a. - Gene annotation. Original data available from GigaScience GigaDB (Stoev et al. 2013). Figure 20a. E-value, identity and species distribution statistics of the sequences that can find homologs on Nr database Figure 20b. COG functional classification of the transcripts Figure 20c. GO categories of the transcripts <br> E-value, identity and species distribution statistics of the sequences that can find homologs on Nr database
Figure 17a. from: Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data - Biodiversity Data Journal 1: e1013 (28 October 2013) https://doi.org/10.3897/BDJ.1.e1013
Figure 17a. - Prefemur of male leg 15. From Stoev et al. (2010). Figure 17a. Eupolybothrus tabularum Figure 17b. Eupolybothrus excellens <br> Eupolybothrus tabularum
Figure 7a. from: Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data - Biodiversity Data Journal 1: e1013 (28 October 2013) https://doi.org/10.3897/BDJ.1.e1013
Figure 7a. - Eupolybothrus cavernicolus Komerički & Stoev sp. n., male paratype. Figure 7a. tarsus 1, tarsus 2 and pretarsus of leg 10, lateral view. Abbreviations: pectinal setae (ps). Figure 7b. pretarsus of leg 15 <br> tarsus 1, tarsus 2 and pretarsus of leg 10, lateral view. Abbreviations: pectinal setae (ps).
Figure 5b. from: Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data - Biodiversity Data Journal 1: e1013 (28 October 2013) https://doi.org/10.3897/BDJ.1.e1013
Figure 5b. - Eupolybothrus cavernicolus Komerički & Stoev sp. n., male paratype. Figure 5a. tergite 7, dorsal view Figure 5b. tergites 12-13, dorsal view <br> tergites 12-13, dorsal view
Figure 11. from: Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data - Biodiversity Data Journal 1: e1013 (28 October 2013) https://doi.org/10.3897/BDJ.1.e1013
Figure 11. - Eupolybothrus cavernicolus Komerički & Stoev sp. n., male paratype. Genitalia, posterio-dorsal view.
Figure 6b. from: Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data - Biodiversity Data Journal 1: e1013 (28 October 2013) https://doi.org/10.3897/BDJ.1.e1013
Figure 6b. - Eupolybothrus cavernicolus Komerički & Stoev sp. n., male paratype. Figure 6a. tergite 14 and intermediate tergite, posteriodorsal view. Abbreviations: seta-free areas (sfa). Figure 6b. pretarsus of leg 10, ventral view. Abbreviations: anterior accessory claw (a), posterior accessory claw (p). <br> pretarsus of leg 10, ventral view. Abbreviations: anterior accessory claw (a), posterior accessory claw (p).
Figure 5a. from: Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data - Biodiversity Data Journal 1: e1013 (28 October 2013) https://doi.org/10.3897/BDJ.1.e1013
Figure 5a. - Eupolybothrus cavernicolus Komerički & Stoev sp. n., male paratype. Figure 5a. tergite 7, dorsal view Figure 5b. tergites 12-13, dorsal view <br> tergite 7, dorsal view
Figure 4b. from: Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data - Biodiversity Data Journal 1: e1013 (28 October 2013) https://doi.org/10.3897/BDJ.1.e1013
Figure 4b. - Eupolybothrus cavernicolus Komerički & Stoev sp. n., male paratype. Figure 4a. forcipules, ventral view Figure 4b. close up of coxosternum, ventral view. Abbreviations: porodonts (po). <br> close up of coxosternum, ventral view. Abbreviations: porodonts (po).
Figure 4a. from: Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data - Biodiversity Data Journal 1: e1013 (28 October 2013) https://doi.org/10.3897/BDJ.1.e1013
Figure 4a. - Eupolybothrus cavernicolus Komerički & Stoev sp. n., male paratype. Figure 4a. forcipules, ventral view Figure 4b. close up of coxosternum, ventral view. Abbreviations: porodonts (po). <br> forcipules, ventral view
Figure 3b. from: Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data - Biodiversity Data Journal 1: e1013 (28 October 2013) https://doi.org/10.3897/BDJ.1.e1013
Figure 3b. - Eupolybothrus cavernicolus Komerički & Stoev sp. n., male paratype. Figure 3a. clypeus, ventral view; most setae broken off Figure 3b. tip of antenna <br> tip of antenna
Figure 14b. from: Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data - Biodiversity Data Journal 1: e1013 (28 October 2013) https://doi.org/10.3897/BDJ.1.e1013
Figure 14b. - Eupolybothrus leostygis (Verhoeff, 1899), male. Figure 14a. ocelli Figure 14b. forcipules, ventral view <br> forcipules, ventral view
Figure 7b. from: Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data - Biodiversity Data Journal 1: e1013 (28 October 2013) https://doi.org/10.3897/BDJ.1.e1013
Figure 7b. - Eupolybothrus cavernicolus Komerički & Stoev sp. n., male paratype. Figure 7a. tarsus 1, tarsus 2 and pretarsus of leg 10, lateral view. Abbreviations: pectinal setae (ps). Figure 7b. pretarsus of leg 15 <br> pretarsus of leg 15
Figure 3a. from: Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data - Biodiversity Data Journal 1: e1013 (28 October 2013) https://doi.org/10.3897/BDJ.1.e1013
Figure 3a. - Eupolybothrus cavernicolus Komerički & Stoev sp. n., male paratype. Figure 3a. clypeus, ventral view; most setae broken off Figure 3b. tip of antenna <br> clypeus, ventral view; most setae broken off
ScienceDex guides
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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)
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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.