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accession-icon GSE19677
Striatum of Huntington's disease model mice
  • organism-icon Mus musculus
  • sample-icon 18 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

Transcriptional changes in Huntington disease identified using genome-wide expression profiling and cross-platform analysis.

Sample Metadata Fields

Age, Specimen part

View Samples
accession-icon GSE47177
Epigenetic determinants of muscle stem cell quiescence and chronological aging
  • organism-icon Mus musculus
  • sample-icon 30 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Skeletal muscle is a post-mitotic tissue that exhibits an extremely low turnover in the absence of disease or injury. At the same time, muscle possesses remarkable regenerative capacity mediated by satellite cells (SCs) that reside in close association with individual myofibers, underneath the fibers basal lamina. Consistent with the low turnover of the muscle, SCs in adult animals are mitotically quiescent and therefore provide an excellent model to study stem cell quiescence. As an organism grows older, the resident stem cells are exposed to a deteriorating environment and experience chronological aging. In stem cells with high turnover, the effects of chronological aging are superimposed upon the effects of the replicative aging that results from DNA replication and cell division. On the contrary, SCs experience minimal replicative aging due to their low turnover. They are thus a good model to study the consequence of chronological aging of quiescent stem cells. We performed microarray analysis of quiescent and activated SCs from both young and aged mice to understand the global gene expression profile underlying stem cell properties such as quiecence and self-renewal, and to understand how the transcriptome of a quiescent stem cell pouplation changes with age.

Publication Title

Chromatin modifications as determinants of muscle stem cell quiescence and chronological aging.

Sample Metadata Fields

Treatment, Time

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accession-icon GSE18551
Striatum of Huntington's disease model mice [Affymetrix data]
  • organism-icon Mus musculus
  • sample-icon 18 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Evaluation of transcriptional changes in the striatum may be an effective approach to understanding the natural history of changes in expression contributing to the pathogenesis of Huntington disease (HD). We have performed genome-wide expression profiling of the YAC128 transgenic mouse model of HD at 12 and 24 months of age using two platforms in parallel; Affymetrix and Illumina. We performed gene expression profiling on the same striatal mRNA across both platforms.

Publication Title

Transcriptional changes in Huntington disease identified using genome-wide expression profiling and cross-platform analysis.

Sample Metadata Fields

Age, Specimen part

View Samples
accession-icon GSE68529
Functionally distinct subsets of lineage-biased multipotent progenitors control blood production in normal and regenerative conditions
  • organism-icon Mus musculus
  • sample-icon 31 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

To identify the molecular characterisitics of parallel lineage-biased MPP populations arising from hematopoietic stem cells (HSC) we conducted genome-wide analyses of hematopoietic stem, progenitor and mature myeloid cell populations using Affymetrix Gene ST1.0 arrays.

Publication Title

Functionally Distinct Subsets of Lineage-Biased Multipotent Progenitors Control Blood Production in Normal and Regenerative Conditions.

Sample Metadata Fields

Specimen part

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accession-icon GSE98224
Placental methylation arrays for the assessment of epigenetic regulation in transcriptional subtypes of human preeclampsia
  • organism-icon Homo sapiens
  • sample-icon 48 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

Preeclampsia (PE) is a complex, heterogeneous disorder of pregnancy, demonstrating considerable variability in observed maternal symptoms and fetal outcomes. We recently identified five clusters of placentas within a large gene expression microarray dataset (N=330, GSE75010), of which four contained a substantial number of PE samples. However, while transcriptional analysis of placentas can subtype patients, we hypothesized that the addition of epigenetic information should reveal gene regulatory mechanisms behind the distinct PE pathologies. We, therefore, subjected 48 of our samples to Infinium Human Methylation 450K arrays and investigated relationships between the gene expression and DNA methylation data.

Publication Title

Epigenetic regulation of placental gene expression in transcriptional subtypes of preeclampsia.

Sample Metadata Fields

Sex, Specimen part, Disease

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accession-icon GSE61284
Gene expression profile of CD4+ T-cells restimulated by anti-CD3 and anti-ICOS compared to anti-CD3 alone
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Engagement of the ICOS receptor represents a key event in a process that culminates in Bcl6 expression and acquisition of the TFH and TFR phenotype. To better understand the essentials of ICOS-mediated signaling pathway, we profiled the changes in gene expression elicited after co-ligation of ICOS and CD3 compared with CD3 ligation alone.

Publication Title

A p85α-osteopontin axis couples the receptor ICOS to sustained Bcl-6 expression by follicular helper and regulatory T cells.

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE75010
Placental gene expression profiling for the identification of clinically relevant subclasses of human preeclampsia
  • organism-icon Homo sapiens
  • sample-icon 157 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

Preeclampsia (PE) is a complex, heterogeneous disorder of pregnancy, demonstrating considerable variability in observed maternal symptoms and fetal outcomes. We hypothesized that this heterogeneity is due to the existence of multiple molecular forms of PE. To address our hypothesis, we created a large (N=330) human placental microarray data set consisting of seven previously published studies (GSE30186, GSE10588, GSE24129, GSE25906, GSE43942, GSE4707, and GSE44711) and 157 highly annotated samples from a BioBank (below).

Publication Title

Unsupervised Placental Gene Expression Profiling Identifies Clinically Relevant Subclasses of Human Preeclampsia.

Sample Metadata Fields

Specimen part, Disease

View Samples
accession-icon GSE100415
Placental gene expression profiling for the identification of subtypes of human fetal growth restriction
  • organism-icon Homo sapiens
  • sample-icon 20 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

Fetal growth restriction (FGR) is a heterogeneous disorder of pregnancy associated with pathologically low fetal and neonatal weights. We hypothesized that FGR consists of multiple placental subtypes, similar to what we have observed in preeclampsia. To address this hypothesis, we assembled a fetal growth-focused human placental microarray data set (N=97) consisting of 20 new normotensive suspected FGR samples (below), in addition to term controls (N=26) and hypertensive suspected FGR samples (N=51) from GSE75010.

Publication Title

Placental transcriptional and histologic subtypes of normotensive fetal growth restriction are comparable to preeclampsia.

Sample Metadata Fields

Specimen part

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accession-icon GSE10263
Mutant huntingtin's effects on striatal gene expression in mice
  • organism-icon Mus musculus
  • sample-icon 31 Downloadable Samples
  • Technology Badge Icon Affymetrix Murine Genome U74A Array (mgu74a), Affymetrix Murine Genome U74A Version 2 Array (mgu74av2), Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Mutant huntingtin's effects on striatal gene expression in mice recapitulate changes observed in human Huntington's disease brain and do not differ with mutant huntingtin length or wild-type huntingtin dosage.

Sample Metadata Fields

Sex, Age, Specimen part

View Samples
accession-icon GSE9857
Striatal gene expression data from 12 weeks-old R6/2 mice and control mice
  • organism-icon Mus musculus
  • sample-icon 17 Downloadable Samples
  • Technology Badge Icon Affymetrix Murine Genome U74A Version 2 Array (mgu74av2), Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Mutant huntingtin's effects on striatal gene expression in mice recapitulate changes observed in human Huntington's disease brain and do not differ with mutant huntingtin length or wild-type huntingtin dosage.

Sample Metadata Fields

No sample metadata fields

View Samples
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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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