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25,372 results for “Transcriptomics”
additional file 3 for De novo transcriptome sequencing of Serangium japonicum (Coleoptera: Coccinellidae)
<p>The different expression unigenes between in summer and in winter. TPM: transcripts per million reads. pValue: statistic test p value. qValue: corrected p value after multiple tests. </p>
Fig. 5 in Transcriptome profiling of Symbion pandora (phylum Cycliophora): insights from a differential gene expression analysis
Fig. 5 Differential transcript expression analysis. Bar charts represent the enriched molecular functions associated with the upregulated genes in a feeding stages with Prometheus larva(e) and b feeding stages alone
Fig. 4 in Transcriptome profiling of Symbion pandora (phylum Cycliophora): insights from a differential gene expression analysis
Fig. 4 Differential transcript expression analysis. Bar charts represent the enriched biological processes associated with the upregulated genes in a feeding stages with Prometheus larva(e) and b feeding stages alone
Fig. 2 in Transcriptome profiling of Symbion pandora (phylum Cycliophora): insights from a differential gene expression analysis
Fig. 2 Scheme of the methodology employed in this study. In a first approach, the reference transcriptome (workflow in grey) was assembled de novo from three distinct life cycle stages: the feeding stage alone (asexual generation; note that in young feeding stages, the buccal funnel is located inside in the trunk), the feeding stage with Prometheus larva(e) attached to its trunk (sexual generation) and the free-swimming chordoid larva. Secondly, in the differential gene expression analysis (workflow in black), only two different conditions were investigated: feeding stages with Prometheus larva(e) attached to its trunk and feeding stages alone. Finally, sequenced reads were mapped to the reference transcriptome
Fig. 6 in Transcriptome profiling of Symbion pandora (phylum Cycliophora): insights from a differential gene expression analysis
Fig. 6 Differential transcript expression analysis. Bar charts represent the enriched cellular components associated with the upregulated genes in a feeding stages with Prometheus larva(e) and b feeding stages alone
Fig. 3 in First comprehensive multi-tissue transcriptome of Cherax quadricarinatus (Decapoda: Parastacidae) reveals unexpected diversity of endogenous cellulase
Fig. 3 Expression of 65 transcripts categorized into 16 GH families measured in log2 of (TPM + 1) values. The descriptions of GH families were assigned based on InterPro annotations of transcripts in each family (Online Resource 3), providing higher confidence of its putative function. In contrast, GH30, GH31, and GH39 do not have descriptions as their corre- sponding transcripts do not pos- sess detectable domains or signatures that point to any enzymatic functions
Fig. 2 in First comprehensive multi-tissue transcriptome of Cherax quadricarinatus (Decapoda: Parastacidae) reveals unexpected diversity of endogenous cellulase
Fig. 2 Annotation and information on the Cherax quadricarinatus transcriptome. a Distribution of transcript lengths with blue bars representing the lengths of all transcripts and red bars showing the length distribution only for transcripts with at least one annotation. b Venn diagram showing the number of shared and unique transcripts in different tissue types expressed at a TPM threshold of 100. c Transcript
Fig. 1 in First comprehensive multi-tissue transcriptome of Cherax quadricarinatus (Decapoda: Parastacidae) reveals unexpected diversity of endogenous cellulase
Fig. 1 Workflow diagram for the analysis of the Cherax quadricarinatus transcriptome. Analyses included the de novo assembly of the transcriptome, annotation of transcripts, expression analysis in multiple tissues, and the identification of putative cellulases
Pancreatic Ductal Adenocarcinoma Spatial Transcriptomics
Open the record for dataset details and reuse information.
Masked Conditional Diffusion Model with GNN for Spatial Transcriptomics Data Imputation
Open the record for dataset details and reuse information.
Fig. 4 in Comparative analysis of peripheral blood reveals transcriptomic adaptations to extreme environments on the Qinghai-Tibetan Plateau in the gray wolf (Canis lupus chanco)
Fig. 4 Reconstructed mitochondrial DNA tree of the worldwide distributed wolves. The numbers at each node are the Bayesian posterior probabilities (right) and ML bootstrap propor- tions (left)
Fig. 3 in Comparative analysis of peripheral blood reveals transcriptomic adaptations to extreme environments on the Qinghai-Tibetan Plateau in the gray wolf (Canis lupus chanco)
Fig. 3 Scatterplot of enriched KEGG pathways for DEGs between the Tibetan and lowland wolves. The enrichment factor is the ratio of the DEG number to the total gene number in the pathway. The dot size and color represent the gene number and the range of the p value respectively
Fig. 1 in Comparative analysis of peripheral blood reveals transcriptomic adaptations to extreme environments on the Qinghai-Tibetan Plateau in the gray wolf (Canis lupus chanco)
Fig. 1 Gene expression profiles of blood in Tibetan and lowland wolves. a Boxplot of the log transformed FPKM expression values across eight wolf blood samples. FPKM: fragments per kilobase of exon per million fragments. The solid horizontal line represents the median, and the box
Single Cell Spatial Transcriptomics Reveals Immunotherapy-Driven Bone Marrow Niche Remodeling in AML
<p>Images utilized in the paper <em>Single Cell Spatial Transcriptomics Reveals Immunotherapy-Driven Bone Marrow Niche Remodeling in AML </em>- by Gui, Bingham et al.<em><br></em></p>
Example dataset and expected outcomes of Spatially resolved in situ profiling of mRNA life cycle at transcriptome scale in intact cells and tissues
<p>Here are the example datasets and expected outcomes included in "<strong>Spatially resolved in situ profiling of mRNA life cycle at transcriptome scale in intact cells and tissues</strong>" from Ren et al. Please refer to the README.txt file for more detailed information. Corresponding computational tools are available at <a href="https://github.com/wanglab-broad/starfinder">https://github.com/wanglab-broad/starfinder.</a></p>
Transcriptome profiling associated with CARD11 overexpres-sion in Colorectal Cancer implicates a potential role for Tumour Immune Microenvironment and Cancer pathways modulation via NF-κB
<p>Images for CARD11 study in IJMS</p>
Combined transcriptomics and metabolomics analysis reveals the mechanism behind the pollen abortion in early stage among male sterile lines of alfalfa
<p><span>This study investigates early-stage anther development in cytoplasmic male sterile (CMS) alfalfa lines (MSJN1A) compared to their isotypic maintainer line (MSJN1B). Histological analyses revealed abnormal degradation of tapetal cells post-meiosis in the CMS line. Notably, during the early mononuclear stage, the central vacuole in the microspores was absent, leading to evident pollen abortion. These findings suggest that pollen abortion in the CMS line is associated with the delayed disintegration of the tapetum and structural anomalies in microspore vacuoles.</span><span> </span><span>Non-targeted metabolomic sequencing was employed to analyze the early anther metabolites of alfalfa, identifying four hundred and one and four hundred and five metabolites in the late tetrad and early mononuclear stages, respectively. Among these, thirty-nine metabolites were consistently up-regulated, while eighty-eight were down-regulated. Differential analysis revealed forty-five and thirty-seven unique metabolites in each respective stage. These metabolites primarily featured in pathways related to energy, phenylpropane, sucrose and starch, and fatty acid metabolism. Integrated analysis demonstrated that differentially expressed genes (DEGs) and differential metabolites (DMs) were co-enriched in these pathways. Additionally, quantitative real-time PCR and physiological index analysis confirmed the down-regulation of key genes during anther development, illustrating that changes in gene regulation upstream could significantly impact downstream metabolite levels, ultimately influencing pollen fertility.</span></p>
Single-cell transcriptome analysis reveals evolving tumor microenvironment induced by immunochemotherapy in nasopharyngeal carcinoma
<p>18 bulks and 11 single-cell RNA sequencing samples from paired before anti-PD-1 contained treatment and on treatment in patients with treatment-naive high-risk metastatic locally advanced NPCs were obtained. We aim to explore the mechanism of response heterogeneity for locally advanced NPCs underwent immunochemotherapy.</p>
Time series transcriptomes resolve metabolic pathways underlying crocin's anti-cancer activity: Control FASTQ sequencing reads
<p><span>Natural products like saffron show promise in treating hepatocellular carcinoma (HCC), but their mechanisms remain unclear. Here, we used time-series transcriptomics to elucidate crocin's anti-cancer mechanisms in HCC cells. We treated HepG2 cells with 1 and 2 mM crocin for 2, 6, 12, and 24 hours and analyzed transcriptomic profiles at each timepoint. The strongest transcriptional response occurred at 2 hours with 1 mM crocin, with diminishing effects at later timepoints. We observed upregulation of metabolic-, adhesion-, and endocytosis-related genes across all timepoints. Pathway analysis revealed activation of DNA damage checkpoints and senescence while proliferation pathways were suppressed. Notably, 52 genes involved in non-alcoholic fatty liver disease were downregulated at 24 hours (FDR p = 8 × 10⁻⁸), suggesting reversal of carcinogenic pathways. Strikingly, crocin consistently downregulated spliceosomal machinery genes across all timepoints while upregulating senescence and autophagy pathways. This spliceosome targeting represents a clinically relevant mechanism, as aberrant splicing drives oncogenesis in more than 90% of cancers. The transcription factor PAX5 was significantly upregulated while oncogenic ELK1 targets were downregulated. Our findings show that crocin treatment is accompanied by HCC cell senescence induction through coordinated spliceosome disruption and metabolic reprogramming, providing novel therapeutic targets for hepatocellular carcinoma.</span></p> <p><strong><span>Keywords: </span></strong><span>Hepatocellular carcinoma (HCC), crocin, transcriptomics, spliceosome, senescence, natural anti-cancer compounds</span></p>
Supplementary Information - Chapter 1. Transcriptomic investigation of the molecular mechanisms underlying resistance to the neonicotinoid thiamethoxam and the pyrethroid lambda-cyhalothrin in Euschistus heros (Hemiptera: Pentatomidae)
<p><span>Laboratory-selected resistant strains of <em>Euschistus heros</em> to thiamethoxam (NEO) and lambda-cyhalothrin (PYR) were recently reported in Brazil. However, the mechanisms conferring resistance to these insecticides in <em>E. heros</em> remain unresolved. We utilized comparative transcriptome profiling and single nucleotide polymorphism (SNP) calling of susceptible and resistant strains of <em>E. heros</em> to investigate the molecular mechanism(s) underlying resistance.</span><span> </span><span>The <em>E. heros</em> transcriptome was assembled, generating 91 673 transcripts with a mean length of 720 bp and N50 of 1795 bp. Comparative gene expression analysis between the susceptible (SUS) and NEO strains identified 215 significantly differentially expressed (DE) transcripts. DE transcripts associated with the xenobiotic metabolism were all up-regulated in the NEO strain. The comparative analysis of the SUS and PYR strains identified 204 DE transcripts, including an esterase (esterase FE4), a glutathione-<em>S</em>-transferase, an ABC transporter (ABCC1) and aquaporins that were up-regulated in the PYR strain. We identified 9588 and 15 043 nonsynonymous SNPs in the PYR and NEO strains. One of the SNPs (D70N) detected in the NEO strain occurs in a subunit (α5) of the nAChRs, the target site of neonicotinoid insecticides. Nevertheless, this residue position in α5 is not conserved among insects.</span><span> </span><span>Neonicotinoid and pyrethroid resistance in laboratory-selected <em>E. heros</em> is associated with a potential metabolic resistance mechanism by the overexpression of proteins commonly involved in the three phases of xenobiotic metabolism. Together these findings provide insight into the potential basis of resistance in <em>E. heros</em> and will inform the development and implementation of resistance management strategies against this important pest.</span></p> <p><strong><span>*Published in: </span></strong><em><span>Pest Management Science</span></em><span><span> 79.12 (2023): 5349-5361</span>. <a href="https://doi.org/10.1002/ps.7745">https://doi.org/10.1002/ps.7745</a></span></p>
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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.