The RIN: an RNA integrity number for assigning integrity values to RNA measurements
Open accessAbstract
Background: The integrity of RNA molecules is of paramount importance for experiments that try to reflect the snapshot of gene expression at the moment of RNA extraction. Until recently, there has been no reliable standard for estimating the integrity of RNA samples and the ratio of 28S:18S ribosomal RNA, the common measure for this purpose, has been shown to be inconsistent. The advent of microcapillary electrophoretic RNA separation provides the basis for an automated high-throughput approach, in order to estimate the integrity of RNA samples in an unambiguous way. Methods: A method is introduced that automatically selects features from signal measurements and constructs regression models based on a Bayesian learning technique. Feature spaces of different dimensionality are compared in the Bayesian framework, which allows selecting a final feature combination corresponding to models with high posterior probability. Results: This approach is applied to a large collection of electrophoretic RNA measurements recorded with an Agilent 2100 bioanalyzer to extract an algorithm that describes RNA integrity. The resulting algorithm is a user-independent, automated and reliable procedure for standardization of RNA quality control that allows the calculation of an RNA integrity number (RIN). Conclusion: Our results show the importance of taking characteristics of several regions of the recorded electropherogram into account in order to get a robust and reliable prediction of RNA integrity, especially if compared to traditional methods.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
9 cortex and 15 cerebellum samples were excluded because they had an RNA Integrity Number (RIN) less than 7.
“In this study, we also excluded 9 cortex and 15 cerebellum samples that had an RNA Integrity Number (RIN)63 less than 7.”
From Pathogenic tau-induced piRNA depletion promotes neuronal death through transposable element dysregulation in neurodegenerative tauopathies (2018) · cites this paper as [63]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Molecular Cloning: A Laboratory Manual
Sambrook, J., Fritsch, E., & Maniatis, T. (1989) · UCLA - Biblioteca de Ciencias de la Salud · Cited by 133,589 · see citing works
Molecular cloning: A laboratory manual
Deininger, P. L. (1990) · Analytical Biochemistry · doi:10.1016/0003-2697(90)90595-z · Cited by 84,684 · see citing works
Elements of Information Theory
Cover, T. M., & Thomas, J. A. (2001) · Wiley eBooks · doi:10.1002/0471200611 · Cited by 37,139 · see citing works
Neural networks for pattern recognition
Bishop, C. (1994) · Choice Reviews Online · doi:10.5860/choice.31-5500 · Cited by 18,537 · see citing works
Density Estimation for Statistics and Data Analysis
Silverman, B. W. (2018) · Routledge eBooks · doi:10.1201/9781315140919 · Cited by 15,938 · see citing works
Neural Networks for Pattern Recognition
Bishop, C. M. (1995) · doi:10.1093/oso/9780198538493.001.0001 · Cited by 12,287 · see citing works
Density Estimation for Statistics and Data Analysis
(1986) · Springer eBooks · doi:10.1007/978-1-4899-3324-9 · Cited by 8,478 · see citing works
Fabrication of microfluidic systems in poly(dimethylsiloxane)
McDonald, J. C., Duffy, D. C., Anderson, J. R., Chiu, D. T., Wu, H., Schueller, O. J. A., & Whitesides, G. M. (2000) · Electrophoresis · doi:10.1002/(sici)1522-2683(20000101)21:1 · Cited by 3,338 · see citing works
Self-citationA practical Bayesian framework for backpropagation networks
MacKay, D. J. C. (1992) · Neural Computation · doi:10.1162/neco.1992.4.3.448 · Cited by 2,917 · see citing works
(1982) · Cited by 1,288 · see citing works
Elements of Information Theory, Wiley Series in Telecommunications
Cover, T. M., & Allen, T. (1991) · Cited by 625 · see citing works
Riedmiller, M. (1994) · Computer Standards & Interfaces · doi:10.1016/0920-5489(94)90017-5 · Cited by 604 · see citing works
Imbeaud, S. (2005) · Nucleic Acids Research · doi:10.1093/nar/gni054 · Cited by 530 · see citing works
Chipping away at the chip bias: RNA degradation in microarray analysis
Auer, H., Liyanarachchi, S., Newsom, D. L., Klisovic, M. I., Marcucci, U., & Kornacker, K. (2003) · Nature Genetics · doi:10.1038/ng1203-292 · Cited by 201 · see citing works
Evaluating RNA status for RT-PCR in extracts of postmortem human brain tissue
Miller, C. L., Diglisic, S., Leister, F. J., Webster, M. J., & Yolken, R. H. (2004) · BioTechniques · doi:10.2144/04364st03 · Cited by 89 · see citing works
Special Issue on Neural Networks
Lisboa, P. J. G. (1993) · Journal of Microcomputer Applications · doi:10.1006/jmca.1993.1009 · Cited by 54 · see citing works
Computer Science and Statistics: Proceedings of the Fifteenth Symposium on the Interface.
Anderson, A. J. B., & Gentle, J. E. (1984) · Biometrics · doi:10.2307/2530952 · Cited by 14 · see citing works
Bayesian learning and evolutionary parameter optimization
Ragg, T. (2002) · Cited by 7 · see citing works
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
Quantification of mRNA using real-time RT-PCR
Nolan, T., Hands, R. E., & Bustin, S. A. (2006) · Nature Protocols · doi:10.1038/nprot.2006.236 · Cited by 2,247 · see citing works
Ramirez, A., Heimbach, A., Gründemann, J., Stiller, B., Hampshire, D., Cid, L. P., Goebel, I., Mubaidin, A. F., Wriekat, A.-L., Roeper, J., et al. (2006) · Nature Genetics · doi:10.1038/ng1884 · Cited by 1,208 · see citing works
Cell-type-specific isolation of ribosome-associated mRNA from complex tissues
Sanz, E., Yang, L., Su, T., Morris, D. R., McKnight, G. S., & Amieux, P. S. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0907143106 · Cited by 982 · see citing works
Review: Activation patterns of microglia and their identification in the human brain
Boche, D., Perry, V. H., & Nicoll, J. A. R. (2012) · Neuropathology and Applied Neurobiology · doi:10.1111/nan.12011 · Cited by 911 · see citing works
Ballgown bridges the gap between transcriptome assembly and expression analysis
Frazee, A. C., Pertea, G. M., Jaffe, A. E., Langmead, B., Salzberg, S. L., & Leek, J. T. (2015) · Nature Biotechnology · doi:10.1038/nbt.3172 · Cited by 853 · see citing works
A Novel Approach to High-Quality Postmortem Tissue Procurement: The GTEx Project
Carithers, L. J., Ardlie, K., Barcus, M., Branton, P. A., Britton, A., Buia, S. A., Compton, C. C., DeLuca, D. S., Peter-Demchok, J., Gelfand, E. T., et al. (2015) · Biopreservation and Biobanking · doi:10.1089/bio.2015.0032 · Cited by 833 · see citing works
Intrinsic Gene Expression Profiles of Gliomas Are a Better Predictor of Survival than Histology
Gravendeel, L. A. M., Kouwenhoven, M. C. M., Gevaert, O., de Rooi, J. J., Stubbs, A., Duijm, J. E., Daemen, A., Bleeker, F. E., Bralten, L. B. C., Kloosterhof, N. K., et al. (2009) · Cancer Research · doi:10.1158/0008-5472.can-09-2307 · Cited by 668 · see citing works
Bleach gel: A simple agarose gel for analyzing RNA quality
Aranda, P. S., LaJoie, D., & Jorcyk, C. L. (2012) · Electrophoresis · doi:10.1002/elps.201100335 · Cited by 580 · see citing works
Fleige, S., Walf-Vorderwülbecke, V., Huch, S., Prgomet, C., Sehm, J., & Pfaffl, M. W. (2006) · Biotechnology Letters · doi:10.1007/s10529-006-9127-2 · Cited by 574 · see citing works
In Posidonia oceanica cadmium induces changes in DNA methylation and chromatin patterning
Greco, M., Chiappetta, A. A. C., Bruno, L., & Bitonti, M. B. (2011) · Journal of Experimental Botany · doi:10.1093/jxb/err313 · Cited by 533 · see citing works
RNA-seq: impact of RNA degradation on transcript quantification
Romero, I. G., Pai, A. A., Tung, J., & Gilad, Y. (2014) · BMC Biology · doi:10.1186/1741-7007-12-42 · Cited by 473 · see citing works
Recent advances in quantitative PCR (qPCR) applications in food microbiology
Postollec, F., Falentin, H., Pavan, S., Combrisson, J., & Sohier, D. (2011) · Food Microbiology · doi:10.1016/j.fm.2011.02.008 · Cited by 479 · see citing works
Vieler, A., Wu, G., Tsai, C.-H., Bullard, B., Cornish, A. J., Harvey, C., Reca, I.-B., Thornburg, C., Achawanantakun, R., Buehl, C. J., et al. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1003064 · Cited by 458 · see citing works
Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons
Krishnaswami, S. R., Grindberg, R. V., Novotny, M., Venepally, P., Lacar, B., Bhutani, K., Linker, S. B., Pham, S., Erwin, J. A., Miller, J. A., et al. (2016) · Nature Protocols · doi:10.1038/nprot.2016.015 · Cited by 445 · see citing works
Kautz, L., Meynard, D., Monnier, A., Darnaud, V., Bouvet, R., Wang, R.-H., Deng, C., Vaulont, S., Mosser, J., Coppin, H., et al. (2008) · Blood · doi:10.1182/blood-2008-03-143354 · Cited by 437 · see citing works
Selective degradation of splicing factor CAPERα by anticancer sulfonamides
Uehara, T., Minoshima, Y., Sagane, K., Sugi, N. H., Mitsuhashi, K. O., Yamamoto, N., Kamiyama, H., Takahashi, K., Kotake, Y., Uesugi, M., et al. (2017) · Nature Chemical Biology · doi:10.1038/nchembio.2363 · Cited by 396 · see citing works
Systems medicine: the future of medical genomics and healthcare
Auffray, C., Zhu, C. H., & Hood, L. (2009) · Genome Medicine · doi:10.1186/gm2 · Cited by 386 · see citing works
Peripheral blood gene expression: it all boils down to the RNA collection tubes
Menke, A., Rex‐Haffner, M., Klengel, T., Binder, E. B., & Mehta, D. (2012) · BMC Research Notes · doi:10.1186/1756-0500-5-1 · Cited by 352 · see citing works
Measures of gene expression in sputum cells can identify TH2-high and TH2-low subtypes of asthma
Peters, M. C., Mekonnen, Z. K., Yuan, S., Bhakta, N. R., Woodruff, P. G., & Fahy, J. V. (2013) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2013.07.036 · Cited by 342 · see citing works
Gene expression in human brain implicates sexually dimorphic pathways in autism spectrum disorders
Werling, D. M., Parikshak, N. N., & Geschwind, D. H. (2016) · Nature Communications · doi:10.1038/ncomms10717 · Cited by 296 · see citing works
Allen, C. E., Li, L., Peters, T., Leung, H. E., Yu, A. K.-T., Man, T., Gurusiddappa, S., Phillips, M. T., Hicks, J. M., Gaikwad, A. S., et al. (2010) · The Journal of Immunology · doi:10.4049/jimmunol.0902336 · Cited by 324 · see citing works
Loss of NF1 in cutaneous melanoma is associated with RAS activation and MEK dependence
Nissan, M. H., Pratilas, C., Jones, A. M., Ramirez, R., Won, H., Liu, C.-L., Tiwari, S., Kong, L., Hanrahan, A. J., Yao, Z., et al. (2014) · Cancer Research · doi:10.1158/0008-5472.can-13-2625 · Cited by 297 · see citing works
Sun, W., Samimi, H., Gamez, M., Zare, H., & Frost, B. (2018) · Nature Neuroscience · doi:10.1038/s41593-018-0194-1 · Cited by 315 · see citing works
The effects of death and post-mortem cold ischemia on human tissue transcriptomes
Ferreira, P. G., Muñoz-Aguirre, M., Reverter, F., Godinho, C. D. S., Sousa, A., Amadoz, A., Sodaei, R., Hidalgo, M. R., Pervouchine, D. D., Carbonell‐Caballero, J., et al. (2018) · Nature Communications · doi:10.1038/s41467-017-02772-x · Cited by 300 · see citing works
Cumulus and granulosa cell markers of oocyte and embryo quality
Uyar, A., Torrealday, S., & Seli, E. U. (2013) · Fertility and Sterility · doi:10.1016/j.fertnstert.2013.01.129 · Cited by 309 · see citing works
Baumann, V., & Winkler, J. (2014) · Future Medicinal Chemistry · doi:10.4155/fmc.14.116 · Cited by 300 · see citing works
Robust MicroRNA Stability in Degraded RNA Preparations from Human Tissue and Cell Samples
Jung, M., Fendler, A., Steiner, I., Kempkensteffen, C., Stephan, C., Erbersdobler, A., & Jung, K. (2010) · Clinical Chemistry · doi:10.1373/clinchem.2009.141580 · Cited by 296 · see citing works
Activation of RNase L is dependent on OAS3 expression during infection with diverse human viruses
Li, Y., Banerjee, S., Wang, Y., Goldstein, S. A., Dong, B., Gaughan, C., Silverman, R. H., & Weiss, S. R. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1519657113 · Cited by 285 · see citing works
Shabihkhani, M., Lucey, G. M., Wei, B., Mareninov, S., Lou, J. J., Vinters, H. V., Singer, E. J., Cloughesy, T. F., & Yong, W. H. (2014) · Clinical Biochemistry · doi:10.1016/j.clinbiochem.2014.01.002 · Cited by 287 · see citing works
Storage conditions of intestinal microbiota matter in metagenomic analysis
Cardona, S. T., Eck, A., Cassellas, M., Gallart, M., Alastrue, C., Dore, J. M., Azpiroz, F., Roca, J., Guarner, F., & Manichanh, C. (2012) · BMC Microbiology · doi:10.1186/1471-2180-12-158 · Cited by 275 · see citing works
mRNA and microRNA quality control for RT-qPCR analysis
Becker, C., Hammerle-Fickinger, A., Riedmaier, I., & Pfaffl, M. W. (2010) · Methods · doi:10.1016/j.ymeth.2010.01.010 · Cited by 272 · see citing works
Recurrent DUX4 fusions in B cell acute lymphoblastic leukemia of adolescents and young adults
Yasuda, T., Tsuzuki, S., Kawazu, M., Hayakawa, F., Kojima, S., Ueno, T., Imoto, N., Kohsaka, S., Kunita, A., Doi, K., et al. (2016) · Nature Genetics · doi:10.1038/ng.3535 · Cited by 267 · see citing works
Truncated stathmin-2 is a marker of TDP-43 pathology in frontotemporal dementia
Prudencio, M., Humphrey, J., Pickles, S., Brown, A.-L., Hill, S. E., Kachergus, J. M., Shi, J., Heckman, M. G., Spiegel, M. R., Cook, C., et al. (2020) · Journal of Clinical Investigation · doi:10.1172/jci139741 · Cited by 231 · see citing works
miR-195 and miR-483-5p Identified as Predictors of Poor Prognosis in Adrenocortical Cancer
Soon, P. S. H., Tacon, L. J., Gill, A. J., Bambach, C. P., Sywak, M. S., Campbell, P. R., Yeh, M. W., Wong, S. G., Clifton-Bligh, R. J., Robinson, B. G., et al. (2009) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-09-1587 · Cited by 262 · see citing works
Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes
Giannoukos, G., Ciulla, D., Huang, K. H., Haas, B. J., Izard, J., Levin, J. Z., Livny, J., Earl, A. M., Gevers, D., Ward, D. V., et al. (2012) · Genome biology · doi:10.1186/gb-2012-13-3-r23 · Cited by 263 · see citing works
Measure transcript integrity using RNA-seq data
Wang, L., Nie, J. J., Sicotte, H., Li, Y., Eckel‐Passow, J. E., Dasari, S., Vedell, P. T., Barman, P., Wang, L., Weinshiboum, R., et al. (2016) · BMC Bioinformatics · doi:10.1186/s12859-016-0922-z · Cited by 256 · see citing works
TREM2 is upregulated in amyloid plaque-associated microglia in aged APP23 transgenic mice
Frank, S., Burbach, G. J., Bonin, M., Walter, M., Streit, W., Bechmann, I., & Deller, T. (2008) · Glia · doi:10.1002/glia.20710 · Cited by 247 · see citing works
Patnaik, S. K., Kannisto, E. D., Knudsen, S., & Yendamuri, S. (2009) · Cancer Research · doi:10.1158/0008-5472.can-09-3153 · Cited by 245 · see citing works
Development of Gene Expression Signatures for Practical Radiation Biodosimetry
Paul, S., & Amundson, S. A. (2008) · International Journal of Radiation Oncology*Biology*Physics · doi:10.1016/j.ijrobp.2008.03.043 · Cited by 245 · see citing works
Preservation of RNA and DNA from mammal samples under field conditions
Camacho‐Sanchez, M., Burraco, P., Gómez-Mestre, I., & Leonard, J. A. (2013) · Molecular Ecology Resources · doi:10.1111/1755-0998.12108 · Cited by 242 · see citing works
Sutherland, G. T., Sheedy, D. L., & Kril, J. J. (2014) · Handbook of clinical neurology · doi:10.1016/b978-0-444-62619-6.00035-5 · Cited by 243 · see citing works
Transcriptomic Responses to Salinity Stress in the Pacific Oyster Crassostrea gigas
Zhao, X., Yu, H., Kong, L., & Li, Q. (2012) · PLoS ONE · doi:10.1371/journal.pone.0046244 · Cited by 237 · see citing works
Attene‐Ramos, M. S., Nava, G. M., Muellner, M. G., Wagner, E. D., Plewa, M. J., & Gaskins, H. R. (2010) · Environmental and Molecular Mutagenesis · doi:10.1002/em.20546 · Cited by 233 · see citing works
Trabzuni, D., Ryten, M., Walker, R., Smith, C., Imran, S., Ramasamy, A., Weale, M. E., & Hardy, J. (2011) · Journal of Neurochemistry · doi:10.1111/j.1471-4159.2011.07432.x · Cited by 229 · see citing works
The power and promise of RNA ‐seq in ecology and evolution
Todd, E. V., Black, M. A., & Gemmell, N. J. (2016) · Molecular Ecology · doi:10.1111/mec.13526 · Cited by 233 · see citing works
Gene expression profiling in human neurodegenerative disease
Cooper‐Knock, J., Kirby, J., Ferraiuolo, L., Heath, P. R., Rattray, M., & Shaw, P. J. (2012) · Nature Reviews Neurology · doi:10.1038/nrneurol.2012.156 · Cited by 218 · see citing works
Johnson, M. T. J., Carpenter, E. J., Tian, Z., Bruskiewich, R., Burris, J. N., Carrigan, C. T., Chase, M. W., Clarke, N. D., Covshoff, S., dePamphilis, C. W., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0050226 · Cited by 218 · see citing works
Principles of transcriptome analysis and gene expression quantification: an RNA ‐seq tutorial
Wolf, J. B. W. (2013) · Molecular Ecology Resources · doi:10.1111/1755-0998.12109 · Cited by 219 · see citing works
Validation of two ribosomal RNA removal methods for microbial metatranscriptomics
He, S., Wurtzel, O., Singh, K., Froula, J. L., Yilmaz, S., Tringe, S. G., Wang, Z., Chen, F., Lindquist, E. A., Sorek, R., et al. (2010) · Nature Methods · doi:10.1038/nmeth.1507 · Cited by 219 · see citing works
Evaluation of isolation methods and RNA integrity for bacterial RNA quantitation
Jahn, C. E., Charkowski, A. O., & Willis, D. K. (2008) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2008.07.004 · Cited by 214 · see citing works
Israeli Acute Paralysis Virus: Epidemiology, Pathogenesis and Implications for Honey Bee Health
Chen, Y. P., Pettis, J. S., Corona, M., Chen, W. P., Li, C., Spivak, M. S., Visscher, P. K., DeGrandi‐Hoffman, G., Boncristiani, H., Zhao, Y., et al. (2014) · PLoS Pathogens · doi:10.1371/journal.ppat.1004261 · Cited by 217 · see citing works
Standardization and quality management in next-generation sequencing
Endrullat, C., Glökler, J., Franke, P., & Frohme, M. (2016) · Applied & Translational Genomics · doi:10.1016/j.atg.2016.06.001 · Cited by 213 · see citing works
Atlas of the aging mouse brain reveals white matter as vulnerable foci
Hahn, O., Foltz, A. G., Atkins, M., Kedir, B., Moran-Losada, P., Guldner, I. H., Munson, C., Kern, F., Pálovics, R., Lu, N., et al. (2023) · Cell · doi:10.1016/j.cell.2023.07.027 · Cited by 213 · see citing works
Biochemical Mechanism on GABA Accumulation During Fruit Development in Tomato
Akihiro, T., Koike, S., Tani, R., Tominaga, T., Watanabe, S., Iijima, Y., Aoki, K., Shibata, D., Ashihara, H., Matsukura, C., et al. (2008) · Plant and Cell Physiology · doi:10.1093/pcp/pcn113 · Cited by 209 · see citing works
Impact of RNA degradation on gene expression profiling
Opitz, L., Salinas, G., Grade, M., Jung, K., Jo, P., Emons, G., Ghadimi, Β. M., Beißbarth, T., & Gaedcke, J. (2010) · BMC Medical Genomics · doi:10.1186/1755-8794-3-36 · Cited by 208 · see citing works
Nucleic acids from long-term preserved FFPE tissues are suitable for downstream analyses
Ludyga, N., Grünwald, B. T., Azimzadeh, O., Englert, S., Höfler, H., Tapio, S., & Aubele, M. M. (2012) · Archiv für Pathologische Anatomie und Physiologie und für Klinische Medicin · doi:10.1007/s00428-011-1184-9 · Cited by 206 · see citing works
Mehta, D. (2011) · Archives of General Psychiatry · doi:10.1001/archgenpsychiatry.2011.50 · Cited by 200 · see citing works
Alvarez‐Erviti, L., Seow, Y., Schapira, A. H. V., Rodríguez‐Oroz, M., Obeso, J. A., & Cooper, J. A. D. (2013) · Cell Death and Disease · doi:10.1038/cddis.2013.73 · Cited by 204 · see citing works
Morgan, X., Kabakchiev, B., Waldron, L., Tyler, A., Tickle, T., Milgrom, R., Stempak, J., Gevers, D., Xavier, R., Silverberg, M., et al. (2015) · Genome Biology · doi:10.1186/s13059-015-0637-x · Cited by 197 · see citing works
arcasHLA: high-resolution HLA typing from RNAseq
Orenbuch, R., Filip, I., Comito, D., Shaman, J. L., Pe’er, I., & Rabadán, R. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz474 · Cited by 202 · see citing works
Lin, R.-J., Yu, H.-P., Chang, B.-L., Tang, W., Liao, C., & Lin, Y. (2009) · The Journal of Immunology · doi:10.4049/jimmunol.0902728 · Cited by 202 · see citing works
Peters, M. C., Kerr, S. C., Dunican, E. M., Woodruff, P. G., Fajt, M. L., Levy, B. D., Israel, E., Phillips, B. R., Mauger, D. T., COMHAIR, S. A. A., et al. (2018) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2017.12.1009 · Cited by 190 · see citing works
Brottveit, M., Beitnes, A.-C. R., Tollefsen, S., Bratlie, J., Jahnsen, F. L., Johansen, F., Sollid, L. M., & Lundin, K. E. A. (2013) · The American Journal of Gastroenterology · doi:10.1038/ajg.2013.91 · Cited by 187 · see citing works
Corkum, C. P., Ings, D. P., Burgess, C. J., Karwowska, S., Kroll, W., & Michalak, T. I. (2015) · BMC Immunology · doi:10.1186/s12865-015-0113-0 · Cited by 188 · see citing works
Gorter, J. A., Iyer, A. M., White, I., Colzi, A., van Vliet, E. A., Sisodiya, S. M., & Aronica, E. (2013) · Neurobiology of Disease · doi:10.1016/j.nbd.2013.10.026 · Cited by 183 · see citing works
Experimental Considerations for Single-Cell RNA Sequencing Approaches
Nguyen, Q. H., Pervolarakis, N., Nee, K., & Kessenbrock, K. (2018) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2018.00108 · Cited by 170 · see citing works
Roedder, S., Sigdel, T. K., Salomonis, N., Hsieh, S., Dai, H., Bestard, O., Metes, D., Zeevi, A., Gritsch, A., Cheeseman, J. A., et al. (2014) · PLoS Medicine · doi:10.1371/journal.pmed.1001759 · Cited by 184 · see citing works
Lenk, G. M., Tromp, G. C., Weinsheimer, S., Gatalica, Z., Berguer, R., & Kuivaniemi, H. (2007) · BMC Genomics · doi:10.1186/1471-2164-8-237 · Cited by 183 · see citing works
Copois, V., Bibeau, F., Mollévi, C., Salvetat, N., Chalbos, P., Bareil, C., Candeil, L., Fraslon, C., Conseiller, E., Granci, V., et al. (2006) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2006.07.032 · Cited by 182 · see citing works
Anglesio, M. S., Wang, Y., Yang, W., Senz, J., Wan, A. N. C., Heravi‐Moussavi, A., Salamanca, C. M., Maines‐Bandiera, S., Huntsman, D. D., & Morin, G. B. (2012) · The Journal of Pathology · doi:10.1002/path.4135 · Cited by 178 · see citing works
Yong, F. L., Law, C. W., & Wang, C. W. (2013) · BMC Cancer · doi:10.1186/1471-2407-13-280 · Cited by 176 · see citing works
Gründemann, J., Schlaudraff, F., Haeckel, O., & Liss, B. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn084 · Cited by 174 · see citing works
Dong, C., He, F., Berkowitz, O., Liu, J., Cao, P., Tang, M., Shi, H., Wang, W., Li, Q., Shen, Z., et al. (2018) · The Plant Cell · doi:10.1105/tpc.18.00051 · Cited by 171 · see citing works
Transcriptional firing helps to drive NETosis
Khan, M. A., & Palaniyar, N. (2017) · Scientific Reports · doi:10.1038/srep41749 · Cited by 172 · see citing works
Current genetic methodologies in the identification of disaster victims and in forensic analysis
Ziętkiewicz, E., Witt, M. M., Daca‐Roszak, P., Żebracka‐Gala, J., Goniewicz, M., Jarząb, B., & Witt, M. (2011) · Journal of Applied Genetics · doi:10.1007/s13353-011-0068-7 · Cited by 173 · see citing works
Paschold, A., Jia, Y., Marcon, C., Lund, S., Larson, N. B., Yeh, C.-T., Ossowski, S., Lanz, C., Nettleton, D., Schnable, P. S., et al. (2012) · Genome Research · doi:10.1101/gr.138461.112 · Cited by 170 · see citing works
Riesenberg, R., Weiler, C., Spring, O., Eder, M., Büchner, A., Popp, T., Castro, M., Kammerer, R., Takikawa, O., Hatz, R. A., et al. (2007) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-07-0942 · Cited by 169 · see citing works
Ach, R. A., Wang, H., & Curry, B. (2008) · BMC Biotechnology · doi:10.1186/1472-6750-8-69 · Cited by 146 · see citing works
Wonodi, I., Stine, O. C., Sathyasaikumar, K. V., Roberts, R. C., Mitchell, B. D., Hong, L. E., Kajii, Y., Thaker, G. K., & Schwarcz, R. M. (2011) · Archives of General Psychiatry · doi:10.1001/archgenpsychiatry.2011.71 · Cited by 166 · see citing works
Effects of Antemortem and Postmortem Variables on Human Brain mRNA Quality: A BrainNet Europe Study
Durrenberger, P. F., Fernando, S., Kashefi, S. N., Ferrer, I., Hauw, J.-J., Seilhean, D., Smith, C., Walker, R., Al-Sarraj, S., Troakes, C., et al. (2010) · Journal of Neuropathology & Experimental Neurology · doi:10.1097/nen.0b013e3181c7e32f · Cited by 161 · see citing works
Clinical microfluidics for neutrophil genomics and proteomics
Kotz, K. T., Xiao, W., Miller‐Graziano, C. L., Qian, W., Russom, A., Warner, E. A., Moldawer, L. L., De, A. K., Bankey, P. E., Petritis, B. O., et al. (2010) · Nature Medicine · doi:10.1038/nm.2205 · Cited by 161 · see citing works
Jung, M., Ramankulov, A., Roigas, J., Johannsen, M., Ringsdorf, M., Kristiansen, G., & Jung, K. (2007) · BMC Molecular Biology · doi:10.1186/1471-2199-8-47 · Cited by 160 · see citing works
Identification of evolutionarily conserved gene networks mediating neurodegenerative dementia
Swarup, V., Hinz, F. I., Rexach, J. E., Noguchi, K.-I., Toyoshiba, H., Oda, A., Hirai, K., Sarkar, A., Seyfried, N. T., Cheng, C., et al. (2019) · Nature Medicine · doi:10.1038/s41591-018-0223-3 · Cited by 136 · see citing works
Gelman, B. B., Chen, T., Lisinicchia, J. G., Soukup, V. M., Carmical, J. R., Starkey, J. M., Masliah, E., Commins, D., Brandt, D., Grant, I., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0046178 · Cited by 155 · see citing works
RNA-Seq: revelation of the messengers
Verk, M. C. V., Hickman, R. J., Pieterse, C. M. J., & Wees, S. C. M. V. (2013) · Trends in Plant Science · doi:10.1016/j.tplants.2013.02.001 · Cited by 156 · see citing works
Tufi, R., Gandhi, S., de Castro, I. P., Lehmann, S., Angelova, P. R., Dinsdale, D. D., Deas, E., Plun‐Favreau, H., Nicotera, P., Abramov, A. Y., et al. (2014) · Nature Cell Biology · doi:10.1038/ncb2901 · Cited by 153 · see citing works
Ernst, C., Nagy, C., Kim, S., Yang, J., Deng, X., Hellstrom, I. C., Choi, K. H., Gershenfeld, H. K., Meaney, M. J., & Turecki, G. (2011) · Biological Psychiatry · doi:10.1016/j.biopsych.2011.03.038 · Cited by 152 · see citing works
Martínez-Conejero, J. A., Morgan, M., Montesinos, M., Fortuño, S., Meseguer, M., Simón, C., Horcajadas, J. A., & Pellicer, A. (2011) · Fertility and Sterility · doi:10.1016/j.fertnstert.2011.07.1088 · Cited by 151 · see citing works
Hebels, D. G. A. J., Georgiadis, P., Keun, H. C., Athersuch, T. J., Vineis, P., Vermeulen, R. C. H., Portengen, L., Bergdahl, I. A., Hallmans, G., Palli, D., et al. (2013) · Environmental Health Perspectives · doi:10.1289/ehp.1205657 · Cited by 149 · see citing works
Middle East Respiratory Syndrome Coronavirus NS4b Protein Inhibits Host RNase L Activation
Thornbrough, J. M., Jha, B. K., Yount, B. L., Goldstein, S. A., Li, Y., Elliott, R., Sims, A. M., Baric, R. S., Silverman, R. H., & Weiss, S. R. (2016) · mBio · doi:10.1128/mbio.00258-16 · Cited by 149 · see citing works
Post-mortem analysis of neuroinflammatory changes in human Alzheimer’s disease
Gomez-Nicola, D., & Boche, D. (2015) · Alzheimer's Research & Therapy · doi:10.1186/s13195-015-0126-1 · Cited by 147 · see citing works
Courts, C., & Madea, B. (2011) · Journal of Forensic Sciences · doi:10.1111/j.1556-4029.2011.01894.x · Cited by 145 · see citing works
Tsuzuki, S., Handa, Y., Takeda, N., & Kawaguchi, M. (2016) · Molecular Plant-Microbe Interactions · doi:10.1094/mpmi-10-15-0234-r · Cited by 144 · see citing works
Fink, T., Lund, P., Pilgaard, L., Rasmussen, J. G., Duroux, M. C., & Zachar, V. (2008) · BMC Molecular Biology · doi:10.1186/1471-2199-9-98 · Cited by 142 · see citing works
Keller, M., Hopp, L., Liu, X.-S., Wohland, T., Rohde, K., Cancello, R., Klös, M., Bacos, K., Kern, M., Eichelmann, F., et al. (2016) · Molecular Metabolism · doi:10.1016/j.molmet.2016.11.003 · Cited by 114 · see citing works
Lyck, R., Ruderisch, N., Moll, A. G., Steiner, O., Cohen, C. D., Engelhardt, B., Makrides, V., & Verrey, F. (2009) · Journal of Cerebral Blood Flow & Metabolism · doi:10.1038/jcbfm.2009.72 · Cited by 140 · see citing works
RNA Toxicity and Missplicing in the Common Eye Disease Fuchs Endothelial Corneal Dystrophy
Du, J., Aleff, R. A., Soragni, E., Kalari, K. R., Nie, J. J., Tang, X., Davila, J. I., Kocher, J.-P. A., Patel, S. V., Gottesfeld, J. M., et al. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m114.621607 · Cited by 141 · see citing works
SpermBase: A Database for Sperm-Borne RNA Contents
Schuster, A., Tang, C., Xie, Y., Ortogero, N., Yuan, S., & Yan, W. (2016) · Biology of Reproduction · doi:10.1095/biolreprod.116.142190 · Cited by 141 · see citing works
Monsieurs, P., Moors, H., Houdt, R. V., Janssen, P., Janssen, A., Coninx, I., Mergeay, M., & Leys, N. (2011) · BioMetals · doi:10.1007/s10534-011-9473-y · Cited by 140 · see citing works
- Authors
- Schroeder, A., Mueller, O., Stocker, S., Salowsky, R., Leiber, M., Gassmann, M., Lightfoot, S., Menzel, W., Granzow, M., & Ragg, T.
- Affiliations
- Agilent Technologies (United States) (US)
- Agilent Technologies (Germany) (DE)
- Karlsruhe Institute of Technology (DE)
- Corresponding author
- Mueller, Odilo
- Ragg, Thomas
- Venue
- BMC Molecular Biology
- Published
- 2006-01-31
- Volume
- 7
- Issue
- 1
- Pages
- 3-3
- ISSN
- 1471-2199 (ISSN-L)
- PMC
- PMC1413964
- OpenAlex
- W1696199194
- Cited by
- 2,623
- References
- 18
- Citations by year
- 2026: 97 · 2025: 106 · 2024: 135 · 2023: 111 · 2022: 132 · 2021: 172 · 2020: 129 · 2019: 108 · 2018: 169 · 2017: 138 · 2016: 166 · 2015: 149 · 2014: 162 · 2013: 180 · 2012: 145
- FWCI
- 33.21
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by
- Locations
- BMC Molecular Biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- Johns Hopkins University
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Molecular Biology Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- RNA integrity number, RNA quality control, Agilent 2100 Bioanalyzer, Bayesian feature selection, regression models, gene expression
- MeSH terms
- Algorithms, Animals, Bayes Theorem, Humans, Quality Control, RNA, Software, Linear Models, Polymerase Chain Reaction, Neural Networks, Computer, Gene Expression Profiling, Electrophoresis, Microchip, Mice, Rats
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
