Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7527110.fastq.gz | Fastqsanger.gz | |||
| SRR7527120.fastq.gz | Fastqsanger.gz | |||
| SRR7527130.fastq.gz | Fastqsanger.gz | |||
| SRR7527140.fastq.gz | Fastqsanger.gz | |||
| SRR7527111.fastq.gz | Fastqsanger.gz |
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Project description:As an adaptive response to the environment, oaks have evolved long taproots that increase their ability to acquire water. Taproots penetrate deeper layers of soil and send out absorptive roots that can then uptake water from these layers. This ability enables taproots to supply trees with water better. Unfortunately, the applied agrotechnical procedures during seedlings production in container nurseries damage the oaks' taproot, leading to changes in the root system structure. That changes may make the seedlings more responsive to chronic or periodic episodes of severe drought. In turn, seedlings that containers do not restrict roots growth, i.e. grown in rhizotron, may elongate because they are not subjected to air-pruning. Despite their significant role, little is known about the internal factors (specific genes) and their interactions that regulate taproot elongation in oaks seedlings. Thus, our study aimed to determine the potential genes regulating growth, cessation and physiology of taproot and check whether there is a difference in the expression level of the genes involved in root development. For this purpose, we performed next-generation sequencing (NGS), taproots and lateral roots, which allowed us to obtain a complete picture of the transcriptomes. Our findings of taproot growth regulations can be used to improve trees production in forest nurseries.
2022-11-23 | GSE181860 | GEO
Project description:Priming of plant defenses provides increased plant protection against herbivores and reduces the allocation costs of defense. Defense priming in woody plants remains obscure, in particular due to plant development traits such as the endogenous rhythmic growth displayed by oaks (Quercus robur). By using bioassays with oak microcuttings, and by combining transcriptomic and metabolomic analyses, we investigated how leaf herbivory by Lymantria dispar and root inoculation with the ectomycorrhizal fungus Piloderma croceum prime oak defenses. We further investigated how defense priming is modulated by rhythmic growth of the oaks. A first herbivory challenge in oak leaves primed newly grown leaves for an enhanced induction of jamonic acid (JA)-related direct defenses, or enhanced emission of volatiles, depending on the specific growth stage at which the plants where challenged. Root inoculation with Piloderma abolished the enhanced induction of JA-related defenses and volatile emission. Our results indicate that a first herbivore attack primes direct and indirect defenses of newly formed oak leaves, and that the specific display of defense priming is modulated by rhythmic growth. Our results further show that the priming memory in oaks can be transmitted to the next growth cycle even to the leaves of the new shoot unit.
2022-08-27 | GSE212157 | GEO
Project description:The utility of RADseq in an experimental setting is also demonstrated, based on our chasacterisation of an APOBEC mutation signature in an APOBEC3A transfected mouse cell line. 0D5 cells, derived from SSM3 cells, were co-transfected with a mixture containing pcDNA3.1 vectors expressing either APOBEC3A or APOBEC3B (kindly donated by Vincent Caval), pcDNA3.1 construct expressing deaminase null APOBEC3A linked to a uracil deglycosylase construct and a plasmid encoding mutant GFP and WT mCherry that is a reporter for APOBEC mutagenesis. Cells were grown, and gDNA extracted, prior to preparation of RADseq libraries using a PstI- MspI double-digest. Libraries underwent a Pippin Prep to select fragments in the size range of 220-520 bp (genomic sequence plus 148 bp of adapters). Single-end sequencing (1x101bp) was performed on an Illumina NovaSeq6000 utilizing v1.5 chemistry. Reads were aligned to mm10 using bwa mem and variants called using the GATK4 pipeline.
2023-06-30 | GSE234146 | GEO
Project description:Multiple individuals sampled from across all 7 species of the American live oaks, and outgroup samples from the white oaks, red oaks, and golden oaks. Raw sequence reads
| PRJNA277574 | ENA
Project description:To study transcriptional profiles in human CD34+ cell in EPO condition on day 7 and day 14. Experiment Overall Design: After obtaining informed consent, human CD34+ cells were isolated in high purity from the peripheral blood of normal human volunteers. The cells were cultured at a concentration of 104 -105 cells/mL in medium supplemented with 4 U/mL EPO (Amgen, Thousand Oaks, CA) as described previously.1 Cells were enumerated using an electronic cell counter (Coulter, Hialeah, FL). Adult and fetal hemoglobin was analysed by HPLC. RNA was extracted using QIAshredder and Rneasy Minikit.
2008-06-15 | E-GEOD-7874 | biostudies-arrayexpress