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1,278 results for “microarray analysis”
The raw microarray data and the differential expression analysis results from "Manipulating the growth environment through co-culture to enhance stress tolerance and viability of probiotic strains in the gastrointestinal tract".
<p>The signal data for each spot were subsequently quantified by using Feature Extraction software (Agilent Technologies).M1.txt to M5.txt: monoculture; C1.txt to C5.txt: co-culture; P1.txt to P5.txt: pH-controlled monoculture. The differential expression analysis results were obtained by using limma.</p>
Analysis of heme and iron influence on Porphyromonas gingivalis A7436 and ATCC 33277 strains genes expression (microarray results)
<p>The aim of this study was to analyze phenotypic differences between <i>P. gingivalis</i> more virulent A7436 and less virulent ATCC 33277 (33277) strains. The analysis comprised the influence of heme and iron on <i>P. gingivalis</i> gene expression. </p><p><i>P. gingivalis</i> A7436 and 33277 strains were cultured in basal medium (3% trypticase soy broth and 0.5% yeast extract), supplemented with 3.6 mM L-cysteine hydrochloride, and 0.5 mg/l menadione, in anaerobic conditions (80% N2, 10% H2 and 10% CO2). To generate heme and iron-limited conditions, the medium was supplemented with 0.16 mM of the iron chelator 2,2-dipyridyl (DIP conditions). To generate heme and iron-rich conditions, the medium was supplemented with 0.0077mM hemin chloride (Hm conditions). Three sample replicates of A7436 and 33277 strains were grown in Hm or DIP conditions for 20 hours. RNA isolation and microarray analysis were performed in IMGM laboratories (Martinsried, Germany), as described by Śmiga et al. (2023).</p><p>The online tool eArray (http://earray.chem.agilent.com/; Agilent Technologies, Santa Clara, CA, USA) was used to design an Agilent Custom <i>Porphyromonas gingivalis</i> A7436 Gene Expression Microarray (8×15K format). Probes were prepared based on <i>P. gingivalis</i> transcriptome information derived from the NCBI reference sequence NZ_CP011995.1. Total RNA isolation, RNA quantity, and quality were determined as described by Curaszkiewicz et al. 2014. For internal labeling control, the total RNA was spiked with <i>in vitro </i>synthesized polyadenylated transcripts (One-Color RNA Spike-In Mix; Agilent Technologies). Subsequently, samples were reverse transcribed into cDNA and then converted into cyanine-3-labeled complementary RNA (cRNA) with Low Input Quick-Amp Labeling Kit One-Color (Agilent Technologies). For microarray hybridization, a Gene Expression Hybridization Kit (Agilent Technologies) was used. Labeled cRNA was hybridized for 17 hours at 65℃ on Agilent Custom GE 8×15K Microarrays, washed according to the manufacturer's protocol, and dried with acetonitrile (Sigma-Aldrich). The fluorescence of samples was detected with Scan Control A.8.4.1 software (Agilent Technologies) on the Agilent DNA Microarray Scanner (Agilent Technologies) and extracted from the images using Feature Extraction 10.7.3.1 software (Agilent Technologies). For data analysis, Feature Extraction 10.7.3.1 (Agilent Technologies), GeneSpring GX 13.1.1 (Agilent Technologies), and Excel 2010 (Microsoft, Redmond, WA, USA) were used. For statistical analysis, Welch's approximate <i>t</i>-test was used. Differences in gene expression are shown as fold change values (FC). The average was calculated from the normalized signal values and they were transformed from the log2 to the linear scale. Increases and decreases in gene expression are shown as positive and negative numbers, respectively. The fold change in gene expression was considered significant for FC ≥ 2 or FC ≤ -2 and <i>P</i>-value ≤ 0.05</p><ul><li>Ciuraszkiewicz J, Śmiga M, Mackiewicz P, Gmiterek A, Bielecki M, Olczak M, Olczak T. 2014. Fur homolog regulates <i>Porphyromonas gingivalis </i>virulence under low-iron/heme conditions through a complex regulatory network. Mol Oral Microbiol 29:333-353. doi: 10.1111/omi.12077.</li><li>Śmiga M, Ślęzak P, Olczak T. 2023. Comparative analysis of <i>Porphyromonas gingivalis</i> A7436 and ATCC 33277 strains reveals differences in the expression of heme acquisition systems. Microbiol Spectr (revised manuscript under revision).</li></ul>
Data and Analysis Files Repository: Repurposing Large-Format Microarrays for Scalable Spatial Transcriptomics
<p>Data and Analysis Files from "Repurposing Large-Format Microarrays for Scalable Spatial Transcriptomics"</p> <p>ArraySeq_Method.zip contains the following folder and contents:</p> <ul> <li>STARSolo: All code and count matrix output from fastq spatial barcode demultiplexing. </li> <li>Images: All resolution-downsampled H&E image scans from analyzed tissues</li> <li>Space_Ranger: All 10x Space Ranger output from Visium datasets generated in the paper. </li> <li>Analysis: All scripts for analyzing and plotting Array-seq and Visium datasets generated in this paper. Also contains output h5ad files. </li> </ul> <p>ArraySeq_Barcode_generation_n12.rmd: The script used to generate the Array-seq probes with 12-mer spatial barcodes. </p>
Galaxy Training Data for "End-to-End Tissue Microarray Image Analysis with Galaxy-ME"
<p>This dataset provides the inputs used in the Galaxy Training Network (GTN) training 'End-to-End Tissue Microarray Image Analysis with Galaxy-ME'. The tutorial demonstrates how to use the Galaxy-ME tool suite for primary image processing, data analysis, and interactive visualization of multiple tissue imaging datasets. Original data was published by <a href="https://pubmed.ncbi.nlm.nih.gov/34824477/">Schapiro <em>et al</em></a>.</p>
Axiom canine microarray data from Australian dingoes and domestic dogs for admixture and population structure analysis
<p>Admixture between species is a cause for concern in wildlife management. Canids are particularly vulnerable to inter-specific hybridisation, and genetic admixture has shaped their evolutionary history. Microsatellite DNA testing, relying on a small number of genetic markers and geographically restricted reference populations, has identified extensive domestic dog admixture in Australian dingoes and driven conservation management policy. There has been concern that geographic variation in dingo genotypes could confound ancestry analyses that use a small number of genetic markers. Here we apply genome-wide single nucleotide polymorphism (SNP) genotyping to a set of 385 wild and captive dingoes from across Australia and then carry out comparisons to domestic dogs, and perform ancestry modelling and biogeographic analyses to characterize population structure in dingoes and investigate the extent of admixture between dingoes and dogs in different regions of the continent. We show that there are at least five distinct dingo populations across Australia. We observed limited evidence of dog admixture in wild dingoes, challenging previous reports regarding the occurrence and extent of dog admixture in dingoes, as our ancestry analyses show that previous assessments severely overestimate the degree of domestic dog admixture in dingo populations, particularly in southeastern Australia. These findings strongly support the use of genome-wide SNP genotyping as a refined method for wildlife managers and policy makers to assess and inform dingo management policy and legislation moving forwards.</p>
Microarray analysis of Quail Embryo Pharyngeal Pouch Endoderm
<p>Anterior endoderm region was isolated from Coturnix japonica embryos at qE3 and 2PP and 3/4PP endoderm separated from central pharynx. Total RNA was isolated from two biological replicate of 2PP and 3/4PP endoderm samples. Transcription profiles were obtained using GeneChip® Chicken Genome Array.</p>
Treatment of Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma (CLL/SLL): DNA Microarray Gene Expression Analysis
ClinicalTrials.gov study NCT00001586. IPD Sharing: Not stated. Countries: 1. Publications: 5.
Axiom canine microarray data from Australian dingoes and domestic dogs for admixture and population structure analysis
Open the record for dataset details and reuse information.
Microarray analysis of EZH2 knockout HaCat cell lines
Open the record for dataset details and reuse information.
Microarray Analysis of microRNA Expression in Basal Cell Carcinoma
ClinicalTrials.gov study NCT01498250. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Genetic Expression Alteration Affect on Lateral Neck Node Metastasis of Thyroid Papillary Microcarcinoma : Microarray Analysis
ClinicalTrials.gov study NCT01384669. IPD Sharing: Not stated. Countries: 1. Publications: 20.
Microarray Analysis of Gene Expression in Idiopathic Pulmonary Fibrosis (IPF)
ClinicalTrials.gov study NCT00258544. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Microarray Analysis of Scalp Biopsies After Minoxidil Treatment
ClinicalTrials.gov study NCT01309191. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Microarray Analysis of IFN-Induced Gene Expression in Obese and Non-Obese Patients With Chronic Hepatitis C
ClinicalTrials.gov study NCT00322179. IPD Sharing: Not stated. Countries: 1. Publications: 5.
The Eshre Study Into The Evaluation of Oocyte Euploidy by Microarray Analysis
ClinicalTrials.gov study NCT01532284. IPD Sharing: UNDECIDED. Countries: 6. Publications: 2.
Microarray Analysis of microRNA Expression Profiles in Cutaneous Squamous Cell Carcinoma
ClinicalTrials.gov study NCT01500954. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Comparative Microarray Analysis in Primary Cutaneous Malignant Melanoma
ClinicalTrials.gov study NCT01482260. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Microarray Analysis in Syndromic Obesity
ClinicalTrials.gov study NCT01043198. IPD Sharing: Not stated. Countries: 1. Publications: 8.
Microarray Analysis for Human Genetic Disease
ClinicalTrials.gov study NCT00001898. IPD Sharing: Not stated. Countries: 4. Publications: 1.
Gene Expression Profiles in Generalized Aggressive Periodontitis: A Gene Network-based Microarray Analysis
ClinicalTrials.gov study NCT02327533. IPD Sharing: Not stated. Countries: 0. Publications: 3.
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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.