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accession-icon GSE38529
Expression data from Drosophila embryos, control vs. dMyc+
  • organism-icon Drosophila melanogaster
  • sample-icon 5 Downloadable Samples
  • Technology Badge Icon Affymetrix Drosophila Genome 2.0 Array (drosophila2)

Description

dMyc is a conserved transcription factor that controls growth and proliferation by regulating its target genes.

Publication Title

MicroRNA miR-308 regulates dMyc through a negative feedback loop in Drosophila.

Sample Metadata Fields

Specimen part

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accession-icon SRP055176
m6A level and isoform characterization sequencing (m6A-LAIC-seq) reveal the census and complexity of the m6A epitranscriptome
  • organism-icon Homo sapiens
  • sample-icon 12 Downloadable Samples
  • Technology Badge IconIlluminaHiSeq2000

Description

N6-methyladenosine (m6A) is a widespread reversible chemical modification of RNAs, implicated in many aspects of RNA metabolism. Little quantitative information exists as to either how many transcript copies of particular genes are m6A modified (“m6A levels”), or the relationship of m6A modification(s) to alternative RNA isoforms. To deconvolute the m6A epitranscriptome, we developed m6A level and isoform-characterization sequencing (m6A-LAIC-seq). We found that cells exhibit a broad range of non-stoichiometric m6A levels with cell type specificity. At the level of isoform characterization, we discovered widespread differences in use of tandem alternative polyadenylation (APA) sites by methylated and nonmethylated transcript isoforms of individual genes. Strikingly, there is a strong bias for methylated transcripts to be coupled with proximal APA sites, resulting in shortened 3’ untranslated regions (3’-UTRs), while nonmethylated transcript isoforms tend to use distal APA sites. m6A-LAIC-seq yields a new perspective on transcriptome complexity and links APA usage to m6A modifications. Overall design: m6A-LAIC-seq of H1-ESC and GM12878 cell lines, each cell line has two replicates

Publication Title

m(6)A-LAIC-seq reveals the census and complexity of the m(6)A epitranscriptome.

Sample Metadata Fields

No sample metadata fields

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accession-icon SRP033269
m6A RNA modification controls cell fate transition in mammalian embryonic stem cells (RNA methylation)
  • organism-icon Mus musculus
  • sample-icon 10 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Here we determine the map of RNA methylation (m6A) in mouse embrionic stem cells, and Mettl3 knock out cells Overall design: Examination of m6A modification sites on the transcriptome of mouse Embryonic stem cells and Embryonic Mettl3 knock out cells, using a m6A specific antibody.

Publication Title

m(6)A RNA modification controls cell fate transition in mammalian embryonic stem cells.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE14280
Comparison of CD4+ T cell function between HIV-1 resistant and HIV-1 susceptible individuals
  • organism-icon Homo sapiens
  • sample-icon 18 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

HIV‐exposed seronegative commercial sex workers show a quiescent phenotype in the CD4+ T cell compartment and reduced expression of HIV‐dependent host factors.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE14278
Comparison of CD4+ T cell function between HIV-1 resistant and HIV-1 susceptible individuals (Affymetrix)
  • organism-icon Homo sapiens
  • sample-icon 18 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Understanding why some indidivual resist HIV-1 infection despite continued exposure is an important goal for vaccine development.

Publication Title

HIV‐exposed seronegative commercial sex workers show a quiescent phenotype in the CD4+ T cell compartment and reduced expression of HIV‐dependent host factors.

Sample Metadata Fields

No sample metadata fields

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accession-icon SRP051072
RNA-Seq of Cultured Mouse Podocytes
  • organism-icon Mus musculus
  • sample-icon 4 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Investigation of mRNA changes in podocytes transfected with a miR-93 mimic or a nontargeting mimic. Overall design: The design was meant to identify biologically significant, novel targets of the miR-93 microRNA in podocytes

Publication Title

miR-93 regulates Msk2-mediated chromatin remodelling in diabetic nephropathy.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE54633
Expression data from M0505 and STOSE murine ovarian surface epithelial cell lines
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Our lab established the M0505 cell line from the ovarian surface epithelium (OSE) of FVB/N mice in May 2005 in order to study OSE biology. This cell line spontaneously transformed into the spontaneously transformed OSE (STOSE) cell line in mid 2012.

Publication Title

A new spontaneously transformed syngeneic model of high-grade serous ovarian cancer with a tumor-initiating cell population.

Sample Metadata Fields

Specimen part

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accession-icon GSE22581
Early gene expression events in ferrets in response to SARS coronavirus infection versus direct interferon-alpha2b stimulation
  • organism-icon Mustela putorius furo
  • sample-icon 20 Downloadable Samples
  • Technology Badge Icon Affymetrix Canine Genome 2.0 Array (canine2)

Description

Background: Type I interferons (IFNs) are essential to the clearance of viral diseases, in part by initiating upregulation of IFN regulated genes (IRGs). A clear distinction between genes upregulated directly by virus and genes upregulated by secondary IFN production has not been made. Here we investigated the genes regulated by IFN-a2b compared to the genes regulated by SARS-CoV infection in ferrets.

Publication Title

Early gene expression events in ferrets in response to SARS coronavirus infection versus direct interferon-alpha2b stimulation.

Sample Metadata Fields

Specimen part

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accession-icon GSE27248
Molecular Characterization of In Vivo Adjuvant Activity in Ferrets Vaccinated against Influenza Virus
  • organism-icon Mustela putorius furo
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Canine Genome 2.0 Array (canine2)

Description

The 2009 H1N1 influenza pandemic has prompted a significant need for the development of efficient, single-dose, adjuvanted vaccines. Here we investigated the adjuvant potential of CpG oligodeoxynucleotide (ODN) when used with a human seasonal influenza virus vaccine in ferrets. We found that the CpG ODNadjuvanted vaccine effectively increased antibody production and activated type I interferon (IFN) responses compared to vaccine alone. Based on these findings, pegylated IFN- 2b (PEG-IFN) was also evaluated as an adjuvant in comparison to CpG ODN and complete Freunds adjuvant (CFA). Our results showed that all three vaccines with adjuvant added prevented seasonal human A/Brisbane/59/2007 (H1N1) virus replication more effectively than did vaccine alone. Gene expression profiles indicated that, as well as upregulating IFN-stimulated genes (ISGs), CpG ODN enhanced B-cell activation and increased Toll-like receptor 4 (TLR4) and IFN regulatory factor 4 (IRF4) expression, whereas PEG-IFN augmented adaptive immunity by inducing major histocompatibility complex (MHC) transcription and Ras signaling. In contrast, the use of CFA as an adjuvant induced limited ISG expression but increased the transcription of MHC, cell adhesion molecules, and B-cell activation markers. Taken together, our results better characterize the specific molecular pathways leading to adjuvant activity in different adjuvant-mediated influenza virus vaccinations.

Publication Title

Molecular characterization of in vivo adjuvant activity in ferrets vaccinated against influenza virus.

Sample Metadata Fields

Specimen part, Treatment

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accession-icon GSE57933
Discovery and validation of a novel expression signature for recurrence in high-risk bladder cancer post-cystectomy
  • organism-icon Homo sapiens
  • sample-icon 199 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Exon 1.0 ST Array [probe set (exon) version (huex10st)

Description

Purpose: Selecting muscle-invasive bladder cancer patients for adjuvant therapy is currently based on clinical variables with limited power. We hypothesized that genomic-based signatures can outperform clinical models to identify patients at higher risk. Method:Transcriptome-wide expression profiles were generated using 1.4 million feature-arrays on archival tumors from 225 patients who underwent radical cystectomy and had muscle-invasive and/or node-positive bladder cancer. A 15-feature GC was developed on the discovery set with area under curve (AUC) of 0.77 in the validation set.

Publication Title

Discovery and validation of novel expression signature for postcystectomy recurrence in high-risk bladder cancer.

Sample Metadata Fields

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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