Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1108077 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Following serious accidents at the Chernobyl and Fukushima nuclear power plants in 1986 and 2011 respectively, local flora and fauna have been chronically exposed to environmental radiation for many years . However, little is known about the environmental effects of low doses of radiation on aquatic organisms. The present study assesses the effect of an environmentally relevant dose range of radiation (Control: 0, Low (L): 0.1, Medium (M): 1 and High (H): 10 mGy/day) of waterborne 32P on early life stages of the 3-spined stickleback, Gasterosteus aculeatus. Here we assess the global effects on gene regulation on the embryo development of fish suffering from differing levels of environmental radiation to identify significantly altered transcriptional networks as a result of sustained radiation exposure.
2020-02-04 | E-MTAB-7872 | biostudies-arrayexpress
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Project description:Base-pair level resolution of DNase susceptibility of the native chromatin state. These maps represent and are dependent upon the nature and the specificity of interaction of the DNA with the regulatory/modulatory proteins binding at specific loci in the genome; thus they represent the native chromatin state of the genome under investigation. The deep sequencing approach has been used to define the footprint landscape of the genome by identifying DNA motifs that interact with known or novel DNA-binding proteins 2 replicates of the erythroid cells were generated and profiled by Dnase I.
2014-03-05 | E-GEOD-55579 | biostudies-arrayexpress
Project description:We developed a multi recombinase engineering rationale, that combines oligonucleotide recombineering with the selective capacity of antibiotic resistance via transient insertion of selector plasmids. We tested this method in Mycoplasma pneumoniae, a bacterium with a very inefficient native recombination machinery. A wide variety of targeted genome modifications were carried out. We did whole genome sequencing of some clones to confirm that the engineering method is not mutagenic and ensure that genome modifications only occurred at the intended loci. Specifically we sequenced clones carrying 1 kb deletion at 4 different chromosomal locations (i.e., M129-GP35-PtetCre Δ1kbmpn088::lox scar, M129-GP35-PtetCre Δ1kbmpn256::lox scar, M129-GP35-PtetCre Δ1kbmpn440::lox scar, M129-GP35-PtetCre Δ1kbmpn583::lox scar), a clone carrying a 30 kb deletion (M129-GP35-PtetCre Δ30kbNE region::pLoxPuro) and a clone carrying a 5.5 kb deletion that was complemented with the two essential genes found in this area (M129-GP35 Δ5.5kbmpn633-mpn638::mpn636-637lox scar)
2022-04-06 | E-MTAB-11600 | biostudies-arrayexpress
Project description:Enhancer function is frequently investigated piecemeal using truncated reporter assays or single deletion analysis, thus it remains unclear to what extent their function is influenced by surrounding genomic context. Using our Big-IN technology for targeted integration of large DNAs, we analyzed the regulatory architecture of the Igf2/H19 locus, a paradigmatic model of enhancer selectivity. We assembled payloads containing a 157-kb functional Igf2/H19 locus and engineered mutations to genetically direct CTCF occupancy at the imprinting control region (ICR) that switches the target gene of the H19 enhancer cluster. Contrasting the activity of payloads delivered to the endogenous locus or to a safe harbor locus (Hprt) revealed that the functional elements comprising the Igf2/H19 locus are highly sensitive to their native context. Exchanging components of the Igf2/H19 locus with the well-studied Sox2 locus showed that the H19 enhancer cluster in particular functioned poorly out of context, and required its native surroundings to activate Sox2 expression. Conversely, the Sox2 locus control region (LCR) could activate both Igf2 and H19 outside its native context, but its activity was only partially modulated by CTCF occupancy at the ICR. Analysis of regulatory DNA actuation across different cell types revealed that, while the H19 enhancers are tightly coordinated within their native locus, the Sox2 LCR acts more independently. We show that these enhancer clusters typify broader classes of loci genome-wide. Our results show that unexpected dependencies may influence even the most studied functional elements, and our synthetic regulatory genomics approach permits large-scale manipulation of complete loci to investigate how locus architecture relates to function.
2024-03-13 | GSE241705 | GEO