Difference between revisions of "Xenopus Genome Project"

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(Assembled transcripts from RNA-seq data)
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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), in coordination with projects funded by the National Institutes of Health, to begin sequencing of the ''X. laevis'' genome. We are primarily working with [https://wikis.utexas.edu/display/GSAF/About+Us Scott Hunicke-Smith] at the [https://wikis.utexas.edu/display/GSAF/Home+Page 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.  
 
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), in coordination with projects funded by the National Institutes of Health, to begin sequencing of the ''X. laevis'' genome. We are primarily working with [https://wikis.utexas.edu/display/GSAF/About+Us Scott Hunicke-Smith] at the [https://wikis.utexas.edu/display/GSAF/Home+Page 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.  
  
= Assembled transcripts from RNA-seq data =
 
 
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If you have any question about this data in general, please contact to [mailto:taejoon.kwon@marcottelab.org Taejoon Kwon].
 
If you have any question about this data in general, please contact to [mailto:taejoon.kwon@marcottelab.org Taejoon Kwon].
 +
 +
 +
= Assembled transcripts from J-strain <i>X. laevis</i> RNA-seq data =
 +
You can see more detailed info at [[Taira201203_XENLA]]
  
 
== J-strain stage data ==
 
== J-strain stage data ==
Contact info: Masanori Taira
+
Courtesy of [mailto:m_taira at biol dot s dot u-tokyo dot ac dot jp Masanori Taira](University of Tokyo, Japan)
 
* cDNA: [[xdata:/final/Taira201103_XENLA_stage_cdna_final.fa]]  
 
* cDNA: [[xdata:/final/Taira201103_XENLA_stage_cdna_final.fa]]  
 
* Protein: [[xdata:/final/Taira201203_XENLA_stage_pep_final.fa]]  
 
* Protein: [[xdata:/final/Taira201203_XENLA_stage_pep_final.fa]]  
  
 
== J-strain tissue data ==
 
== J-strain tissue data ==
Contact info: Masanori Taira
+
Courtesy of [mailto:m_taira at biol dot s dot u-tokyo dot ac dot jp Masanori Taira](University of Tokyo, Japan)
 
* cDNA: [[xdata:/final/Taira201103_XENLA_tissue_cdna_final.fa]]  
 
* cDNA: [[xdata:/final/Taira201103_XENLA_tissue_cdna_final.fa]]  
 
* Protein: [[xdata:/final/Taira201203_XENLA_tissue_pep_final.fa]]  
 
* Protein: [[xdata:/final/Taira201203_XENLA_tissue_pep_final.fa]]  
 +
 +
= Assembled transcripts from wild-type <i>X. laevis</i> RNA-seq data =
  
 
== Amin201106_XENLA ==
 
== Amin201106_XENLA ==
(Courtesy of Nirav Amin & Frank Conlon, University of North Carolina at Chapel Hill)
+
(Courtesy of [mailto:nmamin at email dot unc dot edu Nirav Amin], [mailto:frank_conlon at med dot unc dot edu Frank Conlon] (University of North Carolina at Chapel Hill, USA)
Contact info: [mailto:nmamin@email.unc.edu Nirav Amin], [mailto:frank_conlon@med.unc.edu Frank Conlon]
+
 
<b>Only control samples are used for this assembly.</b>
 
<b>Only control samples are used for this assembly.</b>
  
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== Park201106_XENLA ==
 
== Park201106_XENLA ==
(Courtesy of Tae Joo Park & Richard Harland, University of California at Berkeley)
+
Courtesy of [mailto:tjpark01 at gmail dot com Tae Joo Park] (UNIST, Republic of Korea)
Contact info: [mailto:tjpark01@gmail.com Tae Joo Park], [mailto:harland@berkeley.edu Richard Harland].
+
  
 
* cDNA: [[xdata:/final/Park201106_XENLA_cdna_final.fa]]  
 
* cDNA: [[xdata:/final/Park201106_XENLA_cdna_final.fa]]  
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== Kwon201107_XENLA ==
 
== Kwon201107_XENLA ==
From two clutches of egg.
+
Courtesy of [mailto:edward dot marcotte at gmail dot com Edward Marcotte],[mailto:taejoon dot kwon at marcottelab dot org Taejoon Kwon], [mailto:meii at utexas dot edu Meii Chung], [mailto:wallingford at mail dot utexas dot edu John Wallingford] (University of Texas at Austin, USA)
Contact info:[mailto:edward.marcotte@gmail.com Edward Marcotte],[mailto:taejoon.kwon@marcottelab.org Taejoon Kwon]
+
  
 
* cDNA: [[xdata:/final/Kwon201107_XENLA_cdna_final.fa]]  
 
* cDNA: [[xdata:/final/Kwon201107_XENLA_cdna_final.fa]]  
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== Chung201110_XENLA ==
 
== Chung201110_XENLA ==
(Courtesy of Meii Chung & John Wallingford, University of Texas at Austin)
+
Courtesy of [mailto:meii at utexas dot edu Meii Chung], [mailto:wallingford at mail dot utexas dot edu John Wallingford] (University of Texas at Austin, USA)
Contact info: [mailto:meii@utexas.edu Meii Chung], [mailto:wallingford@mail.utexas.edu John Wallingford]
+
  
 
* cDNA: [[xdata:/final/Chung201110_XENLA_cdna_final.fa]]  
 
* cDNA: [[xdata:/final/Chung201110_XENLA_cdna_final.fa]]  
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== Quigley201112_XENLA ==
 
== Quigley201112_XENLA ==
Courtesy of Ian Quigley, Chris Kintner
+
Courtesy of [mailto:iquigley at salk dot edu Ian Quigley], [mailto:kintner at salk dot edu Chris Kintner] (Salk Institute, USA)
  
 
* cDNA: [[xdata:/final/Quigley201112_XENLA_cdna_final.fa]]  
 
* cDNA: [[xdata:/final/Quigley201112_XENLA_cdna_final.fa]]  
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== Jarikji201201_XENLA ==
 
== Jarikji201201_XENLA ==
Courtesy of Marko Horb
+
Courtesy of [mailto:mhorb at mbl dot edu Marko Horb] (Marine Biological Laboratory, USA)
  
 
* cDNA: [[xdata:/final/Jarikji201101_XENLA_cdna_final.fa]]  
 
* cDNA: [[xdata:/final/Jarikji201101_XENLA_cdna_final.fa]]  
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== TeperekTkacz201202_XENLA ==
 
== TeperekTkacz201202_XENLA ==
Courtesy of Marta Teperek-Tkacz
+
Courtesy of [mailto: mt446 at cam dot ac dot uk Marta Teperek-Tkacz] (University of Cambridge/Gurdon Institute, UK)
  
 
* cDNA: [[xdata:/final/TeperekTkacz201102_XENLA_cdna_final.fa]]  
 
* cDNA: [[xdata:/final/TeperekTkacz201102_XENLA_cdna_final.fa]]  
 
* Protein: [[xdata:/final/TeperekTkacz201102_XENLA_pep_final.fa]]  
 
* Protein: [[xdata:/final/TeperekTkacz201102_XENLA_pep_final.fa]]  
 +
 +
== Ismailoglu201203_XENLA ==
 +
Courtesy of [iismailoglu at rockefeller dot edu Ismail Ismailoglu], [brvnlou at mail dot rockefeller dot edu Ali Brivanlou] (Rockefeller University, USA)
 +
 +
* cDNA: [[xdata:/final/Ismailoglu201203_XENLA_cdna_final.fa]]
 +
* Protein: [[xdata:/final/Ismailoglu201203_XENLA_pep_final.fa]]
  
 
== Veenstra201204_XENLA ==
 
== Veenstra201204_XENLA ==
Courtesy of Gert J Veenstra
+
Courtesy of Gert J Veenstra (Radboud University Nijmegen, The Netherlands)
  
 
* cDNA: [[xdata:/final/Veenstra201104_XENLA_cdna_final.fa]]  
 
* cDNA: [[xdata:/final/Veenstra201104_XENLA_cdna_final.fa]]  
 
* Protein: [[xdata:/final/Veenstra201104_XENLA_pep_final.fa]]
 
* Protein: [[xdata:/final/Veenstra201104_XENLA_pep_final.fa]]
 +
 +
== Audic201207_XENLA ==
 +
Courtesy of [mailto:yann dot audic at univ-rennes1 dot fr Yann Audic] (Université de RENNES I)
 +
 +
* cDNA: [[xdata:/final/Audic201207_XENLA_cdna_final.fa]]
 +
* Protein: [[xdata:/final/Audic201207_XENLA_pep_final.fa]]
 +
 +
== Quigley201207_XENLA ==
 +
Courtesy of [mailto:iquigley at salk dot edu Ian Quigley], [mailto:kintner at salk dot edu Chris Kintner] (Salk Institute, USA)
 +
 +
* cDNA: [[xdata:/final/Quigley201207_XENLA_cdna_final.fa]]
 +
* Protein: [[xdata:/final/Quigley201207_XENLA_pep_final.fa]]
 +
 +
 +
= Assembled transcripts from wild-type <i>S. tropicalis</i> RNA-seq data =
 +
== Tan201204_XENTR ==
 +
Courtesy of [mailto:menghow at stanford dot edu Meng How Tan] (Stanford University, USA)
 +
It is published in Genome Research [http://genome.cshlp.org/content/early/2012/09/07/gr.141424.112.abstract Early Access]
 +
 +
* cDNA: [[xdata:/final/Tan201204_XENTR_cdna_final.fa]]
 +
* Protein: [[xdata:/final/Tan201204_XENTR_pep_final.fa]]
 +
 +
 +
  
 
= CHORI-219 BAC sequencing =
 
= CHORI-219 BAC sequencing =

Revision as of 10:20, 21 September 2012

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), in coordination with projects funded by the National Institutes of Health, 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.

Disclaimer

  • Data users may freely download and analyze data. They may use data in publications focused around individual genes.
  • Data users may use data to analyze their own data, i.e. reference database for MS/MS proteomics data, and/or RNA-seq data.
  • The publication and presentation of global analysis of data with these sequences are not allowed until 'data owner' published the paper. As soon as the paper is accepted, we will post that info on this website.

If you have any question about this data in general, please contact to Taejoon Kwon.


Contents

Assembled transcripts from J-strain X. laevis RNA-seq data

You can see more detailed info at Taira201203_XENLA

J-strain stage data

Courtesy of at biol dot s dot u-tokyo dot ac dot jp Masanori Taira(University of Tokyo, Japan)

J-strain tissue data

Courtesy of at biol dot s dot u-tokyo dot ac dot jp Masanori Taira(University of Tokyo, Japan)

Assembled transcripts from wild-type X. laevis RNA-seq data

Amin201106_XENLA

(Courtesy of at email dot unc dot edu Nirav Amin, at med dot unc dot edu Frank Conlon (University of North Carolina at Chapel Hill, USA) Only control samples are used for this assembly.

Park201106_XENLA

Courtesy of at gmail dot com Tae Joo Park (UNIST, Republic of Korea)

Kwon201107_XENLA

Courtesy of dot marcotte at gmail dot com Edward Marcotte,dot kwon at marcottelab dot org Taejoon Kwon, at utexas dot edu Meii Chung, at mail dot utexas dot edu John Wallingford (University of Texas at Austin, USA)

Chung201110_XENLA

Courtesy of at utexas dot edu Meii Chung, at mail dot utexas dot edu John Wallingford (University of Texas at Austin, USA)

Quigley201112_XENLA

Courtesy of at salk dot edu Ian Quigley, at salk dot edu Chris Kintner (Salk Institute, USA)

Jarikji201201_XENLA

Courtesy of at mbl dot edu Marko Horb (Marine Biological Laboratory, USA)

TeperekTkacz201202_XENLA

Courtesy of [mailto: mt446 at cam dot ac dot uk Marta Teperek-Tkacz] (University of Cambridge/Gurdon Institute, UK)

Ismailoglu201203_XENLA

Courtesy of [iismailoglu at rockefeller dot edu Ismail Ismailoglu], [brvnlou at mail dot rockefeller dot edu Ali Brivanlou] (Rockefeller University, USA)

Veenstra201204_XENLA

Courtesy of Gert J Veenstra (Radboud University Nijmegen, The Netherlands)

Audic201207_XENLA

Courtesy of dot audic at univ-rennes1 dot fr Yann Audic (Université de RENNES I)

Quigley201207_XENLA

Courtesy of at salk dot edu Ian Quigley, at salk dot edu Chris Kintner (Salk Institute, USA)


Assembled transcripts from wild-type S. tropicalis RNA-seq data

Tan201204_XENTR

Courtesy of at stanford dot edu Meng How Tan (Stanford University, USA) It is published in Genome Research Early Access



CHORI-219 BAC 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 the group of 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.

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.

  • Given that we currently see better mapping of the shotgun SA09023 reads to X. tropicalis than to X. laevis (both to BACs and mRNAs), we're confirming the sample identity before continuing with whole genome sequencing. See the 'sanity check' /Species_Identification for details.

J-strain whole genome sequencing

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.

See also

References

Protocol