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accession-icon SRP170102
Homo sapiens Genome sequencing
  • organism-icon Homo sapiens
  • sample-icon 2 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Breast cancer (BRC) is the most invasive cancer in women. Although the survival rate of BRC is gradually increasing due to improved screening systems, development of novel therapeutic targets for inhibition of BRC proliferation, metastasis and recurrence have been constantly needed. Thus, in this study, we identified overexpression of SETDB1, a histone methyltransferase, in RNA-seq data of BRC derived from TCGA portal. In Gene Ontology (GO) analysis, cell migration-related GO terms were enriched, and we confirmed down-regulation of cell migration/invasion and alteration of EMT /MET markers after knockdown of SETDB1. Moreover, gene network analysis showed that SMAD7 expression is regulated by SETDB1 levels, indicating that up-regulation of SMAD7 by SETDB1 knockdown inhibited BRC metastasis. Therefore, development of SETDB1 inhibitors and functional studies may help develop more effective clinical guidelines for BRC treatment

Publication Title

No associated publication

Sample Metadata Fields

Sex, Age, Specimen part, Disease, Cell line, Treatment

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accession-icon SRP044280
Mus musculus Transcriptome or Gene expression
  • organism-icon Mus musculus
  • sample-icon 2 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

RNA-seq of single embryo

Publication Title

No associated publication

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE2192
Differentiation of NIH-3T3 cells to adipocytes by PPARg or EBF1 over-expression.
  • organism-icon Mus musculus
  • sample-icon 53 Downloadable Samples
  • Technology Badge Icon Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)

Description

NIH-3T3 cells transduced with either EBF1-, PPARg2- or empty vector were stimulated with hormones to initiate adipocyte differentiation. RNA extraction was done using TriZol at d0, d2, d4 and d10 after stimulation. Samples were handled according to standard affymetrix protocols.

Publication Title

Gene expression analysis suggests that EBF-1 and PPARgamma2 induce adipogenesis of NIH-3T3 cells with similar efficiency and kinetics.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE55129
The role of Rif1 in ES cells
  • organism-icon Mus musculus
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Purpose:The goals of this study are to understand the mechanisms underlying reduced self-renewal and loss of pluripotency by depletion of Rif1.

Publication Title

Rif1 maintains telomere length homeostasis of ESCs by mediating heterochromatin silencing.

Sample Metadata Fields

Cell line

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accession-icon SRP072829
Transcriptome analysis of CNS leukemia
  • organism-icon Homo sapiens
  • sample-icon 15 Downloadable Samples
  • Technology Badge IconNextSeq 500

Description

The goal of this study is to reveal the characters and therapeutic targets of CNS leukemia.

Publication Title

No associated publication

Sample Metadata Fields

Sex, Age, Specimen part, Disease

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accession-icon SRP045672
RNA-seq transcriptome analysis of mouse cell lines
  • organism-icon Mus musculus
  • sample-icon 7 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Building the gene expression profiles and identifying the differentially expressed genes in specific comparisons.

Publication Title

No associated publication

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE76580
REST knock-out ESCs: a role for REST in embryonic stem cells' cardiac lineage specification
  • organism-icon Mus musculus
  • sample-icon 16 Downloadable Samples
  • Technology Badge IconIllumina MouseRef-8 v2.0 expression beadchip

Description

During development, lineage specification is controlled by several signaling pathways involving various transcription factors (TFs). Here, we studied the RE1-silencing transcription factor (REST) and identified an important role of this TF in cardiac differentiation. Using mouse embryonic stem cells (ESC) to model development, we analyzed the effect of REST knock-out on the ability to these cells to differentiate into the cardiac lineage. Detailed analysis of specific lineage markers expression showed selective down-regulation of endoderm markers in REST-null cells, thus contributing to a loss of cardiogenic signals.

Publication Title

A Role for RE-1-Silencing Transcription Factor in Embryonic Stem Cells Cardiac Lineage Specification.

Sample Metadata Fields

Specimen part, Treatment

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accession-icon GSE43234
Sox7 and Sox17
  • organism-icon Mus musculus
  • sample-icon 11 Downloadable Samples
  • Technology Badge IconIllumina mouseRef-8 v1.1 expression beadchip

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Oct4 switches partnering from Sox2 to Sox17 to reinterpret the enhancer code and specify endoderm.

Sample Metadata Fields

Cell line, Treatment

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accession-icon GSE43233
Gene expression analysis of V5 tagged Sox17 expressing ES cells
  • organism-icon Mus musculus
  • sample-icon 10 Downloadable Samples
  • Technology Badge IconIllumina mouseRef-8 v1.1 expression beadchip

Description

Analysis of the expression of KH2 embryonic stem cells inducibly expressing V5 tagged Sox17 protein. Results provide information on the endodermal gene expression program activated after Sox17 expression in ES cells.

Publication Title

Oct4 switches partnering from Sox2 to Sox17 to reinterpret the enhancer code and specify endoderm.

Sample Metadata Fields

Cell line, Treatment

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accession-icon GSE43232
Gene expression analysis of F9 cells double knock-down for Sox7 and Sox17
  • organism-icon Mus musculus
  • sample-icon 1 Downloadable Sample
  • Technology Badge IconIllumina mouseRef-8 v1.1 expression beadchip

Description

Analysis of the expression of F9 cells after knockdown of Sox7 and Sox17 during their primitive endoderm differnetiation induction with retinoic acid. Results provide information on the endodermal gene expression program regulated by Sox7 and Sox17.

Publication Title

Oct4 switches partnering from Sox2 to Sox17 to reinterpret the enhancer code and specify endoderm.

Sample Metadata Fields

Cell line, Treatment

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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