Libraries, Vectors and Screening - Revision history

Xenbase at 15:02, 6 October 2023

2023-10-06T15:02:48Z

← Older revision		Revision as of 15:02, 6 October 2023
Line 55:		Line 55:

	<span class="newwin">Fluorescent Protein Vectors</span><br />		<span class="newwin">Fluorescent Protein Vectors</span><br />
	The expression of exogenous proteins in sea urchins embryos, by injection of recombinant mRNAs, is routine procedure. The Hamdoun lab has generated a vector set with the major color and tag position variants that is useful for fluorescent protein tagging and expression in urchins. The complete vector set and can be obtained here: [https://www.addgene.org/kits/hamdoun-fluorescent-proteins/]. A description of the vectors can be found in Gokirmak et al., 2012 [http://~~new~~.echinobase.org/literature/article.do?method=display&articleId=42631 Vectors for generation of exogenous mRNAs fused to fluorescent proteins for expression in urchins]		The expression of exogenous proteins in sea urchins embryos, by injection of recombinant mRNAs, is routine procedure. The Hamdoun lab has generated a vector set with the major color and tag position variants that is useful for fluorescent protein tagging and expression in urchins. The complete vector set and can be obtained here: [https://www.addgene.org/kits/hamdoun-fluorescent-proteins/]. A description of the vectors can be found in Gokirmak et al., 2012 [http://www.echinobase.org/literature/article.do?method=display&articleId=42631 Vectors for generation of exogenous mRNAs fused to fluorescent proteins for expression in urchins]

imported>Ctelmer at 15:37, 4 February 2021

2021-02-04T15:37:55Z

imported>Ctelmer: Ctelmer moved page Protocols to Libraries, Vectors and Screening: Wanted a more descriptive title.

2021-02-04T15:25:51Z

Ctelmer moved page Protocols to Libraries, Vectors and Screening: Wanted a more descriptive title.

← Older revision	Revision as of 15:25, 4 February 2021
(No difference)

imported>Ctelmer: /* An index of general molecular biology techniques used in studies of S. purpuratus */

2020-05-21T01:13:06Z

An index of general molecular biology techniques used in studies of S. purpuratus

← Older revision		Revision as of 01:13, 21 May 2020
Line 51:		Line 51:

	<span class="newwin">Fluorescent Protein Vectors</span><br />		<span class="newwin">Fluorescent Protein Vectors</span><br />
	The expression of exogenous proteins in sea urchins embryos, by injection of recombinant mRNAs, is routine procedure. The Hamdoun lab has generated a vector set with the major color and tag position variants that is useful for fluorescent protein tagging and expression in urchins. The complete vector set and can be obtained here: https://www.addgene.org/kits/hamdoun-fluorescent-proteins/. A description of the vectors can be found in Gokirmak et al., 2012 [http://new.echinobase.org/literature/article.do?method=display&articleId=42631 Vectors for generation of exogenous mRNAs fused to fluorescent proteins for expression in urchins]		The expression of exogenous proteins in sea urchins embryos, by injection of recombinant mRNAs, is routine procedure. The Hamdoun lab has generated a vector set with the major color and tag position variants that is useful for fluorescent protein tagging and expression in urchins. The complete vector set and can be obtained here: [https://www.addgene.org/kits/hamdoun-fluorescent-proteins/]. A description of the vectors can be found in Gokirmak et al., 2012 [http://new.echinobase.org/literature/article.do?method=display&articleId=42631 Vectors for generation of exogenous mRNAs fused to fluorescent proteins for expression in urchins]

imported>Ctelmer at 21:08, 16 April 2020

2020-04-16T21:08:08Z

← Older revision		Revision as of 21:08, 16 April 2020
Line 50:		Line 50:
	Vic Vacquier developed a handout for university students on how to observe sea urchin fertilization in a university lab class setting. All that is needed are sea urchin gametes, a microscope, a few solutions and this handout. The handout works well for both 1 or 2 three hour labs. The student reads through the handout, makes the simple observations, and does the simple, direct experiments to gain insight into the fascinating process of sperm-egg interaction and egg activation.		Vic Vacquier developed a handout for university students on how to observe sea urchin fertilization in a university lab class setting. All that is needed are sea urchin gametes, a microscope, a few solutions and this handout. The handout works well for both 1 or 2 three hour labs. The student reads through the handout, makes the simple observations, and does the simple, direct experiments to gain insight into the fascinating process of sperm-egg interaction and egg activation.

	<span class="newwin">~~[http://new.echinobase.org/literature/article.do?method=display&articleId=42631~~ Vectors ~~for generation of exogenous mRNAs fused to fluorescent proteins for expression in urchins]~~</span><br />		<span class="newwin">Fluorescent Protein Vectors</span><br />
	The expression of exogenous proteins in sea urchins embryos, by injection of recombinant mRNAs, is routine procedure. The Hamdoun lab has generated a vector set with the major color and tag position variants that is useful for fluorescent protein tagging and expression in urchins. The complete vector set and can be obtained here: https://www.addgene.org/~~fluorescent_proteins~~/hamdoun/. A description of the vectors can be found in Gokirmak et al., 2012~~, JBC 287~~:~~43876-83~~. ~~PMID: 23124201~~		The expression of exogenous proteins in sea urchins embryos, by injection of recombinant mRNAs, is routine procedure. The Hamdoun lab has generated a vector set with the major color and tag position variants that is useful for fluorescent protein tagging and expression in urchins. The complete vector set and can be obtained here: https://www.addgene.org/kits/hamdoun-fluorescent-proteins/. A description of the vectors can be found in Gokirmak et al., 2012 [http://new.echinobase.org/literature/article.do?method=display&articleId=42631 Vectors for generation of exogenous mRNAs fused to fluorescent proteins for expression in urchins]

imported>Ctelmer at 18:27, 14 April 2020

2020-04-14T18:27:00Z

← Older revision		Revision as of 18:27, 14 April 2020
Line 22:		Line 22:

	<div class="field-item even" property="content:encoded">		<div class="field-item even" property="content:encoded">

			<p>Below is a list of links to common methods. If you would like to add to the list please contact us.</p>



	=== An index of general molecular biology techniques used in studies of ''S. purpuratus'' ===		=== An index of general molecular biology techniques used in studies of ''S. purpuratus'' ===

	[[array\|Arrayed Filter Manual]]<br />		[[array\|Arrayed Filter Manual]]<br />
	The techniques used to hybridize probes to arrays of cDNAs on filters are detailed here. The manual is based on pages from the RZPD with modifications installed at Caltech.		The techniques used to hybridize probes to arrays of cDNAs on filters are detailed here. The manual is based on pages from the RZPD with modifications installed at Caltech.

imported>Echinobase: /* An index of general molecular biology techniques used in studies of S. purpuratus */

2020-02-11T23:52:48Z

An index of general molecular biology techniques used in studies of S. purpuratus

← Older revision		Revision as of 23:52, 11 February 2020
Line 46:		Line 46:
	Vic Vacquier developed a handout for university students on how to observe sea urchin fertilization in a university lab class setting. All that is needed are sea urchin gametes, a microscope, a few solutions and this handout. The handout works well for both 1 or 2 three hour labs. The student reads through the handout, makes the simple observations, and does the simple, direct experiments to gain insight into the fascinating process of sperm-egg interaction and egg activation.		Vic Vacquier developed a handout for university students on how to observe sea urchin fertilization in a university lab class setting. All that is needed are sea urchin gametes, a microscope, a few solutions and this handout. The handout works well for both 1 or 2 three hour labs. The student reads through the handout, makes the simple observations, and does the simple, direct experiments to gain insight into the fascinating process of sperm-egg interaction and egg activation.

	[http://~~www.ncbi.nlm~~.~~nih~~.~~gov~~/~~pubmed~~/?~~term~~=~~23124201~~ Vectors for generation of exogenous mRNAs fused to fluorescent proteins for expression in urchins]<br />		<span class="newwin">[http://new.echinobase.org/literature/article.do?method=display&articleId=42631 Vectors for generation of exogenous mRNAs fused to fluorescent proteins for expression in urchins]</span><br />
	The expression of exogenous proteins in sea urchins embryos, by injection of recombinant mRNAs, is routine procedure. The Hamdoun lab has generated a vector set with the major color and tag position variants that is useful for fluorescent protein tagging and expression in urchins. The complete vector set and can be obtained here: https://www.addgene.org/fluorescent_proteins/hamdoun/. A description of the vectors can be found in Gokirmak et al., 2012, JBC 287:43876-83. PMID: 23124201		The expression of exogenous proteins in sea urchins embryos, by injection of recombinant mRNAs, is routine procedure. The Hamdoun lab has generated a vector set with the major color and tag position variants that is useful for fluorescent protein tagging and expression in urchins. The complete vector set and can be obtained here: https://www.addgene.org/fluorescent_proteins/hamdoun/. A description of the vectors can be found in Gokirmak et al., 2012, JBC 287:43876-83. PMID: 23124201

imported>Echinobase: /* An index of general molecular biology techniques used in studies of S. purpuratus */

2020-02-11T23:46:05Z

An index of general molecular biology techniques used in studies of S. purpuratus

← Older revision		Revision as of 23:46, 11 February 2020
Line 43:		Line 43:
	The BAC vector pBACe3.6 is the one we have used in the preparation of all of our macro-array genomic libraries. Constructed in Pieter J. de Jong's laboratory at the Children's Hospital Oakland Research Center, it has been used extensively for genomic libraries and sequencing projects of many species.		The BAC vector pBACe3.6 is the one we have used in the preparation of all of our macro-array genomic libraries. Constructed in Pieter J. de Jong's laboratory at the Children's Hospital Oakland Research Center, it has been used extensively for genomic libraries and sequencing projects of many species.

	[http://new.echinobase.org/literature/article.do?method=display&articleId=42133 Sea Urchin Fertilization Laboratory]<br />		<span class="newwin">[http://new.echinobase.org/literature/article.do?method=display&articleId=42133 Sea Urchin Fertilization Laboratory]</span><br />
	Vic Vacquier developed a handout for university students on how to observe sea urchin fertilization in a university lab class setting. All that is needed are sea urchin gametes, a microscope, a few solutions and this handout. The handout works well for both 1 or 2 three hour labs. The student reads through the handout, makes the simple observations, and does the simple, direct experiments to gain insight into the fascinating process of sperm-egg interaction and egg activation.		Vic Vacquier developed a handout for university students on how to observe sea urchin fertilization in a university lab class setting. All that is needed are sea urchin gametes, a microscope, a few solutions and this handout. The handout works well for both 1 or 2 three hour labs. The student reads through the handout, makes the simple observations, and does the simple, direct experiments to gain insight into the fascinating process of sperm-egg interaction and egg activation.

	[http://www.ncbi.nlm.nih.gov/pubmed/?term=23124201 Vectors for generation of exogenous mRNAs fused to fluorescent proteins for expression in urchins]<br />		[http://www.ncbi.nlm.nih.gov/pubmed/?term=23124201 Vectors for generation of exogenous mRNAs fused to fluorescent proteins for expression in urchins]<br />
	The expression of exogenous proteins in sea urchins embryos, by injection of recombinant mRNAs, is routine procedure. The Hamdoun lab has generated a vector set with the major color and tag position variants that is useful for fluorescent protein tagging and expression in urchins. The complete vector set and can be obtained here: https://www.addgene.org/fluorescent_proteins/hamdoun/. A description of the vectors can be found in Gokirmak et al., 2012, JBC 287:43876-83. PMID: 23124201		The expression of exogenous proteins in sea urchins embryos, by injection of recombinant mRNAs, is routine procedure. The Hamdoun lab has generated a vector set with the major color and tag position variants that is useful for fluorescent protein tagging and expression in urchins. The complete vector set and can be obtained here: https://www.addgene.org/fluorescent_proteins/hamdoun/. A description of the vectors can be found in Gokirmak et al., 2012, JBC 287:43876-83. PMID: 23124201

imported>Echinobase: /* An index of general molecular biology techniques used in studies of S. purpuratus */

2020-02-11T23:25:54Z

An index of general molecular biology techniques used in studies of S. purpuratus

@@ Line 43: / Line 43: @@
 The BAC vector pBACe3.6 is the one we have used in the preparation of all of our macro-array genomic libraries. Constructed in Pieter J. de Jong's laboratory at the Children's Hospital Oakland Research Center, it has been used extensively for genomic libraries and sequencing projects of many species.
-[[download/Lab_Manual.pdf|Sea Urchin Fertilization Laboratory]]<br />
+[http://new.echinobase.org/literature/article.do?method=display&articleId=42133 Sea Urchin Fertilization Laboratory]<br />
 Vic Vacquier developed a handout for university students on how to observe sea urchin fertilization in a university lab class setting. All that is needed are sea urchin gametes, a microscope, a few solutions and this handout. The handout works well for both 1 or 2 three hour labs. The student reads through the handout, makes the simple observations, and does the simple, direct experiments to gain insight into the fascinating process of sperm-egg interaction and egg activation.
 [http://www.ncbi.nlm.nih.gov/pubmed/?term=23124201 Vectors for generation of exogenous mRNAs fused to fluorescent proteins for expression in urchins]<br />
 The expression of exogenous proteins in sea urchins embryos, by injection of recombinant mRNAs, is routine procedure. The Hamdoun lab has generated a vector set with the major color and tag position variants that is useful for fluorescent protein tagging and expression in urchins. The complete vector set and can be obtained here: https://www.addgene.org/fluorescent_proteins/hamdoun/. A description of the vectors can be found in Gokirmak et al., 2012, JBC 287:43876-83. PMID: 23124201

imported>Echinobase: /* An index of general molecular biology techniques used in studies of S. purpuratus */

2020-02-11T17:34:03Z

An index of general molecular biology techniques used in studies of S. purpuratus

← Older revision		Revision as of 17:34, 11 February 2020
Line 23:		Line 23:
	<div class="field-item even" property="content:encoded">		<div class="field-item even" property="content:encoded">

	=== An index of general molecular biology techniques used in studies of S. purpuratus ===		=== An index of general molecular biology techniques used in studies of ''S. purpuratus'' ===

	[[array\|Arrayed Filter Manual]]<br />		[[array\|Arrayed Filter Manual]]<br />

← Older revision		Revision as of 15:37, 4 February 2021
Line 28:		Line 28:

	=== An index of general molecular biology techniques used in studies of ''S. purpuratus'' ===		=== An index of general molecular biology techniques used in studies of ''S. purpuratus'' ===


	[[array\|Arrayed Filter Manual]]<br />		[[array\|Arrayed Filter Manual]]<br />
	The techniques used to hybridize probes to arrays of cDNAs on filters are detailed here. The manual is based on pages from the RZPD with modifications installed at Caltech.		The techniques used to hybridize probes to arrays of cDNAs on filters are detailed here. The manual is based on pages from the RZPD with modifications installed at Caltech.


	[[download/DIGscreen.pdf\|Non-radioactive library screening protocol]]<br />		[[download/DIGscreen.pdf\|Non-radioactive library screening protocol]]<br />
	The availability of sensitive chemiluminescent detection systems for hybridization screening of arrayed library filters now makes it possible to reach outcomes similar to methods using 32P labeled probes. We have used a digoxygenin based protocol with good success. It is detailed [[download/DIGscreen.pdf\|here]].		The availability of sensitive chemiluminescent detection systems for hybridization screening of arrayed library filters now makes it possible to reach outcomes similar to methods using 32P labeled probes. We have used a digoxygenin based protocol with good success. It is detailed [[download/DIGscreen.pdf\|here]].


	[[subtrmethods\|Subtractive Probe Analysis]]<br />		[[subtrmethods\|Subtractive Probe Analysis]]<br />
	Our techniques for complex probes to be used on arrayed filters for gene discovery have been perfected by Jonathan Rast in the Davidson Laboratory. The investigation underlying this work is published: Rast J. P. et al, Developmental Biology 228 (2): 270-286, 2000. Supplementary data is presented here, as well.		Our techniques for complex probes to be used on arrayed filters for gene discovery have been perfected by Jonathan Rast in the Davidson Laboratory. The investigation underlying this work is published: Rast J. P. et al, Developmental Biology 228 (2): 270-286, 2000. Supplementary data is presented here, as well.


	[[libprepd\|Additional Notes on cDNA Library Preparations]]<br />		[[libprepd\|Additional Notes on cDNA Library Preparations]]<br />
	The procedures used to construct the cDNA libraries are described here.		The procedures used to construct the cDNA libraries are described here.


	[[epgfp\|The Reporter Plasmid, EpGFPII]]<br />		[[epgfp\|The Reporter Plasmid, EpGFPII]]<br />
	The sequence and map of the reporter construct described in: R. A. Cameron, P. Oliveri, J. Wyllie, and E. H. Davidson (2004) cis-Regulatory Activity of Randomly Chosen Genomic Fragments from the Sea Urchin. Gene Expression Patterns 4, 205-213 can be found here.		The sequence and map of the reporter construct described in: R. A. Cameron, P. Oliveri, J. Wyllie, and E. H. Davidson (2004) cis-Regulatory Activity of Randomly Chosen Genomic Fragments from the Sea Urchin. Gene Expression Patterns 4, 205-213 can be found here.


	[[bac_vector_library\|BAC Library Vector]]<br />		[[bac_vector_library\|BAC Library Vector]]<br />
	The BAC vector pBACe3.6 is the one we have used in the preparation of all of our macro-array genomic libraries. Constructed in Pieter J. de Jong's laboratory at the Children's Hospital Oakland Research Center, it has been used extensively for genomic libraries and sequencing projects of many species.		The BAC vector pBACe3.6 is the one we have used in the preparation of all of our macro-array genomic libraries. Constructed in Pieter J. de Jong's laboratory at the Children's Hospital Oakland Research Center, it has been used extensively for genomic libraries and sequencing projects of many species.

	~~<span class="newwin">[http://new.echinobase.org/literature/article.do?method=display&articleId=42133 Sea Urchin Fertilization Laboratory]</span><br />~~
	Vic Vacquier developed a handout for university students on how to observe sea urchin fertilization in a university lab class setting. All that is needed are sea urchin gametes, a microscope, a few solutions and this handout. The handout works well for both 1 or 2 three hour labs. The student reads through the handout, makes the simple observations, and does the simple, direct experiments to gain insight into the fascinating process of sperm-egg interaction and egg activation.

	<span class="newwin">Fluorescent Protein Vectors</span><br />		<span class="newwin">Fluorescent Protein Vectors</span><br />
	The expression of exogenous proteins in sea urchins embryos, by injection of recombinant mRNAs, is routine procedure. The Hamdoun lab has generated a vector set with the major color and tag position variants that is useful for fluorescent protein tagging and expression in urchins. The complete vector set and can be obtained here: [https://www.addgene.org/kits/hamdoun-fluorescent-proteins/]. A description of the vectors can be found in Gokirmak et al., 2012 [http://new.echinobase.org/literature/article.do?method=display&articleId=42631 Vectors for generation of exogenous mRNAs fused to fluorescent proteins for expression in urchins]		The expression of exogenous proteins in sea urchins embryos, by injection of recombinant mRNAs, is routine procedure. The Hamdoun lab has generated a vector set with the major color and tag position variants that is useful for fluorescent protein tagging and expression in urchins. The complete vector set and can be obtained here: [https://www.addgene.org/kits/hamdoun-fluorescent-proteins/]. A description of the vectors can be found in Gokirmak et al., 2012 [http://new.echinobase.org/literature/article.do?method=display&articleId=42631 Vectors for generation of exogenous mRNAs fused to fluorescent proteins for expression in urchins]