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accession-icon GSE35314
Expression data from Control and Six1 expressing MCF7 derived xenograft tumors
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix HT Human Genome U133A Array (hthgu133a)

Description

Although an important association between lymph node metastasis and poor prognosis in breast cancer was observed decades ago, an active role for the lymphatic system in metastatic dissemination has only recently been examined. We demonstrate that the Six1 homeoprotein promotes peri- and intra-tumoral lymphangiogenesis, lymphatic invasion, and distant metastasis of breast cancer cells. We identify the pro-lymphangiogenic factor, VEGF-C, as required for this process, and demonstrate transcriptional induction as the mechanism of regulation of VEGF-C expression by Six1. Using a different, but complementary animal model, we show that while required, VEGF-C is not sufficient for the pro-metastatic effects of Six1. Verifying the clinical significance of this pro-metastatic Six1-VEGF-C axis, we demonstrate co-expression of Six1 and VEGF-C in human breast cancer.

Publication Title

SIX1 induces lymphangiogenesis and metastasis via upregulation of VEGF-C in mouse models of breast cancer.

Alternate Accession IDs

E-GEOD-35314

Sample Metadata Fields

Specimen part, Cell line

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accession-icon GSE142807
Transcriptomic profiling of dermatomyositis lesions.
  • organism-icon Homo sapiens
  • sample-icon 48 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 2.1 ST Array (hugene21st)

Description

The microarray experiment was employed to evaluate the gene expressions in skin lesions of dermatomyositis and healthy controls.

Publication Title

IL18-containing 5-gene signature distinguishes histologically identical dermatomyositis and lupus erythematosus skin lesions.

Alternate Accession IDs

E-GEOD-142807

Sample Metadata Fields

Disease, Subject

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accession-icon SRP187984
Whole blood human transcriptome and virome analysis of ME/CFS patients experiencing post-exertional malaise following cardiopulmonary exercise testing
  • organism-icon Homo sapiens
  • sample-icon 94 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Myalgic encephalomyelitis / chronic fatigue syndrome (ME/CFS) is a syndrome of unknown etiology characterized by profound fatigue exacerbated by physical activity, also known as post-exertional malaise (PEM). Previously, we did not detect evidence of immune dysregulation or virus reactivation outside of PEM periods. Here we sought to determine whether cardiopulmonary exercise stress testing of ME/CFS patients could trigger such changes. ME/CFS patients (n=14) and matched sedentary controls (n=11) were subjected to cardiopulmonary exercise on 2 consecutive days and followed up to 7 days post-exercise, and longitudinal whole blood samples analyzed by RNA-seq. Although ME/CFS patients showed significant worsening of symptoms following exercise versus controls, with 8 of 14 ME/CFS patients showing oxygen consumption (V?O2) on day 2, transcriptome analysis yielded only 6 differentially expressed gene (DEG) candidates when comparing ME/CFS patients to controls across all time points. None of the DEGs were related to immune signaling, and no DEGs were found in ME/CFS patients before and after exercise. Virome composition (P=0.746 by chi-square test) and number of viral reads (P = 0.098 by paired t-test) were not significantly associated with PEM. These observations do not support transcriptionally-mediated immune cell dysregulation or viral reactivation in ME/CFS patients during symptomatic PEM episodes. Overall design: RNAseq of whole blood samples from ME/CFS patients and controls following exercise.

Publication Title

Whole blood human transcriptome and virome analysis of ME/CFS patients experiencing post-exertional malaise following cardiopulmonary exercise testing.

Alternate Accession IDs

GSE128078

Sample Metadata Fields

Specimen part, Disease, Disease stage, Treatment, Subject

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accession-icon GSE13854
Expression profiling of the host and the Ovine Herpesvirus 2 pathogen during malignant catarrhal fever of cattle
  • organism-icon Bos taurus
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon Affymetrix Bovine Genome Array (bovine)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Malignant catarrhal fever of cattle is associated with low abundance of IL-2 transcript and a predominantly latent profile of ovine herpesvirus 2 gene expression.

Alternate Accession IDs

E-GEOD-13854

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE13852
Expression profiling of Bos taurus lymph nodes upon infection with Ovine Herpesvirus 2
  • organism-icon Bos taurus
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon Affymetrix Bovine Genome Array (bovine)

Description

We hypothesized that the relative abundances of host cell transcripts in lymph nodes of animals with malignant catarrhal fever (MCF), compared to healthy controls, may be used to identify pathways that may help to explain the pathogenesis of MCF. Therefore, an abundance of host cell gene expression patterns in lymph nodes of animals with MCF and healthy controls were analyzed by microarray. Indeed, a vast number of genes related to inflammatory processes, lymphocyte activation, cell proliferation and apoptosis were detected at different abundances. However, the IL-2 transcript was eminent among the transcripts, which were, compared to healthy controls, less abundant in animals with MCF. Compared to healthy cattle, bovines with MCF appear to mimic an IL-2 knockout phenotype that has been described in mice. This supports the hypothesis that immunopathogenic events are linked to the pathogenesis of MCF. IL-2-deficiency may play an important role in the process.

Publication Title

Malignant catarrhal fever of cattle is associated with low abundance of IL-2 transcript and a predominantly latent profile of ovine herpesvirus 2 gene expression.

Alternate Accession IDs

E-GEOD-13852

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon SRP068931
Sensory experience restricts cortical plasticity by inducing IGF-1 in VIP neurons
  • organism-icon Mus musculus
  • sample-icon 67 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

RNA-seq libraries purified from the visual cortices of neurons expressing Emx-, GAD2-, PV-, SST-, or VIP-Cre using the Ribotag allele. Seq libraries are provided from mice raised in standard housing, or housed in the dark for two weeks (dark-housed), or dark-housed and then exposed to light for 1, 3, or 7.5 hours. These seq libraries represent the genetic response of distinct types of cortical interneurons to altered sensory experience. Overall design: To explore how sensory experience affects gene expression, we examined this process in the visual cortex of adult mice that were housed in standard conditions, in complete darkness (i.e. dark-housed), or dark-housed and then exposed to light for increasing amounts of time. We generated mice that were heterozygous for alleles of either Emx-,Gad2-,Sst-,Vip- or Pv-Cre, and were also heterozygous for the Rpl22-HA (RiboTag) allele, which expresses an HA-tagged ribosomal protein specifically in Cre-expressing neurons. We performed RNA-Seq on RNA isolated from the dark-housed/light-exposed RiboTag-mice; Experiments were done in 3 biological replicates and the visual cortices of 3 mice were pooled per sample at each time-point and for each Cre line.

Publication Title

Sensory experience regulates cortical inhibition by inducing IGF1 in VIP neurons.

Alternate Accession IDs

GSE77243

Sample Metadata Fields

Age, Specimen part, Cell line, Subject

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accession-icon SRP195777
Identification of HIV Transmitting CD11c+ Human Epidermal Dendritic Cells
  • organism-icon Homo sapiens
  • sample-icon 116 Downloadable Samples
  • Technology Badge Icon

Description

Langerhans cells (LC) represent one of the first lines of contact between the immune system and sexually transmitted pathogens, and in the human epidermis LCs have been thought to represent the only mononuclear phagocyte (MNP) population. Here we show an additional epidermal MNP subset that can be distinguished from LCs phenotypically as CD11chi, CD1c+ MR+ (epidermal CD11c+ DCs). These cells are transcriptionally similar to dermal cDC2 but express higher levels of costimulatory markers and are more efficient at T cell stimulation. Importantly, compared to LC, epidermal CD11c+ DCs are i) enriched in the epithelium of anogenital tissues where they preferentially interact with HIV, ii) express the higher levels of the HIV entry receptor CCR5, iii) support the higher levels of HIV uptake and replication and iv) are more efficient at transferring virus to CD4 T cells. Importantly these findings were observed using both a lab-adapted and transmitted/founder strain of HIV. We also describe a cell population that can be discerned from LCs by their lower surface expression of CD45, HLA-DR and CD33 (epidermal CD33low cells). These are transcriptionally similar to LCs but do not appear to function as APCs as do not secrete cytokines, express negligible amounts of costimulatory molecules and are very weak inducers of T cell proliferation. They also do not act as HIV target cells. Our findings reveal a new subset of epidermal DCs in skin and anogenital tissues with a potential key role in sexual transmission of HIV. Overall design: Sorted cell populations from four donors were captured directly into lysis buffer and polyA RNA transcripts were reverse transcribed, amplified and sequenced using the Smart-seq 2 protocol described by Picelli et al (Nature Methods. 2013;10(11):1096-8). Each sample was sequenced across 4 HiSeq lanes and the data for each lane is represented as an independent sample (GSM).

Publication Title

Identification of HIV transmitting CD11c<sup>+</sup> human epidermal dendritic cells.

Alternate Accession IDs

GSE130804

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE50603
Effect of L-Proline on mouse embryonic stem cells (ESCs)
  • organism-icon Mus musculus
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

We found that the non-essential amino acid L-Proline (L-Pro) acts as a signaling molecule that promotes the conversion of embryonic stem cells (ESCs) into mesenchymal-like, spindle-shaped, highly motile, invasive pluripotent stem cells. This embryonic stem cell-to-mesenchymal-like transition (esMT) is accompanied by a genome-wide remodeling of the transcriptome

Publication Title

L-Proline induces a mesenchymal-like invasive program in embryonic stem cells by remodeling H3K9 and H3K36 methylation.

Alternate Accession IDs

E-GEOD-50603

Sample Metadata Fields

Cell line

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accession-icon GSE47606
Changes in mouse kidney glomerular gene expression following dendrin knockout
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Glomerular podocyte cells are critical for the function of the renal ultrafiltration barrier. The highly specialized cell-cell junction of podocytes, the slit diaphragm, has a central role in the filtration barrier. Dendrin is a poorly characterized cytosolic component of the slit diaphragm in where it interacts with nephrin and Cd2ap. In this study, we have generated a dendrin knockout mouse line and explored the molecular interactions of dendrin. Dendrin-deficient mice were viable, fertile and had normal life span.

Publication Title

Wtip- and gadd45a-interacting protein dendrin is not crucial for the development or maintenance of the glomerular filtration barrier.

Alternate Accession IDs

E-GEOD-47606

Sample Metadata Fields

Age, Specimen part

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accession-icon E-MEXP-2472
Transcription profiling by array of Arabidopsis after growing in dark or light conditions
  • organism-icon Arabidopsis thaliana
  • sample-icon 12 Downloadable Samples
  • Technology Badge IconUNKNOWN, Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

RNA from etiolated seedlings, light-treated seedlings, leaves and flowers was hybridized to ATH1 and AGRONOMICS1 arrays.

Publication Title

AGRONOMICS1: a new resource for Arabidopsis transcriptome profiling.

Alternate Accession IDs

None

Sample Metadata Fields

Age, 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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