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accession-icon GSE18296
Gene Expression Profiling of an Immortalized Human Neural Stem Cell Line HB1.F3
  • organism-icon Homo sapiens
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

Neural stem cells (NSC) with self-renewal and multipotent properties serve as an ideal cell source for transplantation to treat spinal cord injury, stroke, and neurodegenerative diseases. To efficiently induce neuronal lineage cells from NSC for neuron replacement therapy, we should clarify the intrinsic genetic programs involved in a time and place-specific regulation of human NSC differentiation. Recently, we established an immortalized human NSC clone HB1.F3 to provide an unlimited NSC source applicable to genetic manipulation for cell-based therapy. To investigate a role of neurogenin 1 (Ngn1), a proneural basic helix-loop-helix (bHLH) transcription factor, in human NSC differentiation, we established a clone derived from F3 stably overexpressing Ngn1. Genome-wide gene expression profiling identified 250 upregulated genes and 338 downregulated genes in Ngn1-overexpressing F3 cells (F3-Ngn1) versus wild-type F3 cells (F3-WT). Notably, leucine-rich repeat-containing G protein-coupled receptor 5 (LGR5), a novel stem cell marker, showed a robust increase in F3-Ngn1.

Publication Title

Stable expression of neurogenin 1 induces LGR5, a novel stem cell marker, in an immortalized human neural stem cell line HB1.F3.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE2198
Comparison of transcripts from the anterior tibialis, gastrocnemius, and liver of glycogen synthase WT, GSL30 or KO mice
  • organism-icon Mus musculus
  • sample-icon 34 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Expression 430A Array (moe430a)

Description

Anterior tibialis removed from 3-month old muscle glycogen synthase WT or knockout mouse. RNA was extracted using GibcoBRL TRIzol Reagent and a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA. GSM40057-GSM40063 AND GSM40956.

Publication Title

Gene expression profiling of mice with genetically modified muscle glycogen content.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE102949
Expression data of human dermal papilla cell with or without beta-estradiol
  • organism-icon Homo sapiens
  • sample-icon 5 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

The dermal papilla plays a key role in the regulation of the hair biology. Accordingly, human dermal papilla cells (hDPCs) may be functionally impaired in female pattern hair loss. A previous observation that beta-estradiol (E2) increased hair density in ovariectomized mice suggested that E2 might modulate the biological properties of hDPCs. Therefore, to further explore the effect of E2 on hDPCs, a global gene expression analysis was conducted.

Publication Title

Reversal of the hair loss phenotype by modulating the estradiol-ANGPT2 axis in the mouse model of female pattern hair loss.

Sample Metadata Fields

Sex, Age, Specimen part, Treatment, Race

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accession-icon GSE43413
Expression data from the telencephalon of wild-type and rSey2/rSey2 rats
  • organism-icon Rattus norvegicus
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Genome 230 2.0 Array (rat2302)

Description

Pax6 is one of the important transcription factors involved in regional specification and neurogenesis in the developing cortex.

Publication Title

Dmrta1 regulates proneural gene expression downstream of Pax6 in the mammalian telencephalon.

Sample Metadata Fields

Specimen part

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accession-icon E-ATMX-7
Transcription profiling of A. thaliana Col-0 wild-type vs. MYB overexpression plants
  • organism-icon Arabidopsis thaliana
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Comparing the gene expression patterns between wild type plant (Col-0) and MYB Over-expression plants.

Publication Title

Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE26933
Effects of polyglutamine expansion and subcellular localization of C-terminal fragment of Cav2.1 in PC12 rat pheochromocytoma cells
  • organism-icon Rattus norvegicus
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Gene 1.0 ST Array (ragene10st)

Description

Polyglutamine(polyQ) expansion of 1A voltage-dependent calcium channel (Cav2.1) is the causative mutation of spinocerebellar ataxia type 6 (SCA6). The C-terminal fragment (CTF) of Cav2.1 makes aggregates in the cytoplasm of SCA6 Purkinje cells and may relate to the pathogenesis. In order to identify genes associated with polyQ expansion and subcellular localization of CTF, we analyzed gene expression profiles of PC12 rat pheochromocytoma cells using Tet-off system.

Publication Title

Cytoplasmic location of α1A voltage-gated calcium channel C-terminal fragment (Cav2.1-CTF) aggregate is sufficient to cause cell death.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE84900
Differential gene expression on islet transplantation with or without the presence of autologous fibroblasts
  • organism-icon Mus musculus
  • sample-icon 10 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Pancreatic islet transplantation was performed in the subcutaneous space of diabetic nude mice. In order to promote long survival and function of transplanted islets a plasma-based scaffold was developed in combination with fibroblasts as graft-supporting accesory cells. Gene expression analysis was carried out to evaluate expression differences due to the presence of fibroblast which could explain the long-term glycemic control observed under these circumstances.

Publication Title

Fibroblasts accelerate islet revascularization and improve long-term graft survival in a mouse model of subcutaneous islet transplantation.

Sample Metadata Fields

Disease, Time

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accession-icon GSE40529
Expression data from untreated and DSS-treated Adamts12 WT and KO mice
  • organism-icon Mus musculus
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Adamts12-deficient mice undergo more severe colitis than WT mice after induction with DSS.

Publication Title

ADAMTS-12 metalloprotease is necessary for normal inflammatory response.

Sample Metadata Fields

Specimen part, Treatment

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accession-icon GSE66416
Differential gene expression of periostin-overexpressing MC3T3-E1 cells
  • organism-icon Mus musculus
  • sample-icon 2 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 2.0 ST Array (mogene20st)

Description

Periostin participates in different processes involved in connective tissue homeostasis. It is also involved in repairment of damaged tissues. We used the osteoblast murine cell line MC3T3-E1 cell line to show how overexpresion of periostin is able to increase their adhesion properties while diminishing their migration capacity. By differential gene expression we evaluated putative targets involved in those cellular properties.

Publication Title

Role of Periostin in Adhesion and Migration of Bone Remodeling Cells.

Sample Metadata Fields

Specimen part, Cell line

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accession-icon GSE62650
Gene expression profiles in dorsal skin of hairless mice orally administrated collagen hydrolysate
  • organism-icon Mus musculus
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Effect of orally administered collagen hydrolysate on gene expression profiles in mouse skin: a DNA microarray analysis.

Sample Metadata Fields

Sex, Age, Specimen part, 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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