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RNA-Seq Atlas of Glycine max: a guide to the soybean transcriptome.

Severin AJ, Woody JL, Bolon YT, Joseph B, Diers BW, Farmer AD, Muehlbauer GJ, Nelson RT, Grant D, Specht JE, Graham MA, Cannon SB, May GD, Vance CP, Shoemaker RC.

BMC Plant Biol. 2010 Aug 5;10:160. doi: 10.1186/1471-2229-10-160.


Divergent patterns of endogenous small RNA populations from seed and vegetative tissues of Glycine max.

Zabala G, Campos E, Varala KK, Bloomfield S, Jones SI, Win H, Tuteja JH, Calla B, Clough SJ, Hudson M, Vodkin LO.

BMC Plant Biol. 2012 Oct 2;12:177. doi: 10.1186/1471-2229-12-177.


RNA-Seq Atlas--a reference database for gene expression profiling in normal tissue by next-generation sequencing.

Krupp M, Marquardt JU, Sahin U, Galle PR, Castle J, Teufel A.

Bioinformatics. 2012 Apr 15;28(8):1184-5. doi: 10.1093/bioinformatics/bts084. Epub 2012 Feb 17.


Using RNA-Seq to profile soybean seed development from fertilization to maturity.

Jones SI, Vodkin LO.

PLoS One. 2013;8(3):e59270. doi: 10.1371/journal.pone.0059270. Epub 2013 Mar 15.


Sequence mining and transcript profiling to explore differentially expressed genes associated with lipid biosynthesis during soybean seed development.

Chen H, Wang FW, Dong YY, Wang N, Sun YP, Li XY, Liu L, Fan XD, Yin HL, Jing YY, Zhang XY, Li YL, Chen G, Li HY.

BMC Plant Biol. 2012 Jul 31;12:122. doi: 10.1186/1471-2229-12-122.


An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants.

Libault M, Farmer A, Joshi T, Takahashi K, Langley RJ, Franklin LD, He J, Xu D, May G, Stacey G.

Plant J. 2010 Jul 1;63(1):86-99. doi: 10.1111/j.1365-313X.2010.04222.x. Epub 2010 Apr 7.


RNA-Seq profiling of a defective seed coat mutation in Glycine max reveals differential expression of proline-rich and other cell wall protein transcripts.

Kour A, Boone AM, Vodkin LO.

PLoS One. 2014 May 14;9(5):e96342. doi: 10.1371/journal.pone.0096342. eCollection 2014.


RNA-seq analyses of multiple meristems of soybean: novel and alternative transcripts, evolutionary and functional implications.

Wang L, Cao C, Ma Q, Zeng Q, Wang H, Cheng Z, Zhu G, Qi J, Ma H, Nian H, Wang Y.

BMC Plant Biol. 2014 Jun 17;14:169. doi: 10.1186/1471-2229-14-169.


Transcriptome analysis reveals a critical role of CHS7 and CHS8 genes for isoflavonoid synthesis in soybean seeds.

Dhaubhadel S, Gijzen M, Moy P, Farhangkhoee M.

Plant Physiol. 2007 Jan;143(1):326-38. Epub 2006 Nov 10.


Genomic expression profiling of mature soybean (Glycine max) pollen.

Haerizadeh F, Wong CE, Bhalla PL, Gresshoff PM, Singh MB.

BMC Plant Biol. 2009 Mar 6;9:25. doi: 10.1186/1471-2229-9-25.


A comparative transcriptomic study of an allotetraploid and its diploid progenitors illustrates the unique advantages and challenges of RNA-seq in plant species.

Ilut DC, Coate JE, Luciano AK, Owens TG, May GD, Farmer A, Doyle JJ.

Am J Bot. 2012 Feb;99(2):383-96. doi: 10.3732/ajb.1100312. Epub 2012 Feb 1.


Maize gene atlas developed by RNA sequencing and comparative evaluation of transcriptomes based on RNA sequencing and microarrays.

Sekhon RS, Briskine R, Hirsch CN, Myers CL, Springer NM, Buell CR, de Leon N, Kaeppler SM.

PLoS One. 2013 Apr 23;8(4):e61005. doi: 10.1371/journal.pone.0061005. Print 2013. Erratum in: PLoS One. 2014;9(1). doi:10.1371/annotation/0444d495-9231-4097-abe0-4750b9045971.


Comprehensive analysis of RNA-seq data reveals the complexity of the transcriptome in Brassica rapa.

Tong C, Wang X, Yu J, Wu J, Li W, Huang J, Dong C, Hua W, Liu S.

BMC Genomics. 2013 Oct 7;14:689. doi: 10.1186/1471-2164-14-689.


Transcript profiling reveals expression differences in wild-type and glabrous soybean lines.

Hunt M, Kaur N, Stromvik M, Vodkin L.

BMC Plant Biol. 2011 Oct 26;11:145. doi: 10.1186/1471-2229-11-145.


Predicting gene regulatory networks of soybean nodulation from RNA-Seq transcriptome data.

Zhu M, Dahmen JL, Stacey G, Cheng J.

BMC Bioinformatics. 2013 Sep 22;14:278. doi: 10.1186/1471-2105-14-278.


Large-scale analysis of putative soybean regulatory gene expression identifies a Myb gene involved in soybean nodule development.

Libault M, Joshi T, Takahashi K, Hurley-Sommer A, Puricelli K, Blake S, Finger RE, Taylor CG, Xu D, Nguyen HT, Stacey G.

Plant Physiol. 2009 Nov;151(3):1207-20. doi: 10.1104/pp.109.144030. Epub 2009 Sep 15.


The transition from primary siRNAs to amplified secondary siRNAs that regulate chalcone synthase during development of Glycine max seed coats.

Cho YB, Jones SI, Vodkin L.

PLoS One. 2013 Oct 21;8(10):e76954. doi: 10.1371/journal.pone.0076954. eCollection 2013.


Transcript profiling of common bean (Phaseolus vulgaris L.) using the GeneChip Soybean Genome Array: optimizing analysis by masking biased probes.

Yang SS, Valdés-López O, Xu WW, Bucciarelli B, Gronwald JW, Hernández G, Vance CP.

BMC Plant Biol. 2010 May 7;10:85. doi: 10.1186/1471-2229-10-85.

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