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Items: 1 to 20 of 243

1.

Impact of library preparation on downstream analysis and interpretation of RNA-Seq data: comparison between Illumina PolyA and NuGEN Ovation protocol.

Sun Z, Asmann YW, Nair A, Zhang Y, Wang L, Kalari KR, Bhagwate AV, Baker TR, Carr JM, Kocher JP, Perez EA, Thompson EA.

PLoS One. 2013 Aug 19;8(8):e71745. doi: 10.1371/journal.pone.0071745. eCollection 2013.

2.

Characterizing the impact of smoking and lung cancer on the airway transcriptome using RNA-Seq.

Beane J, Vick J, Schembri F, Anderlind C, Gower A, Campbell J, Luo L, Zhang XH, Xiao J, Alekseyev YO, Wang S, Levy S, Massion PP, Lenburg M, Spira A.

Cancer Prev Res (Phila). 2011 Jun;4(6):803-17. doi: 10.1158/1940-6207.CAPR-11-0212.

3.

Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling.

Zhao W, He X, Hoadley KA, Parker JS, Hayes DN, Perou CM.

BMC Genomics. 2014 Jun 2;15:419. doi: 10.1186/1471-2164-15-419.

4.

A comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencing.

Cui P, Lin Q, Ding F, Xin C, Gong W, Zhang L, Geng J, Zhang B, Yu X, Yang J, Hu S, Yu J.

Genomics. 2010 Nov;96(5):259-65. doi: 10.1016/j.ygeno.2010.07.010. Epub 2010 Aug 3.

5.

Alternative splicing detection workflow needs a careful combination of sample prep and bioinformatics analysis.

Carrara M, Lum J, Cordero F, Beccuti M, Poidinger M, Donatelli S, Calogero RA, Zolezzi F.

BMC Bioinformatics. 2015;16 Suppl 9:S2. doi: 10.1186/1471-2105-16-S9-S2. Epub 2015 Jun 1.

6.

Method for improved Illumina sequencing library preparation using NuGEN Ovation RNA-Seq System.

Head SR, Komori HK, Hart GT, Shimashita J, Schaffer L, Salomon DR, Ordoukhanian PT.

Biotechniques. 2011 Mar;50(3):177-80. doi: 10.2144/000113613.

7.

Comparison of library preparation methods reveals their impact on interpretation of metatranscriptomic data.

Alberti A, Belser C, Engelen S, Bertrand L, Orvain C, Brinas L, Cruaud C, Giraut L, Da Silva C, Firmo C, Aury JM, Wincker P.

BMC Genomics. 2014 Oct 20;15:912. doi: 10.1186/1471-2164-15-912.

8.

Comparative transcriptome analysis of epithelial and fiber cells in newborn mouse lenses with RNA sequencing.

Hoang TV, Kumar PK, Sutharzan S, Tsonis PA, Liang C, Robinson ML.

Mol Vis. 2014 Nov 4;20:1491-517. eCollection 2014.

9.

Single read and paired end mRNA-Seq Illumina libraries from 10 nanograms total RNA.

Sengupta S, Bolin JM, Ruotti V, Nguyen BK, Thomson JA, Elwell AL, Stewart R.

J Vis Exp. 2011 Oct 27;(56):e3340. doi: 10.3791/3340.

10.

Gene expression, single nucleotide variant and fusion transcript discovery in archival material from breast tumors.

Norton N, Sun Z, Asmann YW, Serie DJ, Necela BM, Bhagwate A, Jen J, Eckloff BW, Kalari KR, Thompson KJ, Carr JM, Kachergus JM, Geiger XJ, Perez EA, Thompson EA.

PLoS One. 2013 Nov 22;8(11):e81925. doi: 10.1371/journal.pone.0081925. eCollection 2013.

11.

Next generation sequencing analysis of human platelet PolyA+ mRNAs and rRNA-depleted total RNA.

Kissopoulou A, Jonasson J, Lindahl TL, Osman A.

PLoS One. 2013 Dec 11;8(12):e81809. doi: 10.1371/journal.pone.0081809. eCollection 2013.

12.

Comparative analysis of human protein-coding and noncoding RNAs between brain and 10 mixed cell lines by RNA-Seq.

Chen G, Yin K, Shi L, Fang Y, Qi Y, Li P, Luo J, He B, Liu M, Shi T.

PLoS One. 2011;6(11):e28318. doi: 10.1371/journal.pone.0028318. Epub 2011 Nov 30.

13.

RNA-seq identified a super-long intergenic transcript functioning in adipogenesis.

Yi F, Yang F, Liu X, Chen H, Ji T, Jiang L, Wang X, Yang Z, Zhang LH, Ding X, Liang Z, Du Q.

RNA Biol. 2013 Jun;10(6):991-1001. doi: 10.4161/rna.24644. Epub 2013 Apr 11.

14.

Characterization and comparative analyses of muscle transcriptomes in Dorper and small-tailed Han sheep using RNA-Seq technique.

Zhang C, Wang G, Wang J, Ji Z, Liu Z, Pi X, Chen C.

PLoS One. 2013 Aug 30;8(8):e72686. doi: 10.1371/journal.pone.0072686. eCollection 2013.

15.

Identification of large intergenic non-coding RNAs in bovine muscle using next-generation transcriptomic sequencing.

Billerey C, Boussaha M, Esquerré D, Rebours E, Djari A, Meersseman C, Klopp C, Gautheret D, Rocha D.

BMC Genomics. 2014 Jun 19;15:499. doi: 10.1186/1471-2164-15-499.

16.

Evaluation of the coverage and depth of transcriptome by RNA-Seq in chickens.

Wang Y, Ghaffari N, Johnson CD, Braga-Neto UM, Wang H, Chen R, Zhou H.

BMC Bioinformatics. 2011 Oct 18;12 Suppl 10:S5. doi: 10.1186/1471-2105-12-S10-S5.

17.

Exploring the gonad transcriptome of two extreme male pigs with RNA-seq.

Esteve-Codina A, Kofler R, Palmieri N, Bussotti G, Notredame C, Pérez-Enciso M.

BMC Genomics. 2011 Nov 8;12:552. doi: 10.1186/1471-2164-12-552.

18.

Identification of mRNAs and lincRNAs associated with lung cancer progression using next-generation RNA sequencing from laser micro-dissected archival FFPE tissue specimens.

Morton ML, Bai X, Merry CR, Linden PA, Khalil AM, Leidner RS, Thompson CL.

Lung Cancer. 2014 Jul;85(1):31-9. doi: 10.1016/j.lungcan.2014.03.020. Epub 2014 Mar 29.

19.

Evaluating gene expression in C57BL/6J and DBA/2J mouse striatum using RNA-Seq and microarrays.

Bottomly D, Walter NA, Hunter JE, Darakjian P, Kawane S, Buck KJ, Searles RP, Mooney M, McWeeney SK, Hitzemann R.

PLoS One. 2011 Mar 24;6(3):e17820. doi: 10.1371/journal.pone.0017820.

20.

A low-cost library construction protocol and data analysis pipeline for Illumina-based strand-specific multiplex RNA-seq.

Wang L, Si Y, Dedow LK, Shao Y, Liu P, Brutnell TP.

PLoS One. 2011;6(10):e26426. doi: 10.1371/journal.pone.0026426. Epub 2011 Oct 19. Erratum in: PLoS One. 2011;6(11). doi: 10.1371/annotation/e5ef7afc-7e81-4053-8670-1bb3402f63fd.

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