Filters: System Type: Data Release (X) > Categories: NOT Data Release - In Progress (X) > Tags: {"type":"USGS Scientific Topic Keyword","name":"genetics"} (X) > partyWithName: Columbia Environmental Research Center (X)
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Data from metabarcoding assays to detect a suite of mussel species using mitochondrial DNA regions of the cytochrome c oxidase subunit I (COI) and NADH dehydrogenase subunit (ND1) genes sequences.
Data describe a designed environmental DNA (eDNA) survey for the detection of longnose darter (Percina nasuta) in field collected water samples. Parameters described include the limit of detection and limit of quantification of the assay; a list of freshwater fish species tissue samples that were used to test specificity of the assay; and field collected water samples that were tested to detect the presence of longnose darter DNA. Samples were collected from sites on the St. Francis river, Missouri in 2018.
Data consist of genotypes for pallid sturgeon and paddlefish broodstock and artificially-produced larvae at 19 sturgeon microsatellite loci and four paddlefish loci. Microsatellite genotypes allowed confirmation of homozygous sturgeon DNA and absence of paddlefish DNA in haploid gynogens. Data also consist of DNA yield estimates for haploid gynogens for proof of concept that haploid gynogens can provide sufficient DNA quantity for restriction site-associated DNA sequencing studies.
The data describe the technical performance of a designed qPCR assay for the detection of mucket (Actinonaias ligamentina) eDNA from field collected water samples. Parameters described include the sequences of the primers and probes used; the limit of detection and limit of quantification for the assay; a list of freshwater mussels species that were used to test specificity of the assay; and in situ field samples that were tested to the verify assay.
Data describe results of a set of laboratory experiments using polyacrylamide gel electrophoresis with a thiaminase activity stain to test the solubility and thiaminase activity of recombinant putative thiaminases expressed in E. coli. Parameters described include the presence and relative mobility of thiaminases, and the presence and relative mobility of recombinant proteins. Experiments were conducted at the USGS Columbia Environmental Research Center, Columbia, MO in 2012 and 2013.
Whole genome sequence data from ten Neosho madtom originating from three geographically separated populations. A Neosho madtom genome was de novo assembled and genome size and content were assessed. Genomic DNA was used to construct one small insert paired-end library per fish with an approximate insert size of 300 bp. The library was constructed following the manufacturer’s protocol with reagents supplied in Illumina’s TruSeq DNA PCR-Free sample preparation kit (#FC-121-3001).
Ichthyoplankton tows samples collected from Truman reservoir tributaries evaluated for eDNA. Data also includes hydrologic and water quality parameters and morphology of grass carp eggs.
Data consist of flow cytometry files (.FCS) that were generated in the analysis of larval pallid sturgeon specimens. Nuclei from produced larval sturgeon somatic cells were analyzed using flow cytometry to estimate genome size and assign ploidy. Freshly collected rainbow trout (Oncorhynchus mykiss), largemouth bass (Micropterus salmoides), or pallid sturgeon blood were used as external controls, whereby the fish blood samples were analyzed in separate tubes from the cells of prepared sturgeon larvae. All samples at 1 x 10^6 cells/mL were incubated in a propidium iodide solution to stain DNA, then analyzed by flow cytometry. Analysis software generated histograms from the experimental samples and the control standard...
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