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accession-icon SRP181649
Targeting HuH7 cells with JumonjiC Lysine Demethylase Inhibitors (RNA-Seq)
  • organism-icon Homo sapiens
  • sample-icon 12 Downloadable Samples
  • Technology Badge IconNextSeq 500

Description

Characterization of gene expression changes in HuH7 HCC cells upon treatment with the Jumonji KDM inhibitor, JIB-04, GSK-J4 and SD-70. Overall design: Comparison of gene expression changes between HuH7 cells treated with JIB-04, GSK-J4 or SD-70 vs. DMSO

Publication Title

A comprehensive study of epigenetic alterations in hepatocellular carcinoma identifies potential therapeutic targets.

Sample Metadata Fields

Sex, Age, Treatment, Race, Subject

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accession-icon GSE54870
Transcription profiling by array of wild type and arr1,10,12 mutant Arabidopsis seedlings treated with the cytokinin benzyladenine
  • organism-icon Arabidopsis thaliana
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Effect of the cytokinin BA on wt and arr1,10,12 mutant seedlings

Publication Title

Type B response regulators of Arabidopsis play key roles in cytokinin signaling and plant development.

Sample Metadata Fields

Age, Specimen part

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accession-icon GSE59807
Gene expression in the GWAT of ob/ob and ob/ob/Fsp27-/- mice
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

GWAT store most of the TAG in mice, ob/ob mice is an obese mice. Ob/ob/Fsp27-/- mice are lean when compared with ob/ob mice. The GWAT weight was dramatically reduced in ob/ob/Fsp27-/- mice.

Publication Title

Insulin resistance and white adipose tissue inflammation are uncoupled in energetically challenged Fsp27-deficient mice.

Sample Metadata Fields

Sex, Age, Specimen part

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accession-icon GSE25012
WNT pathway activation promotes phenotypic reprogramming of glioblastoma derived cells in zebrafish nervous system microenvironment
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

phenotypic reprogramming ability of teh zebtafish brain microenviroment on GBM derived cells controlled by the activation of endogenous Wnt pathway

Publication Title

Wnt activation promotes neuronal differentiation of glioblastoma.

Sample Metadata Fields

Specimen part, Time

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accession-icon GSE14221
TgFVB vs FVB 6 and 8 week kidneys
  • organism-icon Mus musculus
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Human Immunodeficiency Virus (HIV) associated nephropathy (HIVAN) is characterized clinically by both nephrosis and by rapidly progressive kidney dysfunction. HIVAN is characterized histologically by both collapsing focal segmental glomerulosclerosis and prominent tubular damage. Neutrophil Gelatinase Associated Lipocalin (NGAL) is known to be rapidly expressed in distal segments of the nephron at the onset of different types of acute kidney injury, but few studies have examined NGAL in chronic kidney disease models. We found that urinary NGAL (uNGAL) was highly expressed by patients with biopsy proven HIVAN, whereas HIV+ patients without HIVAN demonstrated lower levels. uNGAL was also highly expressed in the TgFVB mouse model of HIVAN, which demonstrated NGAL gene expression in dilated, microcystic segments of the nephron. These data show that NGAL is markedly upregulated in the setting of HIVAN, and suggest that uNGAL levels may provide a non-invasive screening test to detect HIVAN related tubular disease.

Publication Title

Urinary NGAL marks cystic disease in HIV-associated nephropathy.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE2835
Effect of Retinoic Acid on Gene Expression in Human Conjunctival Epithelial Cell Line
  • organism-icon Homo sapiens
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A Array (hgu133a)

Description

Purpose. How vitamin A contributes to the maintenance of the wet-surfaced phenotype at the ocular surface is not well understood. We sought to identify vitamin A responsive genes in ocular surface epithelia using gene microarray analysis of cultures of a human conjunctival epithelial cell line (HCjE) grown with all-trans-retinoic acid (RA). The analysis showed that the membrane-associated mucin MUC16 was induced by RA and that secretory phospholipase A2 Group IIA (sPLA2-IIA), the gene most upregulated by RA, was induced earlier. Since eicosanoids, metabolites of arachidonic acid, which is produced by sPLA2 catalysis of membrane phospholipids, have been demonstrated to affect mucin production, we sought to determine if the sPLA2 induction in HCjE cells was associated with RA induction of MUC16.

Publication Title

Effect of retinoic acid on gene expression in human conjunctival epithelium: secretory phospholipase A2 mediates retinoic acid induction of MUC16.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE22946
Transcriptome analysis of mouse cerebral cortical neural progenitor cells
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Transcriptome analysis of neural progenitor/stem cells is limited by the lack of a reliable method for cell isolation. We have designed a genetic dual reporter strategy that can allow prospective isolation of cortical neural progenitor cells and their neuronal progeny form the same animals. These cells should be a good cell source for comparative global analysis.

Publication Title

Transcriptome analysis of neural progenitor cells by a genetic dual reporter strategy.

Sample Metadata Fields

Specimen part

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accession-icon GSE17936
Nkx2.5 regulates Jarid2 during outflow tract morphogenesis
  • organism-icon Mus musculus
  • sample-icon 26 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302), Affymetrix Mouse Expression 430A Array (moe430a)

Description

The transcription factor Nkx2.5 is required for specification of pharyngeal arch second heart field (SHF) progenitors that contribute to outflow tract (OFT) and right ventricle (RV) formation. Multiple sets of microarray data were analyzed to identify genes that are candidate targets of Nkx2.5 in the second heart field. These sets are: 1) publicly available data for cardiothoracic tissue from E9.5 Nkx2.5 wild-type, heterozygous and homozygous embryos; 2) an analysis of mouse E10.5 pharyngeal arch tissue; 3) an analysis of mouse E12.5 heart tissue; and 4) a temporal analysis of the cardiogenic cell line P19CL6. This combined analysis identified 11 genes (Lrrn1, Elovl2, Safb, Slc39a6, Khdrbs1, Hoxb4, Fez1, Ccdc117, Jarid2, Nrcam, and Enpp3) expressed in SHF-containing pharyngeal arch tissue whose regulation is dependent on Nkx2.5 expression.

Publication Title

Jarid2 is among a set of genes differentially regulated by Nkx2.5 during outflow tract morphogenesis.

Sample Metadata Fields

Specimen part, Cell line

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accession-icon GSE17910
In vitro differentiation of P19CL6 cardiogenic embryonic carcinoma cells
  • organism-icon Mus musculus
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Pluripotent P19CL6 embryonic carcinoma cells can be differentiated to a cardiac lineage by culture in the presence of DMSO. The goal of this study was to characterize temporal gene expression patterns associated with cardiogenic differentiation. Gene expression analysis was conducted on differentiating P19CL6 cells at several time points following induction with 1% DMSO. Samples were processed for analysis by Affymetrix GeneChip.

Publication Title

Jarid2 is among a set of genes differentially regulated by Nkx2.5 during outflow tract morphogenesis.

Sample Metadata Fields

Cell line

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accession-icon E-MEXP-1195
Transcription profiling of rat to investigate effects of hyperglycaemi and genetic background on gene expression
  • organism-icon Rattus norvegicus
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Expression 230A Array (rae230a)

Description

Effects of hyperglycaemia and genetic background differences on renal gene expression

Publication Title

Comparative analysis of methods for gene transcription profiling data derived from different microarray technologies in rat and mouse models of diabetes.

Sample Metadata Fields

Sex, Age, Specimen part, Disease, 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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