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accession-icon GSE97773
Expression data from human umbilical cord-derived mesenchymal stem cells
  • organism-icon Homo sapiens
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Mesenchymal stem cells (MSCs) have been shown to exert therapeutic effects on various autoimmune diseases. However, such therapeutic effect is not always achieved. Among many reasons, MSC culture methodologies may account for the these differences. It is known that oxygen concentration could profoundly affect the properties of MSCs. Therefore, we compared human umbilical cord derived MSCs cultured under hypoxic and normoxic conditions.

Publication Title

No associated publication

Sample Metadata Fields

Specimen part

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accession-icon GSE24705
mRNA expression data from iPSCs, ntESCs and iPSC-nt-ESCs
  • organism-icon Mus musculus
  • sample-icon 33 Downloadable Samples
  • Technology Badge Icon

Description

We generated three kinds of genetically identical mouse reprogrammed cells: induced pluripotent stem cells (iPSCs), nuclear transfer embryonic stem cells (ntESCs) and iPSC-nt-ESCs that are established after successively reprogramming of iPSCs by nuclear transfer (NT). NtESCs show better developmental potential than iPSCs, whereas iPSC-nt-ESCs display worse developmental potential than iPSCs.

Publication Title

Different developmental potential of pluripotent stem cells generated by different reprogramming strategies.

Sample Metadata Fields

Sex, Specimen part, Cell line

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accession-icon GSE83326
Hepatic gene expression data from cadmium-exposed mice
  • organism-icon Mus musculus
  • sample-icon 10 Downloadable Samples
  • Technology Badge Icon

Description

Environmental cadmium, with a high average dietary intake, is a severe public health risk. However, the long-term health implications of environmental exposure to cadmium in different life stages remain unclear.

Publication Title

Sex-Dependent Effects of Cadmium Exposure in Early Life on Gut Microbiota and Fat Accumulation in Mice.

Sample Metadata Fields

Sex, Specimen part

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accession-icon GSE39401
Expression data of WHV/c-myc transgenic mice at preneoplastic and neoplastic stages
  • organism-icon Mus musculus
  • sample-icon 2 Downloadable Samples
  • Technology Badge Icon

Description

The WHV/c-myc transgenic mouse is an animal model of hepatocarcinogenesis that can exquisitely mimic the cancer staging in human Hepatocellular carcinoma (HCC), in which the c-myc oncogene is activated by adjacent woodchuck hepatitis virus (WHV) DNA sequences. Compared to other models of c-myc transgenic mice, WHV/c-myc mice stably develop HCC with a relatively short latent period of 8 to 12 months, with a high (near 100%) tumor incidence.

Publication Title

No associated publication

Sample Metadata Fields

Age

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accession-icon GSE62887
Expression data from haploid and diploid epiblast stem cells
  • organism-icon Mus musculus
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon

Description

Haploid pluripotent stem cells, such as haploid embryonic stem cells (haESCs), facilitate the genetic study of recessive traits. In vitro, fish haESCs maintain haploidy in both undifferentiated and differentiated states, but whether mammalian haESCs can preserve pluripotency in the haploid state has not been tested. Here, we report that mouse haESCs can differentiate in vitro into haploid epiblast stem cells (haEpiSCs), which maintain an intact haploid genome, unlimited self-renewal potential, and durable pluripotency to differentiate into various tissues in vitro and in vivo. Mechanistically, the maintenance of self-renewal potential depends on the Activin/bFGF pathway. We further show that haEpiSCs can differentiate in vitro into haploid progenitor-like cells.

Publication Title

Durable pluripotency and haploidy in epiblast stem cells derived from haploid embryonic stem cells in vitro.

Sample Metadata Fields

Specimen part

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accession-icon GSE107292
Expression data and genome-wide maps of chromatin in Phf8 knock out and wild type mice
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Phf8 histone demethylase deficiency causes cognitive impairments through the mTOR pathway.

Sample Metadata Fields

Age, Specimen part

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accession-icon GSE107210
Expression data from hippocampus of Phf8 knock out and wild type mice
  • organism-icon Mus musculus
  • sample-icon 1 Downloadable Sample
  • Technology Badge Icon

Description

We used microarrays to detail the global programme gene expression of Phf8 knock out and wild type mice

Publication Title

Phf8 histone demethylase deficiency causes cognitive impairments through the mTOR pathway.

Sample Metadata Fields

Age, Specimen part

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accession-icon GSE90808
Expression data from macrophages of E-selectin+/+ and E-selectin-/- mouse infected with Listeria monocytogenes in vivo on day3
  • organism-icon Mus musculus
  • sample-icon 2 Downloadable Samples
  • Technology Badge Icon

Description

We used microarrays to detail the global gene expression in peritoneal macrophages (PM) from E-selectin+/+ and E-selectin-/- mouse infected with Listeria Monocytogenes in vivo on day3

Publication Title

No associated publication

Sample Metadata Fields

Specimen part

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accession-icon GSE39392
Androgenetic haploid embryonic stem cells
  • organism-icon Mus musculus
  • sample-icon 21 Downloadable Samples
  • Technology Badge Icon

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Androgenetic haploid embryonic stem cells produce live transgenic mice.

Sample Metadata Fields

Specimen part, Cell line

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accession-icon GSE39391
Gene expression data from ahES cells, ES cells, MEF cells and round sperm
  • organism-icon Mus musculus
  • sample-icon 21 Downloadable Samples
  • Technology Badge Icon

Description

Haploid stem cells offer an easy-to-manipulate genetic system and therefore have great values for studies of recessive phenotypes. Here, we show that mouse androgenetic haploid ES (ahES) cell lines can be established by transferring sperm into enucleated oocyte. The ahES cells maintain haploidy and stable growth over 30 passages, express pluripotent markers, possess the ability to differentiate into all three germ-layers in vitro and in vivo, and contribute to germline of chimeras when injected into blastocysts. Although epigenetically distinct from sperm cells, the ahES cells can produce viable and fertile progenies after intracytoplasmic injection into mature oocytes. The oocyte injection procedure can also produce viable transgenic mice from genetically engineered ahES cells.

Publication Title

Androgenetic haploid embryonic stem cells produce live transgenic mice.

Sample Metadata Fields

Specimen part, Cell line

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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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