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accession-icon SRP081074
CD133+ vs. CD133- cells in GBML8, a primary glioblastoma tumorsphere culture
  • organism-icon Homo sapiens
  • sample-icon 8 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

CD133+ and CD133- cells were FACS islated from GBML8 cells to find gene signatures upregulated in cancer stem cells Overall design: After surface immuno staining, CD133+ and CD133- cells were FACS isolated and subjected to RNA isolation. Experiment represent averaged data of 2 independent FACS isolations.

Publication Title

GPR133 (ADGRD1), an adhesion G-protein-coupled receptor, is necessary for glioblastoma growth.

Sample Metadata Fields

Specimen part, Subject

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accession-icon GSE9103
Skeletal Muscle Transcript Profiles in Trained or Sedentary Young and Old Subjects
  • organism-icon Homo sapiens
  • sample-icon 34 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Aging is associated with mitochondrial dysfunction and insulin resistance. We conducted a study to determine the role of long-term vigorous endurance exercise on age-related changes in insulin sensitivity and various indices of mitochondrial functions.

Publication Title

Endurance exercise as a countermeasure for aging.

Sample Metadata Fields

No sample metadata fields

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accession-icon SRP142610
Measuring A-to-I RNA editing and gene expression signatures of neuronal populations within the Drosophila brain
  • organism-icon Drosophila melanogaster
  • sample-icon 29 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

We used an improved INTACT (Isolation of Nuclei Tagged in A specific Cell Type) technique to isolate RNA from purified nuclei from different neuronal populations of the Drosophila brain. Using RNA-seq, we determined gene expression and A-to-I RNA editing levels at editing sites across nine distinct neuronal sub-populations and a pan-neuronal control. Overall design: We crossed UAS-unc84-2XGFP transgenic flies with 10 different GAL4 drivers (Dh44-GAL4, NPF-GAL4, NPFR-GAL4, Tdc2-GAL4, Crz-GALl4, TH-GAL4, Trh-GAL4, Fru-GAL4, OK107-GAL4, and elav-GAL4), immunoprecipitated tagged nuclei and extracted RNA. Three independent replicates of each each cross were performed to isolate RNA for RNA-sequencing.

Publication Title

Illuminating spatial A-to-I RNA editing signatures within the <i>Drosophila</i> brain.

Sample Metadata Fields

Subject

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accession-icon GSE20613
The Sp100 component of ND10/PML bodies is a potent tumor suppressor
  • organism-icon Homo sapiens
  • sample-icon 12 Downloadable Samples
  • Technology Badge IconIllumina human-6 v2.0 expression beadchip

Description

Identifying the functions of proteins, which define specific subnuclear structures and territories, is important for understanding eukaryotic nuclear dynamics. Sp100 is a prototypical protein of ND10/PML bodies and co-localizes with the proto-oncogenic protein PML and Daxx, proteins with critical roles in oncogenic transformation, interferon-mediated viral resistance and response to PML-directed cancer therapeutics. Sp100 isoforms contain PHD, Bromo and HMG domains and are highly sumoylated at ND10/PML bodies, all characteristics suggestive of a role in chromatin mediated gene regulation. However, no clear role for the Sp100 component of PML bodies in oncogenesis has been defined. Using isoform-specific knockdown techniques, we show that most human diploid fibroblasts, which lack Sp100, rapidly senesce and discuss gene expression changes associated with this rapid senescence.

Publication Title

Sp100 as a potent tumor suppressor: accelerated senescence and rapid malignant transformation of human fibroblasts through modulation of an embryonic stem cell program.

Sample Metadata Fields

Cell line, Treatment

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accession-icon GSE45970
Targeting Myc signaling pathway by inhibition of histone demethylase JMJD2B
  • organism-icon Homo sapiens
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix HT HG-U133+ PM Array Plate (hthgu133pluspm)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

The role of histone demethylase KDM4B in Myc signaling in neuroblastoma.

Sample Metadata Fields

Cell line, Treatment

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accession-icon GSE51978
Gene expression profiling in neuroblastoma cells upon CHAF1A silencing
  • organism-icon Homo sapiens
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

We used an inducible ShRNA system and microarrays to detail the global programme of gene expression underlying neuroblastoma differentiation upon CHAF1A silencing .

Publication Title

Histone chaperone CHAF1A inhibits differentiation and promotes aggressive neuroblastoma.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE45969
Targeting Myc signaling pathway by inhibition of histone demethylase JMJD2B (ciclopirox)
  • organism-icon Homo sapiens
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix HT HG-U133+ PM Array Plate (hthgu133pluspm)

Description

Epigenetic alterations appear to modulate Myc signaling. We investigated the role of the histone demethylase JMJD2B in Myc-mediated neuroblastoma pathogenesis. We demonstrate that Myc physically interacts with and recruits this epigenetic modifier, which removes repressive H3K9 methyl marks from Myc-target genes. JMJD2B regulates neuroblastoma proliferation and, together with MYCN amplification, identifies a subgroup of poor prognosis patients. We identify a novel histone demethylase inhibitor, ciclopirox, which targets JMJD2B and, consequently, Myc signaling, thereby inhibiting neuroblastoma proliferation and inducing differentiation. In xenograft studies, genetic and pharmacologic inhibition of JMJD2B resulted in significant tumor growth restriction. Our findings provide insight into epigenetic regulation of Myc via histone methylation and proof-of-concept for pharmacologic inhibition of histone demethylases to target Myc signaling in cancer.

Publication Title

The role of histone demethylase KDM4B in Myc signaling in neuroblastoma.

Sample Metadata Fields

Cell line, Treatment

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accession-icon GSE45967
Targeting Myc signaling pathway by inhibition of histone demethylase JMJD2B (siRNA)
  • organism-icon Homo sapiens
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix HT HG-U133+ PM Array Plate (hthgu133pluspm)

Description

Epigenetic alterations appear to modulate Myc signaling. We investigated the role of the histone demethylase JMJD2B in Myc-mediated neuroblastoma pathogenesis. We demonstrate that Myc physically interacts with and recruits this epigenetic modifier, which removes repressive H3K9 methyl marks from Myc-target genes. JMJD2B regulates neuroblastoma proliferation and, together with MYCN amplification, identifies a subgroup of poor prognosis patients. We identify a novel histone demethylase inhibitor, ciclopirox, which targets JMJD2B and, consequently, Myc signaling, thereby inhibiting neuroblastoma proliferation and inducing differentiation. In xenograft studies, genetic and pharmacologic inhibition of JMJD2B resulted in significant tumor growth restriction. Our findings provide insight into epigenetic regulation of Myc via histone methylation and proof-of-concept for pharmacologic inhibition of histone demethylases to target Myc signaling in cancer.

Publication Title

The role of histone demethylase KDM4B in Myc signaling in neuroblastoma.

Sample Metadata Fields

Cell line

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accession-icon GSE13255
Gene Expression Profiles in Peripheral Blood Mononuclear Cells Can Distinguish Patients with NonSmall Cell Lung Cancer.
  • organism-icon Homo sapiens
  • sample-icon 291 Downloadable Samples
  • Technology Badge IconIllumina human-6 v2.0 expression beadchip

Description

We report a 29-gene diagnostic signature, which distinguishes individuals with NSCLC from controls with non-malignant lung disease with 91% Sensitivity, 79% Specificity and a ROC AUC of 92%. Accuracy on an independent set of 18 NSCLC samples from the same location was 79%. Samples from an independent location including 12 stage 1 NSCLC and 15 controls, achieved an accuracy of 74%. A study of 18 paired samples taken pre and post surgery shows that the PBMC associated cancer signature is significantly reduced after tumor removal, supporting the hypothesis that the signature detected in pre-surgery samples is a response to the presence of the tumor.

Publication Title

Gene expression profiles in peripheral blood mononuclear cells can distinguish patients with non-small cell lung cancer from patients with nonmalignant lung disease.

Sample Metadata Fields

Sex, Age, Race

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accession-icon SRP117060
Quantitative Analysis of Wildtype and Neurog2CKO Heterozygote and Mutant Retinal Transcriptomes by RNA Sequencing
  • organism-icon Mus musculus
  • sample-icon 15 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

To generate an unbiased view of changes to the retinal gene network in Neurog2 retinal mutants, we generated and compared the P2 transcriptomes from control, heterozygote and mutant mice. A pair of P2 retinas from each biologic replicate were used to produce libraries for high throughput sequencing (n = 5 biologic replicates/genotype). Reads were aligned with BWA and Bowtie programs to the mm10 genome. Aligned reads were then analyzed for differentially expressed transcripts using the CuffDiff program in the Galaxy online bioinformatics package (www.usegalaxy.org). Overall design: Total RNA from Neurog2CKO/CKO(wildtype; n = 5), Chx10Cre;Neurog2CKO/+(heterozygote; n = 5), and Chx10Cre;Neurog2CKO/CKO(mutant; n = 5) P2 retinas.

Publication Title

Requirements for Neurogenin2 during mouse postnatal retinal neurogenesis.

Sample Metadata Fields

Specimen part, Cell line, Subject

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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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