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81 results for “Arabidopsis accessions”
Gene expression ATLAS of Arabidopsis thaliana (accession Columbia) across its lifecycle
<p><strong>Abstract: </strong>Arabidopsis thaliana (accession- Columbia) is an important model plant. RNA-Seq based study of 36 gene expression libraries was carried out to explore transcriptional programs operating in different plant parts (seedling, rosette, root, inflorescence, flower, fruit silique, and seed) and developmental stages (2-leaf stage, 6-leaf stage, 12-leaf stage, senescence stage, dry mature and imbibed seed stage). For each tissue type and developmental stage, three individual plants were used as biological replicates.</p> <div><strong><span>Organism part: </span></strong><span>inflorescence, whole plant, seed, root, silique fruit, flower, rosette</span></div> <div> </div> <div><span><strong>Developmental stage:</strong> </span><span>LP.02 two leaves visible stage, IL.00 inflorescence just visible stage, fruit size 30 to 50% stage, LP.12 twelve leaves visible stage, root development stage, fruit size 70% to final stage, LP.06 six leaves visible stage, dry seed stage, flowering stage, seed imbibition stage, sporophyte senescent stage, inflorescence development stage</span></div> <div> </div> <div> <div><strong><span>Organism: </span></strong><span>Arabidopsis thaliana</span></div> <div> </div> <div><span><strong>Ecotype:</strong> </span><span>Col-0</span></div> <div> </div> <div><strong><span>Genotype: </span></strong><span>wild type genotype</span></div> <div> </div> <div><span><strong>Age:</strong> Samples are from </span><span>20-day, 49-day, 39-day, 15-day, 21-day, 9-day, 22-day, 55-day, 26-day, 45-day</span></div> <div> </div> <div><span><strong><span>Experimental Designs: </span></strong><span>growth chamber study<a title="" href="https://www.ebi.ac.uk/ols4/ontologies/efo/terms?iri=http://purl.obolibrary.org/obo/EO_0007269" target="_blank" rel="noopener"> EFO</a></span>, <span>development or differentiation design<a title="" href="https://www.ebi.ac.uk/ols4/ontologies/efo/terms?iri=http://www.ebi.ac.uk/efo/EFO_0001746" target="_blank" rel="noopener"> EFO</a></span>, <span>organism part comparison design<a title="" href="https://www.ebi.ac.uk/ols4/ontologies/efo/terms?iri=http://www.ebi.ac.uk/efo/EFO_0001750" target="_blank" rel="noopener"> EFO</a></span></span></div> <div> </div> <div><span>For more description of the data and sample types see the file <a href="../api/records/11133989/draft/files/PRJEB24664_Sample_descriptors.xlsx/content" target="_blank" rel="noopener noreferrer">PRJEB24664_Sample_descriptors.xlsx or visit </a> or visit <a href="https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-6422/sdrf">https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-6422/sdrf</a></span></div> <div> </div> <div><span>Original data was submitted from </span></div> <div> <ul> <li><span>EMBL-EBI ArraExpress: <a href="https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-6422">https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-6422</a></span></li> <li><span>NCBI SRA: <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJEB24664">https://www.ncbi.nlm.nih.gov/bioproject/PRJEB24664</a></span></li> </ul> <p><strong><span>Protocol description:</span></strong></p> <table> <tbody><tr> <th>Name</th> <th>Type</th> <th>Description</th> <th>Hardware</th> </tr> </tbody><tbody> <tr> <td>P-MTAB-71349</td> <td><span>growth protocol<a title="" href="https://www.ebi.ac.uk/ols4/ontologies/efo/terms?iri=http://www.ebi.ac.uk/efo/EFO_0003789" target="_blank" rel="noopener"> EFO</a></span></td> <td>Seeds were planted in pots containing commercial potting mix with fertilizers. Pots were covered with clear perforated plastic wrap and kept at 4 degrees celsius for 3 days to break the dormancy. After 3 days plants were transferred to the Intellus Ultra growth chamber (Percival Scientific, IA, USA) which was set to temperature 22-23 degrees celsius, light intensity 120-150 micromol/m2sec under the cycle of 16h light and 8h dark. Soil was kept moist by gently spraying with water every 72 hours to maintain humidity to 50-60%. Sampling time point is given in days after germination.</td> <td> </td> </tr> <tr> <td>P-MTAB-71350</td> <td><span>nucleic acid extraction protocol<a title="" href="https://www.ebi.ac.uk/ols4/ontologies/efo/terms?iri=http://www.ebi.ac.uk/efo/EFO_0002944" target="_blank" rel="noopener"> EFO</a></span></td> <td>Total RNA from frozen samples was extracted as a method described in Filichkin et al., 2010. Total RNA was used to isolate large RNA as per manufacturer's protocol for miRNeasy Mini kits (Qiagen Inc., USA), and RNase-free DNase (Life Technologies Inc., USA).</td> <td> </td> </tr> <tr> <td>P-MTAB-71351</td> <td><span>nucleic acid library construction protocol<a title="" href="https://www.ebi.ac.uk/ols4/ontologies/efo/terms?iri=http://www.ebi.ac.uk/efo/EFO_0004184" target="_blank" rel="noopener"> EFO</a></span></td> <td>True-Seq kit (Illumina Inc.) was used to prepare RNA-seq libraries, according to the manufacturer’s protocol.</td> <td> </td> </tr> <tr> <td>P-MTAB-71352</td> <td><span>nucleic acid sequencing protocol<a title="" href="https://www.ebi.ac.uk/ols4/ontologies/efo/terms?iri=http://www.ebi.ac.uk/efo/EFO_0004170" target="_blank" rel="noopener"> EFO</a></span></td> <td>101bp paired-end sequencing of mRNA was performed by using the standard protocols on Illumina HiSeq 3000.</td> <td>Illumina HiSeq 3000</td> </tr> </tbody> </table> </div> </div>
Salt stress responses in 9 Arabidopsis accessions
<p>The dataset is used as an example dataset for the MVApp, previously published the results in Awlia et al., 2016 Frontiers in Plant Science.</p>
GWAS output for early salt stress responses in Arabidopsis thaliana accessions
<p>The output of the Genome Wide Association Study for early responses to salt stress in Arabidopsis accessions. The "_gwas2029.rda" files contain associations found for each trait using single models, where the first part of file name describes the phenotype (e.g. ROUNDNESS), the first number describes the day after stress application, the subsequent C/S indicated whether the association was performed with the trait scored at Control / Salt Stress conditions respectively. The "mtmm_final.rda" files contain the associations found between two traits, indicated as above in the first part of the file name. </p>
Scaling the fitness effects of mutations with respect to differentially adapted Arabidopsis thaliana accessions under natural conditions
Open the record for dataset details and reuse information.
Supplementary File to "Both binding strength and evolutionary accessibility affect the population frequency of transcription factor binding sequences in Arabidopsis thaliana" (Genome Biology and Evolution)
<p>This data is supplementary file 1 of the following publication:</p> <p>Schweizer G, Wagner A. "Both binding strength and evolutionary accessibility affect the population frequency of transcription factor binding sequences in Arabidopsis thaliana" (Genome Biology and Evolution)</p>
Transcriptional and splicing response of two Arabidopsis thaliana natural accessions to ABA-mediated stress.
GEO Series GSE228303. Arabidopsis thaliana. 12 samples. Type: Expression profiling by high throughput sequencing.
Chromatin changes in lateral organ founder cells of Arabidopsis thaliana detected by assay for transposase-accessible chromatin sequencing (ATAC-seq)
GEO Series GSE116972. Arabidopsis thaliana. 8 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Genomic DNA hybridizations of Col-0, Tsu-1, and Kas-1 accessions of Arabidopsis thaliana
GEO Series GSE20340. Arabidopsis thaliana. 18 samples. Type: Genome variation profiling by array.
Natural variation of H3K27me3 modification between two Arabidopsis accessions and its inheritance in hybrid
GEO Series GSE62615. Arabidopsis thaliana. 18 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Global transcriptome of the fungal pathogen Sclerotinia sclerotiorum (strain 1980) during the colonization of 23 Accessions of Arabidopsis thaliana
GEO Series GSE248079. Arabidopsis thaliana. 149 samples. Type: Expression profiling by high throughput sequencing.
H2AK121ub in Arabidopsis favors a less accessible chromatin state at transcriptional regulation hotspots [ATAC-seq]
GEO Series GSE154695. Arabidopsis thaliana. 12 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Spider mite preliminary feeding experiment with mites reared on bean and two Arabidopsis thaliana accessions
GEO Series GSE31525. Tetranychus urticae. 6 samples. Type: Expression profiling by high throughput sequencing.
H2AK121ub in Arabidopsis favors a less accessible chromatin state at transcriptional regulation hotspots [RNA-seq]
GEO Series GSE154697. Arabidopsis thaliana. 12 samples. Type: Expression profiling by high throughput sequencing.
Genomic dna hybridizations of 10 Spring annual accessions of Arabidopsis thaliana
GEO Series GSE27549. Arabidopsis thaliana. 30 samples. Type: Other.
Three classes of Arabidopsis SWI/SNF chromatin remodeling complexes differentially regulate development by affecting chromatin accessibility [RNA-Seq]
GEO Series GSE193095. Arabidopsis thaliana. 36 samples. Type: Expression profiling by high throughput sequencing.
Genomic dna hybridizations of 8 winter annual accessions of Arabidopsis thaliana
GEO Series GSE27551. Arabidopsis thaliana. 24 samples. Type: Other.
Antagonistic action of PHYA and PHYB is involved in FR-dependent leaf senescence in Arabidopsis accessions
GEO Series GSE103946. Arabidopsis thaliana. 12 samples. Type: Expression profiling by array.
Cold priming and triggering of Arabidopsis accessions
GEO Series GSE112225. Arabidopsis thaliana. 36 samples. Type: Expression profiling by high throughput sequencing.
Single cell level analysis of the Arabidopsis root transcriptome and chromatin accessibility
GEO Series GSE155304. Arabidopsis thaliana. 9 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Cadmium (Cd) induced expression changes in the Arabidopsis thaliana accessions Col-0 and Bur-0
GEO Series GSE94314. Arabidopsis thaliana. 8 samples. Type: Expression profiling by array.
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