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accession-icon GSE38381
Chicken neural crest and neural plate
  • organism-icon Gallus gallus
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Chicken Genome Array (chicken)

Description

Neural cest cells are a transient stem cell-like population appearing during vertebrate embryonic development. Generation of the cranial neural crest is known to require a balanced combination of FGF and BMP levels. However, it is poorly understood how the functions of such growth factors are controlled in the extracellular spaces. Anosmin is an extracellular matrix protein implicated in FGF signaling and mutated in Kallmann syndrome. Here, we demonstrate that anosmin (Gga.14976.1.S1_at, clone ChEST132d10) is synthesized locally in the cranial neural crest of chicken embryos and is essential for cranial neural crest formation. Anosmin upregulates FGF8 and BMP5 gene expression; it also enhances FGF8 activity while inhibiting BMP5 and WNT3a signaling. Taken together, our data establish that the matrix protein anosmin is required for cranial neural crest formation, with funtional modulation of FGF, BMP, and WNT.

Publication Title

Extracellular matrix protein anosmin promotes neural crest formation and regulates FGF, BMP, and WNT activities.

Sample Metadata Fields

Specimen part

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accession-icon SRP162113
Characterization of ST2+ and ST2- mTh cells in helminth infection
  • organism-icon Mus musculus
  • sample-icon 12 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 1500

Description

CD4+T cells are differentiated into Th1, Th2, Th17 and Treg cells after Antigen presentation by other cell types such as dendritic cells, macrophages and B cells in Lymph nodes. Those differentiated CD4+T cells are subdivided into cell subsets by their producing cytokines and surface markers. We recently identified that ST2 expressing Th2 cells highly produced IL-5 comparing to ST2- Th2 cells in helminth infection. In this study, we investigated the RNAseq analysis to characterize these Th2 cells. Overall design: Characterization of ST2+ and ST2- mTh cells are assessed by RNA-seq.

Publication Title

CXCR6<sup>+</sup>ST2<sup>+</sup> memory T helper 2 cells induced the expression of major basic protein in eosinophils to reduce the fecundity of helminth.

Sample Metadata Fields

Specimen part, Cell line, Subject

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accession-icon GSE33019
Activated YAP1 stimulates cardiomyocyte proliferation
  • organism-icon Rattus norvegicus
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Gene 1.0 ST Array (ragene10st)

Description

Postnatal day 4 neonatal rat cardiomyocytes transduced with LacZ or flag-tagged, activated YAP1 (S127A) expressing adenovirus

Publication Title

YAP1, the nuclear target of Hippo signaling, stimulates heart growth through cardiomyocyte proliferation but not hypertrophy.

Sample Metadata Fields

Treatment

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accession-icon SRP140855
Systemically administered extremely low HMGN1 with anti-CD4 depleting antibody exerts synergistic anti-tumor effects
  • organism-icon Mus musculus
  • sample-icon 5 Downloadable Samples
  • Technology Badge IconIon Torrent Proton

Description

Recently there has been growing interest in the immunomodulatory effects of endogenous danger signals known as alarmins. In this study, we explore a new combination therapy of anti-CD4 depleting antibody with an alarmin, high mobility group nucleosome binding protein 1 (HMGN1). Extremely low dose of HMGN1 with anti-CD4 depleting antibody exerted robust anti-tumor effects in Colon26 subtaneous murine model. To understand transcriptomic differences of CD8+ T cells in the tumor-bearing mice after treated with anti-CD4 depleting antibody or combination therapy of HMGN1 with anti-CD4 depleting antibody, we performed CD8 T cell transcriptome analysis using 3'SAGE-seq and Ion Proton sequencer. Overall design: CD8+ T cells were purified from single cell suspension of each implanted mouse tumor by lineage sorting (CD45-CD11b-B220-CD49b-Ter119-CD4-CD8+) through FACSAria. CD8 T cell transcriptome analysis were generated by 3'SAGE-seq using Ion Proton sequencer.

Publication Title

Combined treatment with HMGN1 and anti-CD4 depleting antibody reverses T cell exhaustion and exerts robust anti-tumor effects in mice.

Sample Metadata Fields

Specimen part, Cell line, Subject

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accession-icon GSE48595
Expression data analysis of murine pulmonary cryptococcosis induced by C. gattii
  • organism-icon Mus musculus
  • sample-icon 3 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Our previous investigation indicated that high-virulence C. gattii (C. gattii TIMM 4097) tend to reside in the alveoli, whereas low-virulence C. gattii (C. gattii TIMM 4903) tend to be washed out from the alveoli and move into the central side of the respiratory system. To test this hypothesis, we performed microarray assay.

Publication Title

How histopathology can contribute to an understanding of defense mechanisms against cryptococci.

Sample Metadata Fields

Sex, Specimen part

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accession-icon GSE6388
Neocortical and hippocampal gene expression in kainate- and nicotine-injected juvenile mice
  • organism-icon Mus musculus
  • sample-icon 34 Downloadable Samples
  • Technology Badge Icon Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)

Description

To examine irreversible changes in the developing brain following seizures, juvenile inbred mice were intraperitoneally injected with kainate and nicotine.

Publication Title

Increased expression of the lysosomal protease cathepsin S in hippocampal microglia following kainate-induced seizures.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE152616
Expression data from lens epithelial cells (LECs) from Shumiya cataract rats (SCR) with or without cataract (Cat+ or Cat-)
  • organism-icon Rattus norvegicus
  • sample-icon 2 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Gene 2.0 ST Array (ragene20st)

Description

The Shumiya cataract rat (SCR) is a model for hereditary cataract. Two-third of these rats develop lens opacity within 10-11-weeks. Onset of cataract is attributed to the synergetic effect of lanosterol synthase (Lss) and farnesyl-diphosphate farnesyltransferase 1 (Fdft1) mutant alleles that lead to cholesterol deficiency in the lenses, which in turn adversely affects lens biology including the growth and differentiation of lens epithelial cells (LECs). Nevertheless, the molecular events and changes in gene expression associated with the onset of lens opacity in SCR is poorly understood.

Publication Title

Identification of Differential Gene Expression Pattern in Lens Epithelial Cells Derived from Cataractous and Noncataractous Lenses of Shumiya Cataract Rat.

Sample Metadata Fields

Specimen part, Disease

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accession-icon GSE76698
Exon array analysis of control vs. FALS MPC
  • organism-icon Homo sapiens
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)

Description

To assess RNA regulation in FALS for gene expression and alternative processing of RNA in the motor neuron precurssors (MPCs)

Publication Title

Establishment of In Vitro FUS-Associated Familial Amyotrophic Lateral Sclerosis Model Using Human Induced Pluripotent Stem Cells.

Sample Metadata Fields

Specimen part

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accession-icon GSE27913
Overexpression of NUCKS1 in colorectal cancer correlates with recurrence after curative surgery
  • organism-icon Homo sapiens
  • sample-icon 112 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Identification of NUCKS1 as a colorectal cancer prognostic marker through integrated expression and copy number analysis.

Sample Metadata Fields

Specimen part

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accession-icon GSE21510
Clinical Significance of Osteoprotegerin Expression in Human Colorectal Cancer
  • organism-icon Homo sapiens
  • sample-icon 146 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Purpose: This study aimed to identify a novel biomarker or a target of treatment for colorectal cancer (CRC).

Publication Title

Clinical significance of osteoprotegerin expression in human colorectal cancer.

Sample Metadata Fields

Specimen part

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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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