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accession-icon SRP159173
PatchSeq analysis of Pthlh expressing cells of the mouse dorsolateral striatum
  • organism-icon Mus musculus
  • sample-icon 92 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

In order to investigate how electrophysiological properties vary within the Pthlh population in the dorsolateral striatum we performed PatchSeq analysis of neurons labeled in 5HT3a(EGFP) and Pvalb(cre)::RCE/tdTomato mouse lines, which included Th, Npy/Mia, Cck, and Cck/Vip expressing cells. Overall design: 98 FACS-sorted single cells isolated from the dorso-lateral striatum from either a 5ht3a-EGFP mouse line or a Lhx6-cre mouse crossed onto a R26R-tdTomato reporter mouse line

Publication Title

Diversity of Interneurons in the Dorsal Striatum Revealed by Single-Cell RNA Sequencing and PatchSeq.

Sample Metadata Fields

Specimen part, Cell line, Subject

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accession-icon SRP103831
A versatile drug delivery system targeting senescent cells
  • organism-icon Mus musculus
  • sample-icon 14 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Senescent cells accumulate in many ageing-associated diseases such as pulmonary fibrosis, and targeting these cells has recently emerged as a promising therapeutic approach. Here, we take advantage of the high ß-galactosidase activity of senescent cells to design a targeted drug delivery system based on the encapsulation of drugs with galacto-oligosaccharides (GalNP beads). In this experiment we show that gal-encapsulated rhodamine target senescent cells in the context of pulmonary fibrosis in mice. Overall design: 8- to 10-week-old C57BL/6 wild-type mice were intratracheally inoculated with bleomycin at 1.5 U/kg of body weight. Two weeks later mice were i.v. injected with 200 µl of a solution of GalNP beads loaded with rhodamine [GalNP(rho)] at 4 mg/ml, equivalent to 1 mg/kg of deliverable rhodamine. 6 hours later mice were sacrificed and lung cells were analysed by flow cytometry and sorted into Rho+ or Rho- cells, all CD45-CD31-.

Publication Title

A versatile drug delivery system targeting senescent cells.

Sample Metadata Fields

Specimen part, Cell line, Subject

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accession-icon SRP198959
Small extracellular vesicles are key regulators of non-cell autonomous intercellular communication in senescence via the interferon protein, IFITM3
  • organism-icon Homo sapiens
  • sample-icon 45 Downloadable Samples
  • Technology Badge IconNextSeq 500

Description

Senescence is a cellular phenotype present in health and disease, characterized by a stable cell cycle arrest and an inflammatory response, denominated senescence-associated secretory phenotype (SASP). The SASP is important in influencing the behaviour of neighbouring cells and altering the microenvironment; yet, this role has been mainly attributed to soluble factors. Here, we show that both the soluble factors in addition to small extracellular vesicles (sEV) are capable of transmitting paracrine senescence to nearby cells. Analysis of individual cells internalizing sEV, using a Cre-reporter system, show a positive correlation between sEV uptake and senescence activation. Interestingly, we find an increase in the number of multivesicular bodies during senescence in vivo. sEV protein characterization by mass spectrometry (MS) followed by a functional siRNA screen identify the Interferon Induced Transmembrane Protein 3 (IFITM3) as partially responsible for transmitting senescence to normal cells. Altogether, we found that sEV contribute to paracrine senescence. Overall design: SASP related mRNA transcripts in HFFF2 treated with sEV from iRAS cells in comparison with HFFF2 treated with sEV from iC cells

Publication Title

Small Extracellular Vesicles Are Key Regulators of Non-cell Autonomous Intercellular Communication in Senescence via the Interferon Protein IFITM3.

Sample Metadata Fields

Disease, Subject

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accession-icon SRP071754
Transcriptomic analysis of liver of WT and p21KO mice upon 24h fasting
  • organism-icon Mus musculus
  • sample-icon 9 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

We profiled total liver mRNA of WT and p21KO mice that were fed ad libitum or fasted for 24 hours Overall design: 2-3 mice of each genotype were either fed or fasted for 24 hours, sacrificed and total mRNA was extracted from liver (we mapped >12M reads per sample)

Publication Title

p21<sup>Cip1</sup> plays a critical role in the physiological adaptation to fasting through activation of PPARα.

Sample Metadata Fields

Specimen part, Subject

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accession-icon GSE62161
Expression profile from Saccharomyces cerevisiae strains deleted for PMR1 treated with 5mM CaCl2
  • organism-icon Saccharomyces cerevisiae
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Yeast Genome 2.0 Array (yeast2)

Description

Pmr1 is a cis-Golgi Mn/Ca transporter with a key role in protein glycosylation and manganese detoxification.

Publication Title

Manganese redistribution by calcium-stimulated vesicle trafficking bypasses the need for P-type ATPase function.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE77286
Expression data from Arabidopsis plants under varying zinc supply.
  • organism-icon Arabidopsis thaliana
  • sample-icon 41 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Deficiency of the micronutrient zinc is a widespread condition in agricultural soils, generating a negative impact on crop quality and yield. Nevertheless, there is insufficient knowledge on the regulatory and molecular mechanisms underlying the plant response to inadequate zinc nutrition.

Publication Title

Transcriptomic profiling of Arabidopsis gene expression in response to varying micronutrient zinc supply.

Sample Metadata Fields

Age, Specimen part

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accession-icon GSE21765
Expression data from Arabidopsis gapcp mutant treated with ABA
  • organism-icon Arabidopsis thaliana
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Glycolytic Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) catalyzes the conversion of glyceraldehyde 3-phospate to 1,3-bisphosphoglycerate by coupling with the reduction of NAD+ to NADH. We generated mutants of the Arabidopsis plastidial GAPDH isoforms (At1g79530, At1g16300; GAPCp1, GAPCp2). gapcp double mutants (gapcp1 gapcp2) display a drastic phenotype of arrested root development and sterility.Complex interactions occurring between ABA and sugar signal transduction pathways have been shown, but the molecular mechanisms connecting both pathways are not well understood. Since we found drastic carbohydrate changes in gapcp1 gapcp2, we studied their response to ABA. by performing a microarray analysis comparing gapcp1 gapcp2 and wild type seedlings after a long term treatment with ABA.

Publication Title

Arabidopsis plants deficient in plastidial glyceraldehyde-3-phosphate dehydrogenase show alterations in abscisic acid (ABA) signal transduction: interaction between ABA and primary metabolism.

Sample Metadata Fields

Specimen part, Treatment

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accession-icon SRP069812
Transcriptomic analysis of pancreas and kidney upon induction of reprogramming
  • organism-icon Mus musculus
  • sample-icon 30 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

We profiled total mRNA of pancreas and kidney tissues of 3 different strains (p53-null; In4a/Arf-null and WT) of reprogrammable mouse lines (they all express OCT4, SOX2, KLF4, C-MYC under the control of a tetracycline promoter, activated by doxycycline) Overall design: 5 mice of each genotype were treated with doxycycline to induce the expression of the reprogramming factors, they were sacrificed and total mRNA was extracted from pancreas and kidney tissues (we mapped >24M reads per sample)

Publication Title

Tissue damage and senescence provide critical signals for cellular reprogramming in vivo.

Sample Metadata Fields

Specimen part, Cell line, Subject

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accession-icon SRP068417
Effects of in vivo expansion of mouse embryonic stem cells
  • organism-icon Mus musculus
  • sample-icon 8 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Whe embryonic stem cells are in vitro expanded threir telomereres lengthen, in the absence of genetic manipulations, concomitant with the loss of heterochromatic marks. In order to analyze whether there would be changes in gene expression during in vitro expansion we performed RNA-seq and found no substantial differences in gene expression at passage 6 or 16. Overall design: Embryonic stem (ES) cells were derived from blastocysts expressing GFP in the Rosa26 locus. Four independent lines of ES were in vitro expanded to passage 16. Total RNA was extracted from each independent clones, RNA was extracted and prepared for RNA-seq.

Publication Title

Generation of mice with longer and better preserved telomeres in the absence of genetic manipulations.

Sample Metadata Fields

Specimen part, Cell line, Treatment, Subject

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accession-icon GSE84407
Gene expression data from yerba mate treated and non-treated cultured PBMCs activated with phytohemagglutinin
  • organism-icon Homo sapiens
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Transcriptome Array 2.0 (hta20)

Description

Yerba mate (YM) has been shown to have anti-inflammatory properties in several studies. However, this effect has been found mainly in obesity-related in inflammation. The aim of this work was to study the effect of YM in cultured peripheral blood mononuclear cells to see whether it has anti-inflammatory properties. We stimulated peripheral blood mononuclear cells in vitro with phitohemaglutinin in the presence of yerba mate and determined their activation measuring the the expression of CD25 by flow cytometry. We observed that YM treatment produced a dose-dependent reduction in PBMC activation (CD25 positive cells) when they were stimulated with PHA. This effect was also observed in T cells (CD3 positive) subpopulation. Microarray analysis revealed the differential expression of 128 genes in YM-treated cells. According to a protein-protein interaction database, these genes were highly connected and they are involved in inflammatory response. In summary, it was demonstrated that YM produces a reduction in the amount of activated cells under the stimulation of PHA. Therefore, it might be used in diseases with an inflammatory component.

Publication Title

Yerba mate (Ilex paraguariensis) inhibits lymphocyte activation in vitro.

Sample Metadata Fields

Sex, 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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