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54,099 results for “Expression”
ARTISTIC EXPRESSION OF THE IMAGE OF THE MOTHERLAND AND THE NATION IN THE STORY "SOHIBQIRON NABIRASI"
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Expression Pattern and Potential Functional Sites Analysis of ALOX12B Gene in Sheep Horn
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Curated RNA Sequencing Data for Zebrafish (Danio rerio) snoRNA Expression Analysis
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Single cell gene expression data and gene regulatory network
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Supplementary Material: Decoding sequence determinants of gene expression in diverse cellular and disease states
<p>Supplementary material for the following publication:</p> <p><strong>Decoding sequence determinants of gene expression in diverse cellular and disease states</strong></p> <p>Avantika Lal*,1, Alexander Karollus*,1,2,3, Laura Gunsalus1, David Garfield4, Surag Nair1, Alex M Tseng1, M Grace Gordon5, John Blischak6, Bryce van de Geijn6, Tushar Bhangale6, Jenna L Collier1, Nathaniel Diamant1, Tommaso Biancalani1, Hector Corrada Bravo1, Gabriele Scalia1, Gokcen Eraslan1</p> <p>*Equal contributions</p> <p>1Biology Research | AI Development, gRED Computational Sciences, Genentech, South San Francisco, CA 94080, USA</p> <p>2School of Computation, Information and Technology, Technical University of Munich, Germany</p> <p>3Munich Center for Machine Learning </p> <p>4OMNI Bioinformatics and Department of Regenerative Medicine, Genentech, South San Francisco, CA 94080, USA</p> <p>5 Department of Cellular and Tissue Genomics, Genentech Research and Early Development, Genentech, South San Francisco, CA 94080, USA</p> <p>6 Department of Human Genetics, Genentech, South San Francisco, CA 94080, USA</p> <p><strong><br></strong>Correspondence: Avantika Lal (<a href="mailto:lal.avantika@gene.com">lal.avantika@gene.com</a>), Gokcen Eraslan (<a href="mailto:eraslan.gokcen@gene.com">eraslan.gokcen@gene.com</a>)</p>
Increased Expression of Sorbitol Dehydrogenase in Colorectal Cancer Predicts BetterPrognosis (raw data)
<p>COAD/READ/COADREAD_rnaseq_fpkm.txt files contain TCGA RNA-Seq data in FPKM normalisation form for colorectal adenocarcinoma (COAD), rectum adenocarcinoma (READ) or combined (COADREAD).</p> <p>COAD/READ/COADREAD_rnaseq_tpm.txt files contain TCGA RNA-Seq data in TPM normalisation form for colorectal adenocarcinoma (COAD), rectum adenocarcinoma (READ) or combined (COADREAD).</p> <p>COAD/READ/COADREAD_clinical_raw.xlsx files contain TCGA clinical data for patients with colorectal adenocarcinoma (COAD), rectum adenocarcinoma (READ) or combined (COADREAD).</p> <p>COAD/READ/COADREAD_rnaseq_clinical_raw.xlsx files contain corresponding information of TCGA clinical data and RNA-Seq data for patients with colorectal adenocarcinoma (COAD), rectum adenocarcinoma (READ) or combined (COADREAD).</p> <p>Local_cohort_tumour/adenoma_qPCR_rawdata.xlsx files contain our experimental results of qPCR CT values for SORD and GAPDH (as internal ref), shown as separate values for duplicate wells and average values.</p> <p>Local_cohort_tumour_clinical_rawdata.xlsx contains clinical information and calculated SORD relative expression of our recruited patients.</p>
Data from: Orientation of mouse H19 ICR affects imprinted H19 gene expression through promoter methylation–dependent and –independent mechanisms
<p>The mouse <em>Igf2/H19</em> locus is regulated by genomic imprinting, in which the paternally methylated <em>H19</em> imprinting control region (ICR) plays a critical role in mono-allelic expression of the genes in the locus. Although the maternal allele–specific insulator activity of the <em>H19</em> ICR in regulating imprinted <em>Igf2</em> expression has been well established, the detailed mechanism by which the <em>H19</em> ICR controls mono-allelic <em>H19</em> gene expression has not been fully elucidated. In this study, we evaluated the effect of <em>H19</em> ICR orientation on imprinting regulation in mutant mice in which the <em>H19</em> ICR sequence was inverted at the endogenous locus. When the inverted-ICR allele was paternally inherited, the methylation level of the <em>H19</em> promoter was decreased and the <em>H19</em> gene was derepressed, suggesting that methylation of the <em>H19</em> promoter is essential for complete repression of <em>H19</em> gene expression. Unexpectedly, when the inverted allele was maternally inherited, the expression level of the <em>H19</em> gene was lower than that of the WT allele, even though the <em>H19</em> promoter remained fully hypomethylated. These observations suggested that the polarity of the <em>H19</em> ICR is involved in controlling imprinted <em>H19</em> gene expression on each parental allele, dependent or independent on DNA methylation of the <em>H19</em> promoter.</p>
Significant eQTLs and expression TWAS reference panels (AMP-AD brain and EADB Belgian LCL cohorts)
<p>This dataset is part of the manuscript "<em><strong>New insights into the genetic etiology of Alzheimer’s disease and related dementias</strong></em>" by Bellenguez, Küçükali, et al. Nature Genetics 2022.</p> <p>Publication link: <a href="https://www.nature.com/articles/s41588-022-01024-z">https://www.nature.com/articles/s41588-022-01024-z</a></p> <p>GitHub repository of all QTL/TWAS data shared for this study: <a href="https://github.com/SleegersLab-VIBCMN/EADB_GWAS_NatureGenetics_QTL_TWAS">https://github.com/SleegersLab-VIBCMN/EADB_GWAS_NatureGenetics_QTL_TWAS</a></p> <p>For details, please see the publication. For any questions, please contact Fahri Küçükali (<a href="mailto:fahri.kucukali@uantwerpen.vib.be">fahri.kucukali@uantwerpen.vib.be</a>) and Kristel Sleegers (<a href="mailto:Kristel.Sleegers@uantwerpen.vib.be">Kristel.Sleegers@uantwerpen.vib.be</a>).</p> <p>Significant eQTL catalogues are compressed with <em>gzip </em>and tar achieve of expression TWAS reference panels are compressed with <em>bzip2</em>.</p> <p><strong>eQTL catalogues</strong></p> <p>The files show significant eQTL - gene pairs mapped in AMP-AD brain and EADB Belgian LCL cohorts. The catalogues are in hg38/GRCh38 human genome build. Most of the columns in the files are based on FastQTL output (<a href="http://fastqtl.sourceforge.net/">http://fastqtl.sourceforge.net/</a>).</p> <p><em>eQTL file columns:</em></p> <ol> <li>variant_id - ID of the significant eQTL variant based on the dbSNPv151 rsID annotation or hg38/GRCh38 CHR_POS_REF_ALT ID if rsID not available.</li> <li>gene_id - eGene ENSG gene ID based on GENCODEv24 (AMP-AD) or GENCODEv32 (EADB Belgian)</li> <li>tss_distance - Genomic distance between eQTL variant and eGene</li> <li>ma_samples - Number of samples carrying the minor allele</li> <li>ma_count - Total count of minor alleles</li> <li>maf - Minor allele frequency</li> <li>pval_nominal - Nominal <em>P</em>-value of the association</li> <li>slope - Slope of the association with respect to alternative (ALT) allele indicated on column 14</li> <li>slope_se - Standard error of the slope</li> <li>pval_nominal_threshold - Nominal <em>P</em>-value significant threshold for this eGene</li> <li>min_pval_nominal - Most significant <em>P</em>-value observed for this eGene</li> <li>pval_beta - permutation <em>P</em>-value obtained via beta approximation and later used to calculate Storey q-values</li> <li>gene_name - eGene name based on GENCODEv24 (AMP-AD) and GENCODEv32 (EADB Belgian)</li> <li>GRCh38_chr_pos - Genomic position of the variant, separated by underscore</li> <li>ref_alt - Reference (REF) and alternative (ALT) allele of the variant, separated by ">" sign. ALT is the tested (A1) allele</li> </ol> <p>Of note, we also mapped the significant sQTLs in the same datasets (please see the data availability section of the manuscript or the GitHub repository).</p> <p><strong>Expression TWAS reference panels</strong></p> <p>Custom expression TWAS reference panels prepared using FUSION pipeline (<a href="http://gusevlab.org/projects/fusion/">http://gusevlab.org/projects/fusion/</a>) in AMP-AD brain and EADB Belgian LCL cohorts. All data in hg38/GRCh38 genome build. In each directory, you will find ".pos", ."profile", and ".profile.err" files. These are explained in the FUSION website as well, but briefly these are:</p> <ol> <li><strong>.pos:</strong> This is a position file that describes the 1Mb extended gene start and end coordinates for each calculated weight file for each gene expression phenotype. Used for scanning the variants in those coordinates for TWAS.</li> <li><strong>.profile: </strong>This informs about all prediction weights calculated, in terms of number of variants in the model, heritability information, and R2 info for each prediction model used (top1, blup, enet, bslmm, lasso; bslmm was not used therefore has NA values).</li> <li><strong>.profile.err: </strong>This summarizes the reference panel in terms of average hsq (with SD), and which model is the best performing.</li> </ol> <p>Each TWAS weight is provided in a .RDat file under <strong>All_Expression_Weights</strong>, and in this data we included all calculated functional weights independent of the fact that they are heritable features or not. In our TWAS analyses, we included the heritable functional weights at a hsq <em>P</em>-value ≤ 0.05 level.</p> <p>Please also see the splicing TWAS reference panels we prepared in the same datasets (see the data availability section of the manuscript or the GitHub repository). If you need an LD reference data in hg38/GRCh38 genome build based on 1000 Genomes NFE samples (whose variant ID annotation are matching to these functional weights), suitable for running the TWAS/FUSION pipeline, please contact us.</p>
Global gene expression analysis of Streptococcus agalactiae at exponential growth phase_Table 2
<p>Top-100 most expressed genes by functional category.</p>
Figure 2 from: King K, Meuti ME, Johnson NF (2021) Identification and expression of odorant binding proteins in the egg-parasitoid Trissolcus basalis (Wollaston) (Hymenoptera, Scelionidae, Telenominae). In: Lahey Z, Talamas E (Eds) Advances in the Systematics of Platygastroidea III. Journal of Hymenoptera Research 87: 251-266. https://doi.org/10.3897/jhr.87.68954
Figure 2 Maximum likelihood tree illustrating relationships among 136 OBP sequences from Nasonia vitripennis (Nv), Apis mellifera (Am), Cephus cinctus (Cc), Trissolcus japonicus (Tj), Telenomus podisi (Tp), and Trissolcus basalis (Tb). The tree is rooted with CcOBP12. TbOBPs are depicted in bold text and branches highlighted in green, other telenomine species are highlighted in blue. TbOBPs that cluster with single-copy orthologs (SCO), paralog group 2 (P2), and the OBP59a group of McKenzie et al. (2014) are highlighted in yellow, pink, and purple respectively. All bootstrap support values ≥ 85% are indicated at the relevant nodes; lower values are reported to clarify support level at other selected nodes.
Figure 1 from: King K, Meuti ME, Johnson NF (2021) Identification and expression of odorant binding proteins in the egg-parasitoid Trissolcus basalis (Wollaston) (Hymenoptera, Scelionidae, Telenominae). In: Lahey Z, Talamas E (Eds) Advances in the Systematics of Platygastroidea III. Journal of Hymenoptera Research 87: 251-266. https://doi.org/10.3897/jhr.87.68954
Figure 1 Position and orientation of syntenic TbOBPs present on genomic scaffolds 159 and 353. Yellow connected ribbon segments represent exon regions of each TbOBP. The black vertical lines labeled with gene names are located at the 5' end of each sequence.
Figure 3 from: King K, Meuti ME, Johnson NF (2021) Identification and expression of odorant binding proteins in the egg-parasitoid Trissolcus basalis (Wollaston) (Hymenoptera, Scelionidae, Telenominae). In: Lahey Z, Talamas E (Eds) Advances in the Systematics of Platygastroidea III. Journal of Hymenoptera Research 87: 251-266. https://doi.org/10.3897/jhr.87.68954
Figure 3 Expression profiles for 11 TbOBPs across four tissue types as measured with qPCR: female antennae (FA), female bodies (FB), male antennae (MA), and male bodies (MB). Black data points: normalized expression (log2) for each of five biological replicates per tissue; red dots: mean expression level. Significance differences (p < 0.05) are illustrated by differences in letters, calculated using TukeyHSD ANOVA means comparison.
Supplementary material 1 from: King K, Meuti ME, Johnson NF (2021) Identification and expression of odorant binding proteins in the egg-parasitoid Trissolcus basalis (Wollaston) (Hymenoptera, Scelionidae, Telenominae). In: Lahey Z, Talamas E (Eds) Advances in the Systematics of Platygastroidea III. Journal of Hymenoptera Research 87: 251-266. https://doi.org/10.3897/jhr.87.68954
TbOBP sequences; OBP sequences for gene tree; qPCR primers
Inference of molecular mechanisms of transcriptional regulation from co-expression data
<p>The accompanying data for the article "Inference of molecular mechanisms of transcriptional regulation from co-expression data". The article is now live on Research Square <a href="https://doi.org/10.21203/rs.3.rs-1262163/v1">10.21203/rs.3.rs-1262163/v1</a></p>
Endosperm preferentially expressed genes highlight unique activities in the wheat filling endosperm
<p><strong>Supplementary Table</strong></p>
NAME:Endosperm preferentially expressed genes highlight unique activities in the wheat filling endosperm
<p><strong>Supplementary Table</strong></p>
Targeted gene expression profiling of human myeloid cells from blood and lung compartments of patients with Tuberculosis and other lung diseases
<p>This dataset comprises expression profiles of 43 genes related to MSDC functioning and 5 reference genes in 8 blood samples and 8 brochio-alveolar lavage fluid (BALF) samples from TB patients. Also included are results from blood and BALF of 2 'other lung disease' patients each.</p>
Figure 9 from: Dorri K, Modaresi F, Shakibaie MR, Moazamian E (2022) Effect of gold nanoparticles on the expression of efflux pump mexA and mexB genes of Pseudomonas aeruginosa strains by Quantitative real-time PCR. Pharmacia 69(1): 125-133. https://doi.org/10.3897/pharmacia.69.e77608
Figure 9 Results of toxA gene replication in clinical isolates of Pseudomonas aeruginosa. Well 1: marker size 50 bp; Well 2–23: positive samples of size 85 bp; Well 24: negative control; Well 25: positive control of Pseudomonas aeruginosa PTCC 17589.
Figure 8 from: Dorri K, Modaresi F, Shakibaie MR, Moazamian E (2022) Effect of gold nanoparticles on the expression of efflux pump mexA and mexB genes of Pseudomonas aeruginosa strains by Quantitative real-time PCR. Pharmacia 69(1): 125-133. https://doi.org/10.3897/pharmacia.69.e77608
Figure 8 Results of Pela gene replication in clinical isolates of Pseudomonas aeruginosa. Well 1: marker size 50 bp; Well 2–23: positive samples of size 148 bp; Well 24: negative control; Well 25: positive control of Pseudomonas aeruginosa PTCC 17589.
Figure 7 from: Dorri K, Modaresi F, Shakibaie MR, Moazamian E (2022) Effect of gold nanoparticles on the expression of efflux pump mexA and mexB genes of Pseudomonas aeruginosa strains by Quantitative real-time PCR. Pharmacia 69(1): 125-133. https://doi.org/10.3897/pharmacia.69.e77608
Figure 7 Results of lasR gene replication in clinical isolates of Pseudomonas aeruginosa. Well 1: marker size 50 bp; Well 2–26: positive samples of size 130 bp; Well 27: negative control; Well 28: positive control of Pseudomonas aeruginosa PTCC 17589.
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)
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.