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accession-icon GSE49283
Translational activation of developmental mRNAs during neonatal mouse testis development
  • organism-icon Mus musculus
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

The sequence of gene regulatory events that drive neonatal germ cell development in the mammalian testis is not yet clear. We assessed changes in mRNA utilization in the neonatal testis at 1 and 4 dpp, times when the testis contains quiescent gonocytes (1 dpp) and proliferating spermatogonia (4 dpp). There are not thought to be major changes in the nature or number of somatic cells over that interval.

Publication Title

Translational activation of developmental messenger RNAs during neonatal mouse testis development.

Sample Metadata Fields

Age, Specimen part

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accession-icon GSE148088
Effects of STOX1 expression variants on trophoblastic cell lines
  • organism-icon Homo sapiens
  • sample-icon 15 Downloadable Samples
  • Technology Badge Icon Affymetrix Clariom S Human array (clariomshuman)

Description

The STOX1 transcription factor has been involved in a complex human disease of pregnancy, preeclampsia, in human families, and mouse models. However, its mode of action is still largely unknown. Overexpression of either the long (STOX1A) or the short (STOX1B) isoform was obtained in the BeWo villous trophoblast model, a cell line able to fuse in syncytiotrophoblast following induction by forskolin treatment. The effects at the transcriptional level are evaluated in every condition.

Publication Title

Molecular Mechanisms of Trophoblast Dysfunction Mediated by Imbalance between STOX1 Isoforms.

Sample Metadata Fields

Cell line, Treatment

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accession-icon GSE50451
Microarray analysis of Merkel cell carcinoma (MCC) tumors, small cell lung cancer (SCLC) tumors, and MCC cell lines
  • organism-icon Homo sapiens
  • sample-icon 77 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

When using cell lines to study cancer, phenotypic similarity to the original tumor is paramount. Yet, little has been done to characterize how closely Merkel cell carcinoma (MCC) cell lines model native tumors. To determine their similarity to MCC tumor samples, we characterized MCC cell lines via gene expression microarrays. Using whole transcriptome gene expression signatures and a computational bioinformatic approach, we identified significant differences between variant cell lines (UISO, MCC13, and MCC26) and fresh frozen MCC tumors. Conversely, the classic WaGa and Mkl-1 cell lines more closely represented the global transcriptome of MCC tumors. When compared to publicly available cancer lines, WaGa and Mkl-1 cells were similar to other neuroendocrine tumors, but the variant cell lines were not. WaGa and Mkl-1 cells grown as xenografts in mice had histological and immunophenotypical features consistent with MCC, while UISO xenograft tumors were atypical for MCC. Spectral karyotyping and short tandem repeat analysis of the UISO cells matched the original cell line's description, ruling out contamination. Our results validate the use of transcriptome analysis to assess the cancer cell line representativeness and indicate that UISO, MCC13, and MCC26 cell lines are not representative of MCC tumors, whereas WaGa and Mkl-1 more closely model MCC.

Publication Title

Assessment of cancer cell line representativeness using microarrays for Merkel cell carcinoma.

Sample Metadata Fields

Specimen part, Disease, Cell line

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accession-icon GSE6189
Molecular Mechanisms of Early Response in Adaptive Cerebral Arteriogenesis
  • organism-icon Rattus norvegicus
  • sample-icon 15 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Expression 230A Array (rae230a)

Description

This study aims at a comprehensive understanding of the genomic program activated during early-phase of collateral vessel growth in a rat model for cerebral adaptive arteriogenesis (3-VO). While arteriogenesis constitutes a promising therapeutic concept for cerebrovascular ischemia, genomic profiles essential for therapeutic target identification were analysed solely for collateral arteries of the heart and periphery. Despite challenging anatomical conditions of the brain the 3-VO model allows identification of differentially expressed genes during adaptive cerebral arteriogenesis by selective removal of the posterior cerebral artery (PCA).

Publication Title

Induction of cerebral arteriogenesis leads to early-phase expression of protease inhibitors in growing collaterals of the brain.

Sample Metadata Fields

Age

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accession-icon GSE23680
Expression data from hepatocellular carcinoma and adjacent normal liver tissue
  • organism-icon Mus musculus
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Assay of gene expression pattern differences between liver cancer tissue and normal liver tissue from the same mouse by microarray in 4 separate mice injected with recombinant adeno-associated viral (AAV) vector

Publication Title

Assessing the potential for AAV vector genotoxicity in a murine model.

Sample Metadata Fields

Sex, Specimen part

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accession-icon GSE12243
Microvesicles derived from human mesenchymal stem cells protect against acute tubular injury
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina human-6 v2.0 expression beadchip

Description

Administration of exogenous mesenchymal stem cells (MSCs) has been shown to improve the recovery from acute kidney injury (AKI). It has been suggested that the beneficial effect of MSCs is related to the paracrine release of factors favouring proliferation of intrinsic epithelial cells survived to injury rather than to their trans-differentiation. However the factors involved remain to be determined. In the present study we demonstrated that microvesicles (MVs) derived from human bone marrow MSCs are able to stimulate in vitro proliferation and apoptosis resistance of tubular epithelial cells (TEC). In addition, MVs were found to accelerate in vivo the morphological and functional recovery of glycerol induced AKI in SCID mice by inducing TEC proliferation. The effect of MVs on the recovery of AKI was comparable to that of human MSC treatment. In vitro we found that the CD44 and beta1-integrin-dependent incorporation of MVs in TEC was required for their biological action. However, despite their internalization, RNase-treated MVs failed to induce in vitro apoptosis resistance and TEC proliferation, and in vivo recovery from AKI, suggesting an RNA-dependent biological effect. Microarray analysis and quantitative RT-PCR of MV-RNA extract indicated that MVs were shuttling a specific subset of cellular mRNA, such as mRNA associated with the mesenchymal differentiative phenotype and with several cell functions involved in the control of transcription, proliferation, apoptosis and cell immune regulation. These results suggest that MVs derived from MSCs may activate a proliferative program in TEC survived to injury in AKI by an horizontal transfer of mRNA.

Publication Title

Mesenchymal stem cell-derived microvesicles protect against acute tubular injury.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE137176
Time-driven molding of the epidermal stem cell transcriptome
  • organism-icon Mus musculus
  • sample-icon 18 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Epidermal stem cells ensure proper faring of skin homeostatic processes under both physiological and challenging conditions. Currently, the molecular events underpinning ageing within the epidermal stem cell niche are poorly understood.

Publication Title

In Silico Analysis of the Age-Dependent Evolution of the Transcriptome of Mouse Skin Stem Cells.

Sample Metadata Fields

Age, Specimen part

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accession-icon GSE38390
Expression data from leaves of GA-deficient and GA-insensitive transgenic poplar
  • organism-icon Populus tremula x populus alba
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Poplar Genome Array (poplar)

Description

We used whole-genome microarrays to identify differentially expressed genes in leaves of GA-deficient (35S::PcGA2ox) and/or GA-insensitive (35S::rgl1) transgenics as compared to WT poplar (717-1B4 genotype).

Publication Title

Roles of gibberellin catabolism and signaling in growth and physiological response to drought and short-day photoperiods in Populus trees.

Sample Metadata Fields

Specimen part

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accession-icon GSE63624
Expression data for 52 microsatellite stable (MSS) primary tumors from patients with proximal colon cancer.
  • organism-icon Homo sapiens
  • sample-icon 52 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)

Description

Samples were taken from surgically resected tumor specimens from patients with proximal colon cancer. The expression profiles were determined using the Affymetrix GeneChip Human Exon 1.0 ST Array version 2. APC gene mutation status was determined using Sanger sequencing. A classifier for APC mutation status was trained using these expression data.

Publication Title

Wild-type APC predicts poor prognosis in microsatellite-stable proximal colon cancer.

Sample Metadata Fields

Specimen part

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accession-icon GSE42816
Gene expression propionic patients, carriers, and controls
  • organism-icon Homo sapiens
  • sample-icon 83 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

Gene expression in LCLs from PA patients, their parents, and HapMap sex and age match controls at low glucose (9 mg/dL) and normal glucose growth conditions.

Publication Title

Gene expression in cell lines from propionic acidemia patients, carrier parents, and controls.

Sample Metadata Fields

Sex, Age, Disease, Disease stage, Cell line, Treatment

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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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