ABSTRACT: Transcriptom analyses of Arabidopsis altered meritem program1-32 (amp1-32) mutant as well as wild-type Columbia-0 plants via next-generation sequencing (NGS).
Project description:Transcriptome analyses of Arabidopsis ldl1ldl2 (lysine-specific demethylase1 [LSD1]-like1 [ldl1]) double mutants as well as wild-type Columbia-0 plants via next-generation sequencing (NGS)
Project description:Purpose:The goals of this study are to compare transcriptome of amp1-32 mutant with that of wild-type Columbia-0 plant and to identify genes whose expression are tightly regualted by AMP1 in Arabidopsis. Methods: mRNA profiles of 3-week-old wild-type Col-0 and amp1-32 mutant plants were generated by deep sequencing, in duplicate, using Illumina HiSeq2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with a method : TopHat followed by Cufflinks. Results: Using an optimized data analysis workflow, we mapped about 30~53 million sequence reads per sample to the Arabidopsis genome (TAIR10). From the 2 biological replicates, we detected 135 up-regulated genes, and 36 down-regulated genes, in the amp1-32 mutant plant. Conclusions: Our study represents the first detailed analysis of transcriptome of amp1 mutant plants, with biologic replicates. Our results show that AMP1 protein had weak, but significant, effects on transcription of genes important for plant development and responses to stresses.
Project description:We performed a transcriptomic analysis of Pi starvation responses in Arabidopsis thaliana (Columbia-0) wild type plants under phosphate starvation stress and in plants with altered PHR1(-like) activity, comparing mutants of phr1 and phr1-phl1 grown in phosphate-lacking medium. Results show the central role of PHR1 and functionally redundant members of its family in the control of transcriptional responses to Pi starvation.
Project description:Arabiposis plants with conbinations of different FRIGIDA (FRI) and FLOWERING LOCUS C (FLC) alleles grown in short days (9L:15D) for 30 days at 21°C, then shifted to long days (16L:8D). Genotypes: Columbia wild type (Col-0): fri FLC Columbia with introgressed FRI from Sf-2: FRI FLC Columbia with introgressed FRI and deleted FLC (flc-3): FRI flc Columbia with deleted FLC (flc-3): fri flc Time points: 0, 2, and 4 days after shift to long days Keywords = flowering Keywords: time-course
Project description:Investigation of the ecotype difference between Columbia-0 (Col) and Wassilewskija-0 (WS) on whole gene expression level, of PME17 mutation effect (compared to background WS) and of the aphid infestation effect on Col, WS and pme17 (infested plants compared to non-infested plants).
Project description:To gain insight into the biological role of D5RF in plants, we conducted a comprehensive survey of global gene expression employing high throughput-RNA sequencing to quantify the variations in transcript abundance between wild-type Columbia-0 (Col-0) and d5rf.
Project description:The ppi2 mutant introgressed into the Columbia-0 ecotype as previously reported. Doublemutant ppi2xrpn8a was crossed with the above referenced genotypes using heterozygous ppi2 plants. After 2 days of stratification at 4 °C the plants were grown on half-strength Murashige and Skoog (M&S) medium supplemented with 0.8% (w/v) plant agar (Duchefa) and 0.8% (w/v) sucrose under short day conditions.
Project description:To gain further insights into a larger number of processes potentially altered by high nickel (Ni), we performed a transcriptional profiling of whole roots of Arabidopsis thaliana accession Columbia-0 (Col-0) exposed to 100 µM nickel, a concentration that induces slight chlorosis and intermediate inhibition of root and shoot growth.
Project description:Wild type and mutanat Arabiposis plants grown in short days (9L:15D) for 30 days at 21°C, then shifted to long days (16L:8D). Genotypes: Columbia wild type (Col-0) Landsberg erecta (Ler) leafy-12 (lfy-12, in Col-0) constans-2 (co-2, in Ler) flowering locus T-2 (ft-2, in Ler) Time points: 0, 3, 5, and 7 days after shift to long days Keywords = flowering Keywords: time-course
Project description:We profiled transcriptome of seedling samples derived from SALK Col-0 plants and a Col-0 plants reproduced in our lab for at least 10 generations. Using strand-specific RNA-seq analysis, we identified 32 genes were differentially expressed genes (fold-change > 2, DESeq2 P-value < 0.01), including 28 ones (88%) were up-regulated in the Col-0 plants reproduced in our lab. Of them, QUA-QUINE STARCH (QQS) ranked top 2 differentially expressed gene.
