RujakBase project - Myristica database
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB48575 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR7229254.fastq.gz | Fastqsanger.gz | |||
| ERR7229255.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 2 of 2 |
Similar Datasets
Project description:ORG.one project - Myristica yunnanensis
| PRJEB53425 | ENA
Project description:Myristica fragrans Genome sequencing and assembly
| PRJNA778329 | ENA
Project description:Myristica yunnanensis Raw sequence reads
| PRJNA827624 | ENA
Project description:ORG.one project - Mangifera casturi for Whole Genome and Transcriptome Studies
| PRJEB46523 | ENA
Project description:As part of the EcoToxChip project, 49 distinct exposure studies were conducted on three lab model species (Japanese quail, fathead minnow, African clawed frog) and three ecologically relevant species (double crested cormorant, rainbow trout, northern leopard frog), at multiple life stages (embryo, adult), exposed to eight chemicals of environmental concern (ethinyl estradiol-EE2, hexabromocyclododecane-HBCD, lead-Pb, selenomethionine-SeMe, 17β trenbolone-TB, chlorpyrifos-CPF, fluoxetine-FLX, and benzo [a] pyrene-BaP. Whole transcriptome analyses were conducted on these samples resulting in a rich RNA seq dataset covering various species, life stages and chemicals, which is one of the largest purposeful complications of RNA seq data within ecotoxicology. Recently, a unified bioinformatics platform of relevance to ecotoxicology, EcoOmicsAnalyst and ExpressAnalyst, was developed to facilitate RNA Seq analysis of non-model species lacking a reference transcriptome. The platform uses the Seq2Fun algorithm to map RNA-seq reads from eukaryotic species to an ortholog database comprised of protein sequences from >600 eukaryotic species (EcoOmicsDB) with a translated search. The availability of these tools presents a unique opportunity to examine the EcoToxChip RNA Seq dataset for cross species comparisons. This work shows the potential of the EcoOmicsAnalyst and Seq2Fun platform to facilitate fast and simple analysis of RNA Seq datasets from non-model organisms with unannotated genomes and conduct comparative transcriptomic analysis across various species and life stages for cross-species extrapolation.
2023-12-05 | GSE239776 | GEO
Project description:The mouse Reference Transcriptome Database (MRTD) is the result of a multi-institute initiative funded with Federal Funds from the National Cancer Institute (NCI) and National Institutes of Health (NIH). When completed, this database will contain quantitative and comprehensive gene expression data obtained from more than one hundred different mouse samples. These data was initially acquired using the Massively Parallel Signature Sequencing (MPSS™) technology invented by Sidney Brenner and reduced to practice by Lynx Therapeutics, Inc. With recent advent of Illumina's Genome Analyzer technology, it was decided that Illumina?s current Genetic Analyzer is better suited for the project by its Clonal Single Molecule Array (CSMA™) technology. It is therefore adapted for the first 14 samples as displayed here. All samples are and will be sequenced at the Illumina facility in Hayward, CA. The data will be maintained and hosted by both the National Center for Biotechnology Information (NCBI->GEO). The high homology between human and mouse, the wealth of biological information available, the clinical relevance of the disease models, the completion of the genome sequencing, and the ease of manipulation of the genome make mouse the prime animal model for biomedical research. All these factors influenced the decision to choose this small mammalian as the first transcriptome to be sampled to this unprecedented depth. Eventually this database will contain a large collection of normal tissues or cell types that will serve as the basis for further disease state studies. CSMA™ is the ideal technology for establishing such a reference database. It provides superior sensitivity and dynamic range and it is the only technology that can routinely provide the sampling depth (2 to 5 million tags per sample) needed for accurately and quantitatively determining the expression level of every gene in a particular sample. In this database each individual sample has been sequenced to a depth of at least 2 million 20 nucleotide long expressed sequence tags. Unlike most other gene expression technologies that provide analog expression data, CSMA™ provides digital expression information, which is crucial for data exchange, comparison and expansion. Our goal is to enable researchers to directly access accurate expression information without conducting additional bench work. The database should also be useful for investigators interested in comparing their own set of CSMA™ data to the healthy tissues made available here. Because of the additive nature of this database, researchers will be able to gain insights on the expression levels of their gene(s) of interest across nearly a hundred samples while they will only need to conduct a few additional experiments targeted to their own area of interest. Keywords: Illumina Genetic Analyzer Sequencing, Clonal Single Molecule Array
2008-06-27 | GSE8324 | GEO
Project description:Interventions: Genomic test CANCERPLEX-JP OncoGuide NCC oncopanel system FndationONe CDx genome profile GUARDANT360 MSI Analysis System BRACAnalysis
Primary outcome(s): Development of genome database
Study Design: Single arm Non-randomized
| 2643590 | ecrin-mdr-crc