Resources - Revision history

Xenbase at 15:03, 6 October 2023

2023-10-06T15:03:27Z

← Older revision		Revision as of 15:03, 6 October 2023
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	'''cDNA sequences'''<br />		'''cDNA sequences'''<br />
	Approximately 13,000 cDNA sequences were obtained from the primary mesenchyme cell library. These sequences comprise 7,400 unique sequences when all of the overlaps are assembled. When these are searched against the BAC-end sequences, 1087 unique matches occur. Thus, the sequence matches between the BAC-ends, the ESTs, and the published data bases all give results commensurate with the conclusion that the collection of sequences we have obtained are of a quality suitable for gene discovery investigations in the sea urchin embryo. <span class="newwin">[http://~~new~~.echinobase.org/literature/article.do?method=display&articleId=37498 (Cameron et al., Proc. Natl. Acad. Sci. USA, Vol. 97, Issue 17, 9514-9518, August 15, 2000 )]</span>		Approximately 13,000 cDNA sequences were obtained from the primary mesenchyme cell library. These sequences comprise 7,400 unique sequences when all of the overlaps are assembled. When these are searched against the BAC-end sequences, 1087 unique matches occur. Thus, the sequence matches between the BAC-ends, the ESTs, and the published data bases all give results commensurate with the conclusion that the collection of sequences we have obtained are of a quality suitable for gene discovery investigations in the sea urchin embryo. <span class="newwin">[http://www.echinobase.org/literature/article.do?method=display&articleId=37498 (Cameron et al., Proc. Natl. Acad. Sci. USA, Vol. 97, Issue 17, 9514-9518, August 15, 2000 )]</span>

Ctelmer at 19:31, 22 March 2022

2022-03-22T19:31:13Z

← Older revision		Revision as of 19:31, 22 March 2022
Line 13:		Line 13:
	A virtual map of the genome was constructed by sequencing the ends of 76,020 BAC recombinants (average length 125kb). The BAC-end sequence tag connectors (STCs) occur an average of 10kb apart. They can be used to assemble contigs surrounding any gene of interest. Using Blast matches to sequences from Bac-ends and complete BACs, confirmations from cDNA sequences we estimate that the sea urchin genome contains a total of 22+/-5X10<sup>3</sup> genes.		A virtual map of the genome was constructed by sequencing the ends of 76,020 BAC recombinants (average length 125kb). The BAC-end sequence tag connectors (STCs) occur an average of 10kb apart. They can be used to assemble contigs surrounding any gene of interest. Using Blast matches to sequences from Bac-ends and complete BACs, confirmations from cDNA sequences we estimate that the sea urchin genome contains a total of 22+/-5X10<sup>3</sup> genes.

	[[~~Image~~:VirtualMap.gif\|frame\|left\|Recovery of a contig surrounding a known gene by use of the STC database. (A) The arrayed BAC library is screened by using a cDNA probe, and a BAC containing the gene sequence is selected; the most desirable clone would be the longest that has the gene sequence (solid box) toward the middle. The STCs for that BAC (black-triangle, star) are recovered from the database together with the length distribution of restriction fragments produced by the sites (indicated by short, vertical lines). (B) Oligonucleotide probes are created from the left and right STCs and used to scan the BAC library. The selected clones are aligned to overlap in the restriction digest patterns. The probes should not lie within repetitive sequences: if they do, too many BACs will score positive, and their restriction fragment lengths will not align. (C) The clones extending the longest distance left and right plus the original clone (A) constitute a contig surrounding the gene, marked by STC tags at frequent intervals.]].		[[File:VirtualMap.gif\|frame\|left\|Recovery of a contig surrounding a known gene by use of the STC database. (A) The arrayed BAC library is screened by using a cDNA probe, and a BAC containing the gene sequence is selected; the most desirable clone would be the longest that has the gene sequence (solid box) toward the middle. The STCs for that BAC (black-triangle, star) are recovered from the database together with the length distribution of restriction fragments produced by the sites (indicated by short, vertical lines). (B) Oligonucleotide probes are created from the left and right STCs and used to scan the BAC library. The selected clones are aligned to overlap in the restriction digest patterns. The probes should not lie within repetitive sequences: if they do, too many BACs will score positive, and their restriction fragment lengths will not align. (C) The clones extending the longest distance left and right plus the original clone (A) constitute a contig surrounding the gene, marked by STC tags at frequent intervals.]].

	'''Repeats'''<br />		'''Repeats'''<br />

imported>Ctelmer at 20:26, 4 May 2021

2021-05-04T20:26:39Z

← Older revision		Revision as of 20:26, 4 May 2021
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	'''Sea Urchin Codon Usage Table'''<br />		'''Sea Urchin Codon Usage Table'''<br />
	The Sea Urchin codon usage table can be accessed [http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=7668 here].		The Sea Urchin codon usage table can be accessed [http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=7668 here].


			'''The principal investigators who participated in establishment of the Sea Urchin Genome Project:'''<br />
			<p>Dr. Eric Davidson, California Institute of Technology</p>
			<p>Dr. Charles Ettensohn, Carnegie-Mellon University</p>
			<p>Dr. Leroy Hood, Institute for Systems Biology, Seattle Washington</p>
			<p>Dr. Greg Wray Duke University, The Sea Urchin Genome Project</p>
			<p>Dr. Andrew Cameron, California Institute of Technology</p>


			'''Advisory Committee for the HGRI Sea Urchin Sequencing Project:'''<br />
			<p>Eric H. Davidson, California Institute of Technology</p>
			<p>R. Andrew Cameron, California Institute of Technology</p>
			<p>Robert C. Angerer, National Institute of Dental and Craniofacial Research</p>
			<p>Lynne Angerer, National Institute of Dental and Craniofacial Research</p>
			<p>James A. Coffman, Mount Desert Island Biological Laboratory</p>
			<p>William H. Klein, M. D. Anderson Cancer Center</p>
			<p>Donal Manahan, University of Southern California</p>
			<p>David R. McClay, Duke University</p>
			<p>Jonathan P. Rast, University of Toronto</p>
			<p>Victor D. Vacquier, Scripps Institute of Oceanography</p>

imported>Ctelmer at 22:34, 10 February 2021

2021-02-10T22:34:36Z

← Older revision		Revision as of 22:34, 10 February 2021
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	Please read following post to learn about our BACs resource and experimental methods<br />		Please read following post to learn about our BACs resource and experimental methods<br />
	[[recombac\|Recombinant Bacs]]<br />		[[recombac\|Recombinant Bacs]]<br />
	Annotation of BAC Sequences ~~was completed using the~~ Sea Urchin Gene AnnotatoR (SUGAR).		Annotation of BAC Sequences with Sea Urchin Gene AnnotatoR (SUGAR, no longer available)


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	'''Sea Urchin Codon Usage Table'''<br />		'''Sea Urchin Codon Usage Table'''<br />
	The Sea Urchin codon usage table can be accessed [http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=7668 here]		The Sea Urchin codon usage table can be accessed [http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=7668 here].

imported>Ctelmer at 22:32, 10 February 2021

2021-02-10T22:32:38Z

← Older revision		Revision as of 22:32, 10 February 2021
Line 7:		Line 7:
	Please read following post to learn about our BACs resource and experimental methods<br />		Please read following post to learn about our BACs resource and experimental methods<br />
	[[recombac\|Recombinant Bacs]]<br />		[[recombac\|Recombinant Bacs]]<br />
	~~[[bac\|~~Annotation of BAC Sequences ~~with~~ SUGAR]]		Annotation of BAC Sequences was completed using the Sea Urchin Gene AnnotatoR (SUGAR).


	'''BACs, BAC-ends and Gene Number'''<br />		'''BACs, BAC-ends and Gene Number'''<br />
	A virtual map of the genome was constructed by sequencing the ends of 76,020 BAC recombinants (average length 125kb). The BAC-end sequence tag connectors (STCs) occur an average of 10kb apart. They can be used to assemble contigs surrounding any gene of interest.Using Blast matches to sequences from Bac-ends and complete BACs, confirmations from cDNA sequences we estimate that the sea urchin genome contains a total of 22+/-5X10<sup>3</sup> genes.		A virtual map of the genome was constructed by sequencing the ends of 76,020 BAC recombinants (average length 125kb). The BAC-end sequence tag connectors (STCs) occur an average of 10kb apart. They can be used to assemble contigs surrounding any gene of interest. Using Blast matches to sequences from Bac-ends and complete BACs, confirmations from cDNA sequences we estimate that the sea urchin genome contains a total of 22+/-5X10<sup>3</sup> genes.

	[[Image:VirtualMap.gif\|frame\|left\|Recovery of a contig surrounding a known gene by use of the STC database. (A) The arrayed BAC library is screened by using a cDNA probe, and a BAC containing the gene sequence is selected; the most desirable clone would be the longest that has the gene sequence (solid box) toward the middle. The STCs for that BAC (black-triangle, star) are recovered from the database together with the length distribution of restriction fragments produced by the sites (indicated by short, vertical lines). (B) Oligonucleotide probes are created from the left and right STCs and used to scan the BAC library. The selected clones are aligned to overlap in the restriction digest patterns. The probes should not lie within repetitive sequences: if they do, too many BACs will score positive, and their restriction fragment lengths will not align. (C) The clones extending the longest distance left and right plus the original clone (A) constitute a contig surrounding the gene, marked by STC tags at frequent intervals.]].		[[Image:VirtualMap.gif\|frame\|left\|Recovery of a contig surrounding a known gene by use of the STC database. (A) The arrayed BAC library is screened by using a cDNA probe, and a BAC containing the gene sequence is selected; the most desirable clone would be the longest that has the gene sequence (solid box) toward the middle. The STCs for that BAC (black-triangle, star) are recovered from the database together with the length distribution of restriction fragments produced by the sites (indicated by short, vertical lines). (B) Oligonucleotide probes are created from the left and right STCs and used to scan the BAC library. The selected clones are aligned to overlap in the restriction digest patterns. The probes should not lie within repetitive sequences: if they do, too many BACs will score positive, and their restriction fragment lengths will not align. (C) The clones extending the longest distance left and right plus the original clone (A) constitute a contig surrounding the gene, marked by STC tags at frequent intervals.]].


	'''Repeats'''<br />		'''Repeats'''<br />
	Since the first sea urchin genomic sequencing project was undertaken, a number of collections of the repeat sequences in the purple sea urchin have been collected. A survey of the 76,000 BAC ends for repeat sequences is described [http://www.ncbi.nlm.nih.gov/pubmed/10920195 here].		Since the first sea urchin genomic sequencing project was undertaken, a number of collections of the repeat sequences in the purple sea urchin have been collected. A survey of the 76,000 BAC ends for repeat sequences is described [http://www.ncbi.nlm.nih.gov/pubmed/10920195 here].



	'''cDNA Libraries'''<br />		'''cDNA Libraries'''<br />
	We maintain a suite of cDNA libraries from embryonic stages, larval stages and adult tissues of the reference species, Strongylocentrotus purpuratus. A few cDNA libraries from other species are also available [[filters\|(see Table)]] These libraries are stored in 384-well plates permitting easy replication and re-spotting as needed. The libraries are spotted onto filters for screening. Library filters are available to members of the research community. [[Filters\|(How to order)]]. These libraries have been used as the basis for EST sequencing as part of the original genome sequencing project reported in [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159423/?tool=pubmed Science.] Several other smaller EST projects have also been completed [http://dev.biologists.org/content/128/13/2615.long (for example: Zhu, X., Mahairas, G., Cameron, R. A., Davidson, E. H. and Ettensohn, C. A. Large-scale analysis of mRNAs expressed by primary mesenchyme cells of the sea urchin embryo. Development 128, 2615-2627, 2001)]. The clones sequenced in these projects are accessioned into Genbank and SpBase with the plate and well locations attached. Thus one can use sequence search programs to find the clones and then request them from our Resource. In other words "cloning by computer" is enabled here.		We maintain a suite of cDNA libraries from embryonic stages, larval stages and adult tissues of the reference species, Strongylocentrotus purpuratus. A few cDNA libraries from other species are also available [[filters\|(see Table)]] These libraries are stored in 384-well plates permitting easy replication and re-spotting as needed. The libraries are spotted onto filters for screening. Library filters are available to members of the research community. [[Filters\|(How to order)]]. These libraries have been used as the basis for EST sequencing as part of the original genome sequencing project reported in [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159423/?tool=pubmed Science.] Several other smaller EST projects have also been completed [http://dev.biologists.org/content/128/13/2615.long (for example: Zhu, X., Mahairas, G., Cameron, R. A., Davidson, E. H. and Ettensohn, C. A. Large-scale analysis of mRNAs expressed by primary mesenchyme cells of the sea urchin embryo. Development 128, 2615-2627, 2001)]. The clones sequenced in these projects are accessioned into Genbank and SpBase with the plate and well locations attached. Thus one can use sequence search programs to find the clones and then request them from our Resource. In other words "cloning by computer" is enabled here.



	'''BAC Libraries'''<br />		'''BAC Libraries'''<br />
	~~<br />~~		Genomic sequence segments are maintained in bacterial artificial chromosome (BAC) libraries. We currently have libraries for seven species of lower deuterostomes in our resource [[filters\|(see Table)]]The vector used is pBACe3.6 which originates from Children's Hospital Oakland Research Institute in Oakland, California, USA. This vector has chloramphenicol antibiotic resistance and is fully described in an article by [http://www.ncbi.nlm.nih.gov/pubmed/10373322?dopt=Abstract Frengen and colleages]. The vector sequence is available [http://www.ncbi.nlm.nih.gov/nuccore/4878025?report=fasta here]. The average insert size for our BAC libraries is about 140 Kb thus 1X coverage of the 800 Megabase genome of ''S. purpuratus'' is on average 5700 clones. Our libraries are at least 100,000 clones providing about 17X genome coverage.
	Genomic sequence segments are maintained in bacterial artificial chromosome (BAC) libraries. We currently have libraries for seven species of lower deuterostomes in our resource [[filters\|(see Table)]]The vector used is pBACe3.6 which originates from Children's Hospital Oakland Research Institute in Oakland, California, USA. This vector has chloramphenicol antibiotic resistance and is fully described in an article by [http://www.ncbi.nlm.nih.gov/pubmed/10373322?dopt=Abstract Frengen and colleages]. The vector sequence is available [http://www.ncbi.nlm.nih.gov/nuccore/4878025?report=fasta here]. The average insert size for our BAC libraries is about 140 Kb thus 1X coverage of the 800 Megabase genome of S. purpuratus is on average 5700 clones. Our libraries are at least 100,000 clones providing about 17X genome coverage.



	'''cDNA sequences'''<br />		'''cDNA sequences'''<br />
	Approximately 13,000 cDNA sequences were obtained from the primary mesenchyme cell library. These sequences comprise 7,400 unique sequences when all of the overlaps are assembled. When these are searched against the BAC-end sequences, 1087 unique matches occur. Thus, the sequence matches between the BAC-ends, the ESTs, and the published data bases all give results commensurate with the conclusion that the collection of sequences we have obtained are of a quality suitable for gene discovery investigations in the sea urchin embryo. <span class="newwin">[http://new.echinobase.org/literature/article.do?method=display&articleId=37498 (Cameron et al., Proc. Natl. Acad. Sci. USA, Vol. 97, Issue 17, 9514-9518, August 15, 2000 )]</span>		Approximately 13,000 cDNA sequences were obtained from the primary mesenchyme cell library. These sequences comprise 7,400 unique sequences when all of the overlaps are assembled. When these are searched against the BAC-end sequences, 1087 unique matches occur. Thus, the sequence matches between the BAC-ends, the ESTs, and the published data bases all give results commensurate with the conclusion that the collection of sequences we have obtained are of a quality suitable for gene discovery investigations in the sea urchin embryo. <span class="newwin">[http://new.echinobase.org/literature/article.do?method=display&articleId=37498 (Cameron et al., Proc. Natl. Acad. Sci. USA, Vol. 97, Issue 17, 9514-9518, August 15, 2000 )]</span>



	'''Gene Model'''<br />		'''Gene Model'''<br />
	~~<br />~~
	During sea urchin genome project, several groups came up with gene predictions based on diverse approaches (ab initio, homology-based or empirical). Baylor used GLEAN methodology to combine those gene-sets into 28,944 unique genes. Their structures were derived from V0.5 genome assembly. At SpBase, we adopted Baylor's GLEAN genes and renamed each GLEAN IDs as GLEAN3_12345 to SPU_012345. New SPU genes will be added with IDs starting from 030000. This first release only modified the gene IDs from GLEAN and adopted them into SpBase. No real changes of gene structures were done.		During sea urchin genome project, several groups came up with gene predictions based on diverse approaches (ab initio, homology-based or empirical). Baylor used GLEAN methodology to combine those gene-sets into 28,944 unique genes. Their structures were derived from V0.5 genome assembly. At SpBase, we adopted Baylor's GLEAN genes and renamed each GLEAN IDs as GLEAN3_12345 to SPU_012345. New SPU genes will be added with IDs starting from 030000. This first release only modified the gene IDs from GLEAN and adopted them into SpBase. No real changes of gene structures were done.


	'''Genome sequence traces'''<br />		'''Genome sequence traces'''<br />
	~~<br />~~
	Beginning in March 2003, the Baylor College of Medicine, Human Genome Sequencing center ([http://www.hgsc.bcm.tmc.edu www.hgsc.bcm.tmc.edu]) began to produce sea urchin sequences. First, a whole genome shotgun (WGS) project was undertaken and the individual sequences are deposited in the Genbank Trace Repository at [http://www.ncbi.nlm.nih.gov/Traces/home/ NCBI]. We have downloaded these traces,analyzed them by Blast and posted the matches in a searchable form on this web site. We will continue to do so until assembled genome sequences are posted at NCBI.		Beginning in March 2003, the Baylor College of Medicine, Human Genome Sequencing center ([http://www.hgsc.bcm.tmc.edu www.hgsc.bcm.tmc.edu]) began to produce sea urchin sequences. First, a whole genome shotgun (WGS) project was undertaken and the individual sequences are deposited in the Genbank Trace Repository at [http://www.ncbi.nlm.nih.gov/Traces/home/ NCBI]. We have downloaded these traces,analyzed them by Blast and posted the matches in a searchable form on this web site. We will continue to do so until assembled genome sequences are posted at NCBI.



	'''Quantitative PCR primers'''<br />		'''Quantitative PCR primers'''<br />
	~~<br />~~
	The Davidson laboratory at Caltech has generated a panel of quantitative PCR primers useful for measuring the level of mRNA abundance for genes involved in early development in general and the endomesoderm gene regulatory network in particular. A table of primer sequences and comments can be viewed ([[QPCR\|here]]).		The Davidson laboratory at Caltech has generated a panel of quantitative PCR primers useful for measuring the level of mRNA abundance for genes involved in early development in general and the endomesoderm gene regulatory network in particular. A table of primer sequences and comments can be viewed ([[QPCR\|here]]).


	'''Nanostring Codeset'''<br />		'''Nanostring Codeset'''<br />
	~~<br />~~
	The Nanostring nCounter identifies and counts RNA molecules based on a fluorescent barcode attached to a sequence specific hybridization ([http://www.ncbi.nlm.nih.gov/pubmed/?term=18278033 Geiss, G. K. et al,2008]). Our newly designed probe set contains codes for 341 genes covering the majority of active, and spatially restricted regulatory genes in the Strongylocentrotus purpuratus embryo up to pluteus (72 h post-fertilization). A description of the use of our previous code set was published by ([http://www.ncbi.nlm.nih.gov/pubmed/?term=20398801 Materna et al.]). They showed that Nanostring nCounter yields measurements with high fidelity over 5 orders of magnitude at levels down to a few transcripts per embryo. The genes and sequences in the new codeset are tabulated [[Nanostring\|here]].		The Nanostring nCounter identifies and counts RNA molecules based on a fluorescent barcode attached to a sequence specific hybridization ([http://www.ncbi.nlm.nih.gov/pubmed/?term=18278033 Geiss, G. K. et al,2008]). Our newly designed probe set contains codes for 341 genes covering the majority of active, and spatially restricted regulatory genes in the Strongylocentrotus purpuratus embryo up to pluteus (72 h post-fertilization). A description of the use of our previous code set was published by ([http://www.ncbi.nlm.nih.gov/pubmed/?term=20398801 Materna et al.]). They showed that Nanostring nCounter yields measurements with high fidelity over 5 orders of magnitude at levels down to a few transcripts per embryo. The genes and sequences in the new codeset are tabulated [[Nanostring\|here]].


	'''Sea Urchin Codon Usage Table'''<br />		'''Sea Urchin Codon Usage Table'''<br />
	~~<br />~~
	The Sea Urchin codon usage table can be accessed [http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=7668 here]		The Sea Urchin codon usage table can be accessed [http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=7668 here]

imported>Ctelmer at 22:23, 10 February 2021

2021-02-10T22:23:49Z

← Older revision		Revision as of 22:23, 10 February 2021
Line 59:		Line 59:
	'''Sea Urchin Codon Usage Table'''<br />		'''Sea Urchin Codon Usage Table'''<br />
	<br />		<br />
	The Sea Urchin ~~condon~~ usage table can be accessed [http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=7668 here]		The Sea Urchin codon usage table can be accessed [http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=7668 here]

imported>Echinobase at 01:22, 13 February 2020

2020-02-13T01:22:22Z

← Older revision		Revision as of 01:22, 13 February 2020
Line 1:		Line 1:


	The combined resources provided by the preliminary Sea Urchin Genome Project are included on this site. The~~<br />~~		The combined resources provided by the preliminary Sea Urchin Genome Project are included on this site. The individual resources listed below are useful for gene discovery approaches, expressed sequence tag analysis and most importantly, studies of gene regulation in the sea urchin.
	individual resources listed below are useful for gene discovery approaches, expressed sequence tag analysis and most importantly, studies of gene regulation in the sea urchin.

	'''BAC Table'''<br />		'''BAC Table'''<br />

imported>Echinobase at 01:21, 13 February 2020

2020-02-13T01:21:19Z

← Older revision		Revision as of 01:21, 13 February 2020
Line 23:		Line 23:

	'''cDNA Libraries'''<br />		'''cDNA Libraries'''<br />
	We maintain a suite of cDNA libraries from embryonic stages, larval stages and adult tissues of the reference species, Strongylocentrotus purpuratus. A few cDNA libraries from other species are also available [[filters\|(see Table)]] These libraries are stored in 384-well plates permitting easy replication and re-spotting as needed. The libraries are spotted onto filters for screening. Library filters are available to members of the research community. [[~~order-filters~~\|(How to order)]]. These libraries have been used as the basis for EST sequencing as part of the original genome sequencing project reported in [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159423/?tool=pubmed Science.] Several other smaller EST projects have also been completed [http://dev.biologists.org/content/128/13/2615.long (for example: Zhu, X., Mahairas, G., Cameron, R. A., Davidson, E. H. and Ettensohn, C. A. Large-scale analysis of mRNAs expressed by primary mesenchyme cells of the sea urchin embryo. Development 128, 2615-2627, 2001)]. The clones sequenced in these projects are accessioned into Genbank and SpBase with the plate and well locations attached. Thus one can use sequence search programs to find the clones and then request them from our Resource. In other words "cloning by computer" is enabled here.		We maintain a suite of cDNA libraries from embryonic stages, larval stages and adult tissues of the reference species, Strongylocentrotus purpuratus. A few cDNA libraries from other species are also available [[filters\|(see Table)]] These libraries are stored in 384-well plates permitting easy replication and re-spotting as needed. The libraries are spotted onto filters for screening. Library filters are available to members of the research community. [[Filters\|(How to order)]]. These libraries have been used as the basis for EST sequencing as part of the original genome sequencing project reported in [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159423/?tool=pubmed Science.] Several other smaller EST projects have also been completed [http://dev.biologists.org/content/128/13/2615.long (for example: Zhu, X., Mahairas, G., Cameron, R. A., Davidson, E. H. and Ettensohn, C. A. Large-scale analysis of mRNAs expressed by primary mesenchyme cells of the sea urchin embryo. Development 128, 2615-2627, 2001)]. The clones sequenced in these projects are accessioned into Genbank and SpBase with the plate and well locations attached. Thus one can use sequence search programs to find the clones and then request them from our Resource. In other words "cloning by computer" is enabled here.


Line 34:		Line 34:

	'''cDNA sequences'''<br />		'''cDNA sequences'''<br />
	Approximately 13,000 cDNA sequences were obtained from the primary mesenchyme cell library. These sequences comprise 7,400 unique sequences when all of the overlaps are assembled. When these are searched against the BAC-end sequences, 1087 unique matches occur. Thus, the sequence matches between the BAC-ends, the ESTs, and the published data bases all give results commensurate with the conclusion that the collection of sequences we have obtained are of a quality suitable for gene discovery investigations in the sea urchin embryo. [~~[cameronPNAS~~.~~pdf\|~~(Cameron et al., Proc. Natl. Acad. Sci. USA, Vol. 97, Issue 17, 9514-9518, August 15, 2000 )]]		Approximately 13,000 cDNA sequences were obtained from the primary mesenchyme cell library. These sequences comprise 7,400 unique sequences when all of the overlaps are assembled. When these are searched against the BAC-end sequences, 1087 unique matches occur. Thus, the sequence matches between the BAC-ends, the ESTs, and the published data bases all give results commensurate with the conclusion that the collection of sequences we have obtained are of a quality suitable for gene discovery investigations in the sea urchin embryo. <span class="newwin">[http://new.echinobase.org/literature/article.do?method=display&articleId=37498 (Cameron et al., Proc. Natl. Acad. Sci. USA, Vol. 97, Issue 17, 9514-9518, August 15, 2000 )]</span>


Line 42:		Line 42:
	During sea urchin genome project, several groups came up with gene predictions based on diverse approaches (ab initio, homology-based or empirical). Baylor used GLEAN methodology to combine those gene-sets into 28,944 unique genes. Their structures were derived from V0.5 genome assembly. At SpBase, we adopted Baylor's GLEAN genes and renamed each GLEAN IDs as GLEAN3_12345 to SPU_012345. New SPU genes will be added with IDs starting from 030000. This first release only modified the gene IDs from GLEAN and adopted them into SpBase. No real changes of gene structures were done.		During sea urchin genome project, several groups came up with gene predictions based on diverse approaches (ab initio, homology-based or empirical). Baylor used GLEAN methodology to combine those gene-sets into 28,944 unique genes. Their structures were derived from V0.5 genome assembly. At SpBase, we adopted Baylor's GLEAN genes and renamed each GLEAN IDs as GLEAN3_12345 to SPU_012345. New SPU genes will be added with IDs starting from 030000. This first release only modified the gene IDs from GLEAN and adopted them into SpBase. No real changes of gene structures were done.

	~~[[\|]]~~

	'''Genome sequence traces'''<br />		'''Genome sequence traces'''<br />
Line 52:		Line 51:
	'''Quantitative PCR primers'''<br />		'''Quantitative PCR primers'''<br />
	<br />		<br />
	The Davidson laboratory at Caltech has generated a panel of quantitative PCR primers useful for measuring the level of mRNA abundance for genes involved in early development in general and the endomesoderm gene regulatory network in particular. A table of primer sequences and comments can be viewed ([[~~q-pcr.html~~\|here]~~]) or downloaded ([http://whis.caltech.edu/SpBase/resources/methods/qPCR.xlsx here~~]).		The Davidson laboratory at Caltech has generated a panel of quantitative PCR primers useful for measuring the level of mRNA abundance for genes involved in early development in general and the endomesoderm gene regulatory network in particular. A table of primer sequences and comments can be viewed ([[QPCR\|here]]).


	'''Nanostring Codeset'''<br />		'''Nanostring Codeset'''<br />
	<br />		<br />
	The Nanostring nCounter identifies and counts RNA molecules based on a fluorescent barcode attached to a sequence specific hybridization ([http://www.ncbi.nlm.nih.gov/pubmed/?term=18278033 Geiss, G. K. et al,2008]). Our newly designed probe set contains codes for 341 genes covering the majority of active, and spatially restricted regulatory genes in the Strongylocentrotus purpuratus embryo up to pluteus (72 h post-fertilization). A description of the use of our previous code set was published by ([http://www.ncbi.nlm.nih.gov/pubmed/?term=20398801 Materna et al.]). They showed that Nanostring nCounter yields measurements with high fidelity over 5 orders of magnitude at levels down to a few transcripts per embryo. The genes and sequences in the new codeset are tabulated [[~~nanostring~~\|here]].		The Nanostring nCounter identifies and counts RNA molecules based on a fluorescent barcode attached to a sequence specific hybridization ([http://www.ncbi.nlm.nih.gov/pubmed/?term=18278033 Geiss, G. K. et al,2008]). Our newly designed probe set contains codes for 341 genes covering the majority of active, and spatially restricted regulatory genes in the Strongylocentrotus purpuratus embryo up to pluteus (72 h post-fertilization). A description of the use of our previous code set was published by ([http://www.ncbi.nlm.nih.gov/pubmed/?term=20398801 Materna et al.]). They showed that Nanostring nCounter yields measurements with high fidelity over 5 orders of magnitude at levels down to a few transcripts per embryo. The genes and sequences in the new codeset are tabulated [[Nanostring\|here]].

	'''Sea Urchin Codon Usage Table'''<br />		'''Sea Urchin Codon Usage Table'''<br />
	<br />		<br />
	The Sea Urchin condon usage table can be accessed [http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=7668 here]		The Sea Urchin condon usage table can be accessed [http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=7668 here]

imported>Echinobase at 01:08, 13 February 2020

2020-02-13T01:08:38Z

← Older revision		Revision as of 01:08, 13 February 2020
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	'''BACs, BAC-ends and Gene Number'''<br />		'''BACs, BAC-ends and Gene Number'''<br />
	A virtual map of the genome was constructed by sequencing the ends~~<br />~~		A virtual map of the genome was constructed by sequencing the ends of 76,020 BAC recombinants (average length 125kb). The BAC-end sequence tag connectors (STCs) occur an average of 10kb apart. They can be used to assemble contigs surrounding any gene of interest.Using Blast matches to sequences from Bac-ends and complete BACs, confirmations from cDNA sequences we estimate that the sea urchin genome contains a total of 22+/-5X10<sup>3</sup> genes.
	of 76,020 BAC recombinants (average length 125kb) ~~[[virtual-map.php\|{Figure}]]~~. The BAC-end sequence tag connectors (STCs) occur an average of 10kb apart. They can be used to assemble contigs surrounding any gene of interest.Using Blast matches to sequences from Bac-ends and complete BACs, confirmations from cDNA sequences we estimate that the sea urchin genome contains a total of 22+/-5X10<sup>3</sup> genes.

			[[Image:VirtualMap.gif\|frame\|left\|Recovery of a contig surrounding a known gene by use of the STC database. (A) The arrayed BAC library is screened by using a cDNA probe, and a BAC containing the gene sequence is selected; the most desirable clone would be the longest that has the gene sequence (solid box) toward the middle. The STCs for that BAC (black-triangle, star) are recovered from the database together with the length distribution of restriction fragments produced by the sites (indicated by short, vertical lines). (B) Oligonucleotide probes are created from the left and right STCs and used to scan the BAC library. The selected clones are aligned to overlap in the restriction digest patterns. The probes should not lie within repetitive sequences: if they do, too many BACs will score positive, and their restriction fragment lengths will not align. (C) The clones extending the longest distance left and right plus the original clone (A) constitute a contig surrounding the gene, marked by STC tags at frequent intervals.]].


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	Since the first sea urchin genomic sequencing project was undertaken, a number of collections of the repeat sequences in the purple sea urchin have been collected. A survey of the 76,000 BAC ends for repeat sequences is described [http://www.ncbi.nlm.nih.gov/pubmed/10920195 here].		Since the first sea urchin genomic sequencing project was undertaken, a number of collections of the repeat sequences in the purple sea urchin have been collected. A survey of the 76,000 BAC ends for repeat sequences is described [http://www.ncbi.nlm.nih.gov/pubmed/10920195 here].

	~~[[\|]]~~

	'''cDNA Libraries'''<br />		'''cDNA Libraries'''<br />

imported>Echinobase: Created page with " The combined resources provided by the preliminary Sea Urchin Genome Project are included on this site. The
individual resources listed below are useful for gene disco..."

2020-02-13T00:53:26Z

Created page with " The combined resources provided by the preliminary Sea Urchin Genome Project are included on this site. The individual resources listed below are useful for gene disco..."

New page

The combined resources provided by the preliminary Sea Urchin Genome Project are included on this site. The 
individual resources listed below are useful for gene discovery approaches, expressed sequence tag analysis and most importantly, studies of gene regulation in the sea urchin.

'''BAC Table''' 
BAC Table can be accessed here [[BAC_Table|BAC Table]] 
Please read following post to learn about our BACs resource and experimental methods 
[[recombac|Recombinant Bacs]] 
[[bac|Annotation of BAC Sequences with SUGAR]]

'''BACs, BAC-ends and Gene Number''' 
A virtual map of the genome was constructed by sequencing the ends 
of 76,020 BAC recombinants (average length 125kb) [[virtual-map.php|{Figure}]]. The BAC-end sequence tag connectors (STCs) occur an average of 10kb apart. They can be used to assemble contigs surrounding any gene of interest.Using Blast matches to sequences from Bac-ends and complete BACs, confirmations from cDNA sequences we estimate that the sea urchin genome contains a total of 22+/-5X103 genes.

'''Repeats''' 
Since the first sea urchin genomic sequencing project was undertaken, a number of collections of the repeat sequences in the purple sea urchin have been collected. A survey of the 76,000 BAC ends for repeat sequences is described [http://www.ncbi.nlm.nih.gov/pubmed/10920195 here].

[[|]]

'''cDNA Libraries''' 
We maintain a suite of cDNA libraries from embryonic stages, larval stages and adult tissues of the reference species, Strongylocentrotus purpuratus. A few cDNA libraries from other species are also available [[filters|(see Table)]] These libraries are stored in 384-well plates permitting easy replication and re-spotting as needed. The libraries are spotted onto filters for screening. Library filters are available to members of the research community. [[order-filters|(How to order)]]. These libraries have been used as the basis for EST sequencing as part of the original genome sequencing project reported in [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159423/?tool=pubmed Science.] Several other smaller EST projects have also been completed [http://dev.biologists.org/content/128/13/2615.long (for example: Zhu, X., Mahairas, G., Cameron, R. A., Davidson, E. H. and Ettensohn, C. A. Large-scale analysis of mRNAs expressed by primary mesenchyme cells of the sea urchin embryo. Development 128, 2615-2627, 2001)]. The clones sequenced in these projects are accessioned into Genbank and SpBase with the plate and well locations attached. Thus one can use sequence search programs to find the clones and then request them from our Resource. In other words "cloning by computer" is enabled here.

'''BAC Libraries''' 
 
Genomic sequence segments are maintained in bacterial artificial chromosome (BAC) libraries. We currently have libraries for seven species of lower deuterostomes in our resource [[filters|(see Table)]]The vector used is pBACe3.6 which originates from Children's Hospital Oakland Research Institute in Oakland, California, USA. This vector has chloramphenicol antibiotic resistance and is fully described in an article by [http://www.ncbi.nlm.nih.gov/pubmed/10373322?dopt=Abstract Frengen and colleages]. The vector sequence is available [http://www.ncbi.nlm.nih.gov/nuccore/4878025?report=fasta here]. The average insert size for our BAC libraries is about 140 Kb thus 1X coverage of the 800 Megabase genome of S. purpuratus is on average 5700 clones. Our libraries are at least 100,000 clones providing about 17X genome coverage.

'''cDNA sequences''' 
Approximately 13,000 cDNA sequences were obtained from the primary mesenchyme cell library. These sequences comprise 7,400 unique sequences when all of the overlaps are assembled. When these are searched against the BAC-end sequences, 1087 unique matches occur. Thus, the sequence matches between the BAC-ends, the ESTs, and the published data bases all give results commensurate with the conclusion that the collection of sequences we have obtained are of a quality suitable for gene discovery investigations in the sea urchin embryo. [[cameronPNAS.pdf|(Cameron et al., Proc. Natl. Acad. Sci. USA, Vol. 97, Issue 17, 9514-9518, August 15, 2000 )]]

'''Gene Model''' 
 
During sea urchin genome project, several groups came up with gene predictions based on diverse approaches (ab initio, homology-based or empirical). Baylor used GLEAN methodology to combine those gene-sets into 28,944 unique genes. Their structures were derived from V0.5 genome assembly. At SpBase, we adopted Baylor's GLEAN genes and renamed each GLEAN IDs as GLEAN3_12345 to SPU_012345. New SPU genes will be added with IDs starting from 030000. This first release only modified the gene IDs from GLEAN and adopted them into SpBase. No real changes of gene structures were done.

[[|]]

'''Genome sequence traces''' 
 
Beginning in March 2003, the Baylor College of Medicine, Human Genome Sequencing center ([http://www.hgsc.bcm.tmc.edu www.hgsc.bcm.tmc.edu]) began to produce sea urchin sequences. First, a whole genome shotgun (WGS) project was undertaken and the individual sequences are deposited in the Genbank Trace Repository at [http://www.ncbi.nlm.nih.gov/Traces/home/ NCBI]. We have downloaded these traces,analyzed them by Blast and posted the matches in a searchable form on this web site. We will continue to do so until assembled genome sequences are posted at NCBI.

'''Quantitative PCR primers''' 
 
The Davidson laboratory at Caltech has generated a panel of quantitative PCR primers useful for measuring the level of mRNA abundance for genes involved in early development in general and the endomesoderm gene regulatory network in particular. A table of primer sequences and comments can be viewed ([[q-pcr.html|here]]) or downloaded ([http://whis.caltech.edu/SpBase/resources/methods/qPCR.xlsx here]).

'''Nanostring Codeset''' 
 
The Nanostring nCounter identifies and counts RNA molecules based on a fluorescent barcode attached to a sequence specific hybridization ([http://www.ncbi.nlm.nih.gov/pubmed/?term=18278033 Geiss, G. K. et al,2008]). Our newly designed probe set contains codes for 341 genes covering the majority of active, and spatially restricted regulatory genes in the Strongylocentrotus purpuratus embryo up to pluteus (72 h post-fertilization). A description of the use of our previous code set was published by ([http://www.ncbi.nlm.nih.gov/pubmed/?term=20398801 Materna et al.]). They showed that Nanostring nCounter yields measurements with high fidelity over 5 orders of magnitude at levels down to a few transcripts per embryo. The genes and sequences in the new codeset are tabulated [[nanostring|here]].

'''Sea Urchin Codon Usage Table''' 
 
The Sea Urchin condon usage table can be accessed [http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=7668 here]