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Items: 1 to 20 of 94

1.

The impact of RNA sequence library construction protocols on transcriptomic profiling of leukemia.

Kumar A, Kankainen M, Parsons A, Kallioniemi O, Mattila P, Heckman CA.

BMC Genomics. 2017 Aug 17;18(1):629. doi: 10.1186/s12864-017-4039-1.

2.

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.

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.

The use of exome capture RNA-seq for highly degraded RNA with application to clinical cancer sequencing.

Cieslik M, Chugh R, Wu YM, Wu M, Brennan C, Lonigro R, Su F, Wang R, Siddiqui J, Mehra R, Cao X, Lucas D, Chinnaiyan AM, Robinson D.

Genome Res. 2015 Sep;25(9):1372-81. doi: 10.1101/gr.189621.115. Epub 2015 Aug 7.

5.

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.

6.

Mining the Archives: A Cross-Platform Analysis of Gene Expression Profiles in Archival Formalin-Fixed Paraffin-Embedded Tissues.

Webster AF, Zumbo P, Fostel J, Gandara J, Hester SD, Recio L, Williams A, Wood CE, Yauk CL, Mason CE.

Toxicol Sci. 2015 Dec;148(2):460-72. doi: 10.1093/toxsci/kfv195. Epub 2015 Sep 10.

7.

Effect of RNA integrity on uniquely mapped reads in RNA-Seq.

Chen EA, Souaiaia T, Herstein JS, Evgrafov OV, Spitsyna VN, Rebolini DF, Knowles JA.

BMC Res Notes. 2014 Oct 23;7:753. doi: 10.1186/1756-0500-7-753.

8.

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.

9.

A comprehensive assessment of RNA-seq protocols for degraded and low-quantity samples.

Schuierer S, Carbone W, Knehr J, Petitjean V, Fernandez A, Sultan M, Roma G.

BMC Genomics. 2017 Jun 5;18(1):442. doi: 10.1186/s12864-017-3827-y.

10.

Depletion of Ribosomal RNA Sequences from Single-Cell RNA-Sequencing Library.

Fang N, Akinci-Tolun R.

Curr Protoc Mol Biol. 2016 Jul 1;115:7.27.1-7.27.20. doi: 10.1002/cpmb.11.

PMID:
27366895
11.

Transcriptome analysis using RNA-Seq.

Hoeijmakers WA, Bártfai R, Stunnenberg HG.

Methods Mol Biol. 2013;923:221-39.

PMID:
22990781
12.

Analyse multiple disease subtypes and build associated gene networks using genome-wide expression profiles.

Aibar S, Fontanillo C, Droste C, Roson-Burgo B, Campos-Laborie FJ, Hernandez-Rivas JM, De Las Rivas J.

BMC Genomics. 2015;16 Suppl 5:S3. doi: 10.1186/1471-2164-16-S5-S3. Epub 2015 May 26.

13.

An optimized protocol for generation and analysis of Ion Proton sequencing reads for RNA-Seq.

Yuan Y, Xu H, Leung RK.

BMC Genomics. 2016 May 26;17:403. doi: 10.1186/s12864-016-2745-8.

14.

Influence of RNA extraction methods and library selection schemes on RNA-seq data.

Sultan M, Amstislavskiy V, Risch T, Schuette M, Dökel S, Ralser M, Balzereit D, Lehrach H, Yaspo ML.

BMC Genomics. 2014 Aug 11;15:675. doi: 10.1186/1471-2164-15-675.

15.

IVT-seq reveals extreme bias in RNA sequencing.

Lahens NF, Kavakli IH, Zhang R, Hayer K, Black MB, Dueck H, Pizarro A, Kim J, Irizarry R, Thomas RS, Grant GR, Hogenesch JB.

Genome Biol. 2014 Jun 30;15(6):R86. doi: 10.1186/gb-2014-15-6-r86.

16.

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.

17.

Next-Generation Sequencing RNA-Seq Library Construction.

Podnar J, Deiderick H, Huerta G, Hunicke-Smith S.

Curr Protoc Mol Biol. 2014 Apr 14;106:4.21.1-19. doi: 10.1002/0471142727.mb0421s106. Review.

PMID:
24733242
18.

A platform independent RNA-Seq protocol for the detection of transcriptome complexity.

Calabrese C, Mangiulli M, Manzari C, Paluscio AM, Caratozzolo MF, Marzano F, Kurelac I, D'Erchia AM, D'Elia D, Licciulli F, Liuni S, Picardi E, Attimonelli M, Gasparre G, Porcelli AM, Pesole G, Sbisà E, Tullo A.

BMC Genomics. 2013 Dec 5;14:855. doi: 10.1186/1471-2164-14-855.

19.

A simple strand-specific RNA-Seq library preparation protocol combining the Illumina TruSeq RNA and the dUTP methods.

Sultan M, Dökel S, Amstislavskiy V, Wuttig D, Sültmann H, Lehrach H, Yaspo ML.

Biochem Biophys Res Commun. 2012 Jun 15;422(4):643-6. doi: 10.1016/j.bbrc.2012.05.043. Epub 2012 May 15.

20.

Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens.

Liao W, Jordaan G, Nham P, Phan RT, Pelegrini M, Sharma S.

BMC Cancer. 2015 Oct 16;15:714. doi: 10.1186/s12885-015-1708-9.

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