Difference between revisions of "Xenopus Genome Project"

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m (moved Texas Xenopus Genome Project to Xenopus Genome Project: It becomes much more popular than we expect.)
(Assembled transcripts from RNA-seq data)
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* 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.</font>
 
* 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.</font>
 
|}
 
|}
 
  
 
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].
  
== TXGP201107_XENLA_EGG ==
+
== J-strain stage data ==
Contact info:[mailto:edward.marcotte@gmail.com Edward Marcotte],[mailto:taejoon.kwon@marcottelab.org Taejoon Kwon]
+
Contact info: Masanori Taira
 +
* cDNA: [[xdata:/final/Taira201103_XENLA_stage_cdna_final.fa]]
 +
* Protein: [[xdata:/final/Taira201203_XENLA_stage_pep_final.fa]]  
  
* [[xdata:/tx/TXGP201107_XENLA_EGG.pub_all.fasta]] (37,470 sequences)
+
== J-strain tissue data ==
** 9,780 pub_all sequences are mapped to 6,705 v2_ref sequences.
+
Contact info: Masanori Taira
** 13,362 pub_all sequences are mapped to 9,920 v3_ref sequences.
+
* cDNA: [[xdata:/final/Taira201103_XENLA_tissue_cdna_final.fa]]  
 +
* Protein: [[xdata:/final/Taira201203_XENLA_tissue_pep_final.fa]]
  
* [[xdata:/tx/TXGP201107_XENLA_EGG.pub_long.fasta]] (20,005 sequences; only > 400 bp)
+
== Amin201106_XENLA ==
** 7,309 pub_long sequences are mapped to 6,082 v2_ref sequences.
+
(Courtesy of Nirav Amin & Frank Conlon, University of North Carolina at Chapel Hill)
** 9,439 pub_long sequences are mapped to 8,137 v3_ref sequences.
+
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>
 +
 
 +
* cDNA: [[xdata:/final/Amin201106_XENLA_cdna_final.fa]]  
 +
* Protein: [[xdata:/final/Amin201106_XENLA_pep_final.fa]]
  
 
== Park201106_XENLA ==
 
== Park201106_XENLA ==
Line 31: Line 37:
 
Contact info: [mailto:tjpark01@gmail.com Tae Joo Park], [mailto:harland@berkeley.edu Richard Harland].  
 
Contact info: [mailto:tjpark01@gmail.com Tae Joo Park], [mailto:harland@berkeley.edu Richard Harland].  
  
* [[xdata:/tx/Park201106_XENLA.pub_all.fasta]] (109,667 sequences)
+
* cDNA: [[xdata:/final/Park201106_XENLA_cdna_final.fa]]  
** 41,847 pub_all sequences are mapped to 7,522 v2_ref sequences.
+
* Protein: [[xdata:/final/Park201106_XENLA_pep_final.fa]]
** 59,419 pub_all sequences are mapped to 16,332 v3_ref sequences.  
+
  
* [[xdata:/tx/Park201106_XENLA.pub_long.fasta]] (19,716 sequences)
+
== Kwon201107_XENLA ==
** 10,790 pub_long sequences are mapped to 5,283 v2_ref sequences.
+
From two clutches of egg.
** 14,007 pub_long sequences are mapped to 7,977 v3_ref sequences.
+
Contact info:[mailto:edward.marcotte@gmail.com Edward Marcotte],[mailto:taejoon.kwon@marcottelab.org Taejoon Kwon].
  
== Amin201106_XENLA ==
+
* cDNA: [[xdata:/final/Kwon201107_XENLA_cdna_final.fa]]  
(Courtesy of Nirav Amin & Frank Conlon, University of North Carolina at Chapel Hill)
+
* Protein: [[xdata:/final/Kwon201107_XENLA_pep_final.fa]]  
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>
+
 
+
* [[xdata:/tx/Amin201106_XENLA.pub_all.fasta]] (106,189 sequences)
+
** 26,154 pub_all sequences are mapped to 8,312 v2_ref sequences.
+
** 38,535 pub_all sequences are mapped to 17,135 v3_ref sequences.
+
 
+
* [[xdata:/tx/Amin201106_XENLA.pub_long.fasta]] (27,252 sequences)
+
** 10,893 pub_long sequences are mapped to 6,757 v2_ref sequences.
+
** 15,342 pub_long sequences are mapped to 10,955 v3_ref sequences.
+
  
 
== Chung201110_XENLA ==
 
== Chung201110_XENLA ==
 
(Courtesy of Meii Chung & John Wallingford, University of Texas at Austin)
 
(Courtesy of Meii Chung & John Wallingford, University of Texas at Austin)
 
Contact info: [mailto:meii@utexas.edu Meii Chung], [mailto:wallingford@mail.utexas.edu John Wallingford]
 
Contact info: [mailto:meii@utexas.edu Meii Chung], [mailto:wallingford@mail.utexas.edu John Wallingford]
* [[xdata:/tx/Chung201110_XENLA.pub_all.fasta]] (109,258 sequences)
 
** 31,287 pub_all sequences are mapped to 7,126 v2_ref sequences.
 
** 44,577 pub_all sequences are mapped to 15,240 v3_ref sequences.
 
  
* [[xdata:/tx/Chung201110_XENLA.pub_long.fasta]] (20,682 sequences)
+
* cDNA: [[xdata:/final/Chung201110_XENLA_cdna_final.fa]]
** 4,817 pub_long sequences are mapped to 8,614 v2_ref sequences.
+
* Protein: [[xdata:/final/Chung201110_XENLA_pep_final.fa]]  
** 7,680 pub_long sequences are mapped to 11,735 v3_ref sequences.
+
 
 +
== Quigley201112_XENLA ==
 +
Courtesy of Ian Quigley, Chris Kintner
 +
 
 +
* cDNA: [[xdata:/final/Quigley201112_XENLA_cdna_final.fa]]
 +
* Protein: [[xdata:/final/Quigley201112_XENLA_pep_final.fa]]
 +
 
 +
== Jarikji201201_XENLA ==
 +
Courtesy of Marko Horb
 +
 
 +
* cDNA: [[xdata:/final/Jarikji201101_XENLA_cdna_final.fa]]
 +
* Protein: [[xdata:/final/Jarikji201101_XENLA_pep_final.fa]]
 +
 
 +
== TeperekTkacz201202_XENLA ==
 +
Courtesy of Marta Teperek-Tkacz
 +
 
 +
* cDNA: [[xdata:/final/TeperekTkacz201102_XENLA_cdna_final.fa]]
 +
* Protein: [[xdata:/final/TeperekTkacz201102_XENLA_pep_final.fa]]
 +
 
 +
== Veenstra201204_XENLA ==
 +
Courtesy of Gert J Veenstra
 +
 
 +
* cDNA: [[xdata:/final/Veenstra201104_XENLA_cdna_final.fa]]
 +
* Protein: [[xdata:/final/Veenstra201104_XENLA_pep_final.fa]]
  
 
= CHORI-219 BAC sequencing =
 
= CHORI-219 BAC sequencing =

Revision as of 08:19, 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.

Contents

Assembled transcripts from RNA-seq data

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.

J-strain stage data

Contact info: Masanori Taira

J-strain tissue data

Contact info: Masanori Taira

Amin201106_XENLA

(Courtesy of Nirav Amin & Frank Conlon, University of North Carolina at Chapel Hill) Contact info: Nirav Amin, Frank Conlon Only control samples are used for this assembly.

Park201106_XENLA

(Courtesy of Tae Joo Park & Richard Harland, University of California at Berkeley) Contact info: Tae Joo Park, Richard Harland.

Kwon201107_XENLA

From two clutches of egg. Contact info:Edward Marcotte,Taejoon Kwon.

Chung201110_XENLA

(Courtesy of Meii Chung & John Wallingford, University of Texas at Austin) Contact info: Meii Chung, John Wallingford

Quigley201112_XENLA

Courtesy of Ian Quigley, Chris Kintner

Jarikji201201_XENLA

Courtesy of Marko Horb

TeperekTkacz201202_XENLA

Courtesy of Marta Teperek-Tkacz

Veenstra201204_XENLA

Courtesy of Gert J Veenstra

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