Difference between revisions of "XENLA GeneModel2012"

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(Orthologous genes)
(Orthologous genes)
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We used EnsEMBL-66 as main protein sequences. For ''X. laevis'', we used protein sequences from XenBase (downloaded on Dec-2011).  
 
We used EnsEMBL-66 as main protein sequences. For ''X. laevis'', we used protein sequences from XenBase (downloaded on Dec-2011).  
  
* Human: [http://www.marcottelab.org/users/XenopusData/J/blast/Taira201203_XENLA_stage_pep_final.HUMAN_ens66_pep_longest.bp+_summary stage_pep --> Human][[xdata:/J/blast/HUMAN_ens66_pep_longest.Taira201203_XENLA_stage_pep_final.bp+_summary Human --> stage_pep]]
+
* Human: [http://www.marcottelab.org/users/XenopusData/J/blast/Taira201203_XENLA_stage_pep_final.HUMAN_ens66_pep_longest.bp+_summary stage_pep --> Human]
 +
[[xdata:/J/blast/HUMAN_ens66_pep_longest.Taira201203_XENLA_stage_pep_final.bp+_summary Human --> stage_pep]]
  
 
== Micriarray ==
 
== Micriarray ==

Revision as of 13:36, 3 August 2012

Contents

Data summary

Disclaimer

  • Data users may freely download and analyze sequences posted here.
  • 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' (Dr. Masanori Taira) published the paper. As soon as the paper is accepted, we will post that info on this website.
  • If you have more question about this data, please contact Dr. Masanori Taira, Dr. Edward Marcotte, or Dr. Taejoon Kwon.

Taira201203_XENLA_tissue

Collect total RNA from14 Tissue of Xenopus laevis J strain.

  • Brain, eye, heart, intestine, kidney, liver, lung, muscle, ovary, pancreas, skin, spleen, stomach, testis
  • Sons & daughters of single pair of frogs (Their mother frog was used for 1st BAC-end sequencing)
  • Standard Illumina sample prep. (poly-A capture)
  • Illumina HiSeq 2000, 2x100 bp
  • 108.5 billions of nucleotide calls in total.
  • 55M ~ 130M reads/tissue (27M ~ 65M pairs)
  • Brief report for data processing

Taira201203_XENLA_stage

Collect total RNA from 11 different developmental stages of Xenopus laevis J strain embryo.

  • Stage 01, 08, 09, 10.5, 12, 15, 20, 25, 30, 35, 40
  • Sons & daughters of single pair of frogs (their mother frog was used for 1st BAC-end sequencing)
  • Standard Illumina sample prep. (poly-A capture)
  • Illumina HiSeq 2000, 2x100 bp
  • 163.8 billions of nucleotide calls in total.
  • 40M ~ 110M reads/tissue (20M ~ 55M pairs)
  • Brief report for data processing

Assembled transcripts

Raw sequences

Annotation

Orthologous genes

We used EnsEMBL-66 as main protein sequences. For X. laevis, we used protein sequences from XenBase (downloaded on Dec-2011).

[[xdata:/J/blast/HUMAN_ens66_pep_longest.Taira201203_XENLA_stage_pep_final.bp+_summary Human --> stage_pep]]

Micriarray

Contributors

  • Masanori Taira (Graduate School of Science, University of Tokyo)
  • Shuji Takahashi (Komaba Organization for Educational Excellence, College of Arts and Sciences, University of Tokyo)
  • Toshiaki Tanaka (Tokyo Institute of Technology)
  • Atsushi Toyoda and Asao Fujiyama (National Institute of Genetics)
  • Yutaka Suzuki (Graduate School of Frontier Sciences, University of Tokyo)