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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
Single-cell analysis reveals host S phase drives large T antigen expression during BK polyomavirus infection
Open the record for dataset details and reuse information.
Meta-analysis of scRNA-seq Co-expression in Human Neural Organoids Reveals High Variability in Recapitulating Primary Tissue
<p>Contains all code and data for Werner and Gillis, Meta-analysis of scRNA-seq Co-expression in Human Neural Organoids Reveals High Variability in Recapitulating Primary Tissue, 2024. </p> <p>Additionally, the code and data for this paper can be found at https://github.com/JonathanMWerner/meta_organoid_analysis with an easy to view github markdown file containing all the code used to generate all figure panel plots at https://github.com/JonathanMWerner/meta_organoid_analysis/blob/main/figure_plots_with_data_code.md.</p> <p>Due to file size limits on github, there are several data files not available on github, but are available here on zenodo in the data_for_plots.zip file, see below:</p> <pre>umap_embeddings_Fig2A.Rdata<br>cross_dataset_aggregated_exp_metaMarker_all_fetal_SuppFig1B_Fig2E.Rdata<br>organoid_egad_results_ranked_6_26_24_Fig3D.Rdata<br>fetal_egad_results_ranked_6_26_24_Fig3D.Rdata<br>org_eigenvec_matrices_SuppFig3CD.Rdata</pre> <p><br>The R package developed for this paper is available at https://github.com/JonathanMWerner/preservedCoexp</p>
Fig. 4 in Direct somatic embryogenesis of drought resistance pistachio (Pistacia vera L.) and expression analysis of somatic embryogenesis-related genes
Fig. 4. Somatic embryos induction of P. vera L. Sarakhs variety from immature zygotic embryos under dark condition after 60 days. Somatic embryos exhibited by arrows (a) Somatic embryos in globular stage, (b) Somatic embryos in heart stage, (c) Cotyledonary somatic embryos. Bar 2 mm.
Fig. 6 in Direct somatic embryogenesis of drought resistance pistachio (Pistacia vera L.) and expression analysis of somatic embryogenesis-related genes
Fig. 6. Secondary somatic embryos produced from primay somatic embryos of P. vera L. Sarakhs variety. Bar 2 mm.
Fig. 8 in Direct somatic embryogenesis of drought resistance pistachio (Pistacia vera L.) and expression analysis of somatic embryogenesis-related genes
Fig. 8. Relative expression of selected embryogenesis-related genes on embryonic and non-embryonic samples of two genotypes (a: Sarakhs variety and b: Ghazvini cultivar) of P.vera L in three technical replication.ACT was used as a reference gene for data normalization.Mean value and standard deviation (SD) were presented for three biological replicates.The significance differences (p <.01) and non-significant differences showed with two stars and "ns", respectively.
Data from: De novo assembly of a tadpole shrimp (Triops newberryi) transcriptome and preliminary differential gene expression analysis
Next-generation sequencing techniques, such as RNA sequencing, have provided a wealth of genomic information for nonmodel species. Transcriptomic information can be used to quantify the patterns of gene expression, which can identify how environmental differences invoke organismal stress responses and provide a gauge in predicting species adaptability. In our study, we used RNA sequencing to characterize the first transcriptome from a naupliar tadpole shrimp (Triops newberryi) to identify the genes expressed during the early life history stages and which could be important for future genomic studies. RNA was extracted from naupliar T. newberryi that were reared in a laboratory-controlled setting and in two different water types, a native and a non-native condition. A total of six replicates, three per condition, were sequenced with the Illumina Hi-Seq 2000 achieving 365 M 50-nt reads. High-quality reads were produced and de novo assembly was used to construct a T. newberryi transcriptome that was approximately 24.8 M base pairs. More than 10 000 peptides were predicted from the assembly, and genes were sorted into gene ontology categories. The use of different water conditions allowed for a preliminary differential gene expression analysis in order to compare the changes in gene expression between conditions. There were 299 differentially expressed genes between water conditions that might serve as a focal point for future genomic studies of Triops acclimation to different environments. The Triops transcriptome could serve as vital genomic information for additional studies on Branchiopod crustaceans.
Transcriptomic analysis demonstrates the expression, origin and function of lncRNAs in multiple skin diseases
<p>Transcriptomic analysis demonstrates the expression, origin and function of lncRNAs in multiple skin diseases</p>
Assessing Tumor-Infiltrating Lymphocytes in Breast Cancer: A Proposal for Combining Immunohistochemistry and Gene Expression Analysis to Refine Scoring
<p>Whole tissue scans of histochemistry (H&E) and immunohistochemistry (CD3, CD4, CD8 andCD45) images that have been used to calculate TIL scores.</p> <p>All stainings are numbers for each patient..</p>
Fig. 6 in Genome-wide transcriptional analysis unveils the molecular basis of organ-specific expression of isosteroidal alkaloids biosynthesis in critically endangered Fritillaria roylei Hook
Fig. 6. Heatmap representing organ specific significantly enriched genes corresponding to (A) Isosteroidal alkaloid biosynthesis, (B) Sucrose and starch metabolism, (C) UGTs and CYPs, (D) aquaporins, (E) ABC transporters, (F) Transcription factor and Transposable elements. The red-blue scale represents positive enrichment (red) and negative enrichment (Blue) of transcripts. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 5 in Genome-wide transcriptional analysis unveils the molecular basis of organ-specific expression of isosteroidal alkaloids biosynthesis in critically endangered Fritillaria roylei Hook
Fig. 5. Significantly enriched transcripts (nodes) in predicted interactome network. (A) Steroidal alkaloid biosynthesis pathways (B) Isopentenyl diphosphate biosynthesis pathway, (C) Sucrose and starch metabolic pathways and (D) Aquaporins. The nodes encircled in red color represents higher enrichment in the bulb while the nodes encircled in grey and blue represents higher enrichment in arial organs (leaf and stem). (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 7 in Genome-wide transcriptional analysis unveils the molecular basis of organ-specific expression of isosteroidal alkaloids biosynthesis in critically endangered Fritillaria roylei Hook
Fig. 7. qRT-PCR expression-based validation of RNA-seq data using potential 20 genes involved in isosteroidal alkaloid biosynthetic pathway. (A) Bulb vs. Leaf, (B) Leaf vs. Stem and (C) Bulb vs. Stem.
Fig. 3 in Genome-wide transcriptional analysis unveils the molecular basis of organ-specific expression of isosteroidal alkaloids biosynthesis in critically endangered Fritillaria roylei Hook
Fig. 3. Significant KEGG pathway enrichment analysis in tissues from aerial organs (leaf & Stem) and bulb. The green colour enrichment indicates higher expression in aerial tissue while pink represents higher enrichment in bulb. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 4 in Genome-wide transcriptional analysis unveils the molecular basis of organ-specific expression of isosteroidal alkaloids biosynthesis in critically endangered Fritillaria roylei Hook
Fig. 4. Transcriptional protein-protein interactome (PPIN) prediction in F. roylei along the network statistics. (A) Overall prediction of PPI network based on significantly differential expressed transcripts. Spatial PPI network prediction of significantly enriched transcripts in (B) Bulb, (C) Leaf and (D) Stem.
Fig. 1 in Genome-wide transcriptional analysis unveils the molecular basis of organ-specific expression of isosteroidal alkaloids biosynthesis in critically endangered Fritillaria roylei Hook
Fig. 1. Summary of organ specific spatial transcriptome sequencing in F. roylei. (A): Overall quality filtering of sequenced reads; (B): Tissue specific high quality filtered reads obtained after removing low quality/adaptor contaminated sequences; (C): Assembly statistics details; (D): Venn diagram representing functional annotation with six different public protein databases.
Fig. 8 in Genome-wide transcriptional analysis unveils the molecular basis of organ-specific expression of isosteroidal alkaloids biosynthesis in critically endangered Fritillaria roylei Hook
Fig. 8. Representation of isosteroidal alkaloid biosynthesis pathway in F. roylei and heat map representing expression of genes in Stem, Leaf and Bulb tissue using red-blue scale (red: positive enrichment and Blue: negative enrichment of transcripts). (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 2 in Genome-wide transcriptional analysis unveils the molecular basis of organ-specific expression of isosteroidal alkaloids biosynthesis in critically endangered Fritillaria roylei Hook
Fig. 2. Clustering of 2488 significant differentially expressed transcripts in leaf, stem and bulb in F. roylei (A) sub-cluster 1 represent transcripts with significant higher expression in bulb; (B): Sub-cluster 2 in Stem and (C): Sub-cluster 3 in leaf; (D): Pearson's correlation of organ specific significant differentially expressed clustered transcripts in leaf, stem and bulb tissues.
TransBic: extracting bucket trend-preserving biclusters for analysis of gene expression data
<p>Datasets of TransBic: extracting bucket trend-preserving biclusters for analysis of gene expression data</p>
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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)
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.