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accession-icon SRP029262
Global transcriptomic analysis of human pancreatic islets reveals novel genes influencing glucose metabolism [RNA-seq]
  • organism-icon Homo sapiens
  • sample-icon 88 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Here we harnessed the potential of RNA sequencing in 89 human pancreatic islet donors to identify genes and exons regulated in this relevant tissue for T2D. Overall design: mRNA profiles of 89 human pancreatic islet donors having different levels of blood glucose (HbA1c) with and without T2D. The data was generated by deep sequencing using Illumina HiSeq 2000.

Publication Title

Orphan G-protein coupled receptor 183 (GPR183) potentiates insulin secretion and prevents glucotoxicity-induced β-cell dysfunction.

Sample Metadata Fields

Sex, Age, Specimen part, Subject

View Samples
accession-icon GSE19603
Expression data from Arabipdosis msh1 recA3 double mutant under heat stress
  • organism-icon Arabidopsis thaliana
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

In Arabidposis thaliana, the msh1 recA3 double mutant shows an extensive mitochondrial genome rearrangement and displays pronounced thermotolerance.

Publication Title

Extensive rearrangement of the Arabidopsis mitochondrial genome elicits cellular conditions for thermotolerance.

Sample Metadata Fields

Specimen part

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accession-icon E-MEXP-1410
Transcription profiling of Arabidopsis wild type and msh1 mutant plants
  • organism-icon Arabidopsis thaliana
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Single mutant msh1

Publication Title

Extensive rearrangement of the Arabidopsis mitochondrial genome elicits cellular conditions for thermotolerance.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon E-MEXP-1409
Transcription profiling of Arabidopsis wild type and msh1/recA3 double mutant plants
  • organism-icon Arabidopsis thaliana
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Double mutant msh1 and recA3

Publication Title

Extensive rearrangement of the Arabidopsis mitochondrial genome elicits cellular conditions for thermotolerance.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE43863
Expression data from virus-specific mouse Th1 and Tfh CD4 T cell subsets after LCMV infection
  • organism-icon Mus musculus
  • sample-icon 22 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

CD4 T follicular helper (Tfh) cells provide the required signals to B cells for germinal center reactions that are necessary for longlived antibody responses. However, it remains unclear whether there are CD4+ memory T cells committed to the Tfh lineage after antigen clearance.

Publication Title

Distinct memory CD4+ T cells with commitment to T follicular helper- and T helper 1-cell lineages are generated after acute viral infection.

Sample Metadata Fields

Specimen part

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accession-icon SRP110669
Single-cell landscape of transcriptional heterogeneity and cell fate decisions during mouse early gastrulation
  • organism-icon Mus musculus
  • sample-icon 633 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

This study explores lineage and regulatory processes involved in early post implantation mouse embryos using single-cell RNA-seq Overall design: Single cells from C57Bl/6Babr mouse embryos at E3.5, E4.5, E5.5 and E6.5 were isolated and subjected to single-cell RNA-seq protocol.

Publication Title

Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation.

Sample Metadata Fields

Specimen part, Cell line, Subject

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accession-icon GSE68291
Reconstructing divergent retinoid-induced cell fate-regulatory programs in stem cells
  • organism-icon Mus musculus
  • sample-icon 24 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

Reconstructed cell fate-regulatory programs in stem cells reveal hierarchies and key factors of neurogenesis.

Sample Metadata Fields

Specimen part, Time

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accession-icon GSE68290
Reconstructing divergent retinoid-induced cell fate-regulatory programs in stem cells [Affymetrix]
  • organism-icon Mus musculus
  • sample-icon 24 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

We have integrated dynamic RXRa binding, chromatin accessibility and promoter epigenetic status with the transcriptional activity inferred from RNA polymerase II mapping and transcription profiling. This demonstrated a temporal organization structure, in which early events are preferentially enriched for common GRNs, while cell fate specification is reflected by the activation of late programs in a cell-type specific manner. Furthermore, significant differences in cell lines' promoter status of genes associated with cell-line specific programs were inferred. Finally, a variety of transcription factors (TFs) playing a direct role in the signal transduction cascade downstream of the RXR/RAR initiated wiring were identified, several of them commonly regulated in both model systems, but in addition cell-type specific TF drivers were also identified.

Publication Title

Reconstructed cell fate-regulatory programs in stem cells reveal hierarchies and key factors of neurogenesis.

Sample Metadata Fields

Specimen part, Time

View Samples
accession-icon GSE25155
Tribbles 3 - a novel regulator of TLR2-mediated signaling in response to Helicobacter pylori lipopolysaccharide
  • organism-icon Homo sapiens
  • sample-icon 25 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Tribbles 3: a novel regulator of TLR2-mediated signaling in response to Helicobacter pylori lipopolysaccharide.

Sample Metadata Fields

Specimen part, Cell line

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accession-icon GSE25148
Changes in gene expression in HEK-TLR2 cells in response to Helicobacter pylori lipopolysaccharide
  • organism-icon Homo sapiens
  • sample-icon 17 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

This study set out to identify global changes in gene expression in human embryonic kidney (HEK) cells stably transfected with Toll-like receptor 2 (TLR2) over a 48 hour time-course, following stimulation with 10 g/ml lipopolysaccharide (LPS) from the gastric pathogen H. pylori.

Publication Title

Tribbles 3: a novel regulator of TLR2-mediated signaling in response to Helicobacter pylori lipopolysaccharide.

Sample Metadata Fields

Specimen part

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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