Difference between revisions of "XENLA GeneModel2012"
From Marcotte Lab
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= Assembled transcripts = | = Assembled transcripts = | ||
== Raw sequences == | == Raw sequences == | ||
− | * From tissue samples: [ | + | * From tissue samples: [[:xdata:/J/Taira201203_XENLA_tissue_pep_final.fa| Protein FASTA]] & [[:xdata:/J/Taira201203_XENLA_tissue_cdna_final.fa| cDNA FASTA]] (112,045 in total) |
− | * From stage samples: [ | + | * From stage samples: [[:xdata:/J/Taira201203_XENLA_stage_pep_final.fa| Protein FASTA]] &[[:xdata:/J/Taira201203_XENLA_stage_pep_final.fa| cDNA FASTA]] (78,546 in total) |
= Annotation = | = Annotation = |
Revision as of 13:57, 3 August 2012
Contents |
Data summary
Disclaimer
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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
- From tissue samples: Protein FASTA & cDNA FASTA (112,045 in total)
- From stage samples: Protein FASTA & cDNA FASTA (78,546 in total)
Annotation
Orthologous genes
We used EnsEMBL-66 as main protein sequences. For X. laevis, we used protein sequences from XenBase (downloaded on Dec-2011). These are top-3 genes (based on E-value), with > 40% aligned length (based on query sequence). It should be mentioned that this is based on simple BLASTP search. We are currently working on more accurate orthology analysis based on phylgenetic tree based method.
XENLA (X. laevis) | HUMAN | XENTR (X. tropicalis) | MOUSE | DANRE (zebrafish) | CHICK (chicken) | CAEEL (worm) | DROME (fly) | |
---|---|---|---|---|---|---|---|---|
Stage pep as query | Stage pep --> XENLA | Stage pep --> HUMAN | Stage pep --> XENTR | Stage pep --> MOUSE | Stage pep --> DANRE | Stage pep --> CHICK | Stage pep --> CAEEL | Stage pep --> DROME |
Stage pep as target | Stage pep --> XENLA | HUMAN --> Stage pep | XENTR --> Stage pep | MOUSE --> Stage pep | DANRE --> Stage pep | CHICK --> Stage pep | CAEEL --> Stage pep | DROME --> Stage pep |
Tissue pep as query | Tissue pep --> XENLA | Tissue pep --> HUMAN | Tissue pep --> XENTR | Tissue pep --> MOUSE | Tissue pep --> DANRE | Tissue pep --> CHICK | Tissue pep --> CAEEL | Tissue pep --> DROME |
Tissue pep as target | Tissue pep --> XENLA | HUMAN --> Tissue pep | XENTR --> Tissue pep | MOUSE --> Tissue pep | DANRE --> Tissue pep | CHICK --> Tissue pep | CAEEL --> Tissue pep | DROME --> Tissue pep |
Micriarray
- Affymetrix microarray v.1 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL1318)
- Affymetrix microarray v.2 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL10756)
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)