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25,372 results for “Transcriptomics”
Genetic characterization of potential venom resistance proteins in California ground squirrels (Otospermophilus beecheyi) using transcriptome analyses
<p>Understanding the molecular basis of adaptations in coevolving species requires identifying the genes that underlie reciprocally selected phenotypes, such as those involved in venom in snakes and resistance to venom in their prey. In this regard, California ground squirrels (CGS; Otospermophilus beecheyi) are eaten by northern Pacific rattlesnakes (Crotalus oreganus oreganus), but individual squirrels may still show substantial resistance to venom and survive bites. A recent study using proteomics identified venom interactive proteins (VIPs) in the blood serum of CGS. These VIPs represent possible resistance proteins, but the sequences of genes encoding them are unknown despite the value of such data to molecular studies of coevolution. To address this issue, we analyzed a de novo assembled transcriptome from CGS liver tissue—where many plasma proteins are synthesized—and other tissues from this species. We then examined VIP sequences in terms of three characteristics that identify them as possible resistance proteins: evidence for positive selection, high liver expression, and nonsynonymous variation across CGS populations. Based on these characteristics, we identified five VIPs (i.e., alpha-2-macroglobulin, alpha-1-antitrypsin-like protein GS55-LT, apolipoprotein A-II, hibernation-associated plasma protein HP-20, and hibernation-associated plasma protein HP-27) as the most likely candidates for resistance proteins among VIPs identified to date. Four of these proteins have been previously implicated in conferring resistance to venom in mammals, validating our approach. When combined with the detailed information available for rattlesnake venom proteins, these results set the stage for future work focused on understanding coevolutionary interactions at the molecular level between these species.</p>
Data from: "Transcriptomic resources for five shrimp (Crustacea: Atyidae and Alpheidae) species from the anchialine ecosystem" in Genomic Resources Notes accepted 1 June 2014 to 31 July 2014
[No abstract entered]
Data from: "Transcriptome sequences for Campanula gentilis" in Genomic Resources Notes accepted 1 April 2015 – 31 May 2015
In this report, we present the transcriptome of a single accession of Campanula gentilis Kovanda, obtained through the sequencing of both a normalized and a non-normalized cDNA library generated from stem and leaf tissue. The resources we provide include the raw sequence reads, the assembled contigs, the putative open reading frames, the contig/ORF annotations and the normalized as well as non-normalized expression levels.
Data from: "Transcriptome sequencing of the Queensland fruit fly, Bactrocera tryoni (Diptera: Tephritidae)" in Genomic Resources Notes accepted 1 December 2013 to 31 January 2014
[No abstract filled]
An Analysis of Transcriptomic Burden Identifies Biological Progression Roadmaps for Hematological Malignancies and Solid Tumors
<p>Supplementary materials for review.</p>
Profiling the transcriptome with RNA SPOTs
<p>Raw data for profiling mouse ES-E14 cell culture transcripts with RNA SPOTs</p>
A combined transcriptome - miRNAome approach revealed that a kinesin gene is differentially targeted by a novel miRNA in an apomictic genotype of Eragrostis curvula
<p>Weeping lovegrass (<em>Eragrostis curvula</em> [Shrad.] Nees) is a perennial grass typically established in semi-arid regions, with good adaptability to dry conditions and sandy soils. This polymorphic complex includes both sexual and apomictic cytotypes, with different ploidy levels (2x-8x). Diploids are known to be sexual, while most polyploids are facultative apomicts, and full apomicts have also been reported. Plant breeding studies throughout the years have focused on achieving the introgression of apomixis into species of agricultural relevance, but, given the complexity of the trait, a deeper understanding of the molecular basis of regulatory mechanisms of apomixis is still required. Apomixis is thought to be associated with silencing or disruption of the sexual pathway, and studies have shown it is influenced by epigenetic mechanisms. In a previous study, we explored the role of miRNA-mRNA interactions using two contrasting <em>E. curvula</em> phenotypes. Here, the sexual OTA-S, the facultative Don Walter and the obligate apomictic Tanganyika cDNA and sRNA libraries were inquired, searching for miRNA discovery and miRNA expression regulation of genes related to the reproductive mode. This allowed for the characterization of seven miRNAs and the validation of their miRNA-target interactions. Interestingly, a <em>kinesin</em> gene was found to be repressed in the apomictic cultivar Tanganyika, targeted by a novel miRNA that was found to be overexpressed in this genotype, suggestive of an involvement in the reproductive mode expression. Our work provided additional evidence of the contribution of the epigenetic regulation of the apomictic pathway.</p>
Gastric Cancer Spatial Transcriptomics
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Spatial transcriptomic data
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supplemetary_data_ hatching_muscle_transcriptome
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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).
Transcriptome analysis reveals potential molecular mechanisms underlying differences in stalk color among four Gastrodia elata varieties-Supplementary Material
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A combined proteomic and transcriptomic signature is predictive of response to anti-PD-1 treatment in patients with metastatic melanoma
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Figure 6 in Transcriptomic analysis of Bursaphelenchus xylophilus treated by a potential phytonematicide, punicalagin
Figure 6: Annotated, enriched KEGG pathway. (A) Annotated KEGG pathway of phagosome. Genes in blue frames with red borders were up-regulated, genes in blue frames with yellow borders were down-regulated, and genes in blue frames with sky-blue borders were simultaneously up-regulated and down-regulated. (B) Annotated KEGG pathway of oxidative phosphorylation about DEGs. Genes in blue frames with white borders were differentially expressed in the pathway.
Supporting data for SpatialOne: End-to-End Analysis of Spatial Transcriptomics at Scale
<p>Supplementary data supporting the <em>SpatialOne: End-to-End Analysis of Spatial </em><em>Transcriptomics at Scale</em> publication</p> <p> </p> <blockquote> <p>To showcase the capabilities of SpatialOne, two human lung cancer formalin-fixed, paraffin-embedded (FFPE) samples are analyzed. These samples are prepared following the CG000495 protocol (Figure 1b), sequenced with the 10x Visium CytAssist, and processed using the 10x SpaceRanger version 2. We also present analysis of two adult mouse samples sequenced using 10x Visium samples (one fresh frozen brain tissue section processed using SpaceRanger v2 and one FFPE kidney sample processed using the SpaceRanger v1), and 75 internal samples. </p> <p> For the human lung cancer samples, single-cell data from the the Lung Cancer Atlas (Salcher et al., 2022) is used as reference. This dataset is filtered to include only Chromium-generated data. For the mice samples, the GSE107585 single-cell dataset serves as reference. In the human lung cancer datasets, a pathologist annotated regions of interest corresponding to tumors, blood vessels, and alveolar regions.</p> </blockquote> <p> </p> <p>Changelog:</p> <ul> <li>Added a README file describing the zip content.</li> </ul>
Real-time and programmable transcriptome sequencing with PROFIT-seq
<div> <p>Source data for our PROFIT-seq manuscript.</p> </div>
Datasets collected for Masked adversarial neural network for cell type deconvolution in spatial transcriptomics
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Codes and datasets for the comparative transcriptome analysis of venom glands in parasitoid wasps
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Supplementary material 1 from: Felden A, Paris C, Chapple DG, Suarez AV, Tsutsui ND, Lester PJ, Gruber MAM (2019) Native and introduced Argentine ant populations are characterised by distinct transcriptomic signatures associated with behaviour and immunity. NeoBiota 49: 105-126. https://doi.org/10.3897/neobiota.49.36086
: Data type: molecular data
Transcriptome analysis of wild-typ and Osbpl2-/- OC1 cells/ wild-typ and osbpl2b-/- zebrafish inner ear tissues
<p>wild-typ:T01, T02, T03</p> <p>Osbpl2-/-: T04, T05, T06</p>
ScienceDex guides
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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.