U.S. flag

An official website of the United States government

The Ag Data Commons is migrating

The Ag Data Commons is migrating to a new institutional portal on Figshare. The current system is available for search and download only. The new platform is open for submission with assistance from Ag Data Commons curators. Please contact NAL-ADC-Curator@usda.gov, if you need to publish or update your datasets.

License

Creative Commons Attribution Share-Alike
[Open Data]

Other Access

The information on this page (the dataset metadata) is also available in these formats:

JSON RDF

via the DKAN API

Social

Hyalella azteca Official Gene Set v1.2

This dataset presents the Hyalella azteca Official Gene Set OGSv1.2. The Hyalella azteca genome assembly was recently updated to assembly Hazt_2.0 (https://www.ncbi.nlm.nih.gov/assembly/GCF_000764305.1). The Hyalella azteca Official Gene Set v1.0, originally generated from assembly Hyalella azteca Genome Assembly 1.0 (10.15482/USDA.ADC/1415994) was lifted over to Hazt_2.0 using the NCBI's remap service, the CrossMap software (http://crossmap.sourceforge.net/), and remap_gff3 (https://github.com/NAL-i5K/remap-gff3). This resulted in the unreleased OGSv1.1. OGSv1.1 received additional QA/QC during NCBI submission, generating Hyalella azteca OGSv1.2.

This dataset contains the following files:
hyaazt_OGSv1.2.tar.gz

  • hyaazt_OGSv1.2.1.gff - GFF3 file of the Hyalella azteca Official Gene Set OGSv1.2
  • hyaazt_OGSv1.2_cds.fa - CDS fasta file of the Hyalella azteca Official Gene Set OGSv1.2
  • hyaazt_OGSv1.2_pep.fa - Protein fasta file of the Hyalella azteca Official Gene Set OGSv1.2
  • hyaazt_OGSv1.2_trans.fa - Transcript fasta file of the Hyalella azteca Official Gene Set OGSv1.2
  • readme
See all >>
FieldValue
Tags
i5k
Hyalella azteca
arthropods
Modified
2023-09-20
Release Date
2023-09-20
Identifier
a9d0c11b-3e0b-4536-9572-1467eba67d87
Publisher
Ag Data Commons
Temporal Coverage
May 3, 2019
License
Creative Commons Attribution Share-Alike
Contact Name
Poynton, Helen
Contact Email
Helen.Poynton@umb.edu
Public Access Level
Public
Program Code
005:040 - Department of Agriculture - National Research
Bureau Code
005:18 - Agricultural Research Service
Extended Metadata: 
FieldValue
Authors
Poynton, Helen (ORCID)
Bain, Peter (ORCID)
Benoit, Joshua B. (ORCID)
Boucher, Peter
Chen, Mei-Ju May (ORCID)
Chen, Shuai (Scopus Author ID)
Chiang, Li-Mei
Christie, Andrew E. (Scopus Author ID)
Connolly, Joseph (ORCID)
Cridge, Andrew (ORCID)
Etxabe, Amaia (ORCID)
Glazier, Amanda (Scopus Author ID)
Hasenbein, Simone (ORCID)
Hughes, Daniel S.T. (Scopus Author ID)
Jennings, Emily C. (ORCID)
Jones, Jeffery W. (Scopus Author ID)
Kearns, Patrick (ORCID)
Lambert, Faith (Scopus Author ID)
Lin, Yu-Yu
Major, Charles
Manny, Austin (Scopus Author ID)
Mathers, Nick
Mechler-Hickson, Alexandra
Munoz-Torres, Monica (ORCID)
Poelchau, Monica (ORCID)
Robertson, Hugh M. (ORCID)
Scanlan, Jack
Szuter, Elise M. (Scopus Author ID)
Werren, Jack (ORCID)
Wood, Shelly Ann
Winchell, Kristin (ORCID)
Richards, Stephen (ORCID)
Peer Reviewed
No
Equipment or Software Used
CrossMap v0.3.0
remap-gff3
Funding Sources
National Human Genome Research Institute
U54 HG003273
National Science Foundation
CBET-1437409
Related Articles

Poynton, H. C., Hasenbein, S., Benoit, J. B., Sepulveda, M. S., Poelchau, M. F., Hughes, D. S. T., Murali, S. C., Chen, S., Glastad, K. M., Goodisman, M. A. D., Werren, J. H., Vineis, J. H., Bowen, J. L., Friedrich, M., Jones, J., Robertson, H. M., Feyereisen, R., Mechler-Hickson, A., Mathers, N., … Richards, S. (2018). The Toxicogenome of <i>Hyalella azteca</i>: A Model for Sediment Ecotoxicology and Evolutionary Toxicology. Environmental Science &Amp; Technology, 52(10), 6009-6022. https://doi.org/10.1021/acs.est.8b00837

AgID: 6000100
Dataset DOI (digital object identifier)
10.15482/USDA.ADC/1529441
Product Type
Dataset
Related Content
IsVerisonOf: Hyalella azteca Official Gene Set v1.0
HasVersion: Hyalella azteca Official Gene Set v1.3
Hyalella azteca Genome Assembly 1.0
FieldValue
ISO Topic(s)
biota
National Agricultural Library Thesaurus Term
genomics
genes
nucleotide sequences
sequence analysis
Ag Data Commons Keywords
  • Genomics & Genetics
  • Genomics & Genetics
  • Genome
  • Genomics & Genetics
  • Genome
  • Genome annotation
Program
Insects 5K – i5K
Organism project
Hyalella azteca

Suggested Citation:

(dataset) Poynton, Helen; Bain, Peter; Benoit, Joshua B.; Boucher, Peter; Chen, Mei-Ju May; Chen, Shuai; Chiang, Li-Mei; Christie, Andrew E.; Connolly, Joseph; Cridge, Andrew; Etxabe, Amaia; Glazier, Amanda; Hasenbein, Simone; Hughes, Daniel S.T.; Jennings, Emily C.; Jones, Jeffery W.; Kearns, Patrick; Lambert, Faith; Lin, Yu-Yu; Major, Charles; Manny, Austin; Mathers, Nick; Mechler-Hickson, Alexandra; Munoz-Torres, Monica; Poelchau, Monica; Robertson, Hugh M.; Scanlan, Jack; Szuter, Elise M.; Werren, Jack; Wood, Shelly Ann; Winchell, Kristin; Richards, Stephen (2023). Hyalella azteca Official Gene Set v1.2. Ag Data Commons. https://doi.org/10.15482/USDA.ADC/1529441. Accessed 2023-12-10.