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Illumina whole genome sequences | Illumina RNA sequences | Transcriptome sequences | Protein Sequences
Illumina NextGen sequences | Transcriptome sequences | Protein sequences | GeneChip
Whole genome DNA Illumina sequencing
Adipose stromal cells - SRX179264
Vascular smooth muscle endothelial cells Illumina sequencing - SRX179266
The Velvet/ Oases pipeline was used to assemble de novo chimpanzee transcripts from the NextGen mRNA sequences listed above. These sequences were deposited in GenBank.
Chimp protein sequences were obtained by conceptual translation of the transcripts described above.
Animal 17573 (reference animal)
Animal 21353
Animal 002T-NHP
Animal 001T-NHP
mRNA from caudate nucleus Illumina sequencing
mRNA from orbital cerebral cortex Illumina sequencing
Animal BF23762
Animal BF23764
Animal BF23773
Animal BF22215
Animal BF20336
Animal BF21178
The Velvet/ Oases pipeline was used to assemble de novo rhesus macaque transcripts from the NextGen mRNA sequences listed above. These sequences were deposited in GenBank.
Rhesus protein sequences were obtained by conceptual translation of the transcripts described above.
The Affymetrix Rhesus Macaque Genome Array was produced as a result of joint collaboration between the Norgren Lab and Affymetrix
Although Affymetrix provides an annotation of the Rhesus Macaque Genome Array, we have created an alternative annotation using a different approach. Briefly, our annotations are based on BLAST searches using the consensus sequences from the Affymetrix rhesus GeneChip files. We BLASTed these sequences against the human transcript database and identified the best hits.
Click on Probeset to Gene Name to get a list of Probesets from the Rhesus GeneChip and their corresponding Gene Symbols and Gene Names in .xlsx format. This is version 3 (updated June 3, 2010).
The fields include:
Affy Rhesus Probe Set Name
Human GeneSymbol
Proposed Gene Description
This annotation may contain errors and should be used with caution. We welcome user feedback and hope to improve the quality and usefullness of this dataset.
An article describing the development of this array "Novel approach results in first-ever rhesus macaque whole-genome array" was featured in Affymetrix Scientist Spotlight.
Although developed based on rhesus macaque sequences, this genechip has been used for several additional species including: Macaca fascicularis (cynomolgus monkey), Macaca radiata (bonnet monkey), Cercocebus atys (sooty mangabey), and Chlorocebus aethiops (grivet). See listing of experiments by species at EMBL-EBI.
The rhesus macaque genome array has been used for a wide variety of different studies including the following subjects: evolution, SIV/HIV, SARS, Monkeypox, stem cells, reproduction, neuroscience, transplantation and RNA helicase A. See experiments which have used the Rhesus Macaque Genome Array by Subject for more information.
University of Nebraska Medical Center
Dept. Genetics, Cell Biology and Anatomy
985805 Nebraska Medical Center
Omaha, NE 69198-5805email: rnorgren@unmc.edu
The rhesus work was funded by NCRR/ORIP NIH grant R24RR017444.
Zhang, X., Goodsell, J. and Norgren R. B. (2012) Limitations of the rhesus macaque draft genome assembly and annotation. BMC Genomics, 13:206. Get the paper.
Duan, F., Pauley, M. A., Spindel, E. R., Zhang, L. and Norgren R. B. (2010) Large scale analysis of positional effects of single-base mismatches on microarray gene expression data. BioData Mining, 3:2. Get the paper.
Duan, F., Spindel, E. R., Li, Y-H and Norgren, R. B. (2007) Intercenter reliability and validity of the rhesus macaque GeneChip. BMC Genomics, 8:61.Get the paper.
Ferguson, B., Street, S.L., Wright, H., Pearson, C., Jia, Y., Thompson, S.L., Allibone, P., Dubay, C.J., Spindel, E. and Norgren, R.B. (2007) Single nucleotide polymorphisms (SNPs) distinguish Indian-origin and Chinese-origin rhesus macaques (Macaca mulatta). BMC Genomics, 8:44. Get the paper.
Norgren, R. B. Expression arrays for macaque monkeys. (2006) Transplantation Reviews, 20: 115-120.
Spindel, E. R., Pauley, M.A., Jia,Y., Gravett, C.,Thompson, S., Boyle, N., Ojeda, S.R., and Norgren, R. B. (2005) Leveraging human genomic information to identify nonhuman primate sequences for expression array development, BMC Genomics, 6:160. Get the paper.
