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accession-icon GSE48837
Gene expression of fly testes with meiotic arrest from different mutations
  • organism-icon Drosophila melanogaster
  • sample-icon 13 Downloadable Samples
  • Technology Badge Icon Affymetrix Drosophila Genome 2.0 Array (drosophila2)

Description

The role of different proteins, Always Early (Aly), Spermatocyte Arrest (Sa), Ubi-p63E (Magn) on the gene expression in spermatocyte differentation was assessed by microarray

Publication Title

The polyubiquitin gene Ubi-p63E is essential for male meiotic cell cycle progression and germ cell differentiation in Drosophila.

Sample Metadata Fields

Specimen part

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accession-icon GSE89506
Blocking promiscuous activation at cryptic promoters directs cell typespecific gene expression
  • organism-icon Drosophila melanogaster
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Drosophila Genome 2.0 Array (drosophila2)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Blocking promiscuous activation at cryptic promoters directs cell type-specific gene expression.

Sample Metadata Fields

Specimen part

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accession-icon GSE68696
Gene expression of fly testes with dMi-2, kumgang (CG5204) knock downs
  • organism-icon Drosophila melanogaster
  • sample-icon 17 Downloadable Samples
  • Technology Badge Icon Affymetrix Drosophila Genome 2.0 Array (drosophila2)

Description

The effect of different loss of functions; kumgang (kmg or CG5204), dMi-2, and kmg and always early (aly) double on the gene expression in spermatocyte differentation was assessed by microarray.

Publication Title

Blocking promiscuous activation at cryptic promoters directs cell type-specific gene expression.

Sample Metadata Fields

Specimen part

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accession-icon GSE82081
Transcriptome assessment of the Pompe (Gaa-/-) mouse cervical cord confirms widespread neuropathology.
  • organism-icon Mus musculus
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 2.0 ST Array (mogene20st)

Description

The only FDA approved therapy for Pompe is directed at correcting skeletal and cardiac muscle pathology, however, clinical and animal model data show strong histological evidence for a neurological disease component. While neuronal cell death and neuroinflammation are prominent in many lysosomal disorders, these processes have not been evaluated in Pompe disease. There is also no information available regarding the impact of Pompe disease on the fundamental pathways associated with synaptic communication.

Publication Title

Transcriptome assessment of the Pompe (Gaa-/-) mouse spinal cord indicates widespread neuropathology.

Sample Metadata Fields

Age

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accession-icon GSE28728
Sequential changes at differentiation gene promoters as they become active in a stem cell lineage
  • organism-icon Drosophila melanogaster
  • sample-icon 2 Downloadable Samples
  • Technology Badge Icon Affymetrix Drosophila Genome 2.0 Array (drosophila2)

Description

Transcriptional silencing of terminal differentiation genes by the Polycomb group (PcG) machinery is emerging as a key feature of precursor cells in stem cell lineages. How, then, is this epigenetic silencing reversed for proper cellular differentiation? Here we investigate how the developmental program reverses local PcG action to allow expression of terminal differentiation genes in the Drosophila male germline stem cell lineage. We find that the silenced state, set up in precursor cells, is relieved through developmentally regulated sequential events at promoters once cells commit to spermatocyte differentiation. The programmed events include global down-regulation of PRC2, recruitment of hypophosphorylated RNA Polymerase II (Pol II) to promoters, as well as expression and action of cell-type specific homologs of subunits of TFIID (tTAFs). In addition, action of tMAC, a tissue specific version of the MIP/dREAM complex, is required both for recruitment of tTAFs to target differentiation genes and for proper cell-type specific localization of PRC1 components and tTAFs to the spermatocyte nucleolus. Together, action of the tMAC and tTAF cell-type specific chromatin and transcription machinery leads to loss of

Publication Title

Sequential changes at differentiation gene promoters as they become active in a stem cell lineage.

Sample Metadata Fields

Time

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accession-icon SRP055864
Transcriptome analyses of skeletal muscle in aB-crystallin/HspB2 knockout and wild-type mice on a normal or high fat diet
  • organism-icon Mus musculus
  • sample-icon 12 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

We profiled the skeletal muscle transcriptome between wild type and aB-crystallin/HspB2 knock mice exposed to normal chow and high fat diets to examine the role of aB-crystallin/HspB2 in diet induced obesity. Combined with metabolic profiling of the mice, these data reveal that aB-crystallin/HspB2 is involved in the genesis of insulin resistance on a high fat diet, and we provide extensive RNA profiling to illuminate potential mechanistic insights into the muscle-specific role of aB-crystallin/HspB2. Overall design: Hind limb muscle mRNA profiles of wild type and aB-crystallin/HspB2 knock mice exposed to either normal chow or high fat diets using RNAseq analysis

Publication Title

αB-crystallin and HspB2 deficiency is protective from diet-induced glucose intolerance.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE42596
Effect of topographical micropatterning on human endothelial cells
  • organism-icon Homo sapiens
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

Shear stress is known to regulate endothelial cell orientation along the direction of flow. We asked wither cellular patterning along, in the absence of shear could have similar biological effects as shear.

Publication Title

Spatial patterning of endothelium modulates cell morphology, adhesiveness and transcriptional signature.

Sample Metadata Fields

Specimen part, Treatment

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accession-icon GSE40760
The E-myc Mouse Model Represents Heterogeneity Across Human Aggressive B-cell Lymphomas
  • organism-icon Mus musculus
  • sample-icon 115 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

Utilization of the Eμ-Myc mouse to model heterogeneity of therapeutic response.

Sample Metadata Fields

Specimen part

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accession-icon GSE40758
Transgenic E-myc mouse lymphoma expression data for test dataset [Mouse430A_2]
  • organism-icon Mus musculus
  • sample-icon 44 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

We used gene expression data from E-myc mouse lymphomas to test various genomic signatures and select lymphomas for further study

Publication Title

Utilization of the Eμ-Myc mouse to model heterogeneity of therapeutic response.

Sample Metadata Fields

Specimen part

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accession-icon GSE40756
Transgenic E-myc mouse lymphoma expression data for training dataset
  • organism-icon Mus musculus
  • sample-icon 39 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

We used gene expression data from E-myc mouse lymphomas to perform unsupervised analyses that identified two lymphoma subgroups.

Publication Title

Utilization of the Eμ-Myc mouse to model heterogeneity of therapeutic response.

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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