Garneau NL, Wilusz J, Wilusz CJ: The highways and byways of mRNA decay. Nat Rev Mol Cell Biol. 2007, 8: 113-126. 10.1038/nrm2104.
Article
CAS
PubMed
Google Scholar
Schwanhausser B, Busse D, Li N, Dittmar G, Schuchhardt J, Wolf J, Chen W, Selbach M: Global quantification of mammalian gene expression control. Nature. 2011, 473: 337-342. 10.1038/nature10098.
Article
PubMed
Google Scholar
Rabani M, Levin JZ, Fan L, Adiconis X, Raychowdhury R, Garber M, Gnirke A, Nusbaum C, Hacohen N, Friedman N, Amit I, Regev A: Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells. Nat Biotechnol. 2011, 29: 436-442. 10.1038/nbt.1861.
Article
CAS
PubMed Central
PubMed
Google Scholar
Tani H, Mizutani R, Salam KA, Tano K, Ijiri K, Wakamatsu A, Isogai T, Suzuki Y, Akimitsu N: Genome-wide determination of RNA stability reveals hundreds of short-lived non-coding transcripts in mammals. Genome Res. 2012, 22: 947-956. 10.1101/gr.130559.111.
Article
CAS
PubMed Central
PubMed
Google Scholar
Yang E, van Nimwegen E, Zavolan M, Rajewsky N, Schroeder M, Magnasco M, Darnell JE: Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes. Genome Res. 2003, 13: 1863-1872.
Article
CAS
PubMed Central
PubMed
Google Scholar
Micke P, Ohshima M, Tahmasebpoor S, Ren ZP, Ostman A, Pontén F, Botling J: Biobanking of fresh frozen tissue: RNA is stable in nonfixed surgical specimens. Lab Invest. 2006, 86: 202-211. 10.1038/labinvest.3700372.
Article
CAS
PubMed
Google Scholar
Auer H, Liyanarachchi S, Newsom D, Klisovic MI, Marcucci G, Kornacker K: Chipping away at the chip bias: RNA degradation in microarray analysis. Nat Genet. 2003, 35: 292-293. 10.1038/ng1203-292.
Article
CAS
PubMed
Google Scholar
Schroeder A, Mueller O, Stocker S, Salowsky R, Leiber M, Gassmann M, Lightfoot S, Menzel W, Granzow M, Ragg T: The RIN: an RNA integrity number for assigning integrity values to RNA measurements. BMC Mol Biol. 2006, 7: 3-10.1186/1471-2199-7-3.
Article
PubMed Central
PubMed
Google Scholar
Imbeaud S, Graudens E, Boulanger V, Barlet X, Zaborski P, Eveno E, Mueller O, Schroeder A, Auffray C: Towards standardization of RNA quality assessment using user-independent classifiers of microcapillary electrophoresis traces. Nucleic Acids Res. 2005, 33: e56-10.1093/nar/gni054.
Article
PubMed Central
PubMed
Google Scholar
Weis S, Llenos IC, Dulay JR, Elashoff M, Martinez-Murillo F, Miller CL: Quality control for microarray analysis of human brain samples: the impact of postmortem factors, RNA characteristics, and histopathology. J Neurosci Methods. 2007, 165: 198-209. 10.1016/j.jneumeth.2007.06.001.
Article
CAS
PubMed
Google Scholar
Genotype-Tissue Expression Porta. [http://www.gtexportal.org/home/]
Durrenberger PF, Fernando S, Kashefi SN, Ferrer I, Hauw JJ, Seilhean D, Smith C, Walker R, Al-Sarraj S, Troakes C, Palkovits M, Kasztner M, Huitinga I, Arzberger T, Dexter DT, Kretzschmar H, Reynolds R: Effects of antemortem and postmortem variables on human brain mRNA quality: a BrainNet Europe study. J Neuropathol Exp Neurol. 2010, 69: 70-81. 10.1097/NEN.0b013e3181c7e32f.
Article
PubMed
Google Scholar
Harrison PJ, Heath PR, Eastwood SL, Burnet PW, McDonald B, Pearson RC: The relative importance of premortem acidosis and postmortem interval for human brain gene expression studies: selective mRNA vulnerability and comparison with their encoded proteins. Neurosci Lett. 1995, 200: 151-154. 10.1016/0304-3940(95)12102-A.
Article
CAS
PubMed
Google Scholar
Tomita H, Vawter MP, Walsh DM, Evans SJ, Choudary PV, Li J, Overman KM, Atz ME, Myers RM, Jones EG, Watson SJ, Akil H, Bunney WE: Effect of agonal and postmortem factors on gene expression profile: quality control in microarray analyses of postmortem human brain. Biol Psychiatry. 2004, 55: 346-352. 10.1016/j.biopsych.2003.10.013.
Article
CAS
PubMed Central
PubMed
Google Scholar
Miyatake Y, Ikeda H, Michimata R, Koizumi S, Ishizu A, Nishimura N, Yoshiki T: Differential modulation of gene expression among rat tissues with warm ischemia. Exp Mol Pathol. 2004, 77: 222-230. 10.1016/j.yexmp.2004.07.004.
Article
CAS
PubMed
Google Scholar
Lee J, Hever A, Willhite D, Zlotnik A, Hevezi P: Effects of RNA degradation on gene expression analysis of human postmortem tissues. FASEB J. 2005, 19: 1356-1358.
Article
CAS
PubMed
Google Scholar
Inoue H, Kimura A, Tuji T: Degradation profile of mRNA in a dead rat body: basic semi-quantification study. Forensic Sci Int. 2002, 130: 127-132. 10.1016/S0379-0738(02)00352-3.
Article
CAS
PubMed
Google Scholar
Hong SH, Baek HA, Jang KY, Chung MJ, Moon WS, Kang MJ, Lee DG, Park HS: Effects of delay in the snap freezing of colorectal cancer tissues on the quality of DNA and RNA. J Kor Soc Coloproctol. 2010, 26: 316-323. 10.3393/jksc.2010.26.5.316.
Article
Google Scholar
Heinrich M, Matt K, Lutz-Bonengel S, Schmidt U: Successful RNA extraction from various human postmortem tissues. Int J Legal Med. 2007, 121: 136-142. 10.1007/s00414-006-0131-9.
Article
PubMed
Google Scholar
Huang J, Qi R, Quackenbush J, Dauway E, Lazaridis E, Yeatman T: Effects of ischemia on gene expression. J Surg Res. 2001, 99: 222-227. 10.1006/jsre.2001.6195.
Article
CAS
PubMed
Google Scholar
Baechler EC, Batliwalla FM, Karypis G, Gaffney PM, Moser K, Ortmann WA, Espe KJ, Balasubramanian S, Hughes KM, Chan JP, Begovich A, Chang SY, Gregersen PK, Behrens TW: Expression levels for many genes in human peripheral blood cells are highly sensitive to ex vivo incubation. Genes Immun. 2004, 5: 347-353. 10.1038/sj.gene.6364098.
Article
CAS
PubMed
Google Scholar
Bray SE, Paulin FE, Fong SC, Baker L, Carey F, Levison D, Steele RJ, Kernohan NM: Gene expression in colorectal neoplasia: modifications induced by tissue ischaemic time and tissue handling protocol. Histopathology. 2010, 56: 240-250. 10.1111/j.1365-2559.2009.03470.x.
Article
PubMed
Google Scholar
Ibberson D, Benes V, Muckenthaler MU, Castoldi M: RNA degradation compromises the reliability of microRNA expression profiling. BMC Biotechnol. 2009, 9: 102-10.1186/1472-6750-9-102.
Article
PubMed Central
PubMed
Google Scholar
Catts VS, Catts SV, Fernandez HR, Taylor JM, Coulson EJ, Lutze-Mann LH: A microarray study of post-mortem mRNA degradation in mouse brain tissue. Mol Brain Res. 2005, 138: 164-177. 10.1016/j.molbrainres.2005.04.017.
Article
CAS
PubMed
Google Scholar
Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y: RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 2008, 18: 1509-1517. 10.1101/gr.079558.108.
Article
CAS
PubMed Central
PubMed
Google Scholar
Cloonan N, Forrest AR, Kolle G, Gardiner BB, Faulkner GJ, Brown MK, Taylor DF, Steptoe AL, Wani S, Bethel G, Robertson AJ, Perkins AC, Bruce SJ, Lee CC, Ranade SS, Peckham HE, Manning JM, McKernan KJ, Grimmond SM: Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods. 2008, 5: 613-619. 10.1038/nmeth.1223.
Article
CAS
PubMed
Google Scholar
Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL: TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2011, 14: R36-
Article
Google Scholar
Narsai R, Howell KA, Millar AH, O’Toole N, Small I, Whelan J: Genome-wide analysis of mRNA decay rates and their determinants in Arabidopsis thaliana. Plant Cell. 2007, 19: 3418-3436. 10.1105/tpc.107.055046.
Article
CAS
PubMed Central
PubMed
Google Scholar
Bernstein JA, Khodursky AB, Lin PH, Lin-Chao S, Cohen SN: Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc Natl Acad Sci U S A. 2002, 99: 9697-9702. 10.1073/pnas.112318199.
Article
CAS
PubMed Central
PubMed
Google Scholar
Ho-Pun-Cheung A, Bascoul-Mollevi C, Assenat E, Boissière-Michot F, Bibeau F, Cellier D, Ychou M, Lopez-Crapez E: Reverse transcription-quantitative polymerase chain reaction: description of a RIN-based algorithm for accurate data normalization. BMC Mol Biol. 2009, 10: 31-10.1186/1471-2199-10-31.
Article
PubMed Central
PubMed
Google Scholar
Opitz L, Salinas-Riester G, Grade M, Jung K, Jo P, Emons G, Ghadimi BM, Beissbarth T, Gaedcke J: Impact of RNA degradation on gene expression profiling. BMC Med Genet. 2010, 3: 36-
Google Scholar
Thompson KL, Pine PS, Rosenzweig BA, Turpaz Y, Retief J: Characterization of the effect of sample quality on high density oligonucleotide microarray data using progressively degraded rat liver RNA. BMC Biotechnol. 2007, 7: 57-10.1186/1472-6750-7-57.
Article
PubMed Central
PubMed
Google Scholar
Strand C, Enell J, Hedenfalk I, Ferno M: RNA quality in frozen breast cancer samples and the influence on gene expression analysis–a comparison of three evaluation methods using microcapillary electrophoresis traces. BMC Mol Biol. 2007, 8: 38-10.1186/1471-2199-8-38.
Article
PubMed Central
PubMed
Google Scholar
Fleige S, Pfaffl MW: RNA integrity and the effect on the real-time qRT-PCR performance. Mol Aspects Med. 2006, 27: 126-139. 10.1016/j.mam.2005.12.003.
Article
CAS
PubMed
Google Scholar
Auerbach RK, Euskirchen G, Rozowsky J, Lamarre-Vincent N, Moqtaderi Z, Lefrançois P, Struhl K, Gerstein M, Snyder M: Mapping accessible chromatin regions using Sono-Seq. Proc Natl Acad Sci U S A. 2009, 106: 14926-14931. 10.1073/pnas.0905443106.
Article
CAS
PubMed Central
PubMed
Google Scholar
Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead B, Raney BJ, Pohl A, Malladi VS, Li CH, Lee BT, Learned K, Kirkup V, Hsu F, Heitner S, Harte RA, Haeussler M, Guruvadoo L, Goldman M, Giardine BM, Fujita PA, Dreszer TR, Diekhans M, Cline MS, Clawson H, Barber GP, et al: The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res. 2013, 41: D64-D69. 10.1093/nar/gks1048.
Article
CAS
PubMed Central
PubMed
Google Scholar
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B: Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008, 5: 621-628. 10.1038/nmeth.1226.
Article
CAS
PubMed
Google Scholar
Flicek P, Ahmed I, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, Gil L, Garcia-Giron C, Gordon L, Hourlier T, Hunt S, Juettemann T, Kahari AK, Keenan S, Komorowska M, Kulesha E, Longden I, Maurel T, McLaren WM, Muffato M, Nag R, Overduin B, Pignatelli M, Pritchard B, Pritchard E, et al: Ensembl 2013. Nucleic Acids Res. 2013, 41: D48-D55. 10.1093/nar/gks1236.
Article
CAS
PubMed Central
PubMed
Google Scholar
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J: Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004, 5: R80-10.1186/gb-2004-5-10-r80.
Article
PubMed Central
PubMed
Google Scholar
Du P, Kibbe WA, Lin SM: lumi: a pipeline for processing Illumina microarray. Bioinformatics. 2008, 24: 1547-1548. 10.1093/bioinformatics/btn224.
Article
CAS
PubMed
Google Scholar
Ramsköld D, Wang ET, Burge CB, Sandberg R: An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Comput Biol. 2009, 5: e1000598-10.1371/journal.pcbi.1000598.
Article
PubMed Central
PubMed
Google Scholar
Quinlan AR, Hall IM: BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010, 26: 841-842. 10.1093/bioinformatics/btq033.
Article
CAS
PubMed Central
PubMed
Google Scholar
Robinson MD, McCarthy DJ, Smyth GK: edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010, 26: 139-140. 10.1093/bioinformatics/btp616.
Article
CAS
PubMed Central
PubMed
Google Scholar
Robinson MD, Oshlack A: A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 2010, 11: R25-10.1186/gb-2010-11-3-r25.
Article
PubMed Central
PubMed
Google Scholar
Alexa A, Rahnenfuhrer J, Lengauer T: Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics. 2006, 22: 1600-1607. 10.1093/bioinformatics/btl140.
Article
CAS
PubMed
Google Scholar
Storey JD, Tibshirani R: Statistical significance for genomewide studies. Proc Natl Acad Sci U S A. 2003, 100: 9440-9445. 10.1073/pnas.1530509100.
Article
CAS
PubMed Central
PubMed
Google Scholar