Project description:Expression data from two weeks old Arabidopsis wild-type (Nössen:NO) and at4g16790 (here renamed DUF761-1) knock-out mutant RATM11-0975-1_H (here named duf761-1); Expression data from two weeks old Arabidopsis wild-type (Columbia-0) and transgenic plant overexpressing DUF761-1 (at4g16790) plants(here named OE6) Microarray assays can facilitate elucidation of cellular processes and gene network functions in the processes of plant growth and development. To gain further insight into the potential molecular role of the at4g16790 gene (here named DUF761-1), we performed Affymetrix whole-genome microarray analysis (http://www.affymetrix.com/) on Nössen and duf761-1plants, and on Columbia-0 and OE6 plants, to compare their genome-wide expression profiles under 22 °C. The differently expressed genes revealed by transcriptional profiling indicate that DUF761-1 may involve in plant cell wall biology and defense response of Arabidopsis.
Project description:rs06-01_pld - pld - Role of PLDzeta to abiotic stress adaptation - A double mutant PLDzeta1,2 was obtained in a Columbia background. 12-day-old Arabidopsis seedlings, wt or double mutant, were treated with either NaCl (200 mM), mannitol (400 mM) or with 4degreeC temperature during 3 h. 3 biological replicates were pooled. Keywords: gene knock out,treated vs untreated comparison
Project description:Analysis of changes in global transcript abundance profiles of 2 week old tim23 OE (overexpressor) and tim23 KO (knock-out) mutant Arabidopsis plants complared to wild-type (Col-0) using Affymetrix GeneChipﾙ Arabidopsis ATH1 Genome Arrays.
Project description:Comparison of gene expression pattern of Al response genes between the two Arabidopsis genotypes, wild type (Columbia-0) and the AvSAMS1-expressing transformant
Project description:Arabidopsis ATH1 Genome Arrays were used to analyse changes in transcript abundance between Col-0 (wild-type) Arabidopsis seedlings and either single T-DNA insertional KO mutants of LETM1 (At3g59820)(T-DNA lines; SALK_067558C (letm1-1) and SALK_058471 (letm1-2)) or LETM2 (At1g65540) (T-DNA line; SALK_068877 (letm2-1)). Additionally, letm1 and letm2 knock out Arabidopsis lines were crossed to generate double mutants, however a double knock-out of these two genes results in an embryo lethal phenotype. Hemizygous plants were generated that were homozygous knock out for LETM1 and heterozygous knock out for LETM2, and visa versa, termed (letm1(-/-)LETM2(+/-) and (LETM1(+/-)letm2(-/-) respectively. Note that (letm1(-/-)LETM2(+/-) displays a mild developmental defective phenotype in the first 10-14 days of growth, while (LETM1(+/-)letm2(-/-) shows no phenotype. Microarray analysis was carried out on all three single homozygous knock out lines, and also on both combinations of the hemizygous mutation between the two genes, and compared with a wild-type Col-0 control to gain insight into global transcript abundance changes in these mutant lines. Arrays were performed in triplicate for each genotype, from RNA isolated from 3 independent pools of 5-10 Arabidopsis seedlings at 10 days old.
Project description:ra07-03_aba4 - aba4/1 - Identification of genes deregulated in aba4 mutant or overexpressers. - Comparison of different genotypes to wild type Col-0: aba4-3 mutant, two independent 35S-ABA4 transgenic lines and two independent 35S-NCED6 transgenic lines. Keywords: gene knock in (transgenic),gene knock out
Project description:In order to identify genes specifically involved in the photoperiodic control of the mobilisation programme for starch reserve in Arabidopsis thaliana transcription profiling was performed on the following genotypes Columbia wild type (Col-0), CO overexpressor (35S::CO), CO muntant (co-10), GBSSI mutant (gbs-1), aps1 mutant (aps1) and Columbia with sucrose. The different Arabidopsis thaliana genotype seedlings were cultivated in long day conditions (16 h day/ 8 h dark) at 22 C in controlled environment cabinets for two weeks. Samples were collected at ZT 4, immediately frozen in liquid nitrogen and processed.
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:Expression data from two weeks old Arabidopsis wild-type (Columbia-0) and transgenic plant overexpressing NHRGP (at4g16790) plants (OE-N6)
Project description:Purpose: The goals of this study are to compare transcriptome of ldl1ldl2 double mutants with that of wild-type Columbia-0 plants and to identify genes whose expression are tightly regualted by LDL1/LDL2 prtoeins in Arabidopsis. Methods: mRNA profiles of 3-week-old wild-type Col-0 and ldl1ldl2 mutant plants were generated by deep sequencing, in duplicate, using Illumina HiSeq 2000. 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 27~31 million sequence reads per sample to the Arabidopsis genome (TAIR10). Conclusions: Our results show that LDL1 and LDL2 protein had significant effects on transcription of genes important for plant immune reponses against Pseudomonas infection.
