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accession-icon GSE103399
Gene expression data of proliferative cells isolated from the adult human peripheral retina, cultured and differentiated
  • organism-icon Homo sapiens
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 2.0 ST Array (hugene20st)

Description

Proliferative cells isolated from the adult human peripheral retina only transiently upregulate key retinal markers upon induced differentiation.

Publication Title

Proliferative Cells Isolated from the Adult Human Peripheral Retina only Transiently Upregulate Key Retinal Markers upon Induced Differentiation.

Sample Metadata Fields

Specimen part, Time

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accession-icon E-MEXP-215
Transcription profiling of mesenchymal stem cells (MSC) maintained in FCS or autologous serum over time analysed at passage 4 and 10
  • organism-icon Homo sapiens
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A Array (hgu133a)

Description

The purpose of this study was to determine whether the serum condition affected the gene expression in mesenchymal stem cells (MSCs)over time. To that end, we compared gene expression in MSCs maintained in regular growth medium supplemented with fetal calf serum (FCS) for 10 passages with gene expression of MSCs cultured in the same conditions for 4 passages for 2 different donors (i.e. donor3 and donor4). Likewise, we compared gene expression in MSCs maintained in regular growth medium supplemented with autologous serum(AS) for 10 passages with gene expression of MSCs cultured in the same conditions for 4 passages for the same 2 donors (i.e. donor3 and donor4). MSCs were cultured in FCS- or AS-supplemented medium and were analyzed at passage 4 and at passage 10.

Publication Title

In vitro expansion of human mesenchymal stem cells: choice of serum is a determinant of cell proliferation, differentiation, gene expression, and transcriptome stability.

Sample Metadata Fields

Sex, Specimen part, Subject

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accession-icon E-MEXP-214
Transcription profiling of Mesenchymal stem cells (MSC) maintained in FCS vs autologous serum analysed at passage 4
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A Array (hgu133a)

Description

The purpose of this study was to determine whether the serum condition affected the gene expression in mesenchymal stem cells (MSCs). To that end, we compared gene expression in MSCs maintained in regular growth medium supplemented with fetal calf serum (FCS) with gene expression of MSCs cultured in regular growth medium supplemented with autologous serum (AS) for 3 different donors (i.e. donor2, donor3 and donor4). MSCs were cultured in FCS- or AS-supplemented medium and were analyzed at passage 4.

Publication Title

In vitro expansion of human mesenchymal stem cells: choice of serum is a determinant of cell proliferation, differentiation, gene expression, and transcriptome stability.

Sample Metadata Fields

Sex, Specimen part, Subject

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accession-icon GSE18460
Lactobacillus acidophilus induces virus immune defense genes in murine dendritic cells by a TLR-2 dependent mechanism
  • organism-icon Mus musculus
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Lactobacilli are probiotics that, among other health promoting effects, have been ascribed immunostimulating and virus preventive properties. Certain lactobacilli species have been shown to possess strong IL-12 inducing properties. As IL-12 production depends on the up-regulation of type I interferons, we hypothesized that the strong IL-12 inducing capacity of L. acidophilus NCFM in murine bone marrow derived DC is caused by an up-regulation of IFN-, which subsequently stimulates the induction of IL-12 and the dsRNA binding toll like receptor (TLR)-3. The expression of the genes encoding IFN-, IL-12, IL-10 and TLR-3 in DC upon stimulation with L. acidophilus NCFM was measured. L. acidophilus NCFM induced a much stronger expression of ifn-, il-12 and il-10 compared to the synthetic dsRNA ligand Poly I:C, whereas the levels of expressed tlr-3 were similar. By the use of whole genome microarray gene expression, we investigated whether other genes related to the viral defence were up-regulated in DC upon stimulation with L. acidophilus NCFM and found that various virus defence related genes, both early and late, were among the strongest up-regulated genes. The IFN- stimulating capability was also detected in another L. acidophilus strain, but was not a property of other probiotic bacteria tested (B. bifidum and E. coli nissle).The IFN- inducing capacity was markedly reduced in TLR-2 -/- DCs, dependent on endocytosis and the major cause of the induction of il-12 and tlr-3 in L. acidophilus NCFM stimulated cells. Collectively, our results reveal that certain lactobacilli trigger the expression of viral defence genes in DC in a TLR-2 manner through induction of IFN- .

Publication Title

Lactobacillus acidophilus induces virus immune defence genes in murine dendritic cells by a Toll-like receptor-2-dependent mechanism.

Sample Metadata Fields

Treatment, Time

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accession-icon E-MEXP-168
Transcription profiling of human freshly isolated adipose-derived adult stem cells (ADASCs) vs cultured cells
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A Array (hgu133a)

Description

In order to assess whether culturing adipose-derived adult stem cells (ADASCs) affect their gene expression (see Sample Growth Condition Protocol), we wanted to identify possible genes that were differentially expressed between cultured polyclonal CD31- ADASCs and freshly isolated (uncultured) polyclonal CD31- ADASCs. To that end, RNA was isolated from cultured and uncultured ADASCs from three different donors and analyzed using the Affymetrix Microarray HG-U133A. Then, using the Affymetrix program MAS 5.0 we performed three comparisons and could identify differentially expressed transcripts common between the three donors, using the Affymetrix program DMT 3.0.

Publication Title

Isolation and transcription profiling of purified uncultured human stromal stem cells: alteration of gene expression after in vitro cell culture.

Sample Metadata Fields

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

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accession-icon GSE20302
B bifidum actively changes the gene expression profile induced by L acidophilus in murine dendritic cells
  • organism-icon Mus musculus
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Dendritic cells (DC) play a pivotal regulatory role in activation of the innate as well as the adaptive part of the immune system by responding to environmental microorganisms. We have previously shown that some lactobacilli strains induce a strong production of the pro-inflammatory and Th1 polarizing cytokine IL-12 in DC. Contrary, bifidobacteria do not induce IL-12, but are able to inhibit the IL-12 production induced by lactobacilli. In the present study, genome wide microarrays were used to investigate the maturation and gene expression pattern murine bone marrow derived DC stimulated with Lactobacillus acidophilus NCFM and Bifidobacterium bifidum Z9. L. acidophilus NCFM strongly induced expression of interferon (IFN)-, multiple virus defence genes, and cytokine and chemokine genes related to both the adaptive and the innate immune response. Contrary, B. bifidum Z9 mostly up-regulated genes encoding cytokines and chemokines related to the innate immune response. Moreover, B. bifidum Z9 inhibited the expression of the genes initiating the adaptive immune response induced by L. acidophilus NCFM and had an additive effect on genes of the innate immune response and some Th2 skewing genes. The gene encoding Jun dimerization protein 2 (JDP2), a key regulator in cell signalling, was one of the few genes only induced by B. bifidum Z9. Blocking of the JNK1/2 pathway completely inhibited the gene expression of Ifn-. We suggest that B. bifidum Z9 employs an active mechanism to inhibit induction of genes in DC triggering the adaptive immune system and that JPD2 is involved in the regulatory mechanism.

Publication Title

Bifidobacterium bifidum actively changes the gene expression profile induced by Lactobacillus acidophilus in murine dendritic cells.

Sample Metadata Fields

Specimen part, Treatment

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accession-icon GSE27449
Changes of mRNA expressin in rat kidney inner medulla in response to dDAVP stimulation/ withdrawal
  • organism-icon Rattus norvegicus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Gene 1.0 ST Array (ragene10st)

Description

The E3 ubiquitin -protein ligases (E3s) plays a role as regulators of protein trafficking and degradation. We aimed to identify E3s in rat kidney which are associated with dDAVP-induced urine concentration.

Publication Title

E3 ubiquitin-protein ligases in rat kidney collecting duct: response to vasopressin stimulation and withdrawal.

Sample Metadata Fields

Sex, Specimen part

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accession-icon SRP136058
Gene expression in PANC1 cells treated with Rakicidin
  • organism-icon Homo sapiens
  • sample-icon 36 Downloadable Samples
  • Technology Badge IconNextSeq 500

Description

Cells were treated with Rakicidin A or an analogue compound BE-43547 or DMSO (control) in three replicates. Overall design: three groups in triplicates.

Publication Title

APD-Containing Cyclolipodepsipeptides Target Mitochondrial Function in Hypoxic Cancer Cells.

Sample Metadata Fields

Specimen part, Cell line, Subject

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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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