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SRX13298289: GSM5712903: pooled whole embryos 210 ng/L repC; Xenopus laevis; RNA-Seq
1 ILLUMINA (Illumina NovaSeq 6000) run: 22.6M spots, 4.6G bases, 1.4Gb downloads

Submitted by: NCBI (GEO)
Study: Gene expression profiling and developmental outcomes reveals early toxicological mechanisms of lead effects in an early-life stage amphibian, Xenopus laevis
show Abstracthide Abstract
Lead (Pb) is a widespread environmental toxicant that can elicit a wide variety of adverse effects in aquatic species. In fish, exposure to Pb can induce oxidative stress and reduce antioxidant capacity and there is evidence that Pb-induced developmental abnormalities are the result of dysregulated metabolism pathways but to date, no studies have characterised the molecular mechanisms of lead toxicity in amphibians. To investigate this, we coupled transcriptomic responses and early-life stage toxicity testing to identify specific molecular mechanisms that drive the adverse effects of lead, in Xenopus laevis. Embryos were exposed to one of the concentrations (0, 70, 210 and 630 ng/L) of lead (II) nitrate starting from 2 days post fertilization (dpf) until 6 dpf and 21 dpf to examine the transcriptomic and apical responses, respectively. We observed common dysregulated pathways and with similar magnitude at medium and high lead concentrations, but a phenotypic response only with the highest lead level. RNA Seq analysis showed about ~250 differentially expressed genes that could be further categorized into KEGG pathways based on their involvement in key biological processes. The most dysregulated pathways were Glutathione metabolism, Cytochrome P450 (drug/ xenobiotic metabolism) and Steroid hormone biosynthesis. Developmental studies showed that tadpoles exposed to the highest Pb concentration (630 ug/L) had significantly decreased total length and higher proportion of developmental abnormalities. Therefore, evaluating gene expression responses can provide early indication of toxicological mechanisms of lead effects in amphibians. As with fish, dysregulated metabolic pathways are most likely the molecular mechanisms underlying lead toxicity in ELS amphibians and contribute to the altered growth and developmental abnormalities observed in this study. Overall design: In this study we analyzed the gene expression profiles of whole body Xenopus laevis embryos exposed to either of the treatments, water control, 210 ng/L, 630 ng/L of lead (II) nitrate starting from 2 days post-fertilization until 6 days post fertilization. Each treatment had 5 replicates and each replicate had 3 individuals.
Sample: pooled whole embryos 210 ng/L repC
SAMN23577170 • SRS11207980 • All experiments • All runs
Organism: Xenopus laevis
Library:
Instrument: Illumina NovaSeq 6000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: Tissue was homogenized and RNA was extracted using the RNeasy Plus Universal Mini kit (QIAGEN) according to the manufacturer's instructions. Libraries were generated from 250 ng of total RNA as following: mRNA enrichment was performed using the NEBNext Poly(A) Magnetic Isolation Module (New England BioLabs). cDNA synthesis was achieved with the NEBNext RNA First Strand Synthesis and NEBNext Ultra Directional RNA Second Strand Synthesis Modules (New England BioLabs). The remaining steps of library preparation were done using and the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs). Adapters and PCR primers were purchased from New England BioLabs. Libraries were quantified using the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems). Average size fragment was determined using a LabChip GXII (PerkinElmer) instrument.
Experiment attributes:
GEO Accession: GSM5712903
Links:
Runs: 1 run, 22.6M spots, 4.6G bases, 1.4Gb
Run# of Spots# of BasesSizePublished
SRR1711100022,569,6434.6G1.4Gb2024-08-31

ID:
18188876

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