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Figure 9 in Evaluation of the Chilli veinal mottle virus CP gene expressing transgenic Nicotiana benthamiana plants for disease resistance against the virus
Figure 9. ELISA plate readings (O.D at 405nm) of leaf samples of transgenic lines (T1-T8) and control plants after 15 dpi.
Figure 7 in Evaluation of the Chilli veinal mottle virus CP gene expressing transgenic Nicotiana benthamiana plants for disease resistance against the virus
Figure 7. PCR Products of the hpt gene from T0 transgenic plants. Lane 1-9 are transgenic. Lane 10, +ve control. Lane 11, control (untransformed) plant.
Figure 6. DNA bands from T0 in Evaluation of the Chilli veinal mottle virus CP gene expressing transgenic Nicotiana benthamiana plants for disease resistance against the virus
Figure 6. DNA bands from T0 transgenic and Agro-infilterated plants. Lane 1-10, transgenic plants. Lane 11-13, agro-infilterated plants.
Figure 3 in Evaluation of the Chilli veinal mottle virus CP gene expressing transgenic Nicotiana benthamiana plants for disease resistance against the virus
Figure 3. Symptoms development on propagative host plants after mechanical inoculation with ChiVMV isolate ATIPK. (a) N. tabacum showing mosaic, mottling and vein clearing (b) C. annum (cv. Loungi) displays the symptoms of mottling, mosaic, leaf deformation and vein clearing.
Figure 2 in Evaluation of the Chilli veinal mottle virus CP gene expressing transgenic Nicotiana benthamiana plants for disease resistance against the virus
Figure 2. Symptoms of ChiVMV on chilli leaves collected from Islamabad. (a) Shows mottling and severe vein clearing and distortion. (b) Shows reduced leaf size with mottling and distortion.
Pelagomonas calceolata gene expression levels in different nitrogen conditions and differential expression analysis.
<p>These files contains the expression levels and DESeq2 results of <em>Pelagomonas calceolata</em> genes cultivated with different nitrate conditions. Two strains of <em>P. calceolata </em>(RCC100 and RCC697) were cultivated and their RNAs reads were aligned on the predicted genes of <em>P. calceolata</em> RCC100 genome: <a href="https://www.ncbi.nlm.nih.gov/Traces/wgs/CAKKNE01?display=download" rel="nofollow">https://www.ncbi.nlm.nih.gov/Traces/wgs/CAKKNE01?display=download</a></p> <p>The following culture conditions were analysed :</p> <p>882 µM of Nitrate (RCC100 and RCC697) </p> <p>441 µM of Nitrate (RCC100)</p> <p>220 µM of Nitrate (RCC100 and RCC697)</p> <p>50 µM of Nitrate (RCC697)</p> <p>882 µM Cyanate (RCC100)</p> <p>882 µM Ammonia (RCC100)</p> <p>441 µM Urea (RCC100)</p> <p><a href="../api/records/12582059/draft/files/20230427_RCC100-Nitrate_transcriptomes_rawcounts.tsv/content" target="_blank" rel="noopener noreferrer">20230427_RCC100-Nitrate_transcriptomes_rawcounts.tsv</a> : the file contains the raw read counts of RCC100 in 6 culture conditions in triplicate + the gene names = 19 columns.</p> <p><a href="../api/records/12582059/draft/files/20230427_RCC100-Nitrate_transcriptomes_TPM.tsv/content" target="_blank" rel="noopener noreferrer">20230427_RCC100-Nitrate_transcriptomes_TPM.tsv</a> : same data normalized in transcript per kb per million mapped reads (TPM).</p> <p><a href="../api/records/12582059/draft/files/20230427_RCC100-Nitrate_transcriptomes_rawcounts.tsv/content" target="_blank" rel="noopener noreferrer">20230427_RCC697-Nitrate_transcriptomes_rawcounts.tsv</a> : the file contains the raw read counts of RCC697 of 3 culture conditions in triplicate + the gene names = 10 columns.</p> <p><a href="../api/records/12582059/draft/files/20230427_RCC100-Nitrate_transcriptomes_TPM.tsv/content" target="_blank" rel="noopener noreferrer">20230427_RCC697-Nitrate_transcriptomes_TPM.tsv</a> : same data normalized in transcript per kb per million mapped reads (TPM).</p> <p><span>Differential expression analysis (DESeq2) was performed by pairwise comparisons between the standard condition (882 µM nitrate) and low-nitrate conditions (50, 220 or 441 µM nitrate) or changing nitrogen sources (882 µM ammonium, 882 µM cyanate and 441 µM urea). Each DESeq-results_RCCxxx_xxx.tsv file contains 6 columns : <em>P.calceolata </em>gene name, base Mean, log2 Fold Change, standard error value (lfcSE), pvalue and adjusted pvalue (padj).<br></span></p>
Association between Dysregulated Expression of Ca2+ and ROS-Related Gene Pairs and Breast Cancer Patient Survival
<p>This file is composed of two documents:</p> <ul> <li>Supplementary File 1 containing three Excel files with cumulative proportion survival from redox-related genes, calcium-related genes, and redox and calcium-related genes.</li> <li>Supplementary Table 3 including an Excel file with a functional enrichment analysis using redox and calcium correlated genes. Cell cycle regulation (sheet 1) and Cell adhesion and projection (sheet 2) were the biological processes more enriched.</li> </ul> <p>Both supplementary tables belongs to the study <strong>Association between Dysregulated Expression of Ca2+ and ROS-Related Gene Pairs and Breast Cancer Patient Survival</strong>, published in <strong>Molecular Diagnosis and therapy</strong></p>
Fig. 2 in Molecular cloning of heat shock protein gene HSP90 and effects of abamectin and double-stranded RNA on its expression in Panonychus citri (Trombidiformes: Tetranychidae)
Fig. 2. Alignment of HSP90 amino acid sequence of P. citri McGregor and its homologus amino acid sequences from other species (Frankliniella occidentalis, Trialeurodes vaporariorum, Pteromalus puparum, Tetranychus cinabarinus).
Fig. 1 in Effects of nucleopolyhedrovirus infection on the development of Helicoverpa armigera (Lepidoptera: Noctuidae) and expression of its 20-hydroxyecdysone- and juvenile hormone-related genes
Fig. 1. Effect of HaSNPV infection on the larval body weight of Helicoverpa armigera. (A) ♦, ■, ▲, ×, —, and ● indicate larvae infected with HaSNPV at the concentrations 0, 105, 106, 107, 108, and 109 PIB/mL, respectively. (B) a, b, c, d, e, and f show H. armigera larvae on the 5th day afer infection with HaSNPV at the concentrations 0, 105, 106, 107, 108, and 109 PIB/mL, respectively.
Fig. 3 in Effects of nucleopolyhedrovirus infection on the development of Helicoverpa armigera (Lepidoptera: Noctuidae) and expression of its 20-hydroxyecdysone- and juvenile hormone-related genes
Fig. 3. Expression analysis by qRT-PCR of the JH related genes MET, JHEH, HSP90, and JHi in Helicoverpa armigera larvae afer HaSNPV infection at 0, 24, 48, 72, 96, and 120 h. The blank bars represent the larvae infected with sterile water (CK). The black bars represent the larvae infected with NPV at the concentration of 107 PIB/mL (NPV infection). The data represent the mean ± SD of 3 biological replicates. Statistically significant differences from gene expression are denoted by * (0.01 <P £ 0.05) and ** (P £ 0.01) as determined by the pairwise Student's t-test analysis in SPSS 17.0 sofware.
Fig. 2 in Effects of nucleopolyhedrovirus infection on the development of Helicoverpa armigera (Lepidoptera: Noctuidae) and expression of its 20-hydroxyecdysone- and juvenile hormone-related genes
Fig. 2. Expression analysis by qRT-PCR of the 20E related genes ECR, USP, E75, BR, HR3, and NFT2 in Helicoverpa armigera larvae afer HaSNPV infection at 0, 24, 48, 72, 96, and 120 h. The blank bars represent the larvae infected with sterile water (CK). The black bars represent the larvae infected with NPV at the concentration of 107 PIB/mL (NPV infection). The data represent the mean ± SD of 3 biological replicates. Statistically significant differences from gene expression are denoted by * (0.01 <P £ 0.05) and ** (P £ 0.01) as determined by the pairwise Student's t-test analysis in SPSS 17.0 sofware.
Fig. 1 in Changes in midgut gene expression following Bacillus thuringiensis (Bacillales: Bacillaceae) infection in Monochamus alternatus (Coleoptera: Cerambycidae)
Fig. 1. Comparison of the gene expression levels between the control (CK) and Bt-exposed Monochamus alternatus. To compare the gene expression levels between the 2 libraries, each library was normalized to 1 million tags. The x-axis represents log10 of the reads per kb per million reads (RPKM) of the control sample, and the y-axis indicates log10 of the RPKM of the treated sample. The expression level of each gene is included in the volcano plot. The red dots represent transcripts that are more prevalent in the Bt-treated library, the green dots show those present at a lower frequency in the Bt-treated library, and the blue dots indicate transcripts that did not change significantly. The parameters "FDR <0.001" and "absolute value of log2(Treated/Control) ≥ 1" were used as the thresholds to judge the significance of the gene expression difference.
Fig. 10 in A mosaic of conserved and novel modes of gene expression and morphogenesis in mesoderm and muscle formation of a larval bivalve
Fig. 10 Muscle systems in bivalve lineages. a Bivalve phylogeny (after Combosch et al. (2017)) with larval muscle systems in various clades.?: unknown, numbers: number of paired retractors/adductors,>: set of paired mantle retractors, a.m.: after metamorphosis. Colour code indicates individual muscle systems. Comparative analysis implies that five major muscle systems were present in the last common ancestor (LCA) of autobranch bivalve larvae: The velum musculature including three or four pairs of velum retractors and a velum muscle ring, the larval retractors (one or two pairs), the adductor system containing the anterior as well as the posterior adductor,
Fig. 5 in A mosaic of conserved and novel modes of gene expression and morphogenesis in mesoderm and muscle formation of a larval bivalve
Fig. 5 Expression of myosin II heavy chain (Dro-mhc_c1) and myogenesis in Dreissena rostriformis veliger larvae. Lateral view in all images, anterior faces upwards and dorsal to the left except in c which is a dorso-anterior view, e and f which are anterior views (dorsal is up), and i which is a posterior view (dorsal is up). Arrowheads indicate the stomodaeum. Scale bar equals 20 µm. Brightfield images of the gene expression (a and e) and confocal images (b–d and f–i) with F-actin (yellow–red), cilia (green), and cell nuclei staining (cyan). a Expression of Dro-mhc_c1 is in the central and dorsal mesoderm. Velum (ve). b First distinct muscle bundles are the dorsal velum retractor (dv), the ventral velum retractor (vv), and the larval retractor (lr). First appearance of the velum muscle ring (vr), the (pal-
Fig. 3 in A mosaic of conserved and novel modes of gene expression and morphogenesis in mesoderm and muscle formation of a larval bivalve
Fig. 3 Expression of myosin II heavy chain (Dro-mhc_c1) and immunofluorescence staining in Dreissena rostriformis trochophore larvae. Anterior is up. Arrowheads indicate the stomodaeum, sf marks the shell field, dotted line outlines the region of the prototroch (pt). Scale bar equals 20 µm. Brightfield images (a, b) of the gene expression and confocal images (c, d) with F-actin (red), cilia (green; pt: prototroch; tt: telotroch), and cell nuclei staining (cyan). a Dro-mhc_c1 expression is first present in the anterior mesoderm. b Anterior mesodermal expression in dorsal view. c First F-actinpositive domain in the mesoderm below the shell field in the dorso-median region. d Slightly further developed trochophore larva showing two developing myofilaments in the median region. A, anterior; D, dorsal; P, posterior; V, ventral
Cell specificity of human regulatory annotations and their genetic effects on gene expression
<p>Processed data for the manuscript: Cell specificty of regulatory annotations and their genetics effects on gene expression.</p> <p>The code to generate these data is included in the zip-file: regulatoryAnnotations_comparisons-master.zip</p> <p>and at GitHub: https://github.com/ParkerLab/regulatoryAnnotations_comparisons</p> <p>Individual dataset information:</p> <p>numberOfSegments.dat.gz: Number of segments in each annotation</p> <p>lengthDistributionOfSegments.dat.gz: Length distribution of segments in each annnotation</p> <p>genomeCoverage.dat.gz: Total genome coverage of regions in each annoation</p> <p>overlapFraction.dat.gz: Basepair level overlap between two pairs of annotations</p> <p>annotations_chromatinStateOverlap.dat.gz: Overlap of annotations with chromatin states</p> <p>information.fourcells_enhancer.dat.gz: Information content of the mean enhancer chromatin posterior probability for annotation segments across four cell types</p> <p>information.fourcells_promoter.dat.gz: Information content of the mean promoter chromatin posterior probability for annotation segments across four cell types</p> <p>gwas_enrichment_stats.txt.gz: Enrichment of GWAS SNPs in annotations</p> <p>GTEx_v7.ESI_medianTPM_min0.15.dat.gz : ESI for genes across 50 tissues</p> <p>gtexv7_lcleqtl.enrichment.dat.gz: Enrichment of GTEx v7 LCL eQTL in annotations</p> <p>gtexv7_lcleqtl.binned_lclESI.enrichment.dat.gz: Enrichment of GTEx v7 LCL eQTL binned by lclESI in annotations</p> <p>K562.gtexv7_bloodeqtl.fdr0.1.prune0.8.maf0.2.ld0.99.annotations.dat.gz: GTEx v7 blood eQTL effect sizes in K562 annotations </p> <p>GM12878.gtexv7_lcleqtl.fdr0.1.prune0.8.maf0.2.ld0.99.annotations.dat.gz: GTEx v7 LCL eQTL effect sizes in GM12878 annotations</p> <p>GM12878.dsqtl.prune0.8.maf0.2.ld0.99.annotations.dat.gz : GM12878 DNase QTL effect sizes in GM12878 annotations</p> <p>GM12878.allelicBiasResults.FracRef.downsampled30.annotations.withMAF.dat.gz: GM12878 ATAC-seq allelic bias effect sizes in GM12878 annotations </p> <p> <br> <br> <br> </p>
Alterations in Patterns of Gene Expression and Perturbed Pathways Associated With Chemotherapy-Induced Nausea
<p>This dataset contains the supplementary materials describing in detail the methods and the results of the analyses. The manuscript has been submitted for publication. Please cite both the paper as well as the DOI of this dataset if you make use of the data.</p>
Classification of Gene Mutations and Cancer-Types with BioBombe Compressed Gene Expression Features
<p>BioBombe analysis applied to gene expression data from The Cancer Genome Atlas (TCGA) PanCanAtlas.</p> <p>Then, the compressed features learned through the serial compression are fed into several machine learning algorithms.</p> <p>The algorithms are used to predict mutation status (for the top 50 most mutated genes in TCGA) and cancer-type using the compressed gene expression features.</p> <p>Method and results described in https://github.com/greenelab/BioBombe. We use the classification approach outlined in https://github.com/greenelab/pancancer</p>
GTEx gene-level expression summary
<p>GTEx gene-level expression summary from the Snaptron collection. Format is a tab-separated text file compressed and indexed using BGZip. The accompanying Tabix index is also available. Uses GENCODE v25 annotation for quantification. Source data for the quantification are the bigWig files produced as part of recount2. More information at http://snaptron.cs.jhu.edu.</p>
Gene interaction networks from donor and failing heart gene expression
<p>These are the gene-gene interaction networks obtained from gene expression microarray data in the paper "Pathologic gene network rewiring implicates PPP1R3A as a central cardioprotective factor in pressure overload heart failure" by Cordero, Parikh, et al. The dataset contains the following items:</p> <p>* networks.zip: Compressed weighted matrices, in numpy format, for various methods in heart failure and donor cohorts, which are in the file name (ARACNE, JGL [Joint Graphical Lasso], Z-score, Pearson correlation, CLR [Context Likelihood of Relatedness])</p> <p>* wgcna.zip: Compressed weighted matrices, in numpy format, for WGCNA. These are the networks used in the paper.</p> <p>* network_gene_names.txt: Gene names for rows and columns of the gene networks in networks.zip</p> <p>* wgcna</p> <p>Construction of the networks were done as follows for each method:</p> <p>* For Pearson, Z-score, and CLR, we simply computed each relevant statistic in a pairwise manner, no thresholds were applied.</p> <p>* For ARACNE, we performed 500 bootstrapped iterations and searched the MI cutoff automatically using default parameters.</p> <p>* For JGL we performed an Akaike Information Criteria guided model selection by scanning the sparsity and group difference L1 penalty strengths.</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.