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8 results for “molecular marker development”
Data from: Genomic exploration and molecular marker development in a large and complex conifer genome using RADseq and mRNAseq
We combined restriction site associated DNA sequencing (RADseq) using a hypomethylation-sensitive enzyme and messenger RNA sequencing (mRNAseq) to develop molecular markers for the 16 gigabase genome of Cedrus atlantica, a conifer tree species. With each method, Illumina® reads from one individual were used to generate de novo assemblies. SNPs from the RADseq data set were detected in a panel of one single individual and three pools of three individuals each. We developed a flexible script to estimate the ascertainment bias in SNP detection considering the pooling and sampling effects on the probability of not detecting an existing polymorphism. Gene Ontology (GO) and transposable element (TE) search analyses were applied to both data sets. The RADseq and the mRNAseq assemblies represented 0.1% and 0.6% of the genome, respectively. Genome complexity reduction resulted in 17% of the RADseq contigs potentially coding for proteins. This rate was doubled in the mRNAseq data set, suggesting that RADseq also explores noncoding low-repeat regions. The two methods gave very similar GO-slim profiles. As expected, the two assemblies were poor in TE-like sequences (<4% of contigs length). We identified 17,348 single nucleotide polymorphisms (SNPs) in the RADseq data set and 5,714 simple sequence repeats (SSRs) in the transcriptome. A subset of 282 SNPs was validated using the Fluidigm genotyping technology, giving a conversion rate of 50.4%, falling within the expected range for conifers. Increasing sample size had the greatest effect for ascertainment bias reduction. These results validated the utility of the RADseq approach for highly complex genomes such as conifers.
Development of a Next Generation Sequencing (NGS) -Based Assay to Detect Preeclampsia Molecular Markers
ClinicalTrials.gov study NCT02808494. IPD Sharing: NO. Countries: 1. Publications: 1.
Data from: Genomic exploration and molecular marker development in a large and complex conifer genome using RADseq and mRNAseq
Open the record for dataset details and reuse information.
Data from: Identifying differentially expressed genes under heat stress and developing molecular markers in orchardgrass (Dactylis glomerata L.) through transcriptome analysis
Open the record for dataset details and reuse information.
Molecular Markers in Predicting Lung Cancer Development Using Tissue Samples From Healthy Participants
ClinicalTrials.gov study NCT00899457. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Mapping and molecular marker development for the BnaSBT gene controlling inflorescence and plant architectures in B. napus
GEO Series GSE293898. Brassica napus. 12 samples. Type: Expression profiling by high throughput sequencing.
Molecular Marker for predicting development of cancer in ulcerative colitis
GEO Series GSE3629. Homo sapiens. 121 samples. Type: Expression profiling by array.
Development of molecular markers linked to powdery mildew resistance gene Pm4b by combining SNP discovery from transcriptome sequencing data with bulked segretant analysis (BSR-seq) in wheat
GEO Series GSE108697. Triticum aestivum. 2 samples. Type: Genome variation profiling by high throughput sequencing.
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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.