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Protocols

Echinobase specifications

Information


Unique identifier OMICS_19345
Name Echinobase
Restrictions to use None
Database management system PostgreSQL
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Echinobase

Subtool


  • SpBase

Maintainer


  • person_outline Andrew Cameron

Publication for Echinobase

Echinobase citations

 (17)
library_books

AID/APOBEC like cytidine deaminases are ancient innate immune mediators in invertebrates

2018
Nat Commun
PMCID: 5956068
PMID: 29769532
DOI: 10.1038/s41467-018-04273-x

[…] Sequence comparisons to the sea urchin genome were done using BLAST, BLASTP, or BLASTN at https://blast.ncbi.nlm.nih.gov/Blast.cgi or www.echinobase.org using either standard parameters or with low complexity filter turned off. Multiple sequence alignments were performed using CLUSTALW and optimized manually based on predicted secondary […]

library_books

Global analysis of primary mesenchyme cell cis regulatory modules by chromatin accessibility profiling

2018
BMC Genomics
PMCID: 5859501
PMID: 29558892
DOI: 10.1186/s12864-018-4542-z

[…] d adapter sequences were trimmed using Cutadapt (v1.9) []. Reads were mapped to the S. purpuratus genome using Bowtie2 (v2.1.0) [] with default parameters and S. purpuratus genome v3.1, obtained from echinobase.org. This is the latest assembly for which a GFF/GTF annotation exists. The v3.1 genome assembly is 826 Mb in size and consists of 32,008 scaffolds with a N50 of 401.6 kb. On average, ~ 80% […]

call_split

Parkinson disease related ATP13A2 evolved early in animal evolution

2018
PLoS One
PMCID: 5837089
PMID: 29505581
DOI: 10.1371/journal.pone.0193228
call_split See protocol

[…] ere first identified using the Basic Local Alignment Search Tool (BLAST) for sequences in completed genomes in the NCBI non-redundant protein sequence database (http://blast.ncbi.nlm.nih.gov/) and in EchinoBase (http://www.echinobase.org/Echinobase/). P5 ATPases in this dataset were first identified by the presence of fully intact signature motifs characteristic for P-type ATPases [] and for P5-ty […]

library_books

Evolutionary recruitment of flexible Esrp dependent splicing programs into diverse embryonic morphogenetic processes

2017
Nat Commun
PMCID: 5703972
PMID: 29180615
DOI: 10.1038/s41467-017-01961-y

[…] olium castaneum (triCas2, BeetleBase), Apis mellifera (apiMel2, Baylor College of Medicine), Saccoglossus kowalevskii (Skow_1.1, Baylor College of Medicine), Strongylocentrotus purpuratus (Spur_v3.1, EchinoBase), Ciona intestinalis (ci2, Aniseed) and Danio rerio (danRer10, Ensembl). Sequencing of amplicons from genomic DNA and tissue-specific cDNA was also carried out for Branchiostoma lanceolatum […]

library_books

Echinobase: an expanding resource for echinoderm genomic information

2017
PMCID: 5737241
PMID: 29220460
DOI: 10.1093/database/bax074

[…] Published and publicly available sea urchin research papers are regularly collected for updating the literature links and the reagent data in Echinobase. The literature data including title, abstracts, full length text etc. are also used for updating our literature database ‘Textpresso for sea urchin’. First, all the sea urchin research pap […]

library_books

Ocean acidification impacts spine integrity but not regenerative capacity of spines and tube feet in adult sea urchins

2017
R Soc Open Sci
PMCID: 5451823
PMID: 28573022
DOI: 10.1098/rsos.170140

[…] machine (Applied Biosystems). Primers were designed using Primer Express software (v. 3.0, Applied Biosystems) with sequences of L. variegatus genes identified in the echinoderm genome database (www.echinobase.org) (electronic supplementary material, table S1). Differential expression of target genes (msp130, c-lectin, c-lectin/pmc1, sm50, cahb, cara7la, P16) was determined using the ΔΔCt method […]

Citations

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Echinobase institution(s)
Center for Computational Regulatory Genomics, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
Echinobase funding source(s)
Supported by National Institutes of Health; National Institute of Child Health and Human Development (R01HD056016); National Center for Research Resources; Division of Comparative Medicine (RR015044) and the Beckman Institute.

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