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accession-icon SRP062966
SLE lupus RNA-seq
  • organism-icon Homo sapiens
  • sample-icon 117 Downloadable Samples
  • Technology Badge IconIlluminaHiSeq2500

Description

RNA-seq of systemic lupus erythematosus (SLE) whole blood and healthy controls to determine the gene expression changes in these patients. Overall design: RNA-seq of PAXgene blood from SLE and healthy donors.

Publication Title

The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression.

Sample Metadata Fields

No sample metadata fields

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accession-icon SRP062956
Ro60-knockout cells
  • organism-icon Homo sapiens
  • sample-icon 10 Downloadable Samples
  • Technology Badge IconIlluminaHiSeq2500

Description

RNA-seq of Ro60-null GM12878 cell lines in order to determine the gene expression changes resulting from loss of Ro60. Overall design: 3 separate clones of Ro60(Trove2)-null cells derived from zinc finger nuclease targeting of exon 2, two wildtype biological replicates, +/- IFNa for 6 hours.

Publication Title

The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression.

Sample Metadata Fields

No sample metadata fields

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accession-icon SRP062958
Healthy donor PBMC RNA-seq with or without interferon-alpha stimulation
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIlluminaGenomeAnalyzer

Description

Determine the gene expression profile in peripheral blood monocytes isolated from 3 healthy donors +/- 6 hours of interferon-alpha treatment. Overall design: 3 healthy donor PBMCs +/- interferon-alpha.

Publication Title

The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE62459
Heart expression data after short ischemia/reperfusion in WT, Reverb alpha KO and Reverb alpha antagonist-treated mice
  • organism-icon Mus musculus
  • sample-icon 24 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 2.0 ST Array (mogene20st)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Daytime variation of perioperative myocardial injury in cardiac surgery and its prevention by Rev-Erbα antagonism: a single-centre propensity-matched cohort study and a randomised study.

Sample Metadata Fields

Specimen part

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accession-icon GSE62457
Heart expression data from WT and reverb alpha KO mice after short ischemia/reperfusion at ZT0, ZT12
  • organism-icon Mus musculus
  • sample-icon 19 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 2.0 ST Array (mogene20st)

Description

Nuclear receptor Reverb alpha is a component of circadian rythm which could be evolved in cardioprotection strategy. We test if pharmacological modulation of these target could be suitable for cardioprotection after ischemia reperfusion injury

Publication Title

Daytime variation of perioperative myocardial injury in cardiac surgery and its prevention by Rev-Erbα antagonism: a single-centre propensity-matched cohort study and a randomised study.

Sample Metadata Fields

Specimen part

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accession-icon GSE98904
Expression data from Trp53- or Atm-deficient E-TCL1 murine CLL cells
  • organism-icon Mus musculus
  • sample-icon 17 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 2.0 ST Array (mogene20st)

Description

To analyze expression differences between Trp53 pro-and deficient as well as Atm pro- and deficient murine CLL tumors developing in the E-TCL1 mouse model, we analyzed splenocytes isolated from heavily infiltrated spleens of sick mice.

Publication Title

Two mouse models reveal an actionable PARP1 dependence in aggressive chronic lymphocytic leukemia.

Sample Metadata Fields

Specimen part

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accession-icon GSE95544
Evaluation of in vitro macrophage differentiation during space flight
  • organism-icon Mus musculus
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

We differentiated mouse bone marrow cells in the presence of recombinant macrophage colony stimulating (rM-CSF) factor for 14 days during the flight of space shuttle Space Transportation System (STS)-126. We tested the hypothesis that the receptor expression for M-CSF, c-Fms was reduced. We used flow cytometry to assess molecules on cells that were preserved during flight to define the differentiation state of the developing bone marrow macrophages; including CD11b, CD31, CD44, Ly6C, Ly6G, F4/80, Mac2, c-Fos as well as c-Fms. In addition, RNA was preserved during the flight and was used to perform a gene microarray. We found that there were significant differences in the number of macrophages that developed in space compared to controls maintained on Earth. We found that there were significant changes in the distribution of cells that expressed CD11b, CD31, F4/80, Mac2, Ly6C and c-Fos. However, there were no changes in c-Fms expression and no consistent pattern of advanced or retarded differentiation during space flight. We also found a pattern of transcript levels that would be consistent with a relatively normal differentiation outcome but increased proliferation by the bone marrow macrophages that were assayed after 14 days of space flight. There also was a surprising pattern of space flight influence on genes of the coagulation pathway. These data confirm that a space flight can have an impact on the in vitro development of macrophages from mouse bone marrow cells.

Publication Title

Evaluation of in vitro macrophage differentiation during space flight.

Sample Metadata Fields

Specimen part

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accession-icon GSE139871
Infection of monocytes from tuberculosis patients with two virulent clinical isolates of Mycobacterium tuberculosis induces alterations in myeloid effector functions.
  • organism-icon Homo sapiens
  • sample-icon 24 Downloadable Samples
  • Technology Badge IconIllumina HumanHT-12 V4.0 expression beadchip

Description

Monocytes play a critical role during infection with Mycobacterium tuberculosis (Mtb). They are recruited to the lung where they participate in the contention of infection. Alternatively, inflammatory monocytes may help in prolonging inflammation or serve as niches for Mtb infection. Also, monocyte response to infection may vary depending on the particularities of the clinical isolate of Mtb from which they are infected. In this pilot study, using microarrays we have examined the global mRNA profiles of circulating human monocytes from healthy individuals and patients with active tuberculosis (TB).

Publication Title

Infection of Monocytes From Tuberculosis Patients With Two Virulent Clinical Isolates of <i>Mycobacterium tuberculosis</i> Induces Alterations in Myeloid Effector Functions.

Sample Metadata Fields

Specimen part, Disease, Disease stage

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accession-icon GSE13276
Candidate genes for the recurrence of glioblastoma multiforme identified by microarray
  • organism-icon Homo sapiens
  • sample-icon 15 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A Array (hgu133a)

Description

Background: Glioblastoma multiforme (GBM) is the most aggressive and most lethal primary malignant brain tumor, correlated with survival rates of less than one year from the time of diagnosis. Current surgical procedure attempts to remove the bulk of the tumor mass, whereas GBM frequently recurs within 1-3cm from the primary tumor resection site. Molecular mechanisms involved in the recurrence of the tumor are still poorly understood. The aim of the study was to define the molecular signature of GBM surrounding white matter (WM) in order to better understand the molecular mechanisms involved with tumor relapse.

Publication Title

Gene expression profile of glioblastoma peritumoral tissue: an ex vivo study.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE72166
Expression profile of mouse carotid body and adrenal medulla
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Oxygen regulation of breathing through an olfactory receptor activated by lactate.

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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