MarcotteLab - Recent changes [en]

Texas Xenopus Genome Project

Taejoon — Sun, 22 Nov 2009 16:17:48 GMT

Progress Reports:

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	''Xenopus laevis'' is an essential model organism in several areas of biology. In addition to the key attributes of these embryos for ''in vivo'' imaging, cell-free extracts from ''Xenopus'' provide among the most powerful ''in vitro'' systems for studies of cell and molecular biology. A complete sequence of the ''X. laevis'' genome is an essential resource for accurate identification of peptides for mass-spec analyses, for cloning of an ORFeome, for identifying evolutionarily conserved regulatory regions, and for design of morpholino-oligonucleotides for gene knockdowns.		''Xenopus laevis'' is an essential model organism in several areas of biology. In addition to the key attributes of these embryos for ''in vivo'' imaging, cell-free extracts from ''Xenopus'' provide among the most powerful ''in vitro'' systems for studies of cell and molecular biology. A complete sequence of the ''X. laevis'' genome is an essential resource for accurate identification of peptides for mass-spec analyses, for cloning of an ORFeome, for identifying evolutionarily conserved regulatory regions, and for design of morpholino-oligonucleotides for gene knockdowns.

-	The [http://www.bio.utexas.edu/faculty/wallingford/ Wallingford] and Marcotte labs have obtained funding from the [http://www.ti3d.utexas.edu/ Texas Institute for Drug and Diagnostic Development] (TI3D) to begin sequencing of the ''X. laevis'' genome. We are primarily working with [http://gsaf.cssb.utexas.edu/Site/About_Us.html Scott Hunicke-Smith] at the [http://gsaf.cssb.utexas.edu University of Texas Genome Sequencing and Analysis facility], with funding sufficient for ~20x coverage of the ''X. laevis genome'' using ABI SOLiD next-generation sequencing. We have started the first runs by sequencing 96 BACs from the [http://bacpac.chori.org/library.php?id=323 CHORI-219] library at ~100X coverage. The selected BACs include ~70 genes of interest (Shroom3, Wnt5a, Glypican-4, Noggin, Gremlin, Pax6, Formin, etc.), as well as 10 BACs that have already been sequenced by HudsonAlpha to serve as positive controls for the sequencing and assembly pipeline. In addition, we are generating several mate pair libraries of different sizes from genomic DNA from J strain frogs (obtained from [http://www.urmc.rochester.edu/web/index.cfm?event=doctor.profile.show&person_id=1001617&display=for_researchers Jacques Robert] via [http://tropicalis.yale.edu/ Mustafa Khokha]), sequencing each to multiple-fold coverage of the genome.	+	The [http://www.bio.utexas.edu/faculty/wallingford/ Wallingford] and Marcotte labs have obtained funding from the [http://www.ti3d.utexas.edu/ Texas Institute for Drug and Diagnostic Development] (TI3D) to begin sequencing of the ''X. laevis'' genome. We are primarily working with [http://gsaf.cssb.utexas.edu/Site/About_Us.html Scott Hunicke-Smith] at the [http://gsaf.cssb.utexas.edu University of Texas Genome Sequencing and Analysis facility], with funding sufficient for ~20x coverage of the ''X. laevis genome'' using ABI SOLiD next-generation sequencing. We have started the first runs by sequencing 96 BACs from the [http://bacpac.chori.org/library.php?id=323 CHORI-219] library (vector: [http://www.sanger.ac.uk/Teams/Team53/psub/sequences/pbacgk.shtml pBACGK1.1]) at ~100X coverage. The selected BACs include ~70 genes of interest (Shroom3, Wnt5a, Glypican-4, Noggin, Gremlin, Pax6, Formin, etc.), as well as 10 BACs that have already been sequenced by HudsonAlpha to serve as positive controls for the sequencing and assembly pipeline. In addition, we are generating several mate pair libraries of different sizes from genomic DNA from J strain frogs (obtained from [http://www.urmc.rochester.edu/web/index.cfm?event=doctor.profile.show&person_id=1001617&display=for_researchers Jacques Robert] via [http://tropicalis.yale.edu/ Mustafa Khokha]), sequencing each to multiple-fold coverage of the genome.

	The primary data from this project will be made available as soon as possible for use by the community. We plan to periodically post reports on our progress below.		The primary data from this project will be made available as soon as possible for use by the community. We plan to periodically post reports on our progress below.

	== Progress Reports ==		== Progress Reports ==
-	~~[http:~~//~~www~~.~~marcottelab~~.~~org/XenopusData/BACsFor1Percent~~.~~xls List~~ of 96 ~~test~~ BACs]	+	=== SA09023 First test stage of sequencing (Nov/16/2009) ===
		+	Three mate paired libraries were sequenced:
		+	* X_laevis_WG - the ''X. laevis'' whole genome library, 5kb insert size - about 4.4GB raw data, 0.4GB high quality data<br>
		+	* X_laevis_2kb - The set of 96 BACs, with 2kb insert size - about 3.6GB raw data, 0.3GB high quality data<br>
		+	* X_laevis_5kb - The set of 96 BACs, with 5kb insert size - about 2.8GB raw data, 0.2GB high quality data<br>

-	~~11/16/2009 - First test stage of sequencing done! Three mate paired libraries were sequenced:<br>~~
-	~~X_laevis_WG - the ''X. laevis'' whole genome library, 5kb insert size - about 4.4GB raw data, 0.4GB high quality data<br>~~
-	~~X_laevis_2kb - The set of 96 BACs, with 2kb insert size - about 3.6GB raw data, 0.3GB high quality data<br>~~
-	~~X_laevis_5kb - The set of 96 BACs, with 5kb insert size - about 2.8GB raw data, 0.2GB high quality data<br>~~
	This (very roughly) corresponds to >600X coverage by raw data, ~50X coverage by high quality data, of the BAC set.		This (very roughly) corresponds to >600X coverage by raw data, ~50X coverage by high quality data, of the BAC set.
		+
		+	[http://www.marcottelab.org/XenopusData/BACsFor1Percent.xls List of 96 test BACs]

Research

Taejoon — Sat, 21 Nov 2009 02:18:57 GMT

Recent research news:

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	<div style="border:solid green;margin:8px;padding:10px;">		<div style="border:solid green;margin:8px;padding:10px;">
	[[File:Xenopus-PV.jpg\|\|100px\|left]] <br>		[[File:Xenopus-PV.jpg\|\|100px\|left]] <br>
-	'''Read about our [~~http://www.bio.utexas.edu/faculty/wallingford/Pages/Research.html#GenomeSeq Texas <i>Xenopus</i> genome project~~] (!)''', a collaboration with the [http://www.bio.utexas.edu/faculty/wallingford/ Wallingford lab] and the [http://gsaf.cssb.utexas.edu/Site/The_Genomic_Sequencing_and_Analysis_Facility_at_UT_Austin_Main_Page.html UT Genomic Sequencing and Analysis Facility], funded by the [http://www.ti3d.utexas.edu/ Texas Institute for Drug and Diagnostic Development]<br>	+	'''Read about our [[Texas_Xenopus_Genome_Project]] (!)''', a collaboration with the [http://www.bio.utexas.edu/faculty/wallingford/ Wallingford lab] and the [http://gsaf.cssb.utexas.edu/Site/The_Genomic_Sequencing_and_Analysis_Facility_at_UT_Austin_Main_Page.html UT Genomic Sequencing and Analysis Facility], funded by the [http://www.ti3d.utexas.edu/ Texas Institute for Drug and Diagnostic Development]<br>
	<br>		<br>
	<br>		<br>

	</div>		</div>

Texas Xenopus Genome Project

Marcotte — Sat, 21 Nov 2009 00:45:07 GMT

Progress Reports:

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	[[File:Xenopus-PV.jpg\|\|100px\|left]] <br>		[[File:Xenopus-PV.jpg\|\|100px\|left]] <br>
-	''Xenopus laevis'' is an essential model organism in several areas of biology. In addition to the key attributes of these embryos for ''in vivo'' imaging, cell-free extracts from ''Xenopus'' provide among the most powerful in vitro systems for studies of cell and molecular biology. A complete sequence of the ''X. laevis'' genome is an essential resource for accurate identification of peptides for mass-spec analyses, for cloning of an ORFeome, for identifying evolutionarily conserved regulatory ~~region~~, and for design of morpholino-oligonucleotides for gene knockdowns.	+	''Xenopus laevis'' is an essential model organism in several areas of biology. In addition to the key attributes of these embryos for ''in vivo'' imaging, cell-free extracts from ''Xenopus'' provide among the most powerful ''in vitro'' systems for studies of cell and molecular biology. A complete sequence of the ''X. laevis'' genome is an essential resource for accurate identification of peptides for mass-spec analyses, for cloning of an ORFeome, for identifying evolutionarily conserved regulatory regions, and for design of morpholino-oligonucleotides for gene knockdowns.

-	The [http://www.bio.utexas.edu/faculty/wallingford/ Wallingford] and Marcotte labs have ~~now~~ obtained funding ~~to begin sequencing of the ''X. laevis'' genome~~ from the [http://www.ti3d.utexas.edu/ Texas Institute for Drug and Diagnostic Development] (TI3D). We are primarily working with [http://gsaf.cssb.utexas.edu/Site/About_Us.html Scott Hunicke-Smith] at the [http://gsaf.cssb.utexas.edu University of Texas Genome Sequencing and Analysis facility], with funding sufficient for ~20x coverage of the ''X. laevis genome'' using ABI SOLiD next-generation sequencing. We have started the first runs by sequencing 96 BACs from the [http://bacpac.chori.org/library.php?id=323 CHORI-219] library at ~100X coverage. The selected BACs include ~70 genes of interest (Shroom3, Wnt5a, Glypican-4, Noggin, Gremlin, Pax6, Formin, etc.), as well as 10 BACs that have already been sequenced by HudsonAlpha to serve as positive controls for the sequencing and assembly pipeline. In addition, we are generating several mate pair libraries of different sizes from genomic DNA from J strain frogs (obtained from [http://www.urmc.rochester.edu/web/index.cfm?event=doctor.profile.show&person_id=1001617&display=for_researchers Jacques Robert] via [http://tropicalis.yale.edu/ Mustafa Khokha]), sequencing each to multiple-fold coverage of the genome.	+	The [http://www.bio.utexas.edu/faculty/wallingford/ Wallingford] and Marcotte labs have obtained funding from the [http://www.ti3d.utexas.edu/ Texas Institute for Drug and Diagnostic Development] (TI3D) to begin sequencing of the ''X. laevis'' genome. We are primarily working with [http://gsaf.cssb.utexas.edu/Site/About_Us.html Scott Hunicke-Smith] at the [http://gsaf.cssb.utexas.edu University of Texas Genome Sequencing and Analysis facility], with funding sufficient for ~20x coverage of the ''X. laevis genome'' using ABI SOLiD next-generation sequencing. We have started the first runs by sequencing 96 BACs from the [http://bacpac.chori.org/library.php?id=323 CHORI-219] library at ~100X coverage. The selected BACs include ~70 genes of interest (Shroom3, Wnt5a, Glypican-4, Noggin, Gremlin, Pax6, Formin, etc.), as well as 10 BACs that have already been sequenced by HudsonAlpha to serve as positive controls for the sequencing and assembly pipeline. In addition, we are generating several mate pair libraries of different sizes from genomic DNA from J strain frogs (obtained from [http://www.urmc.rochester.edu/web/index.cfm?event=doctor.profile.show&person_id=1001617&display=for_researchers Jacques Robert] via [http://tropicalis.yale.edu/ Mustafa Khokha]), sequencing each to multiple-fold coverage of the genome.

	The primary data from this project will be made available as soon as possible for use by the community. We plan to periodically post reports on our progress below.		The primary data from this project will be made available as soon as possible for use by the community. We plan to periodically post reports on our progress below.

	== Progress Reports ==		== Progress Reports ==
		+	[http://www.marcottelab.org/XenopusData/BACsFor1Percent.xls List of 96 test BACs]
		+
		+	11/16/2009 - First test stage of sequencing done! Three mate paired libraries were sequenced:<br>
		+	X_laevis_WG - the ''X. laevis'' whole genome library, 5kb insert size - about 4.4GB raw data, 0.4GB high quality data<br>
		+	X_laevis_2kb - The set of 96 BACs, with 2kb insert size - about 3.6GB raw data, 0.3GB high quality data<br>
		+	X_laevis_5kb - The set of 96 BACs, with 5kb insert size - about 2.8GB raw data, 0.2GB high quality data<br>
		+	This (very roughly) corresponds to >600X coverage by raw data, ~50X coverage by high quality data, of the BAC set.

File:BACsFor1Percent.xls

Marcotte — Sat, 21 Nov 2009 00:20:34 GMT

uploaded "[[File:BACsFor1Percent.xls]]"

New page

Texas Xenopus Genome Project

Marcotte — Sat, 21 Nov 2009 00:16:37 GMT

New page

[[File:Xenopus-PV.jpg||100px|left]] <br>
''Xenopus laevis'' is an essential model organism in several areas of biology. In addition to the key attributes of these embryos for ''in vivo'' imaging, cell-free extracts from ''Xenopus'' provide among the most powerful in vitro systems for studies of cell and molecular biology. A complete sequence of the ''X. laevis'' genome is an essential resource for accurate identification of peptides for mass-spec analyses, for cloning of an ORFeome, for identifying evolutionarily conserved regulatory region, and for design of morpholino-oligonucleotides for gene knockdowns.

The [http://www.bio.utexas.edu/faculty/wallingford/ Wallingford] and Marcotte labs have now obtained funding to begin sequencing of the ''X. laevis'' genome from the [http://www.ti3d.utexas.edu/ Texas Institute for Drug and Diagnostic Development] (TI3D). We are primarily working with [http://gsaf.cssb.utexas.edu/Site/About_Us.html Scott Hunicke-Smith] at the [http://gsaf.cssb.utexas.edu University of Texas Genome Sequencing and Analysis facility], with funding sufficient for ~20x coverage of the ''X. laevis genome'' using ABI SOLiD next-generation sequencing. We have started the first runs by sequencing 96 BACs from the [http://bacpac.chori.org/library.php?id=323 CHORI-219] library at ~100X coverage. The selected BACs include ~70 genes of interest (Shroom3, Wnt5a, Glypican-4, Noggin, Gremlin, Pax6, Formin, etc.), as well as 10 BACs that have already been sequenced by HudsonAlpha to serve as positive controls for the sequencing and assembly pipeline. In addition, we are generating several mate pair libraries of different sizes from genomic DNA from J strain frogs (obtained from [http://www.urmc.rochester.edu/web/index.cfm?event=doctor.profile.show&person_id=1001617&display=for_researchers Jacques Robert] via [http://tropicalis.yale.edu/ Mustafa Khokha]), sequencing each to multiple-fold coverage of the genome.

The primary data from this project will be made available as soon as possible for use by the community. We plan to periodically post reports on our progress below.

== Progress Reports ==

Publication

Marcotte — Mon, 16 Nov 2009 23:31:06 GMT

2009:

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	\|journal=Molecular BioSystems		\|journal=Molecular BioSystems
	\|pub_year=2009		\|pub_year=2009
-	\|volume=~~in press~~	+	\|volume=5
-	\|page=	+	\|page=1512–1526
	\|pubmed=		\|pubmed=
	\|link=http://www.rsc.org/Publishing/Journals/MB/article.asp?doi=b908315d		\|link=http://www.rsc.org/Publishing/Journals/MB/article.asp?doi=b908315d
		+	\|pdf=MolecularBioSystems_ProteinRNA_2009.pdf
	\|comment=		\|comment=
	}}		}}