Arabidopsis sepal RNA-Seq
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ABSTRACT:
PROVIDER: PRJEB52917 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The aim of this study was to analyze the impact of autotetraploidy on gene expression in Arabidopsis thaliana by comparing diploid versus tetraploid transcriptomes. In particular, this included the comparison of the transcriptome of different tetraploid A. thaliana ecotypes (Col-0 vs. Ler-0). The study was extended to address further aspects. One was the comparison of the transcriptomes in subsequent generations. This intended to obtain information on the genome wide stability of autotetraploid gene expression. Another line of work compared the transcriptomes of different diploid vs. tetraploid tissues. This aimed to investigate whether particular gene groups are specifically affected during the development of A. thaliana autotetraploids. Samples 1-8: Arabidopsis thaliana Col-0 tetraploid transcriptome. Transcriptional profiling and comparison of diploid vs. tetraploid Col-0 seedlings. The experiment was carried out with pedigree of independently generated and assessed tetraploid Col-0 lines. Samples 9-12: Arabidopsis thaliana Ler-0 tetraploid transcriptome. Transcriptional profiling and comparison of diploid vs. tetraploid Ler-0 seedlings. The experiment was carried out with pedigree of independently generated and assessed tetraploid Ler-0 lines. Samples 13-24: Arabidopsis thaliana Col-0 tetraploid transcriptome. Transcriptional profiling and comparison of diploid vs. tetraploid Col-0 leaves (6th - 8th). The experiment was carried out with pedigree of independently generated and assessed tetraploid Col-0 lines. Samples 25-32: Arabidopsis thaliana Ler-0 tetraploid transcriptome. Transcriptional profiling and comparison of diploid vs. tetraploid Ler-0 leaves (6th - 8th). The experiment was carried out with pedigree of independently generated and assessed tetraploid Ler-0 lines. Samples 33-36: Arabidopsis thaliana Ler-0 tetraploid transcriptome. Transcriptional profiling and comparison of tetraploid vs. tetraploid Ler-0 seedlings from the second (F2) and third (F3) generation after induction, respectively. The experiment was carried out with pedigree of independently generated and assessed tetraploid Ler-0 lines. Samples 37-40: Arabidopsis thaliana Col-0 tetraploid transcriptome. Transcriptional profiling and comparison of tetraploid vs. tetraploid Col-0 seedlings from the second (F2) and third (F3) generation after induction, respectively. The experiment was carried out with pedigree of independently generated and assessed tetraploid Col-0 lines. Samples 41-44: Arabidopsis thaliana Col-0/Ler-0 diploid transcriptome. Transcriptional profiling and comparison of diploid Col-0 vs. diploid Ler-0 seedlings. The experiment was carried out with pedigree of esrablished lines. Samples 45-48: Arabidopsis thaliana Col-0/Ler-0 tetraploid transcriptome. Transcriptional profiling and comparison of tetraploid Col-0 vs tetraploid Ler-0 seedlings. The experiment was carried out with pedigree of independently generated and assessed tetraploid Col-0 and Ler-0 lines.
2010-05-01 | GSE18482 | GEO
Project description:Purpose: The goals of this study are to compare the transcriptome profiling and alternative splicing (AS) profiling between Col-0 wild type and SFPS knockout mutant (sfps-2) through RNA-seq to determine the molecular mechanisms of how splicing factor SFPS regulates photomorphogenesis in Arabidopsis. Results: Using an optimized data analysis workflow, we mapped about 100 million sequence reads per sample to the Arabidopsis genome (TAIR10) and identified 1495 differentially expressed genes between Col-0 and mutant dark samples; 1361 differentially expressed genes between Col-0 and mutant red light treated samples; 4291 differentially expressed genes between Col-0 dark and red light treated samples; and 4479 differentially expressed genes between mutant dark and red light treated samples. Except for gene expression, we also discovered 788 differentially spliced bins between Col-0 and mutant dark samples; 827 differentially spliced bins between Col-0 and mutant red light treated samples; 610 differentially spliced bins between Col-0 dark and red light treated samples; and 405 differentially spliced bins between mutant dark and red light treated samples. Altered splicing of 9 genes was confirmed with qRT-PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Conclusions: Our study represents the first detailed analysis of SFPS mutant transcriptomes, with biologic replicates, generated by RNA-seq technology. Our results show that SFPS regulates photomorphogenesis in Arabidopisis through regulating the splicing activity of light signaling genes, which helps us.
2017-08-10 | GSE85883 | GEO
Project description:Paired-end Illumina RNA sequencing of Arabidopsis thaliana Col-0 siliques.
2016-11-16 | GSE89617 | GEO
Project description:Arabidopsis thaliana col-0 14 day old whole seedling RNA-seq control samples. These samples are used alongside publicly available ENCODE and Arabidopsis strand-specific RNA-seq samples to examine antisense expression and correct inaccuracies. See https://github.com/bartongroup/RoSA
2019-05-29 | E-MTAB-7990 | biostudies-arrayexpress
Project description:We used Ribo-seq (Ribosome profiling) combining with RNA-seq to explore the translational landscape of Arabidopsis Col-0 seedling. We generated 6 biological replicates of RNA-seq and Ribo-seq data for Arabidopsis Col-0 seedling. 3 of the replicates were collected after 20 minutes of 0.1% DMSO treatment and the other 3 samples were collected after 60 minutes of DMSO treatmeant. The resulting RNA-seq and Ribo-seq files were used to discover translated up-stream ORFs (uORFs) and analyze the translation efficiency of uORF-containing genes in Arabidopsis.
2023-09-20 | GSE183264 | GEO
Project description:Comparison of gene expression between wild type Arabidopsis ecotype Col-0 plants and transgenic Arabidopsis ecotype col-0 plants expressing AtMYB23SRDX. Keywords: other
2004-07-07 | GSE1544 | GEO
Project description:Using MethylC-Seq to provide single-base resolution of DNA methylation status in Col-0 and some RdDM mutants
2016-03-17 | GSE70912 | GEO
Project description:To investigate genome-wide Arabidopsis TE release, we sequenced the wild-type Col-0 transcriptome under Control, Heat and Recovery conditions
2020-03-25 | GSE132415 | GEO
Project description:Transcriptional profiling of Arabidopsis comparing 1μM 3OC6-HSL-treated Arabidopsis wild-type Col-0 with control untreated Col-0. A transcriptomic analysis for Arabidopsis responses to bacterial quorum sensing molecule N-3oxo-hexanoyl-homoserine lactone (3OC6-HSL).
2016-09-21 | GSE78079 | GEO
Project description:Transcriptional profiling of Arabidopsis comparing 10 μM 3OC8-HSL-treated Arabidopsis wild-type Col-0 with control untreated Col-0. A transcriptomic analysis for Arabidopsis responses to bacterial quorum sensing molecule N-3oxo-octanoyl-homoserine lactone (3OC8-HSL).
2022-03-01 | GSE197485 | GEO