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accession-icon GSE119933
Toxicogenomics directory of rat hepatotoxicants in vivo and in cultivated hepatocytes
  • organism-icon Rattus norvegicus
  • sample-icon 524 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Genome 230 2.0 Array (rat2302)

Description

Transcriptomics is developing into an invaluable tool in toxicology. The aim of this study was, using a transcriptomics approach, to identify genes that respond similarly to chemicals (including drugs and industrial compounds) in both rat liver in vivo and in cultivated hepatocytes, which are up- or downregulated by many different test compounds. For this purpose, we analyzed Affymetrix gene array data from 162 compounds that were previously tested in a concentration-dependent manner in rat livers in vivo and rat hepatocytes cultivated in sandwich culture. These data were obtained from the Japanese Toxicogenomics (TGP) and North-Rhine-Westphalian (NRW) data sets, which consist of 138 and 29 compounds, respectively, and have 5 mutual compounds between them. The in vitro gene array data from the NRW data set were generated in the present study, while TGP is publicly available. For each of the data sets, the overlap between up- or down-regulated genes in vitro and in vivo was identified, further named in vitro-in vivo consensus genes. Interestingly, an overlap of in vivo-in vitro consensus genes was obtained between both data sets, which were 21-times (up-regulated genes) or 12-times (down-regulated genes) en-riched compared to random expectation. This is remarkable since the TGP and NRW data sets contained only five mutual compounds. Finally, the genes in the TGP and NRW overlap were used to identify the upregulated genes with the highest com-pound coverage, resulting in a 7-gene set of Cyp1a1, Ugt2b1, Cdkn1a, Mdm2, Aldh1a1, Cyp4a3, and Ehhad. This 7-gene set was then successfully tested with structural analogues of valproic acid that are not present in the TGP and NRW data sets. In conclusion, the 7-gene set identified in the present study responds similarly in vitro and in vivo and is induced by a wide range of different chemicals. Despite these results, transcriptomics with cultivated rat hepatocytes remains a challenge, because many genes are up- or downregulated by the culture conditions, respond differently to test compounds in vitro and in vivo, and shows a higher variability in the in vitro system compared to the corresponding in vivo data.

Publication Title

No associated publication

Sample Metadata Fields

Sex, Specimen part, Disease, Compound

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accession-icon GSE99860
The effect of GPAM silencing in MCF7 breast cancer cells
  • organism-icon Homo sapiens
  • sample-icon 15 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

GPAM is well characterized in triglyceride synthesis, but has never been implicated in cancer. Our study report a role for GPAM in cell migration. Gene expression changes after GPAM silencing was investigated to gain insight into possible mechanisms underlying GPAM's role in cell migration.

Publication Title

Glycerol-3-phosphate Acyltransferase 1 Promotes Tumor Cell Migration and Poor Survival in Ovarian Carcinoma.

Sample Metadata Fields

Specimen part, Cell line

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accession-icon GSE99861
The effect of EDI3 inhibition in MCF7 breast cancer cells
  • organism-icon Homo sapiens
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

EDI3 was shown to be relevant in cell migration, adhesion and spreading. Gene expression analysis was performed to determine the effect of EDI3 silencing in MCF7 cells in order to gain insight into potential underlying mechanisms.

Publication Title

EDI3 links choline metabolism to integrin expression, cell adhesion and spreading.

Sample Metadata Fields

Specimen part, Cell line

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accession-icon E-MEXP-893
Transcription profiling by array of hepatocytes from mice fed a high fat diet
  • organism-icon Mus musculus
  • sample-icon 22 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Expression 430B Array (moe430b), Affymetrix Mouse Expression 430A Array (moe430a)

Description

Effect of high fat diet feeding on gene expression

Publication Title

Subtle metabolic and liver gene transcriptional changes underlie diet-induced fatty liver susceptibility in insulin-resistant mice.

Sample Metadata Fields

Sex, Age, Specimen part, Subject

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accession-icon E-MEXP-889
Transcription profiling of three strains of rat that are normoglycaemic or hyperglycaemic
  • organism-icon Rattus norvegicus
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Expression 230A Array (rae230a)

Description

Effects of hyperglycaemia and genetic background differences on gene expression in rats

Publication Title

No associated publication

Sample Metadata Fields

Sex, Age, Specimen part, Disease, Disease stage, Subject

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accession-icon E-MTAB-494
Transcription profiling by array of zebra fish embryos at the 5-somite stage treated with aplexone
  • organism-icon Danio rerio
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Zebrafish Genome Array (zebrafish)

Description

Arterial and venous endothelial cells exhibit distinct molecular characteristics at early developmental stages. These lineage-specific molecular programs are instructive to the development of distinct vascular architectures and physiological conditions of arteries and veins, but their roles in angiogenesis remain unexplored. Here, we show that the caudal vein plexus in zebrafish forms by endothelial cell sprouting, migration and anastomosis, providing a venous-specific angiogenesis model. Using this model, we identified a novel compound, aplexone, which effectively suppresses venous, but not arterial, angiogenesis. Multiple lines of evidence indicate that aplexone differentially regulates arteriovenous angiogenesis by targeting the HMG-CoA reductase (HMGCR) pathway. Treatment with aplexone affects the transcription of enzymes in the HMGCR pathway and reduces cellular cholesterol levels. Injecting mevalonate, a metabolic product of HMGCR, reverses the inhibitory effect of aplexone on venous angiogenesis. In addition, aplexone treatment inhibits protein prenylation and blocking the activity of geranylgeranyl transferase induces a venous angiogenesis phenotype resembling that observed in aplexone-treated embryos. Furthermore, endothelial cells of venous origin have higher levels of proteins requiring geranylgeranylation than arterial endothelial cells and inhibiting the activity of Rac or Rho Kinase effectively reduces the migration of venous, but not arterial, endothelial cells. Taken together, our findings indicate that angiogenesis is differentially regulated by the HMGCR pathway via an arteriovenousdependent requirement for protein prenylation in zebrafish and human endothelial cells.

Publication Title

Aplexone Targets the HMG-CoA Reductase Pathway and Differentially Regulates Arteriovenous Angiogenesis

Sample Metadata Fields

Compound

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accession-icon SRP136989
Environmental toxins and colon carcinogenesis.
  • organism-icon Homo sapiens
  • sample-icon 16 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 4000

Description

RNA was isolated from colorectal cancer (HCT116) and normal colon cells (HCoEpic) treated with toxic agents (bisphenol A (BPA), hexabromocyclododecane (HBCD), 4-tert-octylphenol (OP)) or Vehicle (DMSO) and then preformed NGS using Illumina protocol.

Publication Title

No associated publication

Sample Metadata Fields

Sex, Specimen part, Disease, Cell line, Treatment

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accession-icon GSE73331
Analysis of initial step of multiciliogenesis during the differentiation of adult airway progenitors
  • organism-icon Mus musculus
  • sample-icon 18 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Multiciliated cells are crucial for fluid and ion transport in epithelia of a variety of organs and their impaired development and function are seen in human diseases affecting the brain, respiratory, and reproductive tracts. Multiciliogenesis requires activation of a specialized transcription program coupled to complex cytoplasmic events that lead to large-scale centriole amplification to generate multicilia. Yet, it remains unclear how these events are coordinated to initiate multiciliogenesis in epithelial progenitors. Here we identify an unsuspected mechanism orchestrated by the transcription factor E2f4 essential to integrate these processes. We show that after inducing a transcriptional program of centriole biogenesis, E2f4 translocates to the cytoplasm to become a core component of structures classically identified as fibrous granules (FG), acting as organizing centers for deuterosome assembly and centriole amplification. Remarkably, loss of cytoplasmic E2f4 prevents FG aggregation, deuterosome assembly and multicilia formation even when E2f4s transcriptional function is preserved. Moreover, in E2f4-deficient cells multiciliogenesis is rescued only if both nuclear and cytoplasmic E2f4 activities are restored. Thus, E2f4 integrates previously unrelated nuclear and cytoplasmic events of the multiciliated cell program.

Publication Title

Cytoplasmic E2f4 forms organizing centres for initiation of centriole amplification during multiciliogenesis.

Sample Metadata Fields

Specimen part

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accession-icon SRP053216
Danio rerio Transcriptome or Gene expression
  • organism-icon Danio rerio
  • sample-icon 4 Downloadable Samples
  • Technology Badge IconIlluminaHiSeq2000

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

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE80070
Whole transcript expression profiling of short-term and long-term hypoxic neural stem cells (NSCs)
  • organism-icon Mus musculus
  • sample-icon 24 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Transcriptome analysis of murine foetal NSCs (E14) after short-term (48 hours) and long-term (13 days) hypoxic (3% oxygen) culture compared to normoxic culture (21% oxygen)

Publication Title

No associated publication

Sample Metadata Fields

Specimen part

View Samples
...

refine.bio is a repository of uniformly processed and normalized, ready-to-use transcriptome data from publicly available sources. refine.bio is a project of the Childhood Cancer Data Lab (CCDL)

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Cite refine.bio

Casey S. Greene, Dongbo Hu, Richard W. W. Jones, Stephanie Liu, David S. Mejia, Rob Patro, Stephen R. Piccolo, Ariel Rodriguez Romero, Hirak Sarkar, Candace L. Savonen, Jaclyn N. Taroni, William E. Vauclain, Deepashree Venkatesh Prasad, Kurt G. Wheeler. refine.bio: a resource of uniformly processed publicly available gene expression datasets.
URL: https://www.refine.bio

Note that the contributor list is in alphabetical order as we prepare a manuscript for submission.

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