UMB Data Catalog

A project of the Health Sciences and Human Services Library
UMB Dataset

Neuropeptide identification using eyestalk-RNAseq of red deep-sea crab, Chaceon quenquedens

UID: 184
Author(s): Shadaesha Green, Tsvetan Bachvaroff, J. Sook Chung*
* Corresponding Author
Description
This study aimed to understand the role of eyestalk neuropeptides in vitellogenesis. Molt-inhibiting hormone (MIH) and crustacean hyperglycemic hormone (CHH) cDNA sequences were first isolated from the eyestalk ganglia of C. quinquedens using traditional cloning methods and their expression was quantified in the eyestalk ganglia at various ovarian stages. De novo transcriptome assembly of the eyestalk ganglia was conducted to determine if transcripts of other neuropeptides differ by ovarian stages. Samples were collected from the mid-Atlantic Bight region of the United States off the coast of Virginia up to Massachusetts between 2013 and 2015.
Timeframe
2013 - 2015
Geographic Coverage
Mid-Atlantic Bight
Subject of Study
Subject Domain
Brachyura/genetics
Invertebrate Hormones/genetics
Neuropeptides
Keywords
Arthropod Proteins
Crustacean hyperglycemic hormone
Molt-inhibiting hormone
Transcriptome
Vitellogenesis

Access

Restrictions
Unrestricted access
Instructions
The RNA sequencing data sets have been submitted to NCBI Sequence Read Archive (SRA) under the BioProject PRJNA765736. Supplementary data to this article can be found online at https://doi.org/10.1016/j.ygcen.2022.114128
Access via NCBI SRA

RNA sequencing datasets under the BioProject PRJNA765736
Accession #: PRJNA765736

Access via Appendix A.

Supplementary data from the article.

Associated Publications
Green S, Bachvaroff T, Sook Chung J. Eyestalk neuropeptide identification in the female red deep-sea crab, Chaceon quinquedens. Gen Comp Endocrinol. 2023 Jan 1;330:114128. doi: 10.1016/j.ygcen.2022.114128.
Data Type
Genomic
Equipment Used
Agilent Reverse phase HPLC (RP-HPLC)

Used method for the analysis and purification of peptides, proteins, and glycoproteins.

Branson Digital Sonifier

Digital sonifier to disrupt cells, bacteria, spores, or tissue. Ideal for initiating and accelerating chemical, biochemical, and physical reactions, and for degassing liquids. Used to prepare emulsion to 0.01 micron, homogenize immiscible liquids, polymerize some materials, and depolymerize others.

Jouan SpeedVac

Used for removing solvents and concentrating samples while maintaining sample integrit

Jupiter C18 column

Offers optimized reversed phase solutions for protein and peptide characterization and purification.

Thermo Scientific NanoDrop Spectrophotometer

Benchtop spectrophotometer designed for DNA, RNA, and protein quantification.

Software Used
Microsatellite Repeats Finder

Finds microsatellites in DNA sequences.

NCBI BLASTX

Search tool used for identifying potential protein products encoded by a nucleotide query.

Phylogeny.fr

Phylogeny analysis.

RegRNA

Integrated web server for identifying regulatory RNA motifs and elements.

SignalP server v.5.0

Signal peptide prediction.

Trinity v.2.8.6

Used to assemble paired-read sequences using the default parameters.

Study Type
Empirical Research
Dataset Format(s)
Plain Text, FASTQ, DOCX
Dataset Size
8169 Mb
Grant Support
NA11SEC4810002/United States. National Oceanic and Atmospheric Administration