Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of transcriptome changes associated with toxic effects of methanolic coal dust extract on fish early life stage by RNASeq

ABSTRACT: We report the transcriptional changes associated with toxic effects of methanolic coal dust extract on normal zebrafish development. Early exposure of wild type embryos at 4 hpf to coal dust extract led to 3 groups of malformed phenotypes - tail deformity (P1), deformed yolk (P2) and smaller embryos with extruded yolks (P3). RNAseq of each phenotypic group revealed changes in genes involved in xenobiotic metabolism, intermediate filament composition, oxidation-reduction processes, calcium ion binding, focal adhesion and the ECM-receptor interaction pathway.

ORGANISM(S): Danio rerio

PROVIDER: GSE128900 | GEO | 2020/04/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Embryonic exposure to an aqueous coal dust extract results in gene expression alterations associated with development and function of connective tissue and the hematological system in zebrafish

Project description:Coal is a major energy source that generates diverse environmental impacts through its production, primarily by the release of coal dust particles. An aqueous coal dust extract was obtained from a mineral sample taken from one of the largest coal mines in Colombia (La Loma, Cesar), trace elements by ICP/MS were measured, and its toxicity evaluated using the zebrafish (Danio rerio) vertebrate model. In this study, zebrafish embryos were exposed to different concentrations of aqueous coal extract (0, 0.1, 1, 10, 100 and 1000 parts per million (ppm; μg/mL) to establish acute toxicity, as well as morphological and transcriptome alterations. Trace elements within the coal extract yielding the highest concentrations included Sr, Zn, Ba, As, Cu, Se, Li, Ni, Sb, Rb, Co, and Cr. In addition, Cd and Pb were found in lower concentrations. No significant difference in mortality was observed with survival near 90% in all treatments. A significant decrease in rate of hatching was observed in the 0.1 and 1000 ppm treatment groups at 72 hpf. Furthermore, no significant differences in total body length, head length, or head diameter was observed in any of the treatment groups. Transcriptomic results of zebrafish larvae revealed alterations in 77, 61, and 1,376 genes in the 1, 10, and 100 ppm treatments, respectively. Gene ontology analysis revealed gene alterations associated with hematological system development and function, tissue morphology and development, connective tissue development and function, and embryonic development. Overall, these findings are the first to identify gene expression alterations in response to a developmental aqueous coal dust residue from coal mining.

2017-11-30 | GSE94997 | GEO

Buccal epithelial gene expression in smoky and smokeless coal users

Project description:Exposure to indoor air pollution generated from the combustion of solid fuels is a major risk factor for a spectrum of cardiovascular and respiratory diseases, including lung cancer. In Chinaâs rural counties of Xuanwei and Fuyuan, lung cancer rates are among the highest in the country. While the elevated disease risk in this population has been linked to the widespread usage of bituminous (smoky) coal as compared to anthracite (smokeless) coal, the underlying physiologic mechanism that smoky coal induces in comparison to other fuel types is unclear. As we have previously used airway gene-expression profiling to gain molecular insights into the physiologic effects of cigarette smoke, here we profiled the buccal epithelium of residents exposed to the burning of smoky and smokeless coal in order to understand the physiologic effects of solid fuels. Buccal mucosa scrapings were collected from healthy, non-smoking female residents of Xuanwei and Fuyuan counties who burn coal indoors. RNA was isolated and hybridized onto Affymetrix Human gene 1.0 ST GeneChips, capturing the gene-expression response of (n=26) smoky coal users and (n=9) smokeless coal users. 24-hour indoor personal exposure levels (PM2.5, Polycyclic Aromatic Hydrocarbons) were also captured during this sampling period.

2015-11-02 | E-GEOD-64277 | biostudies-arrayexpress

LncRNA-ENST00000501520 promotes the proliferation of malignant-transformed BEAS-2B cells induced with coal tar pitch mediated by target genes

Project description:Coal tar pitch (CTP) is a byproduct of cooking process which is used in making coatings, corrosion protection materials, and electrode. and it has been verified that Coal tar pitch extract (CTPE) constitutes polycyclic aromatic hydrocarbons (PAHs) (87.91%) and monocyclic aromatic hydrocarbons, heterocyclic compounds and alkenes (the remaining total is 12.09%) using gas chromatography/mass spectrometry (GC/MS). In this study, we determine the lncRNA expression profile in CTPE group and control group. The key lncRNAs were screen out by using microarray analysis in defferent group.

2022-07-08 | GSE134069 | GEO

Transcriptional changes in mouse lungs induced by house dust mite

Project description:We examined the transcriptional changes in mouse lungs induced by house dust mite (HDM), D.f. extract and the isolated RNA was utilized for RNA-seq analysis. Our results demonstrated that HDM strongly triggered an inflammatory response.

2019-08-01 | GSE102211 | GEO

Buccal epithelial gene expression in smoky and smokeless coal users

2015-11-02 | GSE64277 | GEO

Gene expression patterns in house dust mite stimulated CD4 T cells and IgG:IgE ratios

Project description:PBMC from house dust mite (HDM) sensitized atopics were cultured in the presence or absence of HDM extract for 24 hours. At the termination of the cultures, CD4 T cells were isolated using immunomagnetic separation. Gene expression was profiled on microarrays.

2015-11-03 | GSE70760 | GEO

Gene expression profiling of the effects of organic dust in lung epithelial and THP-1 cells reveals inductive effects on inflammatory mediators [391 expt: A549 vs BEAS 2B]

Project description:The goal of the study was to characterize gene expression profiles of lung epithelial and THP-1 monocytic cells influenzed by exposure to poultry dust extract. Gene expression profiles were determined by DNA microarrayanalysis using Illumina Human HT-12 v4 Expression bead chip, and changes in significantly induced transcripts validated by real time quantitative RT-PCR, ELISA, Western blotting and immunohistochemical staining. Significantly induced genes included IL-8, IL-6, ICAM-1, CCL2, CCL5, TLR4 and PTGS2. Pathway analysis indicated that dust extract treatment induced changes in gene expression influenced functions related to immune and inflammatory responses. Cells were treated with medium alone (control) or dust extract (0.1% or 0.25%) for 1, 3 or 6 h (reference).

2015-09-16 | E-GEOD-73061 | biostudies-arrayexpress

Gene expression profiling of the effects of organic dust in lung epithelial and THP-1 cells reveals inductive effects on inflammatory mediators [452 expt: THP-1 vs BEAS 2B]

2015-09-16 | E-GEOD-73062 | biostudies-arrayexpress

Gene expression profiling of the effects of organic dust in lung epithelial and THP-1 cells reveals inductive effects on inflammatory mediators [391 expt: A549 vs BEAS 2B]

2015-09-16 | GSE73061 | GEO

Gene expression profiling of the effects of organic dust in lung epithelial and THP-1 cells reveals inductive effects on inflammatory mediators [452 expt: THP-1 vs BEAS 2B]

2015-09-16 | GSE73062 | GEO