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54,099 results for “Expression”
Expression and purification of huntingtin nanobody iVHH4 in E. coli (2017/11/20)
<p>Huntingtin structure function open lab notebook</p>
Full-length huntingtin Q54 and Q145 expression and purification – 29th November 2017
<p>Huntingtin structure-function open lab notebook</p>
Full-length huntingtin Q23 expression and purification – 19th November 2017
<p>Huntingtin structure-function open lab notebook</p>
List of differential expressed genes for the different conditions
Open the record for dataset details and reuse information.
Ectopic expression of murine CD163 enables cell-culture isolation of lactate dehydrogenase-elevating (LDV) virus 63 years after its discovery
<p><span>Arteriviruses are RNA viruses related to coronaviruses but have not yet been associated with human infection. A murine arterivirus (lactate dehydrogenase-elevating virus, LDV) was first described in 1960 and quickly became a promising model for understanding immune failure due to its unique ability to persist in immunocompetent adult mice. However, inability to culture LDV <em>in vitro</em> ultimately limited this system. Here, we demonstrate that the macrophage marker CD163 is essential for LDV infection. Expression of the murine homolog (mCD163) in otherwise mCD163-negative cell lines from mice and nonhuman primates enables productive LDV infection, creating the first immortalized cell-culture system. We also show that mCD163-knockout mice are completely resistant to LDV infection. These findings advance LDV as a model of arterivirus infection viral persistence and add to a growing body of literature suggesting that CD163 utilization is a broad feature of arteriviruses.</span></p>
Gene expression profile at both bulk and single cell level for heterogeneous cell type mixtures of A375, HAP1, THP1, HEK239FT, K562, and A549
<p>We used poly-A bulk RNA sequencing and single-cell RNA sequencing using mixtures of well-characterized purified cell lines to better understand measurement noise between technologies. A375, HAP1, THP1, HEK239FT, K562, and A549 cells were mixed in various proportions to generate four in vivo cell mixtures that mimic tissues. Mixtures of 6, 4, 2, and 1 of the cell types are respectively denoted 6ct, 4ct, 2ct, and 1ct. In the included zip, directories are labeled using this notation, followed by a list of cell types in the mixture after an underscore. In each directory, bulk and single cell count data is included.</p>
Figure 4 in Agrobacterium-mediated gene delivery and transient expression in the red macroalga Chondrus crispus
Figure 4: Effect of cultivation medium, wounding method and acetosyringone on Agrobacterium transformation efficiency. The transformation efficiencies of Chondrus thalli segments co-cultivated with pCAMBIA 1301-transformed Agrobacterium in seawater and Induction Medium (IM) were compared. Using seawater as co-cultivation medium, the wound-related treatments, namely biolistics wounding, wounding using pin-pricks and no wounding, were compared. The effect of acetosyringone (100 µM) was also studied. Data are expressed as means ± SE (n = 4). The Mann-Whitney non-parametric test was conducted to compare between two groups.
Figure 2 in Agrobacterium-mediated gene delivery and transient expression in the red macroalga Chondrus crispus
Figure 2: Intimate contact and adhesion of bacteria to wound sites of Chondrus thalli. Thalli co-cultivated for 48 h in induction medium were fixed and viewed under a scanning electron microscope: (A) control thallus incubated without bacteria showing a clean bacterium-free surface; (B) close up view of rod-shaped bacteria attached to thallus surface at wound site; (C) bacterial film at wound sites on thallus surface.
Figure 1 in Agrobacterium-mediated gene delivery and transient expression in the red macroalga Chondrus crispus
Figure 1: Features of binary vectors for Agrobacterium-mediated transformation. (A) Chondrus-specific expression cassette. Salient features: 1.812 kbp GUS gene modified to match the favoured codon usage of Chondrus, promoter region of the Chondrus actin gene, nopaline synthase (NOS) gene terminator from Genbank accession AF502128.1; (B) Binary vector pCAMBIA 1301. Salient features: GUS gene with castor bean catalase intron driven by a CAMV 35 S promoter and terminated by NOS.
Figure 5 in Agrobacterium-mediated gene delivery and transient expression in the red macroalga Chondrus crispus
Figure 5: GUS expression in Chondrus thallus segments transformed with LBA 4404/pRI 910 (Ac-GUS). (A) Surface view of control thallus not co-cultivated with Agrobacterium, (B) surface view of transformed thallus showing GUS expression at wound sites, (C) section through untransformed thallus, (D) thallus section within wounded area showing blue medullary cells at wound spots, (E) cortical cells from untransformed control thallus, (F) GUS-expressing cortical cells in transformed thallus, (G) medullary filaments from untransformed control thallus, (H) medullary filaments from transformed thallus.
Figure 3 in Agrobacterium-mediated gene delivery and transient expression in the red macroalga Chondrus crispus
Figure 3: Histochemical staining and low-power microscopic analysis of Chondrus thallus segments for transient expression of GUS 7 days after co-cultivation. (A) Pin-pricked thalli co-cultivated without bacteria, (B) pin-pricked thalli co-cultivated with untransformed LBA4404 bacteria, (C) unwounded and untransformed thalli, (D) pin-pricked thalli co-cultivated with LBA4404/pRI 910 (no GUS gene), (E) thalli transformed with LBA4404 (pCAMBIA 1301), scale bar: 1 cm.
Dataset: Induction of Bacterial Expression at the mRNA Level by Light
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New Expression of the Field-line Integrated Rayleigh-Taylor Instability Growth Rate
<p>The data provided in correlation with the journal article bearing the same title.</p>
Knockout of Hsp70 genes significantly affects locomotion speed and gene expression in leg skeletal muscles of Drosophila melanogaster
<p>Supplemental data for a study <strong>Knockout of </strong><em><strong>Hsp70 </strong></em><strong>genes significantly affects locomotion speed and gene expression in leg skeletal muscles of </strong><em><strong>Drosophila melanogaster </strong></em>(Physiol Genomics 56: 567–575, 2024.<br><a href="https://doi.org/10.1152/physiolgenomics.00143.2023">https://doi.org/10.1152/physiolgenomics.00143.2023</a> )</p>
Gene expression data from qPCR analysis of molting relevant genes in Calanus finmarchicus utilizing double delta-Ct method
<p>Gene expression data from qPCR analysis of molting relevant genes in Calanus finmarchicus utilizing double delta-Ct method for calculations of fold change and mean fold change. </p>
Genes with differential expression across ancestries are enriched in ancestry-specific disease effects likely due to gene-by-environment interactions
<p>This repository contains raw data, preprocessing scripts, and analysis code to replicate S-LDXR analysis from Wang et al.</p> <p>The project directory is organized as follows:<br>- `compute_de.r`: The script to compute anc-de genes<br>- `create_annot.100kb.sh`: code to create annotations for S-LDXR<br>- `create_annot.r`: R function used to create annotations for S-LDXR<br>- `DEstats.tgz`: Differential gene expression statistics between EAS and EUR for each 7 main cell types + PCs of each cell within each cell type<br>- `list_genes.txt`: Gene list as QCed as in Gazal et al. 2022 Nat Genet<br>- `Lupus_study_adjusted_compressed.h5ad.gz`: The single-cell dataset of Perez*, Gordon*, Subramaniam* et al. 2022 Science used in this study<br>- `README.sh`: This README file<br>- `sldxr_annotations.tgz`: Main S-LDXR annotations used in this study<br>- `sldxr_ref_files.tgz`: S-LDXR reference files (baseline-LD-X annotations, regression weights and EAS and EUR 1000G genotype reference files)<br>- `sumstats.tgz`: GWAS summary statistics of 31 traits in EAS and EUR populations<br>- `code_figures.tgz`: Code files for main figures</p>
Reconstruction of gene regulatory networks for Caenorhabditis elegans using tree-shaped gene expression data
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Supplementary Materials: High-Quality Genome of a novel species belonging to the family Thermosynechococcaceae from Namibia and characterization of its protein expression patterns at elevated temperatures
<p><strong>Supplementary Materials</strong> to the scientific research article "<strong>High-Quality Genome of a novel species belonging to the family<em> Thermosynechococcaceae </em>from Namibia and characterization of its protein expression patterns at elevated temperatures</strong>" in MicrobiologyOpen.</p> <p>Including raw data of: the BCG analysis with antismash, dbCAN3 analysis of carbohydrate active enzymes, eggNOG mapper and KEGG (blastKOALA) functional annotations, whole genome alignments with progressiveMauve, ortholog-based phylogenetics with OrthoFinder, RAST annotations of the novel <em>Thermosynechococcus</em> sp. Okahandja<em> </em>and the type strains <em>Thermosynechococcus lividus</em> PCC 6715-6717, the full length 16S rRNA sequence extracted from the genome, proteomics analyses, the novel <em>T. </em>sp. Okahandja<em> </em>annotated genome, additional STEM microscopy figures and CRISPR analyses.</p>
Raw Data of Polymerase Chain Reaction (qPCR) results of SCUBE3 and TGF-B expression
<p>This raw data presents the qPCR results of SCUBE3 and TGF-B expression from each sample taken from the patient's pleural tissue. Each sample was divided into 14 groups consisting of two main control groups (control group with 1x1 cm preparation and 2x2 cm preparation) and 12 groups divided based on the length of incubation time (group incubated for 24 hours and group incubated for 72 hours). Each of these groups consisted of two groups divided by preparation size, namely the group with 1x1 cm preparation and 2x2 preparation. Each preparation group was further divided into three small groups based on treatment, namely the control group, the group with 50 µg EGCG administration, and 100 µg EGCG administration. </p>
Genetic alterations and expression programs of oral squamous cell carcinoma associated with betel quid chewing
<p><span>Betel quid (BQ) chewing is a profound risk for</span><span> oral squamous cell carcinoma (OSCC) <span>in Southeast Asia.</span> To decipher contributory genomic abnormalities and transcriptional reprogramming in these malignancies, we conducted a multi-omics survey, including exome sequencing of tumor-normal pairs from <span>261 male </span>patients with OSCC (129 habitual BQ chewers and 132 non-BQ users), alone with integrated single-cell and spatial transcriptomics of a set of tumors. Comparative analyses of the mutational catalog identified enrichment of significantly altered genes (e.g mutations of <em>TP53</em> and <em>CHUK</em>, copy gains of <em>MAP3K13</em> and <em>FADD</em>, copy losses of <em>CDKN2A</em>) and mutational signatures associated with BQ chewing. Assessment of oncogenic and co-occurring actionable alterations demonstrated frequently altered oncogenic pathways (Hippo and p53 signaling) and potential combination therapy opportunities linked to BQ use. In addition, evaluation of epithelial, immune, stromal expression programs in the corresponding tissue compartments revealed a shift of tumor microenvironment in BQ-related OSCC, characterized by induced hypoxia of tumor epithelium, altered immunosuppression of dendritic cells, and raised sprouting angiogenesis of tumor endothelium. Quantitative predictions of intercellular communications inferred a more heterogeneous cell-cell crosstalk among BQ-related OSCC, highlighted by extensive interactions of fibroblasts and dendritic cells with other non-epithelial cell types via mostly extracellular matrix-receptor signaling pathways. Collectively, these differences in genomic landscape and tumor niche suggest that OSCC caused by BQ chewing could be an etiological subtype different from their BQ-negative counterparts.</span></p>
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.