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SRP089876
Danio rerio
3 Downloadable Samples
IlluminaHiSeq2000
Description
Based on the differential comparison of transcriptomes of Homo-, hetero-zygote (Het) and wild type (Wt), in vivo protein-trap mutagenesis system, we have produced series of expression codex of the zebrafish. Here , we reported the transcriptomic characteristic of a line with stable deficits found in homozygote (Homo) expressing the strongest signal of red fluorescent protein (mRFP) in the central neural system and vascular system.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
No sample metadata fields
View Samples- Danio rerio
- 15 Downloadable Samples
- IlluminaHiSeq4000
Description
The present study aims to examine the toxicological effects of phenanthrene in the molecular mechanism in zebrafish. We performed RNA-Seq analysis on zebrafish liver responding to phenanthrene exposure. Genes involved in phenanthrene exposure to zebrafish liver were identified from the transcriptional data. This study provides the completed evaluation of toxic effect of phenanthrene exposure to zebrafish by transcriptional approaches. Our findings could present foundation for further study on molecular mechanism responsible for zebrafish's responses to phenanthrene exposure.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
No sample metadata fields
View Samples- Danio rerio
- 4 Downloadable Samples
- IlluminaHiSeq2000
Description
Groups of adult zebrafish (9 male and 9 female) were exposed for 7 days to 50 ng/L (168.7 pmol/L) of 17a-ethinylestradiol (EE2). Transcriptome response of EE2 in zebrafish liver were analysed.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
No sample metadata fields
View Samples- Danio rerio
- 1 Downloadable Sample
- IlluminaHiSeq2000
Description
Mercury is a widespread toxicant in aquatic environment that can cause deleterious effects on fish. Although a number of mercury-regulated genes have been investigated in adult fish, the transcriptional responses of fish embryos to acute mercury exposure are not well understood. In this study, RNA sequencing was used to examine the transcriptional changes in developing zebrafish under a low concentration of mercury exposure from 24 to120 hpf. Our results provide useful insights to help further understand the transcriptional response and detoxification ability of zebrafish embryos following acute exposure to mercury.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 8 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Keeping imbibed seeds at low temperatures for a certain period, so called seed vernalization (SV) treatment, promotes seed germination and subsequent flowering in various plants. Vernalization-promoting flowering requires GSH. However, the expression patterns analyzed by GeneChip arrays showed that increased GSH biosynthesis partially mimics SV treatment in Arabidopsis thaliana. SV treatment (keeping imbibed seeds at 4C for 24 h) induced a specific pattern of gene expression and promoted subsequent flowering in wild-type plants. A similar pattern was observed at 22C in transgenic plants (35S-GSH1 plants) overexpressing the -glutamylcysteine synthetase gene GSH1, coding an enzyme limiting GSH biosynthesis, under the control of the cauliflower mosaic virus 35S promoter. This pattern was strengthened at 4C but flowering was less responsive to SV treatment. There was a difference in the transcript behaviour of the flowering repressor FLC between wild-type and 35S-GSH1 plants. Unlike other genes responsive to SV treatment, SV-dependent decrease in FLC in wild-type plants was reversed in 35S-GSH1 plants. SV treatment increased GSSG level in wild-type seeds, whereas GSSG level was high in 35S-GSH1 plants, even at a non-vernalizing temperature. Taking into consideration that low temperatures stimulate GSH biosynthesis and bring about oxidative stress, GSSG is considered to trigger low temperature response, but enhanced GSH synthesis was not enough for mimicking SV treatment. To complete it, it essentially required the cellular redox retransition from the oxidized to the reduced state that is observed after the seed vernalization treatment.
Publication Title
Overexpression of GSH1 gene mimics transcriptional response to low temperature during seed vernalization treatment of Arabidopsis.
Alternate Accession IDs
Sample Metadata Fields
Specimen part
View Samples- Rattus norvegicus
- 107 Downloadable Samples
- Illumina ratRef-12 v1.0 expression beadchip
Description
Gene expression was analysed in the colon and brain of normal rat pups from late prenatal through early postnatal development. Tissue was isolated from pups one day prior to the anticipated date of birth and throughout the suckling period until the end of weaning.
Publication Title
Sialic acid utilisation and synthesis in the neonatal rat revisited.
Alternate Accession IDs
Sample Metadata Fields
Specimen part
View Samples- Mus musculus, Rattus norvegicus
- 60 Downloadable Samples
- Affymetrix Murine Genome U74A Version 2 Array (mgu74av2), Affymetrix Rat Genome U34 Array (rgu34a)
Description
Whole tissues corresponding to the ileum, colon and rectum were dissected from adult mice and used for RNA preparation. The aim of experiment was to study the impact of gut microbiota on gene expression in different gut regions.
Publication Title
No associated publication
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
View Samples- Rattus norvegicus
- 60 Downloadable Samples
Affymetrix Rat Genome U34 Array (rgu34a), Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
Ochratoxin A gene expression profiling in liver and kidney, with time points of exposure from 7 days to 12 motnhs
Publication Title
A toxicogenomics approach to identify new plausible epigenetic mechanisms of ochratoxin a carcinogenicity in rat.
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 31 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Background: Even though much progress has been made in the understanding of the molecular nature of glioma, the survival rates of patients affected of this tumour have not changed significantly during these years. Thus, a deeper understanding of this malignancy is still needed in order to predict its outcome and improve patient treatment. Here, we report that VAV1, a GDP/GTP exchange factor for Rho/Rac proteins with oncogenic potential that is involved in the regulation of cytoskeletal dynamics and cell migration.
Publication Title
No associated publication
Alternate Accession IDs
Sample Metadata Fields
Sex, Age
View Samples- Mus musculus
- 21 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Progressive myoclonus epilepsy of Unverricht-Lundborg type (EPM1) is an inherited neurodegenerative disease with myoclonus, seizures and ataxia, caused by the mutations in cystatin B (CSTB) gene. In an approach towards understanding the molecular basis of pathogenic events in EPM1 we have utilized the cystatin B deficient mice (Cstb-/-), a model for the disease. We have characterized the gene expression changes from the cerebellum of Cstb-/- mouse at postnatal day 7 (P7) and P30 as well as in cultured cerebellar granule cells using a pathway-based approach. A marked upregulation of immune response genes was seen at P30, reflecting the ongoing neuropathology, however, the observed alterations in complement cascade genes could also imply defects in synaptic plasticity. Differentially expressed genes in pre-symptomatic Cstb-/- animals at P7 were connected to synaptic function and plasticity and in cultured cerebellar granule cells to cellular biogenesis, cytoskeleton and intracellular transport. Especially GABAergic pathways were affected.
Publication Title
Gene expression alterations in the cerebellum and granule neurons of Cstb(-/-) mouse are associated with early synaptic changes and inflammation.
Alternate Accession IDs
Sample Metadata Fields
Sex, Specimen part
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