A human haploid gene trap collection to study lncRNAs with unusual RNA biology

References

• Ulitsky I, Bartel DP. lincRNAs: genomics, evolution, and mechanisms. Cell 2013; 154:26–46; PMID:23827673; http://dx.doi.org/10.1016/j.cell.2013.06.020
   PubMed Web of Science ®Google Scholar
• Iyer MK, Niknafs YS, Malik R, Singhal U, Sahu A, Hosono Y, Barrette TR, Prensner JR, Evans JR, Zhao S, et al. The landscape of long noncoding RNAs in the human transcriptome. Nat Genet 2015; 47(3):199–208; PMID:25599403; http://dx.doi.org/10.1007/82_2015_444
   PubMed Web of Science ®Google Scholar
• Cheetham SW, Gruhl F, Mattick JS, Dinger ME. Long noncoding RNAs and the genetics of cancer. Br J Cancer 2013; 108:2419–25; PMID:23660942; http://dx.doi.org/10.1038/bjc.2013.233
   PubMed Web of Science ®Google Scholar
• Batista PJ, Chang HY. Long noncoding RNAs: cellular address codes in development and disease. Cell 2013; 152:1298–307; PMID:23498938; http://dx.doi.org/10.1016/j.cell.2013.02.012
   PubMed Web of Science ®Google Scholar
• Prensner JR, Iyer MK, Balbin OA, Dhanasekaran SM, Cao Q, Brenner JC, Laxman B, Asangani IA, Grasso CS, Kominsky HD, et al. Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression. Nat Biotechnol 2011; 29:742–9; PMID:21804560; http://dx.doi.org/10.1038/nbt.1914
   PubMed Web of Science ®Google Scholar
• Roth A, Diederichs S. Long Noncoding RNAs in Lung Cancer. Curr Top Microbiol Immunol 2015; PMID:26037047
   PubMedGoogle Scholar
• Meng L, Ward AJ, Chun S, Bennett CF, Beaudet AL, Rigo F. Towards a therapy for Angelman syndrome by targeting a long non-coding RNA. Nature 2015; 518:409–12; PMID:25470045; http://dx.doi.org/10.1038/nature13975
   PubMed Web of Science ®Google Scholar
• Wahlestedt C. Targeting long non-coding RNA to therapeutically upregulate gene expression. Nat Rev Drug Discov 2013; 12:433–46; PMID:23722346; http://dx.doi.org/10.1038/nrd4018
   PubMed Web of Science ®Google Scholar
• Roberts TC, Wood MJ. Therapeutic targeting of non-coding RNAs. Essays Biochem 2013; 54:127–45; PMID:23829532; http://dx.doi.org/10.1042/bse0540127
   PubMed Web of Science ®Google Scholar
• Quinodoz S, Guttman M. Long noncoding RNAs: an emerging link between gene regulation and nuclear organization. Trends Cell Biol 2014; 24:651–63; PMID:25441720; http://dx.doi.org/10.1016/j.tcb.2014.08.009
   PubMed Web of Science ®Google Scholar
• Poliseno L, Salmena L, Zhang J, Carver B, Haveman WJ, Pandolfi PP. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature 2010; 465:1033–8; PMID:20577206; http://dx.doi.org/10.1038/nature09144
   PubMed Web of Science ®Google Scholar
• Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai MC, Hung T, Argani P, Rinn JL, et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 2010; 464:1071–6; PMID:20393566; http://dx.doi.org/10.1038/nature08975
   PubMed Web of Science ®Google Scholar
• Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, Lajoie BR, Protacio A, Flynn RA, Gupta RA, et al. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 2011; 472:120–4; PMID:21423168; http://dx.doi.org/10.1038/nature09819
   PubMed Web of Science ®Google Scholar
• Latos PA, Pauler FM, Koerner MV, Senergin HB, Hudson QJ, Stocsits RR, Allhoff W, Stricker SH, Klement RM, Warczok KE, et al. Airn transcriptional overlap, but not its lncRNA products, induces imprinted Igf2r silencing. Science 2012; 338:1469–72; PMID:23239737; http://dx.doi.org/10.1126/science.1228110
   PubMed Web of Science ®Google Scholar
• Kornienko AE, Guenzl PM, Barlow DP, Pauler FM. Gene regulation by the act of long non-coding RNA transcription. BMC Biol 2013; 11:59; PMID:23721193; http://dx.doi.org/10.1186/1741-7007-11-59
   PubMed Web of Science ®Google Scholar
• Chu C, Spitale RC, Chang HY. Technologies to probe functions and mechanisms of long noncoding RNAs. Nat Struct Mol Biol 2015; 22:29–35; PMID:25565030; http://dx.doi.org/10.1038/nsmb.2921
   PubMed Web of Science ®Google Scholar
• Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 2011; 25:1915–27; PMID:21890647; http://dx.doi.org/10.1101/gad.17446611
   PubMed Web of Science ®Google Scholar
• Cabili MN, Dunagin MC, McClanahan PD, Biaesch A, Padovan-Merhar O, Regev A, Rinn JL, Raj A. Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution. Genome Biol 2015; 16:20; PMID:25630241; http://dx.doi.org/10.1186/s13059-015-0586-4
   PubMed Web of Science ®Google Scholar
• Tilgner H, Knowles DG, Johnson R, Davis CA, Chakrabortty S, Djebali S, Curado J, Snyder M, Gingeras TR, Guigó R. Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs. Genome Res 2012; 22:1616–25; PMID:22955974; http://dx.doi.org/10.1101/gr.134445.111
   PubMed Web of Science ®Google Scholar
• Seidl CI, Stricker SH, Barlow DP. The imprinted Air ncRNA is an atypical RNAPII transcript that evades splicing and escapes nuclear export. Embo J 2006; 25:3565–75; PMID:16874305; http://dx.doi.org/10.1038/sj.emboj.7601245
   PubMed Web of Science ®Google Scholar
• Kelley D, Rinn J. Transposable elements reveal a stem cell-specific class of long noncoding RNAs. Genome Biol 2012; 13:R107; PMID:23181609; http://dx.doi.org/10.1186/gb-2012-13-11-r107
   PubMed Web of Science ®Google Scholar
• Hacisuleyman E, Goff LA, Trapnell C, Williams A, Henao-Mejia J, Sun L, McClanahan P, Hendrickson DG, Sauvageau M, Kelley DR, et al. Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. Nat Struct Mol Biol 2014; 21:198–206; PMID:24463464; http://dx.doi.org/10.1038/nsmb.2764
   PubMed Web of Science ®Google Scholar
• Guttman M, Donaghey J, Carey BW, Garber M, Grenier JK, Munson G, Young G, Lucas AB, Ach R, Bruhn L, et al. lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 2011; 477:295–300; PMID:21874018; http://dx.doi.org/10.1038/nature10398
   PubMed Web of Science ®Google Scholar
• Ulitsky I, Shkumatava A, Jan CH, Sive H, Bartel DP. Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution. Cell 2011; 147:1537–50; PMID:22196729; http://dx.doi.org/10.1016/j.cell.2011.11.055
   PubMed Web of Science ®Google Scholar
• Tripathi V, Ellis JD, Shen Z, Song DY, Pan Q, Watt AT, Freier SM, Bennett CF, Sharma A, Bubulya PA, et al. The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell 2010; 39:925–38; PMID:20797886; http://dx.doi.org/10.1016/j.molcel.2010.08.011
   PubMed Web of Science ®Google Scholar
• Ohrt T, Muetze J, Svoboda P, Schwille P. Intracellular localization and routing of miRNA and RNAi pathway components. Curr Top Med Chem 2012; 12:79–88; PMID:22196276; http://dx.doi.org/10.2174/156802612798919132
   PubMed Web of Science ®Google Scholar
• Sander JD, Joung JK. CRISPR-Cas systems for editing, regulating and targeting genomes. Nat Biotechnol 2014; 32:347–55; PMID:24584096; http://dx.doi.org/10.1038/nbt.2842
   PubMed Web of Science ®Google Scholar
• Sauvageau M, Goff LA, Lodato S, Bonev B, Groff AF, Gerhardinger C, Sanchez-Gomez DB, Hacisuleyman E, Li E, Spence M, et al. Multiple knockout mouse models reveal lincRNAs are required for life and brain development. Elife 2013; 2:e01749; PMID:24381249; http://dx.doi.org/10.7554/eLife.01749
   PubMed Web of Science ®Google Scholar
• Yin Y, Yan P, Lu J, Song G, Zhu Y, Li Z, Zhao Y, Shen B, Huang X, Zhu H, et al. Opposing roles for the lncRNA haunt and its genomic locus in regulating hoxa gene activation during embryonic stem cell differentiation. Cell Stem Cell 2015; 16:504–16; PMID:25891907; http://dx.doi.org/10.1016/j.stem.2015.03.007
   PubMed Web of Science ®Google Scholar
• Zhang B, Arun G, Mao YS, Lazar Z, Hung G, Bhattacharjee G, Xiao X, Booth CJ, Wu J, Zhang C, et al. The lncRNA Malat1 is dispensable for mouse development but its transcription plays a cis-regulatory role in the adult. Cell Reports 2012; 2:111–23; PMID:22840402; http://dx.doi.org/10.1016/j.celrep.2012.06.003
   PubMed Web of Science ®Google Scholar
• Han J, Zhang J, Chen L, Shen B, Zhou J, Hu B, Du Y, Tate PH, Huang X, Zhang W. Efficient in vivo deletion of a large imprinted lncRNA by CRISPR/Cas9. RNA Biol 2014; 11:829–35; PMID:25137067; http://dx.doi.org/10.4161/rna.29624
   PubMed Web of Science ®Google Scholar
• Bassett AR, Akhtar A, Barlow DP, Bird AP, Brockdorff N, Duboule D, Ephrussi A, Ferguson-Smith AC, Gingeras TR, Haerty W, et al. Considerations when investigating lncRNA function in vivo. Elife 2014; 3:e03058; PMID:25124674; http://dx.doi.org/10.7554/eLife.03058
   PubMed Web of Science ®Google Scholar
• Skarnes WC, von Melchner H, Wurst W, Hicks G, Nord AS, Cox T, Young SG, Ruiz P, Soriano P, Tessier-Lavigne M, et al. A public gene trap resource for mouse functional genomics. Nat Genet 2004; 36:543–4; PMID:15167922; http://dx.doi.org/10.1038/ng0604-543
   PubMed Web of Science ®Google Scholar
• Stanford WL, Cohn JB, Cordes SP. Gene-trap mutagenesis: past, present and beyond. Nat Rev Genet 2001; 2:756–68; PMID:11584292; http://dx.doi.org/10.1038/35093548
   PubMed Web of Science ®Google Scholar
• Schuster-Gossler K, Simon-Chazottes D, Guenet JL, Zachgo J, Gossler A. Gtl2lacZ, an insertional mutation on mouse chromosome 12 with parental origin-dependent phenotype. Mamm Genome 1996; 7:20–4; PMID:8903723; http://dx.doi.org/10.1007/s003359900006
   PubMed Web of Science ®Google Scholar
• Barlow DP, Bartolomei MS. Genomic imprinting in mammals. Cold Spring Harb Perspect Biol 2014; 6:a018382; PMID:24492710; http://dx.doi.org/10.1101/cshperspect.a018382
   PubMed Web of Science ®Google Scholar
• Kanduri C. Long noncoding RNAs: Lessons from genomic imprinting. Biochim Biophys Acta 2015; PMID:26004516; http://dx.doi.org/10.1016/j.bbagrm.2015.05.006
   PubMed Web of Science ®Google Scholar
• da Rocha ST, Edwards CA, Ito M, Ogata T, Ferguson-Smith AC. Genomic imprinting at the mammalian Dlk1-Dio3 domain. Trends Genet 2008; 24:306–16; PMID:18471925; http://dx.doi.org/10.1016/j.tig.2008.03.011
   PubMed Web of Science ®Google Scholar
• Benetatos L, Vartholomatos G, Hatzimichael E. DLK1-DIO3 imprinted cluster in induced pluripotency: landscape in the mist. Cell Mol Life Sci 2014; 71:4421–30; PMID:25098353; http://dx.doi.org/10.1007/s00018-014-1698-9
   PubMed Web of Science ®Google Scholar
• Sleutels F, Zwart R, Barlow DP. The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature 2002; 415:810–3; PMID:11845212; http://dx.doi.org/10.1038/415810a
   PubMed Web of Science ®Google Scholar
• Mancini-Dinardo D, Steele SJ, Levorse JM, Ingram RS, Tilghman SM. Elongation of the Kcnq1ot1 transcript is required for genomic imprinting of neighboring genes. Genes Dev 2006; 20:1268–82; PMID:16702402; http://dx.doi.org/10.1101/gad.1416906
   PubMed Web of Science ®Google Scholar
• Meng L, Person RE, Huang W, Zhu PJ, Costa-Mattioli M, Beaudet AL. Truncation of Ube3a-ATS unsilences paternal Ube3a and ameliorates behavioral defects in the Angelman syndrome mouse model. PLoS Genet 2013; 9:e1004039; PMID:24385930; http://dx.doi.org/10.1371/journal.pgen.1004039
   PubMed Web of Science ®Google Scholar
• Shin JY, Fitzpatrick GV, Higgins MJ. Two distinct mechanisms of silencing by the KvDMR1 imprinting control region. Embo J 2008; 27:168–78; PMID:18079696; http://dx.doi.org/10.1038/sj.emboj.7601960
   PubMed Web of Science ®Google Scholar
• Gutschner T, Baas M, Diederichs S. Noncoding RNA gene silencing through genomic integration of RNA destabilizing elements using zinc finger nucleases. Genome Res 2011; 21:1944–54; PMID:21844124; http://dx.doi.org/10.1101/gr.122358.111
   PubMed Web of Science ®Google Scholar
• Burckstummer T, Banning C, Hainzl P, Schobesberger R, Kerzendorfer C, Pauler FM, Chen D, Them N, Schischlik F, Rebsamen M, et al. A reversible gene trap collection empowers haploid genetics in human cells. Nat Methods 2013; 10:965–71; PMID:24161985; http://dx.doi.org/10.1038/nmeth.2609
   PubMed Web of Science ®Google Scholar
• Santoro F, Mayer D, Klement RM, Warczok KE, Stukalov A, Barlow DP, Pauler FM. Imprinted Igf2r silencing depends on continuous Airn lncRNA expression and is not restricted to a developmental window. Development 2013; 140:1184–95; PMID:23444351; http://dx.doi.org/10.1242/dev.088849
   PubMed Web of Science ®Google Scholar
• Andersson BS, Beran M, Pathak S, Goodacre A, Barlogie B, McCredie KB. Ph-positive chronic myeloid leukemia with near-haploid conversion in vivo and establishment of a continuously growing cell line with similar cytogenetic pattern. Cancer Genet Cytogenet 1987; 24:335–43; PMID:3466682; http://dx.doi.org/10.1016/0165-4608(87)90116-6
   PubMed Web of Science ®Google Scholar
• Schuster-Gossler K, Bilinski P, Sado T, Ferguson-Smith A, Gossler A. The mouse Gtl2 gene is differentially expressed during embryonic development, encodes multiple alternatively spliced transcripts, and may act as an RNA. Dev Dyn 1998; 212:214–28; PMID:9626496; http://dx.doi.org/10.1002/(SICI)1097-0177(199806)212:2%3c214::AID-AJA6%3e3.0.CO;2-K
   PubMed Web of Science ®Google Scholar
• Vlatkovic I. PhD thesis: Mapping and characterization of macro non-protein coding RNAs in human imprinted gene regions, University of Vienna; available for download at http://othes.univie.ac.at/12494/1/2010-09-01_0642621.pdf 2010
   Google Scholar
• Smith RJ, Dean W, Konfortova G, Kelsey G. Identification of novel imprinted genes in a genome-wide screen for maternal methylation. Genome Res 2003; 13:558–69; PMID:12670997; http://dx.doi.org/10.1101/gr.781503
   PubMed Web of Science ®Google Scholar
• Andergassen D, Dotter CP, Kulinski TM, Guenzl PM, Bammer PC, Barlow DP, Pauler FM, Hudson QJ. Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data. Nucleic Acids Res 2015; 43(21): e146; PMID:26202974
   PubMed Web of Science ®Google Scholar
• Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum MJ, McGarvey KM, et al. RefSeq: an update on mammalian reference sequences. Nucleic Acids Res 2014; 42:D756–63; PMID:24259432; http://dx.doi.org/10.1093/nar/gkt1114
   PubMed Web of Science ®Google Scholar
• Mattick JS, Rinn JL. Discovery and annotation of long noncoding RNAs. Nat Struct Mol Biol 2015; 22:5–7; PMID:25565026; http://dx.doi.org/10.1038/nsmb.2942
   PubMed Web of Science ®Google Scholar
• Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res 2012; 22:1760–74; PMID:22955987; http://dx.doi.org/10.1101/gr.135350.111
   PubMed Web of Science ®Google Scholar
• Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 2013; 29:15–21; PMID:23104886; http://dx.doi.org/10.1093/bioinformatics/bts635
   PubMed Web of Science ®Google Scholar
• Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 2012; 22:1775–89; PMID:22955988; http://dx.doi.org/10.1101/gr.132159.111
   PubMed Web of Science ®Google Scholar
• Curinha A, Oliveira Braz S, Pereira-Castro I, Cruz A, Moreira A. Implications of polyadenylation in health and disease. Nucleus 2014; 5:508–19; PMID:25484187; http://dx.doi.org/10.4161/nucl.36360
   PubMed Web of Science ®Google Scholar
• Brockdorff N, Ashworth A, Kay GF, McCabe VM, Norris DP, Cooper PJ, Swift S, Rastan S. The product of the mouse Xist gene is a 15 kb inactive X-specific transcript containing no conserved ORF and located in the nucleus. Cell 1992; 71:515–26; PMID:1423610; http://dx.doi.org/10.1016/0092-8674(92)90519-I
   PubMed Web of Science ®Google Scholar
• Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 2012; 7:562–78; PMID:22383036; http://dx.doi.org/10.1038/nprot.2012.016
   PubMed Web of Science ®Google Scholar
• Gregory TR. Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma. Biol Rev Camb Philos Soc 2001; 76:65–101; PMID:11325054; http://dx.doi.org/10.1017/S1464793100005595
   PubMed Web of Science ®Google Scholar
• Huang R, Jaritz M, Guenzl P, Vlatkovic I, Sommer A, Tamir IM, Marks H, Klampfl T, Kralovics R, Stunnenberg HG, et al. An RNA-Seq strategy to detect the complete coding and non-coding transcriptome including full-length imprinted macro ncRNAs. PLoS One 2011; 6:e27288; PMID:22102886; http://dx.doi.org/10.1371/journal.pone.0027288
   PubMed Web of Science ®Google Scholar
• Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Pachter L. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol 2013; 31:46–53; PMID:23222703; http://dx.doi.org/10.1038/nbt.2450
   PubMed Web of Science ®Google Scholar
• Kowalczyk MS, Higgs DR, Gingeras TR. Molecular biology: RNA discrimination. Nature 2012; 482:310–1; PMID:22337043; http://dx.doi.org/10.1038/482310a
   PubMed Web of Science ®Google Scholar
• Wutz A. Gene silencing in X-chromosome inactivation: advances in understanding facultative heterochromatin formation. Nat Rev Genet 2011; 12:542–53; PMID:21765457; http://dx.doi.org/10.1038/nrg3035
   PubMed Web of Science ®Google Scholar
• Alen C, Kent NA, Jones HS, O'Sullivan J, Aranda A, Proudfoot NJ. A role for chromatin remodeling in transcriptional termination by RNA polymerase II. Mol Cell 2002; 10:1441–52; PMID:12504018; http://dx.doi.org/10.1016/S1097-2765(02)00778-5
   PubMed Web of Science ®Google Scholar
• Luco RF, Misteli T. More than a splicing code: integrating the role of RNA, chromatin and non-coding RNA in alternative splicing regulation. Curr Opin Genet Dev 2011; 21:366–72; PMID:21497503; http://dx.doi.org/10.1016/j.gde.2011.03.004
   PubMed Web of Science ®Google Scholar
• Weber EL, Cannon PM. Promoter choice for retroviral vectors: transcriptional strength vs. trans-activation potential. Hum Gene Ther 2007; 18:849–60; PMID:17767401; http://dx.doi.org/10.1089/hum.2007.067
   PubMed Web of Science ®Google Scholar
• Zwart R, Sleutels F, Wutz A, Schinkel AH, Barlow DP. Bidirectional action of the Igf2r imprint control element on upstream and downstream imprinted genes. Genes Dev 2001; 15:2361–6; PMID:11562346; http://dx.doi.org/10.1101/gad.206201
   PubMed Web of Science ®Google Scholar
• Nagano T, Mitchell JA, Sanz LA, Pauler FM, Ferguson-Smith AC, Feil R, Fraser P. The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin. Science 2008; 322:1717–20; PMID:18988810; http://dx.doi.org/10.1126/science.1163802
   PubMed Web of Science ®Google Scholar
• Babak T, DeVeale B, Tsang EK, Zhou Y, Li X, Smith KS, Kukurba KR, Zhang R, Li JB, van der Kooy D, et al. Genetic conflict reflected in tissue-specific maps of genomic imprinting in human and mouse. Nat Genet 2015; 47:544–9; PMID:25848752; http://dx.doi.org/10.1038/ng.3274
   PubMed Web of Science ®Google Scholar
• Baran Y, Subramaniam M, Biton A, Tukiainen T, Tsang EK, Rivas MA, Pirinen M, Gutierrez-Arcelus M, Smith KS, Kukurba KR, et al. The landscape of genomic imprinting across diverse adult human tissues. Genome Res 2015; 25:927–36; PMID:25953952; http://dx.doi.org/10.1101/gr.192278.115
   PubMed Web of Science ®Google Scholar
• Charrin S, Jouannet S, Boucheix C, Rubinstein E. Tetraspanins at a glance. J Cell Sci 2014; 127:3641–8; PMID:25128561; http://dx.doi.org/10.1242/jcs.154906
   PubMed Web of Science ®Google Scholar
• Karlsson G, Rorby E, Pina C, Soneji S, Reckzeh K, Miharada K, Karlsson C, Guo Y, Fugazza C, Gupta R, et al. The tetraspanin CD9 affords high-purity capture of all murine hematopoietic stem cells. Cell Rep 2013; 4:642–8; PMID:23954783; http://dx.doi.org/10.1016/j.celrep.2013.07.020
   PubMed Web of Science ®Google Scholar
• Carette JE, Pruszak J, Varadarajan M, Blomen VA, Gokhale S, Camargo FD, Wernig M, Jaenisch R, Brummelkamp TR. Generation of iPSCs from cultured human malignant cells. Blood 2010; 115:4039–42; PMID:20233975; http://dx.doi.org/10.1182/blood-2009-07-231845
   PubMed Web of Science ®Google Scholar
• Akutsu H, Miura T, Machida M, Birumachi J, Hamada A, Yamada M, Sullivan S, Miyado K, Umezawa A. Maintenance of pluripotency and self-renewal ability of mouse embryonic stem cells in the absence of tetraspanin CD9. Differentiation 2009; 78:137–42; PMID:19716222; http://dx.doi.org/10.1016/j.diff.2009.08.005
   PubMed Web of Science ®Google Scholar
• Kennaway DJ. Clock genes at the heart of depression. J Psychopharmacol 2010; 24:5–14; PMID:20663803; http://dx.doi.org/10.1177/1359786810372980
   PubMed Web of Science ®Google Scholar
• Baek SH, Kim KI. Emerging roles of orphan nuclear receptors in cancer. Annu Rev Physiol 2014; 76:177–95; PMID:24215441; http://dx.doi.org/10.1146/annurev-physiol-030212-183758
   PubMed Web of Science ®Google Scholar
• Wang A, Huang K, Shen Y, Xue Z, Cai C, Horvath S, Fan G. Functional modules distinguish human induced pluripotent stem cells from embryonic stem cells. Stem Cells Dev 2011; 20:1937–50; PMID:21542696; http://dx.doi.org/10.1089/scd.2010.0574
   PubMed Web of Science ®Google Scholar
• Carette JE, Guimaraes CP, Wuethrich I, Blomen VA, Varadarajan M, Sun C, Bell G, Yuan B, Muellner MK, Nijman SM, et al. Global gene disruption in human cells to assign genes to phenotypes by deep sequencing. Nat Biotechnol 2011; 29:542–6; PMID:21623355; http://dx.doi.org/10.1038/nbt.1857
   PubMed Web of Science ®Google Scholar
• Sultan M, Dokel S, Amstislavskiy V, Wuttig D, Sultmann H, Lehrach H, Yaspo ML. A simple strand-specific RNA-Seq library preparation protocol combining the Illumina TruSeq RNA and the dUTP methods. Biochem Biophysical Res Commun 2012; 422:643–6; PMID:22609201; http://dx.doi.org/10.1016/j.bbrc.2012.05.043
   PubMed Web of Science ®Google Scholar
• Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 2002; 30:207-10; PMID:11752295; http://dx.doi.org/10.1093/nar/30.1.207
   Google Scholar
• Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M, et al. A promoter-level mammalian expression atlas. Nature 2014; 507:462–70; PMID:24670764; http://dx.doi.org/10.1038/nature13182
   PubMed Web of Science ®Google Scholar