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accession-icon GSE52399
Affymetrix gene chip analysis for the whole mouse genome transcripts of epithelial and stromal cells from mouse uterine primary co-culture treated with either vehicle or E2
  • organism-icon Mus musculus
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

In the present study, to identify potential paracrine factor for the stromal regulation of E2-induced epithelial cell proliferation, we treated epithelial and stromal cell populations of mouse uterine primary co-culture with either oil or E2. Three independent RNA pools prepared for each population were then subjected to the Affymetrix gene chip analysis for the whole mouse genome transcripts. Our data revealed up-regulation of 119 genes and down-regulation of 28 genes in epithelial cell populations and up-regulation of 144 genes and down-regulation of 192 genes in stromal cell population.

Publication Title

Estrogen mediated epithelial proliferation in the uterus is directed by stromal Fgf10 and Bmp8a.

Alternate Accession IDs

E-GEOD-52399

Sample Metadata Fields

Specimen part, Treatment

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accession-icon GSE42892
Microarray Analysis of a Familial Hypertrophic Cardiomyopathy Mouse Model Rescued by a Phospholamban Knockout
  • organism-icon Mus musculus
  • sample-icon 24 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Familial hypertrophic cardiomyopathy (FHC) is a disease characterized by ventricular hypertrophy, fibrosis, and aberrant systolic and/or diastolic function. Our laboratories have previously developed 2 mouse models that affect cardiac performance. One transgenic mouse model encodes an FHC-associated mutation in -tropomyosin (Tm180) that displays severe cardiac hypertrophy with fibrosis and impaired physiological performance. The other model was a gene knockout of phospholamban (PLB), a regulator of calcium uptake in the sarcoplasmic reticulum of cardiomyocytes; the hearts of these mice exhibit hypercontractility with no pathological abnormalities. Previous work in our laboratories show that the hearts of mice that were genetically crossed between the Tm180 and PLB KO mice rescues the hypertrophic phenotype and improves their cardiac morphology and function.

Publication Title

Microarray analysis of active cardiac remodeling genes in a familial hypertrophic cardiomyopathy mouse model rescued by a phospholamban knockout.

Alternate Accession IDs

E-GEOD-42892

Sample Metadata Fields

Age, Specimen part

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accession-icon SRP073797
Polycomb repressive complex 1 (PRC1) mediated regualtion of uterine stromal cells decidualization.
  • organism-icon Mus musculus
  • sample-icon 4 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

We extract RNA from mouse implantation sites (IS) on D8 of pregnancy. Mice were treated with or without PRT4165, an inhibitior of PRC1. Total RNAs were analyzed by RNA sequncing. Overall design: There are four samples to be analyzed:Control group 1) "D8ISCOT-1" and 2) "D8ISCOT-2” ; PRT4165 treated groups 3) "D8ISPRT4165-1", 4)”D8ISPRT4165-2”

Publication Title

Polycomb repressive complex 1 controls uterine decidualization.

Alternate Accession IDs

GSE80623

Sample Metadata Fields

Specimen part, Cell line, Subject

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accession-icon GSE46995
Molecular signature with high accuracy for biliary atresia identifies a role for Interleukin-8 in pathogenesis of disease
  • organism-icon Mus musculus, Homo sapiens
  • sample-icon 110 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st), Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Gene expression signature for biliary atresia and a role for interleukin-8 in pathogenesis of experimental disease.

Alternate Accession IDs

E-GEOD-46995

Sample Metadata Fields

Specimen part, Time

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accession-icon GSE46960
Comprehensive gene expression profile of human livers from patients with biliary atresia at the time of diagnosis and the corresponding disease and normal controls
  • organism-icon Homo sapiens
  • sample-icon 92 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

Liver biopsy samples were obtained from 64 infants with biliary atresia at the time of intraoperative cholangiogram. Liver biopsy samples were obtained from 14 age-matched infants with other causes of intrahepatic cholestasis, and from 7 deceased-donor children. GeneChip Human Gene 1.0 ST Array (Affymetrix, CA) were used to screen mRNAs whose expression was specifically regulated in the livers from patients with biliary atresia.

Publication Title

Gene expression signature for biliary atresia and a role for interleukin-8 in pathogenesis of experimental disease.

Alternate Accession IDs

E-GEOD-46960

Sample Metadata Fields

Specimen part

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accession-icon GSE46967
Comprehensive gene expression profile of extrahepatic bile ducts in mice with experimental biliary atresia
  • organism-icon Mus musculus
  • sample-icon 18 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st), Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Newborn Balb/c mice were injected intraperitoneally with 1.5x10^6 fluorescent-forming units (ffu) of type- A Rhesus Rotavirus (RRV) or 0.9% normal saline (NS; control) within 24 hours of birth to induce experimental model of biliary atresia. Extrahepatic bile ducts including gallbladder were microdissected en bloc at 3, 7 and 14 days after RRV or saline injections. GeneChip Mouse Gene 1.0 ST Array (Affymetrix, CA) were used to screen mRNAs whose expression was differently regulated after RRV challenge compared to normal saline controls.

Publication Title

Gene expression signature for biliary atresia and a role for interleukin-8 in pathogenesis of experimental disease.

Alternate Accession IDs

E-GEOD-46967

Sample Metadata Fields

Specimen part, Time

View Samples
accession-icon SRP072041
IL-31 regulation of transcripts in skin
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 1000

Description

Interleukin-31 (IL-31), a T cells derived cytokine which is mainly produced by CD4+ T cells skewed towards Th2 phenotypes. It signals via a heterodimeric receptors composed of IL-31RA and OSMR that is expressed constitutively in epithelial cells and keratinocytes. IL-31 is shown to play a pathogenic role in allergic and inflammatory diseases. Transgenic mice overexpressing IL-31 have a phenotype similar to atopic dermatitis. Here, we studied the role of IL-31 in skin damage by intradermal administration of recombinant IL-31. Notably, IL-31 was sufficient to increase epidermal basal cell proliferation and thickening of the epidermal layer of skin in mice. Analysis of skin transcriptome indicates a significant increase in the transcripts involved in epidermal cell proliferation and pathological skin remodeling. Thus, our study revealed an important role of IL-31 signaling in activating transcriptional programs involved in the pathophysiology of skin diseases. Overall design: mRNA profiles of C57BL/6 mice skin injected with saline and rIL-31 (20µg) via i.d.

Publication Title

IL-31-Driven Skin Remodeling Involves Epidermal Cell Proliferation and Thickening That Lead to Impaired Skin-Barrier Function.

Alternate Accession IDs

GSE79403

Sample Metadata Fields

Specimen part, Treatment, Subject

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accession-icon GSE41595
Integrative genomics identifies candidate microRNAs for pathogenesis of experimental biliary atresia
  • organism-icon Mus musculus
  • sample-icon 18 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Integrative genomics identifies candidate microRNAs for pathogenesis of experimental biliary atresia.

Alternate Accession IDs

E-GEOD-41595

Sample Metadata Fields

Specimen part, Treatment, Time

View Samples
accession-icon GSE41594
Comprehensive gene expression profile of mouse extrahepatic bileducts and gallbladder during a mouse model of biliary atresia.
  • organism-icon Mus musculus
  • sample-icon 18 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Newborn Balb/c mice were injected with 1.5x10^6 fluorescent-forming units (ffu) of Rhesus rotavirus type-A or 0.9% NaCl (normal saline) intraperitoneally within 24 hours of birth to induce experimental model of biliary atresia. The extrahepatic bile ducts including gallbladder were microdissected en bloc at 3, 7 and 14 days after rhesus rotavirus or saline injection. GeneChip Mouse Gene 1.0 ST Array (Affymetrix, CA) were used to screen mRNAs whose expression was differently regulated after rhusus rotavirus injection compare to the normal saline controls.

Publication Title

Integrative genomics identifies candidate microRNAs for pathogenesis of experimental biliary atresia.

Alternate Accession IDs

E-GEOD-41594

Sample Metadata Fields

Specimen part, Treatment, Time

View Samples
accession-icon GSE15235
Staging of biliary atresia at diagnosis by molecular profiling of the liver
  • organism-icon Homo sapiens
  • sample-icon 45 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

BACKGROUND: Young age at portoenterostomy has been linked to improved outcome in biliary atresia, but pre-existing biological factors may influence the rate of disease progression. In this study, we aimed to determine whether molecular profiling of the liver identifies stages of disease at diagnosis. METHODS: We examined liver biopsies from 47 infants with biliary atresia enrolled in a prospective observational study. Biopsies were scored for inflammation and fibrosis, used for gene expression profiles, and tested for association with indicators of disease severity, response to surgery, and survival at 2 years. RESULTS: Fourteen of 47 livers displayed prominent features of inflammation (N=9) or fibrosis (N=5), with the remainder showing similar levels of both simultaneously. Differential profiling of gene expression of the 14 livers displayed a unique molecular signature containing 150 gene probes. Applying prediction analysis models, the probes classified 29 of the remaining 33 livers into inflammation or fibrosis. Molecular classification into the two groups was validated by the findings of increased hepatic population of lymphocyte subsets or tissue accumulation of matrix substrates. The groups had no association with traditional markers of liver injury or function, response to surgery, or complications of cirrhosis. However, infants with an inflammation signature were younger, while those with a fibrosis signature had decreased transplant-free survival. CONCLUSION: Molecular profiling at diagnosis of biliary atresia uncovers a signature of inflammation or fibrosis in most livers. This signature may relate to staging of disease at diagnosis and has implications to clinical outcomes.

Publication Title

Staging of biliary atresia at diagnosis by molecular profiling of the liver.

Alternate Accession IDs

E-GEOD-15235

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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