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]
Project description:Identification of new and unpredicted full length Arabidopsis genes. Examination of cRNA prepared from Arabidopsis thaliana ecotype Columbia light grown 7-day old seedlings using whole genome tiling arrays. Keywords: other
Project description:This study evaluates the transcriptome of Arabidopsis thaliana seedlings (Col-0 ecotype) treated with methyl jasmonate (MeJA) or with the salicylic acid analog benzothiadiazole (BTH). Overall design: Two-week-old Arabidopsis thaliana seedlings (Col-0 ecotype) grown under short day conditions (9h of light at 21°C - 15h of dark at 18°C) were sprayed with 50 μM MeJA (Sigma), 300 μM BTH (Actigard 50WG) or a mock solution (0.02% Silwet, 0.1% ethanol). Samples were harvested 1h, 5h and 8h after spraying and used for RNA extraction and Illumina sequencing. The experiment includes two independent biological replicates per condition. Each replicate corresponds to approximately 30 seedlings grown in the same pot.
Project description:To investigate differences in plant responses to salt and ABA stimulus, differences in gene expression in Arabidopsis in response to salt and ABA were compared using an Agilent oligo microarray. Four-week-old Arabidopsis thaliana ecotype Columbia (Col-0) seedlings were treated with either 150 mM NaCl or 10 μM ABA for 6 hours; unstressed seedlings (control sample) were collected in parallel to avoid the possible effects of circadian rhythms. The results revealed that 31 genes were up regulated by both NaCl and ABA stress, and 23 genes were down-regulated by these stressors. To provide further validation of our microarray experiment data, ten genes from this signature were quantified in the same RNA samples by quantitative real-time PCR. Differentially expression genes of Arabidopsis thaliana were measured under salt stressed, ABA stressed and normal condition for 6 hours, respectively. Three independent experiments were performed at each treatment using different plants for each experiment.
Project description:We sequenced the poly(A)+ and poly(A)- samples of the roots and shoots from 10-day-old WT seedlings grown under P+ and P- condition. The WT plant refers to Columbia ecotype Arabidopsis seedlings. Each condition has two replicates. After total RNA extraction, ribosomal RNAs were removed using RiboMinus™ Plant Kit repeated two times. The poly(A)+ and poly(A)- constituent were separated with oligo(dT) magnetic beads (Oligotex mRNA Mini Kit, QIAGEN). Using a 2-fold change and a P-value <0.05 as the cut-off for selecting the differentially expressed transcripts, we globally identified novel noncoding lncRNAs. Overall design: We performed a RNA-seq analysis on Columbia WT plants. Total RNAs were extracted from the shoots and roots of 10-day-old P+ and P- WT seedlings (i.e., seedling grown on P-sufficient and P-deficient media). The extracted RNAs were subjected to polyA(+) and polyA(-) RNA purification, library construction and RNA deep sequencing. We used Tophat to map reads to TAIR10 genome and used Cufflinks to assemble transcripts based on 16 datasets of RNA-seq samples.
Project description:Wild-type A. thaliana plants (Arabidopsis thaliana L. ecotype-Columbia) were grown in plastic pots filled with peat moss for 3 weeks (principal growth stage 1.071.08) under a 16 h light/8 h dark regimen (40 ± 10 umol photons/m2/s) at 22C. Dehydration treatment: The 3-week-old plants were grown for 6 days without watering.
Project description:Wild-type A. thaliana plants (Arabidopsis thaliana L. ecotype-Columbia) were grown in plastic pots filled with peat moss for 3 weeks (principal growth stage 1.071.08) under a 16 h light/8 h dark regimen (40 ± 10 umol photons/m2/s) at 22C. Cold treatment: The 3-week-old plants were transferred from 22C to 4C and were grown for 1 day.
Project description:Identification of new and unpredicted full length Arabidopsis genes. Examination of cRNA prepared from Arabidopsis thaliana ecotype Columbia light grown 7-day old seedlings, light grown 7-day old seedlings treated at 4 degrees C for 24hrs, and etiolated 7-day old seedlings using pilot genome tiling arrays. Total RNA was isolated from seedlings with the TRIzol reagent procedure of Invitrogen, then poly(A)+ RNA was purified with Qiagen oligotex. One microgram poly(A)+ RNA was converted into ds-cDNA using T7-oligo(dT) primers. Biotin-labeled cRNA was generated by in vitro transcription reactions using ENZO labeling kit, fragmented and then 20 micrograms of fragmented cRNA were hybridized to the arrays according to Affymetrix instructions. Keywords: other
Project description: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
Project description:This study evaluates the transcriptome of Arabidopsis thaliana infected with the Pseudomonas syringae strain DC3000 cor- carrying the type three secretion system effector HopBB1 Overall design: Two-week-old Arabidopsis thaliana seedlings (Col-0 ecotype) were sprayed with a mock solution (10 mM MgCl2) or bacteria [Pto DC3000 (EV), Pto DC3000 cor- (EV); Pto DC3000 cor- (HopBB1); Pto DC3000 cor- (HopBB1G126D)] at OD600=0.2 with 10mM MgCl2 and 0.04% Silwet L-77. Samples were harvested 24 hours after infection. This experiment included three biological replicates, each one corresponding to approximately 30 seedlings grown in the same pot.
Project description:Identification of nutrient-specific microRNA expressed in Arabidopsis seedlings Overall design: Small RNA sequencing of Arabidopsis wild type ecotype Columbia (Col-0) seedling under different nutrient limitation conditions