Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13069519_1.fastq.gz | Fastqsanger.gz | |||
| SRR13069519_2.fastq.gz | Fastqsanger.gz | |||
| SRR13069520_1.fastq.gz | Fastqsanger.gz | |||
| SRR13069520_2.fastq.gz | Fastqsanger.gz | |||
| SRR13069521_1.fastq.gz | Fastqsanger.gz |
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Project description:Affymetrix single nucleotide polymorphism (SNP) array data were used to study genes that underlie human adaptation to climatic stress, with a focus on genetic changes that lead to long-term cold tolerance. Siberia provides the best opportunity to investigate the genetic mechanisms of cold resistance because of the long-term ancestry of indigenous populations in some of the coldest climates on earth. While much of northern Europe was under ice throughout the last glacial period, Siberia remained relatively ice free, and archaeological evidence suggests that people inhabited this region for more than 40,000 years. We gathered SNP data from ~200 individuals from 15 indigenous Siberian populations that inhabit a range of arctic climates and compare their patterns of genetic variation with those from other world populations from warmer climates.Particular attention is paid to regions containing genes that have been previously implicated in cold adaptation or that function in known pathways connected to energy metabolism or cold adapted phenotypes (e.g., those involved in basal metabolic rate and brown adipose tissue function).
2016-09-15 | GSE73996 | GEO
Project description:This experiment has been annotated by TAIR (http://arabidopsis.org). We examined transcript profiles triggered by three different arabidopsis R genes that recognize distinct Peronospora parasitica isolates. Experimenter name = Thomas Eulgem Experimenter phone = 43 1 4277 54622 Experimenter fax = 43 1 4277 9546 Experimenter department = Institute of Microbiology and Genetics Experimenter address = Institute of Microbiology and Genetics Experimenter address = Dr. Bohrgasse 9 Experimenter address = Vienna Experimenter zip/postal_code = A-1030 Experimenter country = Austria Keywords: strain_or_line_design
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Project description:Semiconductor sequencing of alkaline degraded total RNA from Pyrococcus furiosus annotated for ”The 23S ribosomal RNA from Pyrococcus furiosus is circularly permuted” published in Frontiers in Microbiology”
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Project description:Background: The halophyte Mesembryanthemum crystallinum (ice plant) is a model for studying salt tolerance. The morphology, physiology, metabolism, and gene expression of ice plant have been studied for over 40 years. Although the complete genome sequence has not been revealed, large-scale analyses of gene expression profiling have drawn an outline of salt tolerance in ice plant. Despite ample information in the transcriptome, miRNA information has not been documented. Results: We examined responses to a sudden increase in salinity in ice plant seedlings. Using a fluorescent dye to detect Na+, we found that ice plant roots respond to an increased flux of Na+ by either secreting or storing Na+ in specialized cells. High-throughput sequencing was used to identify small RNA profiles in three-day-old seedlings treated with or without 200 mM NaCl. Totally 132 conserved miRNAs belonging to 22 families were found. The hairpin precursor of 19 conserved mcr-miRNAs and 12 novel mcr-miRNAs were identified. Target genes are involved in a broad range of biological processes: transcription factors that regulate growth and development, enzymes that catalyze miRNA biogenesis for the most conserved mcr-miRNA, and proteins that are involved in ion homeostasis and drought-stress responses for some novel mcr-miRNAs. After 6 h of salt stress, the expressions of most mcr-miRNAs were down-regulated, whereas the expressions of their corresponding target genes were up-regulated. Analyses of the functions of target genes revealed that cellular processes, including growth and development, metabolism, and ion transport activity were up-regulated in roots under salt stress. Conclusions: Analyses of small RNA profile of ice plant seedlings identified many conserved miRNA families and several novel miRNAs. The expression of ten conserved miRNAs and three novel miRNAs were reciprocally correlated to predicted targets hourly after salt stress. Based on the expression pattern of miRNA and target genes in combination with the observation of Na+ distribution, we suggest that ice plant roots respond effectively to increased salinity by using Na+ as an osmoticum for cell expansion and guard cell opening. Excessive Na+ could either be secreted through root epidermis or stored in specialized leaf epidermal cells. These responses are partially regulated at the miRNA-mediated post-transcriptional level.
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