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2-week-old Arabidopsis seedlings (Columbia ecotype)

ABSTRACT: Comparison of TopHat alignments and assessment of spurious splice junctions for 32nt and 76nt read lengths. Total RNA from 2-week-old Arabidopsis thaliana (ecotype Columbia) seedlings grown on MS plates was isolated using RNeasy Plant Mini Kit from Qiagen. To remove any contaminating DNA, RNA was treated with DNAse. Isolation of poly (A) mRNA and preparation of cDNA library were carried out using the Illumina TrueSeq RNA kit. Sequencing (72 cycle) was done on Illumina Genome Analyzer II. 2 replicates

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Mark Rogers

PROVIDER: E-GEOD-32318 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data.

Rogers Mark F MF Thomas Julie J Reddy Anireddy Sn AS Ben-Hur Asa A

Genome biology 20120131 1

We propose a method for predicting splice graphs that enhances curated gene models using evidence from RNA-Seq and EST alignments. Results obtained using RNA-Seq experiments in Arabidopsis thaliana show that predictions made by our SpliceGrapher method are more consistent with current gene models than predictions made by TAU and Cufflinks. Furthermore, analysis of plant and human data indicates that the machine learning approach used by SpliceGrapher is useful for discriminating between real and ...[more]

PMID: 22293517

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