Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA143725 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:gnp07_regeneome_microdissectionbias - microdissection vs no microdissection - Transcriptome bias induce by protocols used in microdissection - To compare RNA from flowers and RNA from microdissected flowers to know bias induce by microdissection (dissection from all tissues were collected to have a representation of entire flower)
2012-06-01 | GSE30265 | GEO
Project description:gnp07_regeneome_microdissectionbias - microdissection vs no microdissection - Transcriptome bias induce by protocols used in microdissection - To compare RNA from flowers and RNA from microdissected flowers to know bias induce by microdissection (dissection from all tissues were collected to have a representation of entire flower) 2 dye-swap - treated vs untreated comparison
2012-05-31 | E-GEOD-30265 | biostudies-arrayexpress
Project description:Laser capture microdissection (LCM) provides a useful method for isolating specific cells or tissues from biological samples. Here, we adapted microdissection protocols to allow high-resolution transcript analysis of different tissues from developing Arabidopsis seed. However, to obtain enough RNA for microarray analyses it was necessary to amplify the RNA. Microarray analyses, using endosperm derived RNA amplified by two-round IVT, reproducibly identified endosperm enriched marker genes. Keywords: LCM Endosperm Arabidopsis
2007-04-02 | GSE6663 | GEO
Project description:We report the application of laser capture microdissection (LCM) for high resolution transcriptome profiling of the second internode of the Arabidopsis thaliana inflorescence stem. In this series, we used LCM to determine and compare the transcriptome profiles of the phloem cap, the pith, and the remaining vascular bundle area.
2020-02-10 | GSE142033 | GEO
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:Comparison of IND induced vs. mock treated seedlings: Transcriptome profiling upon induction of the transcription factor IND
| PRJNA140653 | ENA
Project description:Arabidopsis thaliana vs P. megaterium - Transcriptome
| PRJNA816506 | ENA
Project description:Microdissection: Transdifferentiation of Root Apical Meristem to Shoot Apical Meristem
| PRJNA143755 | ENA
Project description:Small RNA-seq is increasingly being used for profiling of small RNAs. Quantitative characteristics of long RNA-seq have been extensively described, but small RNA-seq involves fundamentally different methods for library preparation, with distinct protocols and technical variations that have not been fully and systematically studied. Using common sets of reference samples, we evaluated the accuracy, reproducibility and bias of small RNA-seq library preparation for five distinct protocols and across nine different laboratories. As part of this larger study, we assessed sequencing bias and reproducibility using an equimolar pool of 1,152 small RNA sequences ranging from 15-90 nt, and primarily comprised of annotated human microRNAs. We observed extensive protocol-specific and sequence-specific bias that was largely mitigated in protocols employing sequencing adapters with randomized end-nucleotides. We find that sequencing bias is highly reproducible across labs using the same library preparation technologies, and use the data to calculate inter-protocol bias correction factors. These results provide strong evidence for the feasibility of reproducible cross-laboratory small RNA-seq studies, even those involving analysis of data generated using different protocols.
2018-07-09 | GSE94584 | GEO
Project description:Arabidopsis dark-induced senescence: wild type (Col-0) vs. pif quadruple (pif1pif3pif4pif5) mutant
| PRJNA229514 | ENA