UN-NHPGC

University of Nebraska Nonhuman Primate Genome Center

This data is provided to the research community under the Bermuda, Ft. Lauderdale and Toronto agreements.

Contact | Funding | Publications

 

 

Rhesus macaque (Macaca mulatta)

New Rhesus Genome (MacaM) | v7.8_Annotation | GeneChip | NextGen Sequences | Transcriptome sequences | Protein sequences

Marmoset (Callithrix jacchus)

NextGen Sequences | Transcriptome sequences | Protein sequences

Chimpanzee (Pan Troglodytes) - "Clint"

NexGen Sequences | Transcriptome sequences | Protein Sequences

 

Rhesus macaque (Macaca mulatta)

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 Chromosome FASTA file

MacaM Chromosome fai file

MacaM v7.6.8 GTF annotation file

MacaM_v7.6.8_GFF_annotation_file

MacaM_v7.6.8_TRANSCRPTS.fa

MacaM_v7.6.8_PROTEINS.

MacaM_v7_bowtie_index

MacaM_v7_bwa_index

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New MacaM Annotation for mRNA_seq!

MacaM_v7.8_README

MacaM_v7.8.2_GTF_annotation_file

MacaM_v7.8.2_GTF_annotation file_zipped

MacaM_v7.8_TRANSCRPTS.fa

MacaM_v7.8_PROTEINS.fa

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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

Whole genome DNA PGM sequencing

Exome Illumina sequencing

Animal 21353

Exome Ilumina sequencing

Animal 002T-NHP

mRNA from caudate nucleus Illumina sequencing

Exome Illumina sequencing

Animal 001T-NHP

mRNA from caudate nucleus Illumina sequencing

mRNA from orbital cerebral cortex Illumina sequencing

mRNA from thymus Illumina sequencing

mRNA from testes Illumina sequencing

Animal 8408

Exome Illumina sequencing

Animal BF23762

mRNA from frontal cerebral cortex Illumina sequencing

Animal BF23764

mRNA from frontal cerebral cortex Illumina sequencing

Animal BF23773

mRNA from frontal cerebral cortex Illumina sequencing

Animal BF22215

mRNA from frontal cerebral cortex Illumina sequencing

Animal BF20336

mRNA from frontal cerebral cortex Illumina sequencing

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 transcript sequences

Rhesus Proteins

Rhesus protein sequences were obtained by conceptual translation of the transcripts described above.

Rhesus protein sequences

 

Marmoset (Callithrix jacchus)

Marmoset NextGen Sequences

Animal 186/17066 (reference animal)

Whole genome DNA PGM sequencing

Exome Illumina sequencing

Animal 2218

mRNA from Skeletal muscle Illumina sequencing

mRNA from Bladder Illumina sequencing

mRNA from Hippocampus Illumina sequencing

Animal 2219

mRNA from Cerebral cortex Illumina sequencing

mRNA from Cerebellum Illumina sequencing

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.

Marmoset Transcript sequences

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

Marmoset protein sequences

Chimpanzee (Pan troglodytes) - Clint

Chimp NexGen Sequences

Whole genome DNA Illumina sequencing

mRNA from Adipose stromal cells Illumina sequencing

mRNA from Vascular smooth muscle endothelial cells Illumina sequencing

mRNA from Skin fibroblasts Illumina sequencing

mRNA from Muscle myoblasts 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 Transcript sequences

Chimp Proteins

Chimp protein sequences were obtained by conceptual translation of the transcripts described above.

Chimp Protein sequences

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.

Contact

Rob Norgren

University of Nebraska Medical Center
Dept. Genetics, Cell Biology and Anatomy
985805 Nebraska Medical Center
Omaha, NE 69198-5805

email: rnorgren@unmc.edu

Funding

The rhesus work was funded by NCRR/ORIP NIH grant R24RR017444. The marmoset work was funded by the Nebraska Research Initiative.

Related Publications

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.