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
Wang Z, Gerstein M, Snyder M: RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009, 10: 57-63. 10.1038/nrg2484.
Article
PubMed Central
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
PubMed Central
CAS
PubMed
Google Scholar
Hawkins RD, Hon GC, Ren B: Next-generation genomics: an integrative approach. Nat Rev Genet. 2010, 11: 476-486.
PubMed Central
CAS
PubMed
Google Scholar
van Bakel H, Nislow C, Blencowe BJ, Hughes TR: Most “dark matter” transcripts are associated with known genes. Plos Biology. 2010, 8: 21-
Article
Google Scholar
Hallegger M, Llorian M, Smith CWJ: Alternative splicing: global insights. Febs J. 2010, 277: 856-866. 10.1111/j.1742-4658.2009.07521.x.
Article
CAS
PubMed
Google Scholar
Pepke S, Wold B, Mortazavi A: Computation for ChIP-seq and RNA-seq studies. Nat Methods. 2009, 6: S22-S32. 10.1038/nmeth.1371.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ouyang ZQ, Zhou Q, Wong WH: ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells. Proc Natl Acad Sci USA. 2009, 106: 21521-21526. 10.1073/pnas.0904863106.
Article
PubMed Central
CAS
PubMed
Google Scholar
Sharma CM, Vogel J: Experimental approaches for the discovery anal characterization of regulatory small RNA. Curr Opin Microbiol. 2009, 12: 536-546. 10.1016/j.mib.2009.07.006.
Article
CAS
PubMed
Google Scholar
Boyle AP, Song LY, Lee BK, London D, Keefe D, Birney E, Iyer VR, Crawford GE, Furey TS: High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. Genome Res. 2011, 21: 456-464. 10.1101/gr.112656.110.
Article
PubMed Central
CAS
PubMed
Google Scholar
Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Morales DR, Thomas K, Presser A, Bernstein BE, van Oudenaarden A: Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci USA. 2009, 106: 11667-11672. 10.1073/pnas.0904715106.
Article
PubMed Central
CAS
PubMed
Google Scholar
Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai MC, Hung T, Argani P, Rinn JL: Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature. 2010, 464: 1071-U1148. 10.1038/nature08975.
Article
PubMed Central
CAS
PubMed
Google Scholar
Tsai MC, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, Shi Y, Segal E, Chang HY: Long noncoding RNA as modular scaffold of histone modification complexes. Science. 2010, 329: 689-693. 10.1126/science.1192002.
Article
PubMed Central
CAS
PubMed
Google Scholar
Guttman M, Donaghey J, Carey BW, Garber M, Grenier JK, Munson G, Young G, Lucas AB, Ach R, Bruhn L: lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature. 2011, 477: 295-U260. 10.1038/nature10398.
Article
PubMed Central
CAS
PubMed
Google Scholar
Pauli A, Rinn JL, Schier AF: Non-coding RNAs as regulators of embryogenesis. Nat Rev Genet. 2011, 12: 136-149.
Article
PubMed Central
CAS
PubMed
Google Scholar
Nagano T, Fraser P: No-nonsense functions for long noncoding RNAs. Cell. 2011, 145: 178-181. 10.1016/j.cell.2011.03.014.
Article
CAS
PubMed
Google Scholar
Li H, Lovci MT, Kwon YS, Rosenfeld MG, Fu XD, Yeo GW: Determination of tag density required for digital transcriptome analysis: application to an androgen-sensitive prostate cancer model. Proc Natl Acad Sci USA. 2008, 105: 20179-20184. 10.1073/pnas.0807121105.
Article
PubMed Central
CAS
PubMed
Google Scholar
Blencowe BJ, Ahmad S, Lee LJ: Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes. Genes Dev. 2009, 23: 1379-1386. 10.1101/gad.1788009.
Article
CAS
PubMed
Google Scholar
Tarazona S, Garcia-Alcalde F, Dopazo J, Ferrer A, Conesa A: Differential expression in RNA-seq: a matter of depth. Genome Res. 2011, 21: 2213-2223. 10.1101/gr.124321.111.
Article
PubMed Central
CAS
PubMed
Google Scholar
Haas BJ, Chin M, Nusbaum C, Birren BW, Livny J: How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?. Bmc Genomics. 2012, 13: 734-10.1186/1471-2164-13-734.
Article
PubMed Central
CAS
PubMed
Google Scholar
Tang F, Barbacioru C, Bao S, Lee C, Nordman E, Wang X, Lao K, Surani MA: Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis. Cell Stem Cell. 2010, 6: 468-478. 10.1016/j.stem.2010.03.015.
Article
PubMed Central
CAS
PubMed
Google Scholar
Tang F, Barbacioru C, Nordman E, Li B, Xu N, Bashkirov VI, Lao K, Surani MA: RNA-Seq analysis to capture the transcriptome landscape of a single cell. Nat Protoc. 2010, 5: 516-535.
Article
CAS
PubMed
Google Scholar
Westermann AJ, Gorski SA, Vogel J: Dual RNA-seq of pathogen and host. Nat Rev Microbiol. 2012, 10: 618-630. 10.1038/nrmicro2852.
Article
CAS
PubMed
Google Scholar
Iourov IY, Vorsanova SG, Yurov YB: Single cell genomics of the brain: focus on neuronal diversity and neuropsychiatric diseases. Curr Genomics. 2012, 13: 477-488. 10.2174/138920212802510439.
Article
PubMed Central
CAS
PubMed
Google Scholar
Tischler J, Surani MA: Investigating transcriptional states at single-cell-resolution. Curr Opin Biotechnol. 2013, 24: 69-78. 10.1016/j.copbio.2012.09.013.
Article
CAS
PubMed
Google Scholar
Crawford JE, Guelbeogo WM, Sanou A, Traore A, Vernick KD, Sagnon N, Lazzaro BP: De novo transcriptome sequencing in anopheles funestus using illumina RNA-Seq technology. Plos One. 2010, 5 (12): e14202-10.1371/journal.pone.0014202.
Article
PubMed Central
CAS
PubMed
Google Scholar
Winbush A, Reed D, Chang PL, Nuzhdin SV, Lyons LC, Arbeitman MN: Identification of gene expression changes associated with long-term memory of courtship rejection in drosophila males. G3-Genes Genomes Genetics. 2012, 2: 1437-1445.
PubMed Central
CAS
Google Scholar
Bouvaine S, Behmer ST, Lin GG, Faure ML, Grebenok RJ, Douglas AE: The physiology of sterol nutrition in the pea aphid Acyrthosiphon pisum. J Insect Physiol. 2012, 58: 1383-1389. 10.1016/j.jinsphys.2012.07.014.
Article
CAS
PubMed
Google Scholar
Chen X, Hu Y, Zheng HQ, Cao LF, Niu DF, Yu DL, Sun YQ, Hu SN, Hu FL: Transcriptome comparison between honey bee queen- and worker-destined larvae. Insect Biochem Mol Biol. 2012, 42: 665-673. 10.1016/j.ibmb.2012.05.004.
Article
CAS
PubMed
Google Scholar
Teets NM, Peyton JT, Colinet H, Renault D, Kelley JL, Kawarasaki Y, Lee RE, Denlinger DL: Gene expression changes governing extreme dehydration tolerance in an Antarctic insect. Proc Natl Acad Sci USA. 2012, 109: 20744-20749. 10.1073/pnas.1218661109.
Article
PubMed Central
CAS
PubMed
Google Scholar
Dunning LT, Dennis AB, Park D, Sinclair BJ, Newcomb RD, Buckley TR: Identification of cold-responsive genes in a New Zealand alpine stick insect using RNA-Seq. Comp Biochem Physiol D-Genomics Proteomics. 2013, 8: 24-31. 10.1016/j.cbd.2012.10.005.
Article
CAS
Google Scholar
Hoffman DR: Hymenoptera venom allergens. Clin Rev Allergy Immunol. 2006, 30 (2): 109-128. 10.1385/CRIAI:30:2:109.
Article
CAS
PubMed
Google Scholar
Peiren N, de Graaf DC, Vanrobaeys F, Danneels EL, Devreese B, Van Beeurnen J, Jacobs FJ: Proteomic analysis of the honey bee worker venom gland focusing on the mechanisms of protection against tissue damage. Toxicon. 2008, 52 (1): 72-83. 10.1016/j.toxicon.2008.05.003.
Article
CAS
PubMed
Google Scholar
Bonizzoni M, Dunn WA, Campbell CL, Olson KE, Marinotti O, James AA: Complex modulation of the Aedes aegypti transcriptome in response to dengue virus infection. Plos One. 2012, 7 (11): e50512-10.1371/journal.pone.0050512.
Article
PubMed Central
CAS
PubMed
Google Scholar
Fontana JR, Crews ST: Transcriptome analysis of drosophila CNS midline cells reveals diverse peptidergic properties and a role for castor in neuronal differentiation. Dev Biol. 2012, 372: 131-142. 10.1016/j.ydbio.2012.09.010.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hughes ME, Grant GR, Paquin C, Qian J, Nitabach MN: Deep sequencing the circadian and diurnal transcriptome of Drosophila brain. Genome Res. 2012, 22: 1266-1281. 10.1101/gr.128876.111.
Article
PubMed Central
CAS
PubMed
Google Scholar
Su Y-L, Li J-M, Li M, Luan J-B, Ye X-D, Wang X-W, Liu S-S: Transcriptomic analysis of the salivary glands of an invasive whitefly. Plos One. 2012, 7 (6): e39303-10.1371/journal.pone.0039303.
Article
PubMed Central
CAS
PubMed
Google Scholar
Huang ZY, Robinson GE: Honey bee colony integration: worker-worker interactions mediate plasticity in endocrine and behavioral development. Proc Natl Acad Sci USA. 1992, 89: 11726-11729. 10.1073/pnas.89.24.11726.
Article
PubMed Central
CAS
PubMed
Google Scholar
Whitfield CW, Ben-Shahar Y, Brillet C, Leoncini I, Crauser D, Le Conte Y, Rodriguez-Zas S, Robinson GE: Genomic dissection of behavioral maturation in the honey bee. Proc Natl Acad Sci USA. 2006, 103 (44): 16068-16075. 10.1073/pnas.0606909103.
Article
PubMed Central
CAS
PubMed
Google Scholar
Crailsheim K: Interadult feeding of jelly in honeybee (Apis mellifera) colonies. J Comp Physiol B-Biochemical Systemic Environ Physiol. 1991, 161: 55-60. 10.1007/BF00258746.
Article
Google Scholar
Wegener J, Huang ZY, Lorenz MW, Bienefeld K: Regulation of hypopharyngeal gland activity and oogenesis in honey bee (Apis mellifera) workers. J Insect Physiol. 2009, 55: 716-725. 10.1016/j.jinsphys.2009.05.003.
Article
CAS
PubMed
Google Scholar
Johnson BR: Division of labor in honeybees: form, function, and proximate mechanisms. Behav Ecol Sociobiol. 2010, 64 (3): 305-316. 10.1007/s00265-009-0874-7.
Article
PubMed Central
PubMed
Google Scholar
Trapnell C, Pachter L, Salzberg SL: TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009, 25: 1105-1111. 10.1093/bioinformatics/btp120.
Article
PubMed Central
CAS
PubMed
Google Scholar
Martin M: Cutadapt removes adapter sequences from high-throughput sequencing reads. 2011, North America: EMBnet.journal, Available at: http://journal.embnet.org/index.php/embnetjournal/article/view/200
Google Scholar
Anders S, Huber W: Differential expression analysis for sequence count data. Genome Biol. 2010, 11: R106-10.1186/gb-2010-11-10-r106.
Article
PubMed Central
CAS
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
PubMed Central
CAS
PubMed
Google Scholar