XENLA GeneModel2012
From Marcotte Lab
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Data summary
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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
- From stage samples: Protein FASTA cDNA FASTA
Annotation
Orthologous genes
We used EnsEMBL-66 as main protein sequences. For X. laevis, we used protein sequences from XenBase (downloaded on Dec-2011).
- Human: stage_pep --> Human[[xdata:/J/blast/HUMAN_ens66_pep_longest.Taira201203_XENLA_stage_pep_final.bp+_summary Human --> stage_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)