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accession-icon SRP062768
Gene expression in the developing murine utricle
  • organism-icon Mus musculus
  • sample-icon 9 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

We report a gene expression changes during development and maturation of the murine utricle Overall design: Using RNA-sequencing, we examined the gene expression in the murine utricle at E17.5, p0, and p9

Publication Title

SoxC transcription factors are essential for the development of the inner ear.

Sample Metadata Fields

Specimen part, Cell line, Subject

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accession-icon GSE55853
Dynamic gene expression by putative hair-cell progenitors during regeneration in the zebrafish lateral line
  • organism-icon Danio rerio
  • sample-icon 52 Downloadable Samples
  • Technology Badge Icon Zebrafish Gene 1.0 ST Array (zebgene10st)

Description

Hearing loss is most commonly caused by the destruction of mechanosensory hair cells in the ear. This condition is usually permanent: Despite the presence of putative hair-cell progenitors in the cochlea, hair cells are not naturally replenished in adult mammals. Unlike those of the mammalian ear, the progenitor cells of nonmammalian vertebrates can regenerate hair cells through- out life. The basis of this difference remains largely unexplored but may lie in molecular dissimilarities that affect how progenitors respond to hair-cell death.

Publication Title

Dynamic gene expression by putative hair-cell progenitors during regeneration in the zebrafish lateral line.

Sample Metadata Fields

Specimen part

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accession-icon GSE41469
Mapping and genome-wide profiling of human NKp46+ cells
  • organism-icon Homo sapiens
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Understanding Natural Killer (NK) cell anatomical distribution is key to dissect the role of these unconventional lymphocytes in physiological and disease conditions. In mouse, NK cells have been detected in various lymphoid and non-lymphoid organs, while in humans the current knowledge of NK cell distribution at steady state is mainly restricted to lymphoid tissues. The translation to humans of findings obtained in mice is facilitated by the identification of NK cell markers conserved between these two species. The Natural Cytotoxicity Receptor (NCR) NKp46 is a marker of the NK cell lineage evolutionary conserved in mammals. In mice, NKp46 is also present on rare T cell subsets and on a subset of gut Innate Lymphoid Cells (ILCs) expressing the retinoic acid receptor-related orphan receptor gammat (RORgammat) transcription factor. Here, we documented the distribution and the phenotype of human NKp46+ cells in lymphoid and non-lymphoid tissues isolated from healthy donors. Human NKp46+ cells were found in splenic red pulp, in lymph nodes, in lungs and gut lamina propria, thus mirroring mouse NKp46+ cell distribution. We identified a novel cell subset of CD56dimNKp46low cells that includes RORgammat+ILCs with a lineage-CD94-CD117brightCD127bright phenotype.We also included data regarding the genome-wide transcriptional profiles of human healthy colonic NK cells and RORgammat+ILCs.The use of NKp46 thus contributes to establish the basis for analyzing quantitative and qualitative changes of NK cell and ILC subsets in human diseases.

Publication Title

Mapping of NKp46(+) Cells in Healthy Human Lymphoid and Non-Lymphoid Tissues.

Sample Metadata Fields

Specimen part

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accession-icon GSE110811
Distinct Gene Expression Profiles Define Anaplastic Grade in Retinoblastoma
  • organism-icon Homo sapiens
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 2.0 ST Array (hugene20st)

Description

Morbidity and mortality associated with retinoblastoma have decreased drastically in recent decades, in large part due to better prediction of high-risk disease and appropriate treatment stratification. High-risk histopathologic features and severe anaplasia both predict the need for more aggressive treatment; however, not all centers are able to easily assess tumor samples for degree of anaplasia. Instead, identification of genetic signatures able to distinguish among anaplastic grades and thus predict high versus low risk retinoblastoma would facilitate appropriate risk stratification in a wider patient population. A better understanding of genes dysregulated in anaplasia would also yield valuable insights into pathways underlying the development of more severe retinoblastoma. Here, we present the histopathologic and gene expression analysis of 28 retinoblastoma cases using microarray analysis. Tumors of differing anaplastic grade show clear differential gene expression, with significant dysregulation of unique genes and pathways in severe anaplasia. Photoreceptor and nucleoporin expression in particular are identified as highly dysregulated in severe anaplasia and suggest particular cellular processes contributing to the development of increased retinoblastoma severity. A limited set of highly differentially expressed genes are also able to accurately predict severe anaplasia in our dataset. Together, these data contribute to the understanding of the development of anaplasia and facilitate the identification of genetic markers of high-risk retinoblastoma.

Publication Title

Distinct Gene Expression Profiles Define Anaplastic Grade in Retinoblastoma.

Sample Metadata Fields

Specimen part

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accession-icon SRP082228
Molecular Analysis of Sink Limited Soybeans
  • organism-icon Glycine max
  • sample-icon 38 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Soybean plants that do not produce a sink, such as depodded or male sterile plants, exhibit physiological and morphological changes during the reproductive stages, including increased levels of nitrogen and starch in the leaves and a delayed senescence. To identify transcriptional changes that occur in leaves of sink-limited plants, we used RNAseq to compare gene expression levels in trifoliate leaves from depodded and ms6 male sterile plants and control plants. In sink-limited tissues, we observed a deferral of the expression of senescence-associated genes and a continued high expression of genes associated with the maturity phase of leaf development. We identified GO-terms associated with growth and development and storage protein in sink limited tissues. We also identified that the bHLH. ARFs, and SBP transcription factors were expressed in sink limited tissues while the senescing control leaves expressed WRKY and NAC transcription factors. We identified genes that were not expressed during normal leaf development but highly expressed in sink-limited plants, including the D4 “non-yellowing” gene. These changes highlighted several metabolic pathways that were involved in distinct modes of resource parttioning in the “stay green” leaves. Overall design: Timecourse gene expression analysis of sink-limited soybean leaves. Gene expression was profiled from R2 growth stage (flowering) until the onset of leaf seenscence, and contrasted between mechanically and genetically sink-limited soybeans.

Publication Title

Transcriptional profiling of mechanically and genetically sink-limited soybeans.

Sample Metadata Fields

Specimen part, Subject, Time

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accession-icon SRP048326
Gene Expression Profiling of Glycine max Cotyledons and Trifoliate Leaves to Determine Genes Associated with Senescence
  • organism-icon Glycine max
  • sample-icon 41 Downloadable Samples
  • Technology Badge IconIllumina HiScanSQ, Illumina HiSeq 2500

Description

We use RNA sequencing technology in a time course study to measure transcript abundance from three developmental stages in cotyledons and five stages in the trifoliate leaf of Glycine max to identify genes with distinct temporal patterns of expression during leaf or cotyledon development. We also examine the diffrences between these two photosynthetic tissues. Overall design: Timecourse Expression analysis of Cotyledon Development and Leaf Development using RNAseq on distinct timepoints. 3 stages of the cotyledon were sequenced with 3 biological replicates in each stage. Five stages of the leaf were sequenced with 3 biological replicates for each stage.

Publication Title

Developmental profiling of gene expression in soybean trifoliate leaves and cotyledons.

Sample Metadata Fields

Specimen part, Subject

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accession-icon GSE29529
Transcriptome profiling of Saccharomyces cerevisiae during a transition from fermentative to glycerol-based respiratory growth reveals extensive metabolic and structural remodeling.
  • organism-icon Saccharomyces cerevisiae
  • sample-icon 10 Downloadable Samples
  • Technology Badge Icon Affymetrix Yeast Genome S98 Array (ygs98)

Description

Transcriptome analyses using a wild-type strain of Saccharomyces cerevisiae were performed to assess the overall pattern of gene expression during the transition from glucose-based fermentative to glycerol-based respiratory growth. These experiments revealed a complex suite of metabolic and structural changes associated with the adaptation process. Alterations in gene expression leading to remodeling of various membrane transport systems and the cortical actin cytoskeleton were observed. Transition to respiratory growth was accompanied by alterations in transcript patterns demonstrating not only a general stress response, as seen in earlier studies, but also the oxidative and osmotic stress responses. In some contrast to earlier studies, these experiments identified modulation of expression for many genes specifying transcription factors during the transition to glycerol-based growth. Importantly and unexpectedly, an ordered series of changes was seen in transcript levels from genes encoding components of the TFIID, SAGA (Spt-Ada-Gcn5-Acetyltransferase), and SLIK (Saga LIKe) complexes and all three RNA polymerases, suggesting a modulation of structure for the basal transcriptional machinery during adaptation to respiratory growth. In concert with data given in earlier studies, the results presented here highlight important aspects of metabolic and other adaptations to respiratory growth in yeast that are common to utilization of multiple carbon sources. Importantly, they also identify aspects specific to adaptation of this organism to growth on glycerol as sole carbon source.

Publication Title

Transcriptome profiling of Saccharomyces cerevisiae during a transition from fermentative to glycerol-based respiratory growth reveals extensive metabolic and structural remodeling.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE10031
mRNA expression data in rsf1mutant during growth on, and transition to growth on glycerol as sole carbon source
  • organism-icon Saccharomyces cerevisiae
  • sample-icon 22 Downloadable Samples
  • Technology Badge Icon Affymetrix Yeast Genome S98 Array (ygs98)

Description

Rsf1p is a putative transcription factor required for efficient growth using glycerol as sole carbon source but not for growth on the alternative respiratory carbon source ethanol.

Publication Title

Rsf1p is required for an efficient metabolic shift from fermentative to glycerol-based respiratory growth in S. cerevisiae.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE5145
Genes regulated by vitamin D in bronchial smooth muscle cells
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Studied gene regulation in bronchial smooth muscle cells following vitamin D stimulation.

Publication Title

1alpha,25-dihydroxy-vitamin D3 stimulation of bronchial smooth muscle cells induces autocrine, contractility, and remodeling processes.

Sample Metadata Fields

Sex, Age, Specimen part, Race

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accession-icon GSE29530
The YJR127C/ZMS1 gene product is involved in glycerol-based respiratory growth of the yeast Saccharomyces cerevisiae.
  • organism-icon Saccharomyces cerevisiae
  • sample-icon 5 Downloadable Samples
  • Technology Badge Icon Affymetrix Yeast Genome S98 Array (ygs98)

Description

A putative yeast mitochondrial upstream activating sequence (UAS) was used in a one-hybrid screening procedure that identified the YJR127C ORF on chromosome X. This gene was previously designated ZMS1 and is listed as a transcription factor on the SGD website. Real time RT-PCR assays showed that expression of YJR127C/ZMS1 was glucose-repressible, and a deletion mutant for the gene showed a growth defect on glycerol-based but not on glucose- or ethanol-based medium. Real time RT-PCR analyses identified severely attenuated transcript levels from GUT1 and GUT2 to be the source of that growth defect, the products of GUT1 and GUT2 are required for glycerol utilization. mRNA levels from a large group of mitochondria- and respiration-related nuclear genes also were shown to be attenuated in the deletion mutant. Importantly, transcript levels from the mitochondrial OLI1 gene, which has an associated organellar UAS, were attenuated in the DeltaYJR127C mutant during glycerol-based growth, but those from COX3 (OXI2), which lacks an associated mitochondrial UAS, were not. Transcriptome analysis of the glycerol-grown deletion mutant showed that genes in several metabolic and other categories are affected by loss of this gene product, including protein transport, signal transduction, and others. Thus, the product of YJR127C/ZMS1 is involved in transcriptional control for genes in both cellular genetic compartments, many of which specify products required for glycerol-based growth, respiration, and other functions.

Publication Title

The YJR127C/ZMS1 gene product is involved in glycerol-based respiratory growth of the yeast Saccharomyces cerevisiae.

Sample Metadata Fields

No sample metadata fields

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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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