title: The baboon kidney transcriptome: analysis of transcript sequence, splice variants, and abundance.
abstract: The baboon is an invaluable model for the study of human health and disease, including many complex diseases of the kidney. Although scientists have made great progress in developing this animal as a model for numerous areas of biomedical research, genomic resources for the baboon, such as a quality annotated genome, are still lacking. To this end, we characterized the baboon kidney transcriptome using high-throughput cDNA sequencing (RNA-Seq) to identify genes, gene variants, single nucleotide polymorphisms (SNPs), insertion-deletion polymorphisms (InDels), cellular functions, and key pathways in the baboon kidney to provide a genomic resource for the baboon. Analysis of our sequencing data revealed 45,499 high-confidence SNPs and 29,813 InDels comparing baboon cDNA sequences with the human hg18 reference assembly and identified 35,900 cDNAs in the baboon kidney, including 35,150 transcripts representing 15,369 genic genes that are novel for the baboon. Gene ontology analysis of our sequencing dataset also identified numerous biological functions and canonical pathways that were significant in the baboon kidney, including a large number of metabolic pathways that support known functions of the kidney. The results presented in this study catalogues the transcribed mRNAs, noncoding RNAs, and hypothetical proteins in the baboon kidney and establishes a genomic resource for scientists using the baboon as an experimental model.
authors: Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, United States of America. kspradli@txbiomedgenetics.org
authors: Kimberly D
authors: KD
authors: Spradling
authors: Jeremy P
authors: JP
authors: Glenn
authors: Roy
authors: R
authors: Garcia
authors: Robert E
authors: RE
authors: Shade
authors: Laura A
authors: LA
authors: Cox
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D030541:Databases, Genetic; D005260:Female; D020869:Gene Expression Profiling; D006801:Humans; D054643:INDEL Mutation; D007668:Kidney / Q000378:metabolism*; D008297:Male; D009928:Organ Specificity; D010215:Papio; D020641:Polymorphism, Single Nucleotide; D020033:Protein Isoforms / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D022661:RNA, Untranslated / Q000235:genetics; D012015:Reference Standards; D017423:Sequence Analysis, RNA
chemical_list: D020033:Protein Isoforms; D012333:RNA, Messenger; D022661:RNA, Untranslated
references: Genomics. 2006 Sep;88(3):274-81
references: 16697552
references: Nephrology (Carlton). 2012 May;17(4):311-21
references: 22288610
references: J Lipid Res. 2009 Jul;50(7):1420-8
references: 19270339
references: Am J Physiol Regul Integr Comp Physiol. 2011 Nov;301(5):R1229-41
references: 21832206
references: Nature. 2010 Jan 28;463(7280):536-9
references: 20072128
references: Genome Res. 2002 Nov;12(11):1693-702
references: 12421756
references: Kidney Int. 2012 Jan;81(1):22-39
references: 21881558
references: Hypertension. 2008 Dec;52(6):987-93
references: 18981331
references: Methods. 2009 Sep;49(1):63-9
references: 19596448
references: Nat Methods. 2011 Jun;8(6):469-77
references: 21623353
references: BMC Genomics. 2007 Jun 12;8:166
references: 17565689
references: Cancer Genet Cytogenet. 2004 Mar;149(2):114-9
references: 15036886
references: Endocrinology. 2002 Jun;143(6):1983-9
references: 12021158
references: Am J Pathol. 2006 Aug;169(2):433-44
references: 16877346
references: Biochem Genet. 2010 Jun;48(5-6):538-47
references: 20390338
references: J Exp Clin Cancer Res. 2008 Jul 16;27:19
references: 18631387
references: Nucleic Acids Res. 2009 Jul;37(12):e90
references: 19474342
references: Nature. 2006 Apr 20;440(7087):1045-9
references: 16625196
references: Exp Biol Med (Maywood). 2009 Dec;234(12):vi, 1519-24
references: 19934372
references: Science. 2008 Aug 15;321(5891):956-60
references: 18599741
references: Genome Biol. 2009;10(3):R25
references: 19261174
references: Nat Rev Urol. 2010 May;7(5):277-85
references: 20448661
references: Nature. 2007 Jun 14;447(7146):799-816
references: 17571346
references: Nat Biotechnol. 2010 May;28(5):511-5
references: 20436464
references: Am J Physiol Renal Physiol. 2009 Nov;297(5):F1137-52
references: 19570878
references: Clin Exp Pharmacol Physiol. 2010 Feb;37(2):178-84
references: 19650795
references: J Lipid Res. 2008 Jun;49(6):1295-302
references: 18334716
references: Virology. 2006 Nov 10;355(1):44-51
references: 16904151
references: Cell. 2010 Oct 1;143(1):46-58
references: 20887892
references: Am J Hum Biol. 1995;7(2):149-158
references: 28557219
references: Nature. 2006 May 18;441(7091):315-21
references: 16710414
references: Am J Pathol. 2003 Dec;163(6):2303-17
references: 14633604
references: Kidney Int. 2010 Aug;78(3):231-4
references: 20631733
references: Am J Primatol. 2008 Aug;70(8):796-802
references: 18481256
references: Curr Drug Targets Immune Endocr Metabol Disord. 2002 Jul;2(2):181-92
references: 12476791
references: Genomics. 2003 May;81(5):519-24
references: 12706110
references: Genome Res. 2010 Sep;20(9):1297-303
references: 20644199
references: Bioinformatics. 2011 Sep 1;27(17):2325-9
references: 21697122
references: Hypertension. 1993 Jun;21(6 Pt 2):1076-9
references: 8505095
references: Cell Biochem Biophys. 2004;40(3):371-88
references: 15211033
references: Am J Physiol Renal Physiol. 2002 Jan;282(1):F1-9
references: 11739106
references: Nat Rev Neurol. 2009 Dec;5(12):639-40
references: 19953110
references: J Med Primatol. 2008 Dec;37(6):337-45
references: 19017195
references: Int J Nephrol. 2012;2012:465897
references: 22577546
references: Am J Clin Nutr. 2007 Sep;86(3):597-603
references: 17823422
references: Mol Syst Biol. 2010 Dec 21;6:450
references: 21179022
references: J Am Soc Nephrol. 2008 Nov;19(11):2069-75
references: 18832437
references: J Med Primatol. 2008 Jun;37(3):146-53
references: 18642436
references: J Lab Clin Med. 1989 Sep;114(3):215-21
references: 2671214
references: Atherosclerosis. 2011 Aug;217(2):387-94
references: 21762917
references: Primates Med. 1976;9:41-65
references: 813210
references: Proc Natl Acad Sci U S A. 2010 Aug 10;107(32):14339-44
references: 20651252
references: Obes Res. 2003 Jan;11(1):75-80
references: 12529488
references: Nat Rev Genet. 2011 Nov 18;12(12):861-74
references: 22094949
references: Diabet Med. 2010 Feb;27(2):136-42
references: 20546255
references: BMC Biol. 2011 May 31;9:34
references: 21627854
references: Nature. 2008 Nov 27;456(7221):470-6
references: 18978772
references: Curr Med Chem. 2006;13(4):449-54
references: 16475932
references: Atherosclerosis. 2008 Feb;196(2):667-73
references: 17767937
references: Science. 1995 Oct 20;270(5235):467-70
references: 7569999
references: Hum Reprod Update. 1997 Nov-Dec;3(6):575-92
references: 9584947
references: Genome Biol. 2010;11(7):125
references: 20624272
references: Genomics. 2000 Aug 1;67(3):237-47
references: 10936045
references: Genome Biol. 2009;10(11):R124
references: 19895688
references: Nat Genet. 2011 May;43(5):491-8
references: 21478889
references: Nature. 2004 Apr 1;428(6982):529-35
references: 15057824
references: Nat Med. 2004 Feb;10(2):168-74
references: 14716305
references: Genome Res. 2008 Sep;18(9):1509-17
references: 18550803
references: Parasitol Today. 1999 Dec;15(12):478-82
references: 10557147
references: Arteriosclerosis. 1985 Sep-Oct;5(5):481-93
references: 3899070
references: PLoS One. 2011;6(11):e28318
references: 22140575
references: Bioinformatics. 2009 May 1;25(9):1105-11
references: 19289445
references: J Pathol. 2010 Jan;220(2):152-63
references: 19918805
references: Arterioscler Thromb Vasc Biol. 1999 Apr;19(4):1134-41
references: 10195946
references: Womens Health (Lond). 2007 Sep;3(5):637-46
references: 19804041
references: Hum Pathol. 2009 Sep;40(9):1296-303
references: 19386349
references: Annu Rev Genomics Hum Genet. 2009;10:135-51
references: 19715439
references: Front Genet. 2012 Jan 09;2:107
references: 22303401
references: J Am Soc Nephrol. 2008 Nov;19(11):2159-69
references: 18776119
references: Curr Opin Nephrol Hypertens. 2010 Jul;19(4):393-402
references: 20489613
references: PLoS Comput Biol. 2009 Dec;5(12):e1000598
references: 20011106
references: J Am Soc Nephrol. 2012 May;23(5):834-41
references: 22323644
references: Genomics. 2009 Apr;93(4):291-8
references: 19071207
references: J Cell Mol Med. 2001 Jan-Mar;5(1):18-32
references: 12067448
references: J Med Primatol. 2009 Apr;38(2):107-13
references: 18671766
references: Genome Biol. 2010;11(7):R78
references: 20653958
references: Genomics. 2011 Oct;98(4):266-71
references: 21515359
references: J Med Primatol. 2008 Feb;37(1):18-25
references: 18199068
references: Diabetologia. 2007 Sep;50(9):1969-1976
references: 17604976
references: BMC Bioinformatics. 2007 Jun 04;8:180
references: 17547750
references: J Biol Chem. 2011 Jul 22;286(29):26003-15
references: 21613219
references: Hippokratia. 2011 Jan;15(Suppl 1):50-2
references: 21897759
references: Hypertension. 2001 Feb;37(2 Pt 2):398-402
references: 11230307
references: Bioinformatics. 2009 Aug 15;25(16):2078-9
references: 19505943
references: Hum Reprod Update. 1998 Jul-Aug;4(4):420-9
references: 9825856
references: Proc Natl Acad Sci U S A. 2008 Jul 29;105(30):10513-8
references: 18663219
references: Curr Opin Lipidol. 2005 Jun;16(3):301-6
references: 15891391
references: J Am Soc Nephrol. 2009 Jan;20(1):131-44
references: 18987305
references: Am J Clin Nutr. 2004 Feb;79(2):185-97
references: 14749222
references: Diabetes Res Clin Pract. 2011 Aug;93 Suppl 1:S66-72
references: 21864754
references: J Physiol. 2006 Apr 1;572(Pt 1):67-85
references: 16513668
references: J Biol Chem. 2008 Sep 12;283(37):25671-25681
references: 18586672
references: Genetics. 2008 Sep;180(1):619-28
references: 18757921