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Results: 1 to 20 of 110

1.

Comparative analysis of RNA sequencing methods for degraded or low-input samples.

Adiconis X, Borges-Rivera D, Satija R, DeLuca DS, Busby MA, Berlin AM, Sivachenko A, Thompson DA, Wysoker A, Fennell T, Gnirke A, Pochet N, Regev A, Levin JZ.

Nat Methods. 2013 Jul;10(7):623-9. doi: 10.1038/nmeth.2483. Epub 2013 May 19. Erratum in: Nat Methods. 2014 Feb;11(2):210.

PMID:
23685885
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data.

Wang L, Feng Z, Wang X, Wang X, Zhang X.

Bioinformatics. 2010 Jan 1;26(1):136-8. doi: 10.1093/bioinformatics/btp612. Epub 2009 Oct 24.

PMID:
19855105
[PubMed - indexed for MEDLINE]
Free Article
3.

Zinc-mediated RNA fragmentation allows robust transcript reassembly upon whole transcriptome RNA-Seq.

Wery M, Descrimes M, Thermes C, Gautheret D, Morillon A.

Methods. 2013 Sep 1;63(1):25-31. doi: 10.1016/j.ymeth.2013.03.009. Epub 2013 Mar 21.

PMID:
23523657
[PubMed - indexed for MEDLINE]
4.

Comprehensive comparative analysis of strand-specific RNA sequencing methods.

Levin JZ, Yassour M, Adiconis X, Nusbaum C, Thompson DA, Friedman N, Gnirke A, Regev A.

Nat Methods. 2010 Sep;7(9):709-15. doi: 10.1038/nmeth.1491. Epub 2010 Aug 15.

PMID:
20711195
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Transcriptome analysis using next-generation sequencing.

Mutz KO, Heilkenbrinker A, Lönne M, Walter JG, Stahl F.

Curr Opin Biotechnol. 2013 Feb;24(1):22-30. doi: 10.1016/j.copbio.2012.09.004. Epub 2012 Sep 25. Review.

PMID:
23020966
[PubMed - indexed for MEDLINE]
6.
7.

Next-generation sequencing facilitates quantitative analysis of wild-type and Nrl(-/-) retinal transcriptomes.

Brooks MJ, Rajasimha HK, Roger JE, Swaroop A.

Mol Vis. 2011;17:3034-54. Epub 2011 Nov 23.

PMID:
22162623
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Full-length transcriptome assembly from RNA-Seq data without a reference genome.

Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A.

Nat Biotechnol. 2011 May 15;29(7):644-52. doi: 10.1038/nbt.1883.

PMID:
21572440
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

A mixture model for expression deconvolution from RNA-seq in heterogeneous tissues.

Li Y, Xie X.

BMC Bioinformatics. 2013;14 Suppl 5:S11. doi: 10.1186/1471-2105-14-S5-S11. Epub 2013 Apr 10.

PMID:
23735186
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Towards the integration, annotation and association of historical microarray experiments with RNA-seq.

Chavan SS, Bauer MA, Peterson EA, Heuck CJ, Johann DJ Jr.

BMC Bioinformatics. 2013;14 Suppl 14:S4. doi: 10.1186/1471-2105-14-S14-S4. Epub 2013 Oct 9.

PMID:
24268045
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

A systematic comparison and evaluation of high density exon arrays and RNA-seq technology used to unravel the peripheral blood transcriptome of sickle cell disease.

Raghavachari N, Barb J, Yang Y, Liu P, Woodhouse K, Levy D, O'Donnell CJ, Munson PJ, Kato GJ.

BMC Med Genomics. 2012 Jun 29;5:28. doi: 10.1186/1755-8794-5-28.

PMID:
22747986
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

RNA-Seq: a method for comprehensive transcriptome analysis.

Nagalakshmi U, Waern K, Snyder M.

Curr Protoc Mol Biol. 2010 Jan;Chapter 4:Unit 4.11.1-13. doi: 10.1002/0471142727.mb0411s89.

PMID:
20069539
[PubMed - indexed for MEDLINE]
13.

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.

PMID:
22064688
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

NSMAP: a method for spliced isoforms identification and quantification from RNA-Seq.

Xia Z, Wen J, Chang CC, Zhou X.

BMC Bioinformatics. 2011 May 16;12:162. doi: 10.1186/1471-2105-12-162.

PMID:
21575225
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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.

PMID:
22165852
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer.

Asmann YW, Klee EW, Thompson EA, Perez EA, Middha S, Oberg AL, Therneau TM, Smith DI, Poland GA, Wieben ED, Kocher JP.

BMC Genomics. 2009 Nov 16;10:531. doi: 10.1186/1471-2164-10-531.

PMID:
19917133
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

RNA sequencing and quantitation using the Helicos Genetic Analysis System.

Raz T, Causey M, Jones DR, Kieu A, Letovsky S, Lipson D, Thayer E, Thompson JF, Milos PM.

Methods Mol Biol. 2011;733:37-49. doi: 10.1007/978-1-61779-089-8_3.

PMID:
21431761
[PubMed - indexed for MEDLINE]
18.

RNA-seq analysis of transcriptomes in thrombin-treated and control human pulmonary microvascular endothelial cells.

Cheranova D, Gibson M, Chaudhary S, Zhang LQ, Heruth DP, Grigoryev DN, Ye SQ.

J Vis Exp. 2013 Feb 13;(72). pii: 4393. doi: 10.3791/4393.

PMID:
23426025
[PubMed - indexed for MEDLINE]
19.

Designing a transcriptome next-generation sequencing project for a nonmodel plant species.

Strickler SR, Bombarely A, Mueller LA.

Am J Bot. 2012 Feb;99(2):257-66. doi: 10.3732/ajb.1100292. Epub 2012 Jan 19. Review.

PMID:
22268224
[PubMed - indexed for MEDLINE]
Free Article
20.

Retinal transcriptome profiling by directional next-generation sequencing using 100 ng of total RNA.

Brooks MJ, Rajasimha HK, Swaroop A.

Methods Mol Biol. 2012;884:319-34. doi: 10.1007/978-1-61779-848-1_23.

PMID:
22688717
[PubMed - indexed for MEDLINE]

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