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accession-icon GSE40248
Expression data from control and heat shocked mouse spermatocytes and hepatocytes
  • organism-icon Mus musculus
  • sample-icon 13 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

In somatic cells elevated temperature induces activation of the heat shock transcription factor 1 (HSF1) what leads to heat shock proteins synthesis and cytoprotection. However, in the male germ cells (spermatocytes) upon HSF1 activation, caspase-3 dependent apoptosis is induced and spermatogenic cells are actively eliminated.

Publication Title

Impact of heat shock transcription factor 1 on global gene expression profiles in cells which induce either cytoprotective or pro-apoptotic response following hyperthermia.

Sample Metadata Fields

Sex, Specimen part

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accession-icon GSE56257
High-fat diet-mediated dysbiosis promotes intestinal carcinogenesis independent of obesity
  • organism-icon Mus musculus
  • sample-icon 18 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Several aspects common to a Western lifestyle, including obesity and decreased physical activity, are known risks for gastrointestinal cancers. There is an increasing amount of evidence suggesting that diet profoundly affects the composition of the intestinal microbiota. Moreover, there is now unequivocal evidence linking a dysbiotic gut to cancer development. Yet, the mechanisms through which high-fat diet (HFD)-mediated changes in the microbial community impact the severity of tumorigenesis in the gut, remain to be determined.

Publication Title

High-fat-diet-mediated dysbiosis promotes intestinal carcinogenesis independently of obesity.

Sample Metadata Fields

Sex, Age, Specimen part, Treatment

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accession-icon SRP080997
Wnt-responsive mesenchymal cells in dorsal back skin and ventral foot skin
  • organism-icon Mus musculus
  • sample-icon 9 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Canonical WNT-signaling is essential for placode formation irrespective of appendage type. At sites of placode initiation, Although WNT-signaling occurs in both epithelium and mesenchyme, the site of most intense activity as revealed by the WNT reporter Axin2-LacZ was in a zone just below the epithelial-mesenchymal interface. In ventral foot-skin, this WNT activity peaked at E17.5, concomitant with sweat bud fate commitment, while in dorsal back-skin, it began at E14.5, concomitant with HF fate specification. Overall design: To address whether WNT-signaling within this zone might regionally influence the transcriptional landscape of body-site mesenchymes to support distinct epithelial fates, we transcriptionally profiled the Axin2-positive and Axin2-negative dermal cells following their FACS-purification from E17.5 ventral foot-skin and E14.5 dorsal back-skin

Publication Title

Spatiotemporal antagonism in mesenchymal-epithelial signaling in sweat versus hair fate decision.

Sample Metadata Fields

Specimen part, Subject

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accession-icon GSE26396
Specific MicroRNAs Are Preferentially Expressed by Skin Stem Cells To Balance Self-Renewal and Early Lineage Commitment
  • organism-icon Mus musculus
  • sample-icon 6 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

Specific microRNAs are preferentially expressed by skin stem cells to balance self-renewal and early lineage commitment.

Sample Metadata Fields

Sex, Specimen part, Treatment

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accession-icon GSE26394
Gene Expression data of P4 stage hair follicle ORS cells from DTG (K14-rtTA,TRE-miR-125b) and control littermates
  • organism-icon Mus musculus
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Increasing evidence suggests that microRNAs may play important roles in regulating self-renewal and differentiation in mammalian stem cells (SCs). Here, we explore this issue in skin. We first characterize microRNA expression profiles of skin SCs versus their committed proliferative progenies and identify a microRNA subset associating with stemness. Of these, miR-125b is dramatically downregulated in early SC-progeny. We engineer an inducible mice system and show that when miR-125b is sustained in SC-progenies, tissue balance is reversibly skewed towards stemness at the expense of epidermal, oil-gland and HF differentiation. Using gain-and-loss of function in vitro, we further implicate miR-125b as a repressor of SC differentiation. In vivo, transcripts repressed upon miR-125b induction are enriched >700% for predicted miR-125b targets normally downregulated upon SC-lineage commitment. We verify some of these miR-125b targets, and show that Blimp1 and VDR in particular can account for many tissue imbalances we see when miR-125b is deregulated.

Publication Title

Specific microRNAs are preferentially expressed by skin stem cells to balance self-renewal and early lineage commitment.

Sample Metadata Fields

Sex, Specimen part, Treatment

View Samples
accession-icon GSE41704
Transcriptional profiling of bulge stem cells
  • organism-icon Mus musculus
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Expression 430A Array (moe430a)

Description

In adult skin, each hair follicle contains a reservoir of stem cells (the bulge), which can be mobilized to regenerate the new follicle with each hair cycle and to reepithelialize epidermis during wound repair. Here we report new methods that permit their clonal analyses and engraftment and demonstrate the two defining features of stem cells, namely self-renewal and multi-potency. We also show that, within the bulge, there are two distinct populations, one of which maintains basal lamina contact and temporally precedes the other, which is suprabasal and arises only after the start of the first postnatal hair cycle. This spatial distinction endows them with discrete transcriptional programs, but surprisingly, both populations are growth inhibited in the niche but can self-renew in vitro and make epidermis and hair when grafted. These findings suggest that the niche microenvironment imposes intrinsic stemness features without restricting the establishment of epithelial polarity and changes in gene expression.

Publication Title

Self-renewal, multipotency, and the existence of two cell populations within an epithelial stem cell niche.

Sample Metadata Fields

Specimen part

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accession-icon GSE9621
Comparison of global gene expression between Pseudomonas aeruginosa strains 383 and 2192
  • organism-icon Pseudomonas aeruginosa
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Pseudomonas aeruginosa Array (paeg1a)

Description

At mid-log phase (OD600 of 0.5), unique gene expression patterns were observed between these two strains with 3.4% of the transcripts (188/5570) expressed differentially.

Publication Title

A novel oxidized low-density lipoprotein-binding protein from Pseudomonas aeruginosa.

Sample Metadata Fields

No sample metadata fields

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accession-icon SRP027384
In vivo transcriptional goverance of hair follicle stem cells by canonical Wnt regulators
  • organism-icon Mus musculus
  • sample-icon 2 Downloadable Samples
  • Technology Badge Icon

Description

Mouse hair follicles undergo synchronized cycles. Cyclical regeneration and hair growth is fueled by hair follicle stem cells (HFSCs). HFSCs regenerate hair in response to canonical Wnt signalling. We used RNA-seq to unfold genome-wide chromatin landscapes of ß-catenin within the native HFSC-niche. Overall design: ß-catenin control and cKO hair follicle stem cells (HFSCs) at the onset of anagen skins were FACS-purified for RNA-sequcencing. Telogen quiescent hair follicle stem cells (HFSCs) were FACS-purified for ChIP-sequcencing. Telogen>anagen activated bulge hair follicle stem cells (HFSCs) were FACS-purified for RNA-sequcencing.

Publication Title

In vivo transcriptional governance of hair follicle stem cells by canonical Wnt regulators.

Sample Metadata Fields

No sample metadata fields

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accession-icon SRP130953
Differential miRNA Expression in B Cells/T Cells Associated with Inter-individual Differences in Humoral Immune Response to Measles Vaccination
  • organism-icon Homo sapiens
  • sample-icon 88 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Through Next Generation Sequencing (mRNA-Seq) of intracellular miRNAs in measles virus-stimulated B and CD4+ T cells isolated from high and low antibody responders to measles vaccination, we identified a set of B cell-specific miRNAs (e.g., miR-151a-5p, miR-223, miR-29, miR-15a-5p, miR-199a-3p, miR-103a, and miR-15a/16 cluster) associated with measles-specific antibody response after vaccination. No CD4+ T cell-specific miRNA expression differences between high and low antibody responders were found. DIANA tool was used for gene/target prediction and pathway enrichment analysis and this yielded several biological processes/pathways, including regulation of adherens junction proteins, Fc-receptor signaling pathway, phosphatidylinositol-mediated signaling pathway, growth factor signaling pathway/pathways, transcriptional regulation, apoptosis and virus-related processes, that were significantly associated with neutralizing antibody titers after measles vaccination. This study demonstrates that miRNA expression directly or indirectly influences humoral immunity to measles vaccination and suggests that B cell-specific miRNAs may potentially serve as predictive biomarkers of vaccine response. Overall design: Examination of miRNA expression differences in/between purified B and CD4+ T cells of high and low responders to measles vaccination.

Publication Title

Differential miRNA expression in B cells is associated with inter-individual differences in humoral immune response to measles vaccination.

Sample Metadata Fields

Specimen part, Subject

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accession-icon GSE61149
Ikaros mediates gene silencing in T cells through Polycomb Repressive Complex 2
  • organism-icon Mus musculus
  • sample-icon 10 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

Ikaros mediates gene silencing in T cells through Polycomb repressive complex 2.

Sample Metadata Fields

Specimen part, Cell line

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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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