Links to Additional Echinoderm Datasets and CRISPR/Cas in Echinoderms: Difference between pages

From EchinoWiki
(Difference between pages)
Jump to navigation Jump to search
imported>Ctelmer
No edit summary
 
imported>Ctelmer
No edit summary
 
Line 1: Line 1:
This page will provide links to additional datasets for various echinoderms organized by class.


Welcome to the Echinobase CRISPR/Cas resource. A brief literature and method review is followed by tables of gRNA spacer sequences.


<p>'''Subphylum Echinozoa'''</p>
Updated December 2020
:Class '''Echinoidea''' (sea urchins)


:Class '''Holothuroidea''' (sea cucumbers)


::''Apostichopus parvimensis'' (warty sea cucumber)
'''''S. purpuratus'' genome editing to create insertions and deletions'''
:::Accession: [https://www.ncbi.nlm.nih.gov/assembly/GCA_000934455.1/ GCA_000934455.1]


 
To date CRISPR/Cas9 has been used to introduce insertion and deletion mutations (indels) into ''S. purpuratus nodall'' ([https://www.echinobase.org/literature/article.do?method=display&articleId=44372 Lin and Su 2016]), ''polyketide synthase 1'', ''gcml'' (Oulhen and Wessel 2016), ''nanos2l'' ([https://www.echinobase.org/literature/article.do?method=display&articleId=45207 Oulhen et al. 2017]) and ''dll1'' (''delta'') ([https://www.echinobase.org/literature/article.do?method=display&articleId=45720 Mellott et al. 2017]) genes. Attempts to mutate ''foxy'' ([https://www.echinobase.org/literature/article.do?method=display&articleId=47178 Oulhen et al. 2019]) were unsuccessful. A number of different methods were used for gRNA synthesis (several using pT7-gRNA)  and NLS-SpCas9-NLS (pCS2-nCas9n (zebrafish codon-optimized), or pCS2-3xFLAG-NLS-SpCas9-NLS (codon optimized for human with a 3XFLAG-tag) were used in these studies (see below for details). The gRNAs and mRNAs were microinjected into fertilized eggs.
<p>'''Subphylum Asterozoa'''</p>
:Class '''Asteroidea''' (sea stars)
 
::''Acanthaster planci'' (crown-of-thorns sea star)
:::Accession: [https://www.ncbi.nlm.nih.gov/genome/?term=GCA_001949145.1 GCA_001949145.1]
:::Publication: [http://doi.org/10.1038/nature22033 2017]
:::[https://www.ncbi.nlm.nih.gov/sra/?term=Acanthaster+planci SRA]
:::[https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL23315 GEO]
 
::''Asterias rubens'' (European sea star)
:::Accession: [https://www.ncbi.nlm.nih.gov/genome/?term=GCA_902459465.3 GCA_902459465.3]
:::[https://www.ncbi.nlm.nih.gov/sra/?term=Asterias+rubens SRA]
 
::''Patiriella regularis'' (New Zealand sea star)
:::Accession: [https://www.ncbi.nlm.nih.gov/genome/?term=GCA_900067625.1 GCA_900067625.1]
:::Publication: [http://doi.org/10.1186/s13742-016-0125-6 2016]
:::[https://www.ncbi.nlm.nih.gov/sra/?term=Patiriella+regularis SRA]
 
::''Pisaster ochraceus'' (purple sea star)
:::Accession: [https://www.ncbi.nlm.nih.gov/genome/?term=GCA_010994315.1 GCA_010994315.1]
:::Publication: [http://doi.org/10.1111/mec.15386 2020]
:::[http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=848819311_uTfQQofCxtzMRnKAidqhoYa6eexL UCSC genome browser]
:::[https://www.ncbi.nlm.nih.gov/sra/?term=Pisaster+ochraceus SRA]
:::[https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE144422 GEO]
 
:Class '''Ophiuroidea''' (brittle stars)
 
::''Ophiothrix spiculata'' (spiny brittle star)
:::Accession: [https://www.ncbi.nlm.nih.gov/assembly/GCA_000969725.1/ GCA_000969725.1]
 
 
<p>'''Subphylum Crinozoa'''</p>
:Class '''Crinoidea'''

Revision as of 10:37, 1 December 2020

Welcome to the Echinobase CRISPR/Cas resource. A brief literature and method review is followed by tables of gRNA spacer sequences.

Updated December 2020


S. purpuratus genome editing to create insertions and deletions

To date CRISPR/Cas9 has been used to introduce insertion and deletion mutations (indels) into S. purpuratus nodall (Lin and Su 2016), polyketide synthase 1, gcml (Oulhen and Wessel 2016), nanos2l (Oulhen et al. 2017) and dll1 (delta) (Mellott et al. 2017) genes. Attempts to mutate foxy (Oulhen et al. 2019) were unsuccessful. A number of different methods were used for gRNA synthesis (several using pT7-gRNA) and NLS-SpCas9-NLS (pCS2-nCas9n (zebrafish codon-optimized), or pCS2-3xFLAG-NLS-SpCas9-NLS (codon optimized for human with a 3XFLAG-tag) were used in these studies (see below for details). The gRNAs and mRNAs were microinjected into fertilized eggs.

Retrieved from "https://wiki.echinobase.org/echinowiki/index.php?title=Links_to_Additional_Echinoderm_Datasets&oldid=456"