Ontology highlight
ABSTRACT:
PROVIDER: PRJEB12813 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:phenanthrene anaerobic biodegradation community Raw sequence reads
| PRJNA416026 | ENA
Project description:au10-04_phytoremediation; impact of sucrose on the tolerance of phenanthrene Effect of phenanthrene and sucrose - We test 3 conditions plants non-treated (C or t0), plants treated with phenanthrene (P) and plants tread with phenanthrene and sucrose (S). The plants were grown on MS/2 media for 17 days and then transferred on the corresponding condition. We took a sample of 30 plants at different times (0, 30 min, 2h, 4h, 8h and 24h).
2013-06-28 | GSE48181 | GEO
Project description:Studying eight enzymes involved in the degradation of polycyclic aromatic hydrocarbons from the model strain Sphingomonas paucimobilis sp. EPA505 using a designed microarray of 8,048 probes. During the biodegradation kinetics with phenanthrene, fluoranthene or a mix of both pollutants, we identified the targeted set of genes induced by these pollutants, compared to basal expression detected with glucose. Hybridizing total DNA extracted from S3, we show the efficiency of our probe design to study a complex environment. Despite the relative small size of our probes (23-mers), their sensitivity is reliable as we can detect the presence of genes in this complex mixture. Obtained results are further described in Sébastien Terrat, Eric Peyretaillade, Olivier Gonçalves, Eric Dugat-Bony, Fabrice Gravelat, and Pierre Peyret. 2010 - Studying the ‘Unkown’ with Metabolic Design, a new probe design software for explorative functional microarrays development. Nucleic Acids Research (submited).
2010-10-01 | GSE21402 | GEO
Project description:Studying eight enzymes involved in the degradation of polycyclic aromatic hydrocarbons from the model strain Sphingomonas paucimobilis sp. EPA505 using a designed microarray of 8,048 probes. During the biodegradation kinetics with phenanthrene, fluoranthene or a mix of both pollutants, we identified the targeted set of genes induced by these pollutants, compared to basal expression detected with glucose. Hybridizing total DNA extracted from S3, we show the efficiency of our probe design to study a complex environment. Despite the relative small size of our probes (23-mers), their sensitivity is reliable as we can detect the presence of genes in this complex mixture. Obtained results are further described in Sébastien Terrat, Eric Peyretaillade, Olivier Gonçalves, Eric Dugat-Bony, Fabrice Gravelat, and Pierre Peyret. 2010 - Studying the ‘Unkown’ with Metabolic Design, a new probe design software for explorative functional microarrays development. Nucleic Acids Research (submited). A 17 chip study was realized using total RNA recovered from separate cultures of Sphingomonas paucimobilis sp. EPA505 with phenanthrene, fluoranthene or a mix of these both pollutants as sole carbon and energy source. A negative kinetic expermient was realized with glucose as sole carbon and energy source. Each chip measures the expression level of 8 genes from Sphingomonas paucimobilis sp. EPA505 with 23-mer probes (a total of 8,048 probes) using a new design approach. We also assess metabolic capacities of microbial communities in an aromatic hydrocarbons contaminated soil named S3. Each probe was spotted in triplicate, and a total of 8,863 random probes was used to determine the background noise.
2010-10-01 | E-GEOD-21402 | biostudies-arrayexpress
Project description:FHMs were exposed to three concentrations of phenanthrene (average measured 29, 287, 1006 ng/L) and fish were sampled after 48hr. There were 20 samples analyzed 5) control liver tissues 5) 29 ng/L phenanthrene exposed liver tissues 5) 287 ng/L phenanthrene exposed liver tissues 5)1006 ng/L phenanthrene exposed liver tissues. There was a total of 20 microarrays processed. In this study, gene expression to a 'dose-response' was investigated after in vivo exposure of fish to phenanthrene.
2013-08-27 | E-GEOD-44839 | biostudies-arrayexpress
Project description:au10-04_phytoremediation; impact of sucrose on the tolerance of phenanthrene Effect of phenanthrene and sucrose - We test 3 conditions plants non-treated (C or t0), plants treated with phenanthrene (P) and plants tread with phenanthrene and sucrose (S). The plants were grown on MS/2 media for 17 days and then transferred on the corresponding condition. We took a sample of 30 plants at different times (0, 30 min, 2h, 4h, 8h and 24h). 22 dye-switch - treated vs untreated comparison
2013-06-28 | E-GEOD-48181 | biostudies-arrayexpress
Project description:In this study, female fathead minnows (FHM) were exposed to waterbourne phenanthrene (201.8 µg/L) or a solvent control for 7 weeks. Fish were tested for behavioral differences in a modified behavioral test prior to euthansia. Hypothalami were excised and stored for microarray analyses. Fish were exposed to one dose of phenanthrene. Female and male hypothalami were analyzed (n=8 per group, control vs. treatment); liver was also analyzed. N=7 control and 8 phenanthrene. In this study, a subchronic exposure to phenanthrene was investigated
2016-08-25 | E-GEOD-85993 | biostudies-arrayexpress
Project description:It has been reported that polycyclic aromatic hydrocarbons (PAHs) act on calcified tissue and suppress osteoblastic activity in the scales of teleost fish. In the present study, the differentially-expressed genes in the zebrafish scales treated with benzo[c]phenanthrene (BcP), a kind of PAH, or its metabolite 3-hydroxybenzo[c]phenanthrene (3-OHBcP) were investigated using GeneChip® oligonucleotide microarrays.
2020-11-12 | GSE161253 | GEO
Project description:Synthetic lethality (SL) has shown great promise for the discovery of novel targets in cancer. CRISPR double-knockout (CDKO) technologies can only screen several hundred genes and their combinations, but not genome-wide. Therefore, good SL prediction models are highly needed for genes and gene pairs selection in CDKO experiments. In this paper, we develop a novel multi-layer encoder for individual sample-specific SL prediction (MLEC-iSL). Unlike existing SL prediction models, MLEC-iSL is built to predict SL connectivity first. Because SL connectivity is scalable from existing genes in the training data to new genes in validation data, we hypothesize MLEC-iSL has better SL prediction performance. MLEC-iSL has three encoders, namely gene encoder, graph encoder, and transformer encoder. MLEC-iSL has high performance in K562 (AUPR, 0.73; AUC, 0.72) and Jurkat (AUPR, 0.73; AUC, 0.71) cells while no existing methods exceed 0.62 AUPR and AUC in either cell. MLEC-iSL guided CDKO experiment in 22Rv1 cells yielded a 46.8% SL ratio amongst its selected gene pairs. Six of top ten SL connectivity hub genes are validated in 22Rv1 cells. It reveals SL gene pairs and dependency between apoptosis and mitosis cell death pathways.
2024-09-13 | GSE262953 | GEO