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accession-icon GSE101854
Dpy30 regulates Myc binding to targets and Myc-driven tumorigenesis
  • organism-icon Mus musculus, Homo sapiens
  • sample-icon 2 Downloadable Samples
  • Technology Badge IconIllumina HumanHT-12 V4.0 expression beadchip

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Hijacking a key chromatin modulator creates epigenetic vulnerability for MYC-driven cancer.

Alternate Accession IDs

E-GEOD-101854

Sample Metadata Fields

Specimen part, Treatment

View Samples
accession-icon GSE101852
Dpy30 regulates Myc binding to targets and Myc-driven tumorigenesis (Illumina HumanHT-12 V4.0 expression)
  • organism-icon Homo sapiens
  • sample-icon 2 Downloadable Samples
  • Technology Badge IconIllumina HumanHT-12 V4.0 expression beadchip

Description

It remains unclear how epigenetic modulators impact the tumorigenic potential of Myc. Here we show that the core subunits, including Dpy30, of the major H3K4 methyltransferase complexes are selectively upregulated in Burkitt lymphoma, and Dpy30 is important for efficient genomic binding of Myc. Dpy30 heterozygosity does not affect normal animal physiology, but significantly suppressed lymphomagenesis and reduced expression of a subset of key pro-survival genes when Myc is hyper-activated. Dpy30 heterozygosity also impedes cellular transformation without affecting normal cell growth. These results suggest that Myc hijacks this chromatin modulator to coordinate its oncogenic program for efficient tumorigenesis, meanwhile creating epigenetic vulnerability, which we then exploited by specifically targeting Dpy30s activity to inhibit growth of the Burkitt lymphoma cell model.

Publication Title

Hijacking a key chromatin modulator creates epigenetic vulnerability for MYC-driven cancer.

Alternate Accession IDs

E-GEOD-101852

Sample Metadata Fields

Specimen part, Treatment

View Samples
accession-icon SRP015640
Comprehensive comparative analysis of RNA sequencing methods for degraded or low input samples
  • organism-icon Homo sapiens
  • sample-icon 64 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500, Illumina HiSeq 2000

Description

RNA-Seq is an effective method to study the transcriptome, but can be difficult to apply to scarce or degraded RNA from fixed clinical samples, rare cell populations, or cadavers. Recent studies have proposed several methods for RNA-Seq of low quality and/or low quantity samples, but their relative merits have not been systematically analyzed. Here, we compare five such methods using a comprehensive set of metrics, relevant to applications such as transcriptome annotation, transcript discovery, and gene expression. Using a single human RNA sample, we constructed and deeply sequenced 10 libraries with these methods and two control libraries. We find that the RNase H method performed best for low quality RNA, and can even effectively replace oligo (dT) based methods for standard RNA-Seq. SMART and NuGEN had distinct strengths for low quantity RNA. Our analysis allows biologists to select the most suitable methods and provides a benchmark for future method development. Overall design: Examination of 9 different RNA-Seq libraries starting from total RNA from 5 distinct methods; also 3 control RNA-Seq libraries

Publication Title

Comparative analysis of RNA sequencing methods for degraded or low-input samples.

Alternate Accession IDs

GSE40705

Sample Metadata Fields

Specimen part, Cell line, Subject

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accession-icon GSE6189
Molecular Mechanisms of Early Response in Adaptive Cerebral Arteriogenesis
  • organism-icon Rattus norvegicus
  • sample-icon 15 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Expression 230A Array (rae230a)

Description

This study aims at a comprehensive understanding of the genomic program activated during early-phase of collateral vessel growth in a rat model for cerebral adaptive arteriogenesis (3-VO). While arteriogenesis constitutes a promising therapeutic concept for cerebrovascular ischemia, genomic profiles essential for therapeutic target identification were analysed solely for collateral arteries of the heart and periphery. Despite challenging anatomical conditions of the brain the 3-VO model allows identification of differentially expressed genes during adaptive cerebral arteriogenesis by selective removal of the posterior cerebral artery (PCA).

Publication Title

Induction of cerebral arteriogenesis leads to early-phase expression of protease inhibitors in growing collaterals of the brain.

Alternate Accession IDs

E-GEOD-6189

Sample Metadata Fields

Age

View Samples
accession-icon GSE23680
Expression data from hepatocellular carcinoma and adjacent normal liver tissue
  • organism-icon Mus musculus
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Assay of gene expression pattern differences between liver cancer tissue and normal liver tissue from the same mouse by microarray in 4 separate mice injected with recombinant adeno-associated viral (AAV) vector

Publication Title

Assessing the potential for AAV vector genotoxicity in a murine model.

Alternate Accession IDs

E-GEOD-23680

Sample Metadata Fields

Sex, Specimen part

View Samples
accession-icon GSE12243
Microvesicles derived from human mesenchymal stem cells protect against acute tubular injury
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina human-6 v2.0 expression beadchip

Description

Administration of exogenous mesenchymal stem cells (MSCs) has been shown to improve the recovery from acute kidney injury (AKI). It has been suggested that the beneficial effect of MSCs is related to the paracrine release of factors favouring proliferation of intrinsic epithelial cells survived to injury rather than to their trans-differentiation. However the factors involved remain to be determined. In the present study we demonstrated that microvesicles (MVs) derived from human bone marrow MSCs are able to stimulate in vitro proliferation and apoptosis resistance of tubular epithelial cells (TEC). In addition, MVs were found to accelerate in vivo the morphological and functional recovery of glycerol induced AKI in SCID mice by inducing TEC proliferation. The effect of MVs on the recovery of AKI was comparable to that of human MSC treatment. In vitro we found that the CD44 and beta1-integrin-dependent incorporation of MVs in TEC was required for their biological action. However, despite their internalization, RNase-treated MVs failed to induce in vitro apoptosis resistance and TEC proliferation, and in vivo recovery from AKI, suggesting an RNA-dependent biological effect. Microarray analysis and quantitative RT-PCR of MV-RNA extract indicated that MVs were shuttling a specific subset of cellular mRNA, such as mRNA associated with the mesenchymal differentiative phenotype and with several cell functions involved in the control of transcription, proliferation, apoptosis and cell immune regulation. These results suggest that MVs derived from MSCs may activate a proliferative program in TEC survived to injury in AKI by an horizontal transfer of mRNA.

Publication Title

Mesenchymal stem cell-derived microvesicles protect against acute tubular injury.

Alternate Accession IDs

E-GEOD-12243

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon SRP048640
EZH2 inhibitor efficacy in non-Hodgkin lymphoma does not require suppression of H3K27 mono-methylation [RNA-Seq]
  • organism-icon Homo sapiens
  • sample-icon 8 Downloadable Samples
  • Technology Badge IconIlluminaHiSeq2000

Description

Here we report the discovery of highly potent and selective EZH2 small molecule inhibitors, their validation by a cellular thermal shift assay, their application across a large lymphoma cell panel and their efficacy in GCBDLBCL xenograft models. Overall design: RNA-seq of KARPAS-422 cell line RNA, in duplicate, treated with DMSO as control, and EZH2 inhibitors CPI360, EPZ-6438 and GSK126. Eight samples in total.

Publication Title

EZH2 inhibitor efficacy in non-Hodgkin's lymphoma does not require suppression of H3K27 monomethylation.

Alternate Accession IDs

GSE62056

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE137176
Time-driven molding of the epidermal stem cell transcriptome
  • organism-icon Mus musculus
  • sample-icon 18 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Epidermal stem cells ensure proper faring of skin homeostatic processes under both physiological and challenging conditions. Currently, the molecular events underpinning ageing within the epidermal stem cell niche are poorly understood.

Publication Title

In Silico Analysis of the Age-Dependent Evolution of the Transcriptome of Mouse Skin Stem Cells.

Alternate Accession IDs

E-GEOD-137176

Sample Metadata Fields

Age, Specimen part

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accession-icon GSE38390
Expression data from leaves of GA-deficient and GA-insensitive transgenic poplar
  • organism-icon Populus tremula x populus alba
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Poplar Genome Array (poplar)

Description

We used whole-genome microarrays to identify differentially expressed genes in leaves of GA-deficient (35S::PcGA2ox) and/or GA-insensitive (35S::rgl1) transgenics as compared to WT poplar (717-1B4 genotype).

Publication Title

Roles of gibberellin catabolism and signaling in growth and physiological response to drought and short-day photoperiods in Populus trees.

Alternate Accession IDs

E-GEOD-38390

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE42816
Gene expression propionic patients, carriers, and controls
  • organism-icon Homo sapiens
  • sample-icon 83 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

Gene expression in LCLs from PA patients, their parents, and HapMap sex and age match controls at low glucose (9 mg/dL) and normal glucose growth conditions.

Publication Title

Gene expression in cell lines from propionic acidemia patients, carrier parents, and controls.

Alternate Accession IDs

E-GEOD-42816

Sample Metadata Fields

Sex, Age, Disease, Disease stage, Cell line, Treatment

View Samples
...

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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