Difference between revisions of "XENLA GeneModel2012"

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(Original sequences)
(Raw sequences)
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= Assembled transcripts =
 
= Assembled transcripts =
 
== Raw sequences ==
 
== Raw sequences ==
* From tissue samples: [http://www.marcottelab.org/users/XenopusData/J/Taira201203_XENLA_stage_pep_final.fa protein FASTA] [http://www.marcottelab.org/users/XenopusData/J/Taira201203_XENLA_stage_cdna_final.fa cDNA FASTA]
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* From tissue samples: [http://www.marcottelab.org/users/XenopusData/J/Taira201203_XENLA_stage_pep_final.fa Protein FASTA] [http://www.marcottelab.org/users/XenopusData/J/Taira201203_XENLA_stage_cdna_final.fa cDNA FASTA]
* From stage samples: [http://www.marcottelab.org/users/XenopusData/J/Taira201203_XENLA_stage_pep_final.fa protein FASTA] [http://www.marcottelab.org/users/XenopusData/J/Taira201203_XENLA_stage_pep_final.fa cDNA FASTA]
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* From stage samples: [http://www.marcottelab.org/users/XenopusData/J/Taira201203_XENLA_stage_pep_final.fa Protein FASTA] [http://www.marcottelab.org/users/XenopusData/J/Taira201203_XENLA_stage_pep_final.fa cDNA FASTA]
  
 
= Annotation =
 
= Annotation =

Revision as of 15:20, 18 July 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)

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)

Assembled transcripts

Raw sequences

Annotation


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)