Difference between revisions of "XENLA GeneModel2012"
From Marcotte Lab
(→Data summary) |
|||
Line 6: | Line 6: | ||
* Data users may freely download and analyze sequences posted here. | * 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. | * 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' ([http://www.xenbase.org/community/person.do?method=display&personId=756 Dr. Masanori Taira]) 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' ([http://www.xenbase.org/community/person.do?method=display&personId=756 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 [http://www.xenbase.org/community/person.do?method=display&personId=756 Dr. Masanori Taira], [http://www.cm.utexas.edu/edward_marcotte Dr. Edward Marcotte], or [mailto:taejoon.kwon_at_marcottelab_dot_org Dr. Taejoon Kwon]. | ||
+ | </font> | ||
|} | |} | ||
Revision as of 01:06, 15 July 2012
Contents |
Data summary
Disclaimer
|
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
Original sequences
- From tissue samples Taira201203_XENLA_tissue_pep_final.fa Taira201203_XENLA_tissue_cdna_final.fa
- From stage samples: Taira201203_XENLA_stage_pep_final.fa Taira201203_XENLA_stage_cdna_final.fa
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)
- Edward M. Marcotte (University of Texas at Austin)
- John B. Wallingford (University of Texas at Austin)
- Taejoon Kwon (University of Texas at Austin)
- Texas Advanced Computing Center (TACC)