Arabidopsis thaliana strain:Columbia-0
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ABSTRACT:
PROVIDER: PRJNA194429 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This study investigates extent and functional significance of alternative splicing in Arabidopsis thaliana defense against the bacterial pathogen Pseudomonas syringae pv tomato (Pst). We have provided a detailed characterization of the Arabidopsis thaliana transcriptional response to Pseudomonas syringae infection in both susceptible and resistant hosts. We carried out two independent inoculation experiments (biological replicates) for each treatment. Col-0 is susceptible to virulent Pst DC3000 but has a functional RPS4 resistance gene effective against DC3000 expressing AvrRps4
2013-03-06 | E-MTAB-4450 | biostudies-arrayexpress
Project description:Pollen grains of Arabidopsis thaliana contain two haploid sperm cells enclosed in a haploid vegetative cell. Upon germination, the vegetative cell extrudes a pollen tube that carries the sperm to an ovule for fertilization. Knowing the identity, relative abundance, and splicing patterns of pollen transcripts will improve understanding of pollen and allow investigation of tissue-specific splicing in plants. Most Arabidopsis pollen transcriptome studies have used the ATH1 microarray, which does not assay splice variants and lacks specific probe sets for many genes. To investigate the pollen transcriptome, we performed high-throughput sequencing (RNA-Seq) of Arabidopsis pollen and seedlings for comparison. Gene expression was more diverse in seedling, and genes involved in cell wall biogenesis were highly expressed in pollen. RNA-Seq detected at least 4,172 protein coding genes expressed in pollen, including 289 assayed only by non-specific probe sets. Additional exons and previously unannotated 5’ and 3’ UTRs for pollen-expressed genes were revealed. We detected regions in the genome not previously annotated as expressed; 14 were tested and 12 confirmed by PCR. Gapped read alignments revealed 1,908 high-confidence new splicing events supported by 10 or more spliced read alignments. Alternative splicing patterns in pollen and seedling were highly correlated. For most alternatively spliced genes, the ratio of variants in pollen and seedling was similar, except for some encoding proteins involved in RNA splicing. This study highlights the robustness of splicing patterns in plants and the importance of on-going annotation and visualization of RNA-Seq data using interactive tools such as Integrated Genome Browser.
2013-05-25 | E-MTAB-4242 | biostudies-arrayexpress
Project description:During sexual reproduction in flowering plants, the two haploid sperm cells embedded within the cytoplasm of a growing pollen tube are carried to the embryo sac for double fertilization. Pollen development in flowering plants is a dynamic process that encompasses changes at transcriptome and epigenome level. While the transcriptome of pollen and sperm cells in Arabidopsis thaliana is well documented, previous analyses were mostly based on expression at gene level. In-depth transcriptome analysis, particularly the extent of alternative splicing at the resolution of sperm cell and vegetative nucleus was still lacking. Therefore, we performed RNA-seq analysis to generate a spliceome map of Arabidopsis sperm cells and vegetative nuclei isolated from mature pollen grains. Based on our de-novo transcriptome assembly we identified 58039 transcripts, including 9681 novel transcripts, of which 2091were expressed in sperm cells and 3600 in vegetative nuclei. Our data from sperm cell and vegetative nucleus identified 468 genes that were regulated both at gene and splicing level, with many having functions in mRNA splicing, chromatin modification, and protein localization. Moreover, a comparison with egg cell RNA-seq data uncovered sex-specific regulation of transcription and splicing factors. Our study provides novel insights into a gamete specific alternative splicing landscape at unprecedented resolution.
2022-12-14 | GSE201115 | GEO
Project description:This experiment has been annotated by TAIR (http://arabidopsis.org). In this experiment, different tissue preparations of wild type Columbia-0 Arabidopsis thaliana plants were hybridized and run on the ATH1 Affymetrix platform. Experimenter name = Chris Somerville Experimenter phone = 650-325-1521 ext203 Experimenter fax = 650-325-6857 Experimenter address = Plant Biology Experimenter address = Carnegie Institution Experimenter address = 260 Panama Street Experimenter address = Stanford Experimenter zip/postal_code = CA 94305-1297 Experimenter country = USA Keywords: organism_part_comparison_design;
2006-08-15 | GSE5533 | GEO
Project description:Transcriptome survey of alternative splicing-contributed proteome diversity in Arabidopsis thaliana
| PRJNA266359 | ENA
Project description:Sexual reproduction in angiosperms requires the production and delivery of two male gametes by a three-celled haploid male gametophyte. This demands synchronised gene expression in a short developmental window to ensure double fertilization and seed set. While transcriptomic changes in developing pollen are known for Arabidopsis, no studies have integrated RNA and proteomic data in this model. Further, the role of alternative splicing has not been fully addressed, yet post-transcriptional and post-translational regulation may have a key role in gene expression dynamics during microgametogenesis. We have refined and substantially updated global transcriptomic and proteomic changes in developing pollen for two Arabidopsis accessions. Despite the superiority of RNA-seq over microarray-based platforms, we demonstrate high reproducibility and comparability. We identify thousands of long non-coding RNAs as potential regulators of pollen development, hundreds of changes in alternative splicing and provide insight into mRNA translation rate and storage in developing pollen. Our analysis delivers an integrated perspective of gene expression dynamics in developing Arabidopsis pollen and a foundation for studying the role of alternative splicing in this model.
2022-11-01 | PXD033305 | Pride
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.
2011-09-24 | GSE32318 | GEO
Project description:Patterns of alternative splicing during heat stress in Arabidopsis thaliana and Boechera depauperata indicate complex and species-specific interactions between differential expression and alternative splicing.
2018-03-21 | GSE107820 | GEO
Project description:Through alternative splicing, most human genes express multiple isoforms that may have distinct or even antagonistic functions. To infer isoform regulation based on data from high-throughput sequencing of cDNA fragments (RNA-Seq), we have developed MISO, a computational model that estimates the expression level of alternatively spliced exons and mRNA isoforms and provides intuitive measures of confidence in these estimates. Incorporation of the length distribution of inserted cDNA fragments in paired-end RNA-Seq analysis in MISO enables dramatic improvements in estimation of alternative splicing levels relative to previous methods. We show that one lane of paired-end RNA-Seq data can provide far more information about splicing than two lanes of single-end data, depending critically on properties of the distribution of cDNA fragment lengths in the sequenced library. MISO also leads to an intuitive method to detect differentially regulated exons or isoforms. Application of this method implicates the RNA splicing factor hnRNP H in regulation of alternative cleavage and polyadenylation, a role that is supported by UV crosslinking/immunoprecipitation/high-throughput sequencing (CLIP-Seq) analysis. Together, our results provide a probabilistic framework for RNA-Seq analysis, derive functional insights into pre-mRNA processing, and yield guidelines for the optimal design of RNA-Seq experiments for studies of gene and isoform expression.
2010-11-07 | GSE23694 | GEO
Project description:Pig is an important animal model for human obesity and diseases. However, the complexity of the porcine transcriptome is not yet fully elucidated. Here we have used massively parallel high-throughput sequencing of cDNA (RNA-Seq) to generate a high-resolution map of the porcine transcriptome and miRNA in liver (LI), longissimus dorsi (LD) and abdominal fat (AF) from an F2 female full-sib pair with extreme phenotypes in growth and fat deposit. On the basis of the porcine annotated genes against the UCSC database, we identified 21,414 annotated genes in our RNA-Seq analysis and 48,045-122,931 novel transcript fragments, which could be clustered into 17,085-29,499 novel transcriptional active regions (nTARs). We found that ~18.8% of the detected known genes showed alternative splicing patterns, and alternative 3’ splicing was the most common type of alternative splicing events in pigs. We also detected that more than 22.7% of the known genes identified here were extended at their 5’ and/or 3’ end. We identified 2,796, 1,551 and 835 differentially expressed genes (DEGs), respectively, in AF, LI and LD between the two individuals. Examining the complexity of the pig transcriptome in three organs (liver, abdominal fat, longissimus dorsi muscle) from a female full-sib pair.
2011-01-12 | E-GEOD-26382 | biostudies-arrayexpress