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355 results for “data extraction”
Data from: Direct PCR meets high-throughput sequencing - metabarcoding of chironomid communities without DNA extraction
<p>Abstract</p> <p>Metabarcoding is a valuable tool for investigating insect community compositions. However, high-throughput applications, such as for biomonitoring, require cost-effective and user-friendly procedures. To investigate if the time-consuming and labour-intensive DNA isolation step can be omitted in metabarcoding, we studied the difference in detection rates and individual read abundance using standard DNA isolation versus direct PCR protocols. Metabarcoding with and without DNA isolation was performed on artificially created communities with known composition as well as on natural communities both of the dipteran family Chironomidae to compare detection rates, individual read abundances and presence-absence community composition. The data sets include read abundances of all artificial and natural community samples. Compositions of the samples per data set are described in the respective README files. ASVs/OTUs and their respective DNA sequences are given. R Scripts for bioinformatic processing (dada2 for ASVs, JAMP for OTUs) are provided.</p> <p>Methods</p> <p>Chironomidae were retrieved from artificial ponds of the Eußerthal Ecosystem Research Station (EERES) near Landau, Germany, in 2019 and 2020. Adult specimens were collected from passive emergence traps. Chironomid samples were stored in 70% ethanol and later dried at 60°C. Samples were then finely ground using a bead mill. PCR-grade water was added to each tissue sample and thoroughly vortexed. The tissue-water mixes were frozen at -20°C until further analysis. Artificial communities were created by pipetting tissue-water mixes of individual chironomids. Natural communities from eight ponds and five consecutive sampling dates were selected to assess the applicability of the dPCR approach compared to standard metabarcoding protocols on natural chironomid communities. Four of the artificial ponds were treated with the mosquito control agent <em>Bacillus thuringiensis israelensis</em> (Bti). Tissue-water mixes of artificial and natural communities were both directly applied to PCR and used for DNA isolation. Illumina sequencing was performed and raw data were bioinformatically prepared. For more details see "Direct PCR meets high-throughput sequencing - metabarcoding of chironomid communities without DNA extraction" (Röder & Schwenk 2023). Raw sequences are available through GenBank SRA archive (BioProject accession number PRJNA989176). </p>
Platform for Medical Information Extraction From Incomplete Data
ClinicalTrials.gov study NCT01813942. IPD Sharing: Not stated. Countries: 1. Publications: 0.
A Clinical Study to Investigate the Reliability of Fetal Heart Rate and Maternal Heart Rate Signals Extracted From Biopotential Data
ClinicalTrials.gov study NCT05498298. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
With the Development of Research, New Algorithms and Technologies Have Emerged, One of Which is Machine Learning. Machine Learning Can Extract Key Factors From Vast Amounts of Data, Identify Underlyin
ClinicalTrials.gov study NCT07121309. IPD Sharing: NO. Countries: 1. Publications: 0.
Expression data from ethanol extract of Aurantiochytrium Sp. (EEA)-treated human amnion epithelial cells (hAECs)
GEO Series GSE188411. Homo sapiens. 6 samples. Type: Expression profiling by array.
Expression data from mouse adrenal glands extracted from wild-type and sf1:Cre; Ezh2 Fl/Fl (KO) adrenals
GEO Series GSE109578. Mus musculus. 7 samples. Type: Expression profiling by array.
Data from: Extraction and separation of active ingredients in Schisandra chinensis (Turcz.) Baill and the study of their antifungal effects
Open the record for dataset details and reuse information.
Data from: Anthocyanin extracted from black soybean seed coats prevents autoimmune arthritis by suppressing the development of Th17 cells and synthesis of proinflammatory cytokines by such cells, via inhibition of NF-κB
Open the record for dataset details and reuse information.
RNA-sequencing data of caecum tissue of mice infected with helminths and administered garlic extract
GEO Series GSE178499. Mus musculus. 19 samples. Type: Expression profiling by high throughput sequencing.
Expression data from mouse adrenal glands extracted from wild-type (WT) and Cyp11b2tm1.1(cre)Brlt;Prkar1afl/fl(KO) adrenals
GEO Series GSE103899. Mus musculus. 24 samples. Type: Expression profiling by array.
Expression data from WT and Elektra (Slfn2 mutant, loss of function) homozygous hematopoietic multipotent progenitor cells extracted from mice.
GEO Series GSE224122. Mus musculus. 8 samples. Type: Expression profiling by array.
Expression data from HUVEC treated with combinations of IL-1 plus P. santalinus extract
GEO Series GSE178106. Homo sapiens. 4 samples. Type: Expression profiling by array.
RNA sequence data in whole cell extracts of differentiated human podocytes
GEO Series GSE129666. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Expression data from WT and BMPR2 knockout hematopoietic stem cells extracted from mice.
GEO Series GSE209862. Mus musculus. 8 samples. Type: Expression profiling by array.
RNA-Seq data for 35 controls using total RNA extracted using RNAZol
GEO Series GSE169359. Homo sapiens. 35 samples. Type: Expression profiling by high throughput sequencing.
Expression data of exosomal miRNAs extracted from plasma [Affymetrix miRNA 4.0]
GEO Series GSE291442. Homo sapiens; synthetic construct. 10 samples. Type: Non-coding RNA profiling by array.
Expression data of mice ovarian tissue cell treated with Red Ginseng Extract fraction (RGE)
GEO Series GSE144954. Mus musculus. 12 samples. Type: Expression profiling by array.
Expression data from WT and Elektra (Slfn2 mutant, loss of function) homozygous hematopoietic stem cells extracted from mice.
GEO Series GSE224120. Mus musculus. 8 samples. Type: Expression profiling by array.
RNA-sequencing data of macrophages exposed to LPS and/or garlic extract
GEO Series GSE178282. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing.
RNA-sequencing data of CMT-93 cells exposed to LPS and/or garlic extract
GEO Series GSE178655. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing.
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.