Contact | Funding | Publications
New Rhesus Genome (MacaM) | v7.8_Annotation | GeneChip | NextGen Sequences | Transcriptome sequences | Protein sequences
NextGen Sequences | Transcriptome sequences | Protein sequences
NexGen Sequences | Transcriptome sequences | Protein Sequences
New Rhesus Genome (MacaM)
In collaboration with Aleksey Zimin and other colleagues, we have produced an entirely new assembly and annotation of the rhesus macaque genome - MacaM. A paper describing this work has been published:
Zimin, A. V., Cornish, A. S., Maudhoo, M.D., Gibbs, R. M. Zhang, X., Pandey, S., Meehan, D. T.,Wipfler, K., Bosinger, S. E., Johnson, Z. P., Tharp, G. K., Marcais, G., Roberts, M., Ferguson, B., Fox, H., Treangen, T., Salzberg, S. L., Yorke, J. A. and Norgren, R. B. (2014) A new rhesus macaque assembly and annotation for next-generation sequencing analyses. Biology Direct, 9:20.
Here, we provide the necessary files for mRNA-seq and other Next Generation Sequencing studies:
MacaM v7.6.8 GTF annotation file
MacaM_v7.6.8_GFF_annotation_file
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New MacaM Annotation for mRNA_seq!
MacaM_v7.8.2_GTF_annotation_file
MacaM_v7.8.2_GTF_annotation file_zipped
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We ask that any investigators who access these files or acquire them from others acknowledge the source in any papers or presentations by citing the Biology Direct paper.
There are three additional papers related to this work:
Sandler, N. G., Bosinger, S. E., Estes J. D., Zhu, R. T. R., Tharp, G. K., Boritz, E., Levin, D., Wijeyesinghe, S., Makamdop, K. N., Del Prete G. Q., Hill, B. J., Timmer, J. K., Reiss E., Darko, S., Contijoch, E., Todd, J. P., Silvestri, G., Nason, M., Norgren, R. B. , Keele, B. F., Rao, S., Langer, J. A., Lifson, J. D., Schreiber, G. and Douek, D. C. (2014) Type I IFN responses in rhesus macaques prevent SIV transmission and slow disease progression. Nature, 51: 601-605.
[This paper utilized the new MacaM genome for gene expression studies.]
Norgren, R. B. (2013) Improving genome assemblies and annotations for nonhuman primates. ILAR J. 54: 144-153. Get the paper.
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.
Rhesus GeneChip
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 usefulness of this dataset.
There are four papers related to development and validation of the Affymetrix Rhesus Macaque Genome Array:
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.
Norgren, R. B. Expression arrays for macaque monkeys. (2006) Transplantation Reviews, 20: 115-120.
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.
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.
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), Macaca nemestrina (pigtail macaque), 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.
Rhesus macaque NextGen Sequences
Animal 17573 (reference animal)
Whole genome DNA Illumina sequencing
Animal 21353
Animal 002T-NHP
Animal 001T-NHP
mRNA from caudate nucleus Illumina sequencing
mRNA from orbital cerebral cortex Illumina sequencing
Animal 8408
Animal BF23762
Animal BF23764
Animal BF23773
Animal BF22215
Animal BF20336
Animal BF21178
mRNA from frontal cerebral cortex Illumina sequencing
Yerkes Colony Exome Sequences
This dataset includes exome sequences from 62 animals at the Yerkes National Primate Research Center.
Tulane Colony Exome Sequences
This dataset includes exome sequences from 78 animals at the Tulane National Primate Research Center.
Rhesus Transcripts
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 Proteins
Rhesus protein sequences were obtained by conceptual translation of the transcripts described above.
Marmoset NextGen Sequences
Animal 186/17066 (reference animal)
Animal 2218
mRNA from Skeletal muscle Illumina sequencing
Animal 2219
Marmoset transcripts
The Velvet/ Oases pipeline was used to assemble de novo marmoset transcripts from the NextGen mRNA sequences listed above. These sequences were deposited in GenBank.
We ask that users of our marmoset sequences or transcripts cite the following paper:
Maudhoo, M. D., Ren, D., Gradnigo, J. S. Gibbs, R. M., Lubker, A. C., Moriyama, E. N., French, J. A. and Norgren, R. B. (2014) De novo assembly of the common marmoset transcriptome from NextGen mRNA sequences. GigaScience, 3:14. Get the paper.
Marmoset proteins
Chimp NexGen Sequences
mRNA from Adipose stromal cells Illumina sequencing
mRNA from Vascular smooth muscle endothelial cells Illumina sequencing
Chimp Transcripts
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 Proteins
Chimp protein sequences were obtained by conceptual translation of the transcripts described above.
Related paper:
Maudhoo, M. D., Madison, J. D, and Norgren, R. B. (2015) De novo assembly of the chimpanzee transcriptome from NextGen mRNA sequences. GigaScience, 4:18. Get the paper.
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. The marmoset work was funded by the Nebraska Research Initiative.
Cornish, A. S., Gibbs, R. M., Norgren, R. B. (2016) Exome screening to identify loss-of-function mutations in the rhesus macaque for development of preclinical models of human disease. BMC Genomics, 17:170. Get the paper.
Maudhoo, M. D., Madison, J. D, and Norgren, R. B. (2015) De novo assembly of the chimpanzee transcriptome from NextGen mRNA sequences. GigaScience, 4:18. Get the paper.
Zimin, A. V., Cornish, A. S., Maudhoo, M.D., Gibbs, R. M. Zhang, X., Pandey, S., Meehan, D. T.,Wipfler, K., Bosinger, S. E., Johnson, Z. P., Tharp, G. K., Marcais, G., Roberts, M., Ferguson, B., Fox, H., Treangen, T., Salzberg, S. L., Yorke, J. A. and Norgren, R. B. (2014) A new rhesus macaque assembly and annotation for next-generation sequencing analyses. Biology Direct, 9:20. Get the paper.
Maudhoo, M. D., Ren, D., Gradnigo, J. S. Gibbs, R. M., Lubker, A. C., Moriyama, E. N., French, J. A. and Norgren, R. B. (2014) De novo assembly of the common marmoset transcriptome from NextGen mRNA sequences. GigaScience, 3:14. Get the paper.
Norgren, R. B. (2013) Improving genome assemblies and annotations for nonhuman primates. ILAR J. 54: 144-153. Get the paper.
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.
