Difference between revisions of "Xenopus Genome Project"

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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 (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 initially identified by extensive probing of the CHORI-219 library by [http://www.jgi.doe.gov/whoweare/cheng.html Jan-Fang Cheng]), as well as 10 BACs that have already been sequenced by the [http://www.jgi.doe.gov/ DOE Joint Genome Institute]/[http://www.hudsonalpha.org/genome-sequencing-center HudsonAlpha Genome Sequencing Center] 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 prepared by [http://tropicalis.yale.edu/ Mustafa Khokha] 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], sequencing each to multiple-fold coverage of the genome.
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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 initially identified by [http://www.jgi.doe.gov/whoweare/cheng.html Jan-Fang Cheng] via probing the CHORI-219 library), as well as 10 BACs that have already been sequenced by the [http://www.jgi.doe.gov/ DOE Joint Genome Institute]/[http://www.hudsonalpha.org/genome-sequencing-center HudsonAlpha Genome Sequencing Center] 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 prepared by [http://tropicalis.yale.edu/ Mustafa Khokha] 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], 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.

Revision as of 13:43, 30 November 2009

Xenopus-PV.jpg

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 Wallingford and Marcotte labs have obtained funding from the Texas Institute for Drug and Diagnostic Development (TI3D) to begin sequencing of the X. laevis genome. We are primarily working with Scott Hunicke-Smith at the 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 CHORI-219 library (vector: pBACGK1.1) at ~100X coverage. The selected BACs include ~70 genes of interest (Shroom3, Wnt5a, Glypican-4, Noggin, Gremlin, Pax6, Formin, etc., as initially identified by Jan-Fang Cheng via probing the CHORI-219 library), as well as 10 BACs that have already been sequenced by the DOE Joint Genome Institute/HudsonAlpha Genome Sequencing Center 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 prepared by Mustafa Khokha from J strain frogs obtained from Jacques Robert, 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

CHORI-219 BACs

List of 96 test BACs (MS Excel file)

XENLA_SA09023 First test stage of sequencing (Nov/16/2009)

See /XENLA_SA09023 for more details. 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
  • X_laevis_2kb - The set of 96 BACs, with 2kb insert size - about 3.6GB raw data, 0.3GB high quality data
  • X_laevis_5kb - The set of 96 BACs, with 5kb insert size - about 2.8GB raw data, 0.2GB high quality data

This (very roughly) corresponds to >600X coverage by raw data, ~50X coverage by high quality data, of the BAC set.