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accession-icon GSE55028
CMPF alters expression of genes related to metabolism in isolated mouse islets
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

CMPF is elevated in diabetes and is associated with impaired insulin secretion. We used microarrays to determine the effect of CMPF on gene expression in isolated islets.

Publication Title

The furan fatty acid metabolite CMPF is elevated in diabetes and induces β cell dysfunction.

Sample Metadata Fields

Sex, Age, Specimen part, Treatment

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accession-icon GSE69815
Expression array of glucosamine-fed Drosophila heart/nephrocyte complexes
  • organism-icon Drosophila melanogaster
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Drosophila Genome 2.0 Array (drosophila2)

Description

Examined the expression effects of supplementing Drosophila food on heart and nephrocyte complexes

Publication Title

Diet-Induced Podocyte Dysfunction in Drosophila and Mammals.

Sample Metadata Fields

Sex, Specimen part, Treatment

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accession-icon GSE70271
caArray_jacks-00113: Murine KRASLA lung cancer gene expression
  • organism-icon Mus musculus
  • sample-icon 58 Downloadable Samples
  • Technology Badge Icon Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)

Description

Tumors from 5-6 month old KrasLA mice were dissected. Gene expression analysis on U74A affy chips. 19 normal lungs from age matched controls were also includeed

Publication Title

Comparison of gene expression and DNA copy number changes in a murine model of lung cancer.

Sample Metadata Fields

Sex, Age, Disease, Disease stage

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accession-icon SRP128647
Dazl maintains proliferating germ cells through a network of polyA-proximal mRNA interactions [Spermatogonia PolyA-Seq]
  • organism-icon Mus musculus
  • sample-icon 2 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Dazl (deleted in azoospermia like) is a member of the DAZ family of germ cell-restricted RNA binding proteins required for gametogenesis from worm to human. The direct RNA targets and functions of these essential proteins are poorly understood. Here, we generated high-resolution, transcriptome-wide maps of Dazl-RNA interactions in mouse testes. These maps provide important insights into the mechanism of Dazl recruitment to mRNA and reveal Dazl binding to thousands of mRNAs predominantly through sequence-specific interactions near the polyA tail. Using transgenic mice and fluorescence activated cell sorting (FACS), we isolated DAZL knockout germ cells and used RNA-Seq to identify mRNAs sensitive to DAZL-ablation. Intersecting the RNA-Seq and Dazl-RNA interaction datasets revealed that Dazl enhances expression of a subset of directly-bound transcripts, namely mRNAs for a network of essential cell cycle regulatory genes. Collectively, our integrative analysis delineates a Dazl-dependent post-transcriptional gene regulatory program essential for mammalian germ cell maintenance. Overall design: PolyA Seq libraries generated from isolated spermatogonial cells

Publication Title

DAZL Regulates Germ Cell Survival through a Network of PolyA-Proximal mRNA Interactions.

Sample Metadata Fields

Sex, Specimen part, Cell line, Subject

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accession-icon SRP108941
Construction of a synthetic RNA-seq data set for testing of fusion detection algorithms
  • organism-icon Homo sapiens
  • sample-icon 1 Downloadable Sample
  • Technology Badge IconIllumina Genome Analyzer II

Description

Gene fusions are known to play critical roles in tumor pathogenesis. However, sensitive and specific algorithms to detect gene fusions in cancer do not currently exist. Although real RNA-seq data from cell lines or tumors can be used in testing new fusion detection algorithms, it is impossible to know the true sensitivity or specificity of an algorithm without knowing the "ground truth". For this reason we designed a synthetic control data set to assess the true and false positive and negative fusions of a a new fusion detection algorithm.

Publication Title

Statistical algorithms improve accuracy of gene fusion detection.

Sample Metadata Fields

Sex, Specimen part

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accession-icon GSE49200
An oncogenic Kras expression signature identified by cross-species
  • organism-icon Mus musculus
  • sample-icon 50 Downloadable Samples
  • Technology Badge Icon Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)

Description

Mouse lung cancers were generated using the KrasLA model, in which a latent mutated Kras2 allele (resulting in the amino acid substitution G12D) is sporadically activated through spontaneous homologous recombination. These mice develop lung adenomas with full penetrance; over time, the tumors acquire morphologic characteristics reminiscent of those of human adenocarcinoma, such as nuclear atypia and a high mitotic index.

Publication Title

An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis.

Sample Metadata Fields

Specimen part

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accession-icon GSE18534
Mouse small cell lung cancer model
  • organism-icon Mus musculus
  • sample-icon 15 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

A mouse model for human small cell lung carcinoma (SCLC) has been developed based on evidence in human tumors that the tumor suppressor functions of RB and p53 are defective in more than 90% of SCLC cases. We also developed another mouse model also combines loss of p130 (Rbl2), an RB-related gene, with deletion of RB and p53. These two mouse tumors were shown to closely resemble human SCLC.

Publication Title

Loss of p130 accelerates tumor development in a mouse model for human small-cell lung carcinoma.

Sample Metadata Fields

Specimen part

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accession-icon SRP147931
Determination of global decay rates of yeast transcriptome and identification of factors impact mRNA stability
  • organism-icon Saccharomyces cerevisiae
  • sample-icon 10 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

In this work, we determine total mRNA decay rates in rpb1-1 and rpb1-1/caf1? cells, calculate half-lives in rpb1-1/caf1? cells relative to rpb1-1 cells and correlate them with codon optimality. Overall design: mRNA profiling was done on 10 time points in rpb1-1/caf1 cells and sequenced using a paired end protocol on an Illumina HiSeq2000 instrument. A biological duplicate was performed.

Publication Title

mRNA Deadenylation Is Coupled to Translation Rates by the Differential Activities of Ccr4-Not Nucleases.

Sample Metadata Fields

Cell line, Subject

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accession-icon GSE11061
Colony Stimulating Factor 1 (CSF-1) responses in human monocyte derived macrophages
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconSentrix Human-6 Expression BeadChip

Description

Although the role of macrophage colony stimulating factor (M-CSF/CSF-1) in homeostasis and disease processes has been studied extensively in mice, little is known of the impact of this cytokine on differentiated human macrophages. Here we show that, in contrast to its effects on mouse bone marrow-derived macrophages (BMM), CSF-1 did not induce expression of urokinase plasminogen activator mRNA, repress expression of apolipoprotein E mRNA, or prime LPS-induced TNF secretion in human monocyte-derived macrophages (HMDM) from several independent donors. Using expression profiling, we show that CSF-1 dynamically regulated the expression of several genes that encode chemokines and chemokine receptors (e.g. CXCL10/IP-10, CXCL2, CCL7, SDF2L1, CXCR4) in HMDM. CSF-1 also upregulated the expression of several genes encoding enzymes of the cholesterol biosynthetic pathway (HMGCR, MVD, IDI1, FDPS, SQLE, CYP51A1, EBP, NSDHL, DHCR7 and DHCR24), while expression of ABCG1, encoding a cholesterol efflux transporter, was repressed. Although the CSF-1/CSF-1R system has been proposed as a target for the treatment of inflammatory and metastatic disease based on studies in rodents, this is the first systematic analysis of the effects of CSF-1 on mature human macrophages. Our data demonstrates that CSF-1 represents a further link between inflammation and cardiovascular disease, inflammtion and immunity.

Publication Title

Colony-stimulating factor-1 (CSF-1) delivers a proatherogenic signal to human macrophages.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE10246
GNF Mouse GeneAtlas V3
  • organism-icon Mus musculus
  • sample-icon 181 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

High-throughput gene expression profiling has become an important tool for investigating transcriptional activity in a variety of biological samples. To date, the vast majority of these experiments have focused on specific biological processes and perturbations. Here, we profiled gene expression from a diverse array of normal tissues, organs, and cell lines in mice. Keywords: multiple tissues

Publication Title

Expression analysis of G Protein-Coupled Receptors in mouse macrophages.

Sample Metadata Fields

No sample metadata fields

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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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