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accession-icon GSE136883
Gene expression from MS5 stroma cells co-cultured with normal human hematopoietic progenitors/stem cells (HSPCs) and AML
  • organism-icon Mus musculus
  • sample-icon 3 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Acute myeloid leukemia remodels the bone marrow non-hematopoietic microenvironment which disrupts niche archiecture and normal hematopoiesis The precise interactions underlying this process are not well understood

Publication Title

No associated publication

Sample Metadata Fields

Specimen part, Cell line

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accession-icon GSE76296
ATMIN function in p53-deficient GBM
  • organism-icon Mus musculus
  • sample-icon 8 Downloadable Samples
  • Technology Badge IconIllumina MouseRef-8 v2.0 expression beadchip

Description

We report the expression anaysis of neural stem cells lacking p53, ATMIN, or both. p53-deficent cells form GBM, which is significanly delayed in the absence of ATMIN.

Publication Title

Inactivation of the ATMIN/ATM pathway protects against glioblastoma formation.

Sample Metadata Fields

Specimen part

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accession-icon GSE89809
Multi-tissue transcriptomics delineates the diversity of airway T cells functions in asthma
  • organism-icon Homo sapiens
  • sample-icon 145 Downloadable Samples
  • Technology Badge Icon Affymetrix HT HG-U133+ PM Array Plate (hthgu133pluspm)

Description

Asthma arises from the complex interplay of inflammatory pathways in diverse cell types and tissues including epithelial and T cells.

Publication Title

Multitissue Transcriptomics Delineates the Diversity of Airway T Cell Functions in Asthma.

Sample Metadata Fields

Sex, Subject

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accession-icon GSE64913
Altered epithelial gene expression in peripheral airways of severe asthma
  • organism-icon Homo sapiens
  • sample-icon 70 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Management of severe asthma remains a challenge despite treatment with glucocorticosteroid therapy. The majority of studies investigating disease mechanisms in treatment-resistant severe asthma have previously focused on the large central airways, with very few utilizing transcriptomic approaches. The small peripheral airways, which comprise the majority of the airway surface area, remain an unexplored area in severe asthma and were targeted for global epithelial gene expression profiling in this study.

Publication Title

Altered Epithelial Gene Expression in Peripheral Airways of Severe Asthma.

Sample Metadata Fields

Sex, Age, Specimen part, Disease, Subject

View Samples
accession-icon GSE91012
UV-Irradiation Induces a Noncoding RNA that Functionally Opposes the Protein Encoded by the Same Gene
  • organism-icon Homo sapiens
  • sample-icon 13 Downloadable Samples
  • Technology Badge IconIllumina HumanHT-12 V4.0 expression beadchip

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

UV Irradiation Induces a Non-coding RNA that Functionally Opposes the Protein Encoded by the Same Gene.

Sample Metadata Fields

Cell line, Treatment, Time

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accession-icon GSE37387
Transcript levels in mouse liver
  • organism-icon Mus musculus
  • sample-icon 24 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Total RNA was isolated from liver samples of C57/BL6 mice over a circadian time course, 3 biological replicate samples per time point were collected and processed individually. RNA from each individual biological replicate sample was extracted using RNeasy mini kit (Qiagen Cat# 74106) and hybridized on an Affymetrix mouse Gene ST1.0 microarray.

Publication Title

Histone methyltransferase MLL3 contributes to genome-scale circadian transcription.

Sample Metadata Fields

Specimen part, Time

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accession-icon GSE114669
OnPLS-based multi-block data integration: a multivariate approach to interrogating biological interactions in asthma
  • organism-icon Homo sapiens
  • sample-icon 22 Downloadable Samples
  • Technology Badge Icon Affymetrix HT HG-U133+ PM Array Plate (hthgu133pluspm)

Description

Integration of multi-omics data remains a key challenge in fulfilling the potential of comprehensive systems biology.

Publication Title

OnPLS-Based Multi-Block Data Integration: A Multivariate Approach to Interrogating Biological Interactions in Asthma.

Sample Metadata Fields

Sex, Age, Specimen part, Disease, Disease stage

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accession-icon GSE119650
Transcriptomes of microglia in experimental cerebral malaria in mice in the presence and absence of Type I Interferon signaling
  • organism-icon Mus musculus
  • sample-icon 22 Downloadable Samples
  • Technology Badge IconIllumina MouseWG-6 v2.0 expression beadchip

Description

Plasmodium berghei ANKA infection in mice is used as a model for human cerebral malaria, the most severe complication of Plasmodium falciparum infection. The response of brain cells such as microglia has been little investigated, and may play a role in the pathogenesis or regulation of cerebral malaria. We showed previously that microglia are activated in P. berghei infections, and that Type 1 Interferon signaling is important for activation. This dataset contains the transcriptome of brain microglia of infected mice in the presence and absence of Type I interferon signaling, with the aim of identifying the genes involved in this pathway in microglia during experimental cerebral malaria. Refererence: Capuccini et al 2016, Scientific Reports, 6:39258

Publication Title

Transcriptomic profiling of microglia reveals signatures of cell activation and immune response, during experimental cerebral malaria.

Sample Metadata Fields

Sex, Specimen part, Treatment

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accession-icon GSE148414
Eye-antenna early L3 disc expression profiling in combinations of COX7a-LoF, ATF4-LoF and Notch-GoF
  • organism-icon Drosophila melanogaster
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Drosophila Genome 2.0 Array (drosophila2)

Description

Gene expression in larval, early third instar eye-antenna discs was assessed to reveal an ATF4 contribution to target gene induction following COX7a knockdown. As hypothesised, these COX7a-RNAi induced target genes require the transcription factor ATF4 for induction, irrespective of concomitant Notch pathway activation through Delta over-expression.

Publication Title

ATF4-Induced Warburg Metabolism Drives Over-Proliferation in Drosophila.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE92325
Illumina bead array -/+ UV ASCC3 short isoform knockout cells
  • organism-icon Homo sapiens
  • sample-icon 1 Downloadable Sample
  • Technology Badge IconIllumina HumanHT-12 V4.0 expression beadchip

Description

The transcription-related DNA damage response was analyzed on a genome-wide scale with great spatial and temporal resolution. Upon UV irradiation, a slowdown of transcript elongation and restriction of gene activity to the promoter-proximal ~25 kilobases is observed. This is associated with a shift from expression of long mRNAs to shorter isoforms, incorporating alternative last exons (ALEs) that are more proximal to the transcription start site. Notably, this includes a shift from a protein-coding ASCC3 mRNA to a shorter transcript isoform of which the RNA, rather than an encoded protein, is critical for the eventual recovery of transcription. The protein-coding ASCC3 isoform counteracts the function of the non-coding isoform, indicating crosstalk between them. Thus, the ASCC3 gene expresses both coding and noncoding transcript isoforms with opposite effects on transcription recovery after UV-induced DNA damage

Publication Title

UV Irradiation Induces a Non-coding RNA that Functionally Opposes the Protein Encoded by the Same Gene.

Sample Metadata Fields

Cell line, Treatment, Time

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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