Bin-Hard
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB21768 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The aim of this study was to determine the changes in gene expression of rice root tips when they came in to contact with a hard layer (60% wax layer). Three categories of root tips were sampled; tips before the hard layer, tips that had come into contact with the hard layer and root tips which had buckled after coming into contact with the hard layer. Two genotypes (Azucena and Bala) that vary in there ability to penetrate a hard layer were selected for a genotype comparison of gene expression at the hard layer. Keywords: Genotype comparison, root impedance response
2008-03-19 | GSE10857 | GEO
Project description:The aim of this study was to determine the changes in gene expression of rice root tips when they came in to contact with a hard layer (60% wax layer). Three categories of root tips were sampled; tips before the hard layer, tips that had come into contact with the hard layer and root tips which had buckled after coming into contact with the hard layer. Two genotypes (Azucena and Bala) that vary in there ability to penetrate a hard layer were selected for a genotype comparison of gene expression at the hard layer. Experiment Overall Design: A chamber with the internal dimensions of 10 x 5 x 25cm consisting of a glass back, Perspex front and aluminium spacers with an open bottom and top was set at an angle of 15o in a large sand filled tray and filled up to 19.5 cm with dry sand. The sand was watered with nutrient solution, the sand was levelled and then a 5mm thick 60% wax layer (prepared using a ratio of 3:2 (w/w) of pastillated paraffin wax / white soft wax) was poured on the sand. Once the wax layer had set, two small holes were placed at the back of the wax layer to allow water drainage and water exchange via capillary action. The chamber was then filled up with more dry sand, and then watered using nutrient solution. Nutrient solution was then added to the large tray which the chamber had been placed; this was regularly topped up and allowed the watering of the chamber by capillary action. Light was eliminated from the chambers using white (exterior face)/black (interior face) plastic sheeting. Experiment Overall Design: Azucena and Bala seeds were surface sterilized with 1% (v/w) sodium hypochlorate for 5 minutes, then rinsed thoroughly three times with water and then germinated on moist tissue paper for 48 hours at 37oC. A single germinated seed was then sown 1 cm below the surface of the sand in each chamber. Experiment Overall Design: The plants were grown in a controlled environment room with a 12 hour day and night, with a day temperature of 30oC and a night temperature of 24oC with 300 µmol m-2 s-1 PAR. After 24 days the chamber was dismantled and the root tips of 5 mm length were harvested from Azucena plants for subsequent RNA extractions from the three categories as follows; a) roots which were between 5-10 mm above the wax layer; b) roots at the wax layer; c) roots which had buckled at the wax layer and grown 7-10 mm after buckling. From Bala plants, only root tips at the layer were harvested. Experiment Overall Design: Each condition was indsependently replicated 3 times.
2008-11-06 | E-GEOD-10857 | biostudies-arrayexpress
Project description:The growth behavior of plant roots on tilted, hard agar surfaces is determined by many basic cellular processes, including microtubule dynamics and cell wall expansion. Among Arabidopsis thaliana accessions there is natural variation for these behaviors, including one known as skewing or slanting. The root skewing pattern on hard, tilted agar surfaces may be a clue to adaptations of an accession to its environment. Here, we compare expression profiles of two accessions with diverse skewing behavior grown on the wave assay, which consists of seedlings growing two days vertically and 3 days tilted on hard agar plates. Cvi has a strong skew on tilted, hard agar sufaces, and Ler-2 has a weaker one. We also include a near isogenic line, 170G-55-16 a.k.a HGI2.1, that is mostly Ler-2 in background but has a segment of Cvi introgressed into chromosome 2. This line has an intermediate skew between its two parents. 3 biological replicates of each of 3 genotypes (Cvi, Ler-2, and 170G-55-16/HGI2.1) were subjected to the wave assay. After the assay, approximately 600 root tips from each biological replicate were pooled for RNA extraction and hybridization on the Affymetrix ATH1 microarray.
2011-03-31 | E-GEOD-28275 | biostudies-arrayexpress
Project description:The growth behavior of plant roots on tilted, hard agar surfaces is determined by many basic cellular processes, including microtubule dynamics and cell wall expansion. Among Arabidopsis thaliana accessions there is natural variation for these behaviors, including one known as skewing or slanting. The root skewing pattern on hard, tilted agar surfaces may be a clue to adaptations of an accession to its environment. Here, we compare expression profiles of two accessions with diverse skewing behavior grown on the wave assay, which consists of seedlings growing two days vertically and 3 days tilted on hard agar plates. Cvi has a strong skew on tilted, hard agar sufaces, and Ler-2 has a weaker one. We also include a near isogenic line, 170G-55-16 a.k.a HGI2.1, that is mostly Ler-2 in background but has a segment of Cvi introgressed into chromosome 2. This line has an intermediate skew between its two parents.
2011-03-31 | GSE28275 | GEO
Project description:uncultured and hard to cultured bacteria Genome sequencing
| PRJNA793610 | ENA
Project description:Identification of RBPs proteome in HEK293 cells and adult mouse brain and kidney which were not treated with UV light before isolation with HARD beads.
2024-08-26 | PXD053382 | Pride
Project description:next generation RNAseq data from human hepatic sinusoidal endothelial cells and primary mouse sinusoidal endothelial cells plated on soft vs hard gels reveals the chemokine CXCL1 being among the top up-regulated genes from granulocyte and agranulocyte migration/diapedesis pathway.
2022-03-31 | GSE198462 | GEO
Project description:Whole-genome sequencing is an important way to understand the genetic information, gene function, biological characteristics, and living mechanisms of organisms. There is no difficulty to have mega-level genomes sequenced at present. However, we encountered a hard-to-sequence genome of Pseudomonas aeruginosa phage PaP1. The shotgun sequencing method failed to dissect this genome. After insisting for 10 years and going over 3 generations of sequencing techniques, we successfully dissected the PaP1 genome with 91,715 bp in length. Single-molecule sequencing revealed that this genome contains lots of modified bases, including 51 N6-methyladenines (m6A) and 152 N4-methylcytosines (m4C). At the same time, further investigations revealed a novel immune mechanism of bacteria, by which the host bacteria can recognize and repel the modified bases containing inserts in large scale, and this led to the failure of the shotgun method in PaP1 genome sequencing. Strategy of resolving this problem is use of non-library dependent sequencing techniques or use of the nfi- mutant of E. coli DH5M-NM-1 as the host bacteria to construct the shotgun library. In conclusion, we unlock the mystery of phage PaP1 genome hard to be sequenced, and discover a new mechanism of bacterial immunity in present study. Methylation profiling of Pseudomonas aeruginosa phage PaP1 using kinetic data generated by single-molecule, real-time (SMRT) sequencing on the PacBio RS.
2013-08-22 | E-GEOD-50100 | biostudies-arrayexpress
Project description:16S rRNA, metagenomic, and metatranscriptomic analysis of the human hard palate following death
| PRJEB44678 | ENA
Project description:To help malaria parasites survive unpredictable host immune responses, it is known that genes for surface proteins express stochastically in Plasmodium falciparum. Here, we demonstrate that gene expression for intracellular metabolic functions may be preordained and insensitive to specific metabolic perturbations. In a tightly-controlled, large microarray study involving over 100 hybridizations to isogenic drug-sensitive and drug-resistant parasites, the lethal antifolate WR99210 failed to over-produce RNA for the biochemically and genetically proven target dihydrofolate reductase-thymidylate synthase (DHFR-TS). Beyond the target, this transcriptional obstinacy carried over to the rest of the parasite genome, including genes for target pathways of folate and pyrimidine metabolism. Even 12 hours after commitment to death, the transcriptome remained faithful to evolutionarily entrained paths. A system-wide transcriptional disregard for metabolic perturbations in malaria parasites may contribute to selective vulnerabilities of the parasite to lethal antimetabolites. While large protective metabolic responses were not detected, DNA microarrays helped capture small, but reproducible drug-dependent perturbations within hours of drug exposure. In addition, in Plasmodium cells that had adapted to long-term drug exposure, DNA microarrays revealed new, large genome-wide transcriptional adjustments in the hard-wired transcriptional program itself. Keywords: Plasmodium falciparum treated with pyrimethamine RNA from pyrimethamine-treated parasite vs RNA from untreated control, Pyr-sensitive TM4/8.2 strain, pyrimethamine concentration at IC50 and treated for 0 h and 24 h, microarray data were obtained from at least four hybridizations using RNA from at lease two independent parasite cultures
2010-05-16 | E-GEOD-9853 | biostudies-arrayexpress