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accession-icon E-MTAB-1419
Transcription profiling by array of X. laevis at stage 23 treated with BMS453 and control to investigate putative target genes of retinoic acid
  • organism-icon Xenopus laevis
  • sample-icon 2 Downloadable Samples
  • Technology Badge Icon Affymetrix Xenopus laevis Genome 2.0 Array (xlaevis2)

Description

To identify RA regulated genes in endoderm, we did microarray analysis comparing gene expression levels between wild-type and RA-deficient embryos, which were treated with BMS453 at the beginning of gastrulation and were collected at stages 23.

Publication Title

No associated publication

Sample Metadata Fields

Sex, Age, Compound

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accession-icon GSE32994
Oct4 and jhdm1b infected MEF with or without vitamin C treatment
  • organism-icon Mus musculus
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Investigate the effect of jhdm1b on Oct4 mediated reprogramming

Publication Title

The histone demethylases Jhdm1a/1b enhance somatic cell reprogramming in a vitamin-C-dependent manner.

Sample Metadata Fields

Specimen part, Treatment

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accession-icon GSE19379
DNA microarrays time course of SKO-infected MEFs and MaF pre-iPSCs treated with Vc
  • organism-icon Mus musculus
  • sample-icon 22 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Vitamin C enhances the generation of mouse and human induced pluripotent stem cells.

Sample Metadata Fields

Specimen part, Treatment, Time

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accession-icon GSE19604
Expression profile of early stage druing induced pluripotency regulated by BMP/FBS
  • organism-icon Mus musculus
  • sample-icon 15 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

FBS and BMP influence the somatic reprogramming induced by Oct4/Sox2/Klf4/c-Myc similarly. Bone morphogenetic proteins (BMPs) are abundant in serum and activate Smad1/5/8 to regulated target genes.

Publication Title

H3K9 methylation is a barrier during somatic cell reprogramming into iPSCs.

Sample Metadata Fields

Cell line

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accession-icon GSE19377
DNA microarrays time course of SKO-infected MEFs treated with Vc
  • organism-icon Mus musculus
  • sample-icon 14 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

In order to understand the global gene expression changes resulting from the addition of vitamin C (Vc) to SKO (sox2, klf4 and oct4)-transduced mouse embryonic fibroblasts (MEFs), we used microarray to compare the gene expression profile at different time points with or without Vc.

Publication Title

Vitamin C enhances the generation of mouse and human induced pluripotent stem cells.

Sample Metadata Fields

Specimen part, Treatment, Time

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accession-icon GSE23692
DNA microarrays (time course) of MEFs transduced with SKO plus HDAC7 or MEF2C
  • organism-icon Mus musculus
  • sample-icon 14 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Overexpression HDAC7 can enhance iPS efficiency in SKO by supressing MEF2 factors

Publication Title

No associated publication

Sample Metadata Fields

Specimen part, Time

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accession-icon GSE23104
DNA microarrays (time course) in the iPS process treated with microRNA clusters
  • organism-icon Mus musculus
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Treatment with MicroRNA cluster B and C increase the iPS efficiency

Publication Title

MicroRNA cluster 302-367 enhances somatic cell reprogramming by accelerating a mesenchymal-to-epithelial transition.

Sample Metadata Fields

Specimen part, Treatment, Time

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accession-icon GSE21067
Molecular mechanisms underlying reprogramming of mouse fibroblasts into pluripotent stem cells
  • organism-icon Mus musculus
  • sample-icon 9 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

A mesenchymal-to-epithelial transition initiates and is required for the nuclear reprogramming of mouse fibroblasts.

Sample Metadata Fields

Cell line

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accession-icon GSE15267
Expression data of induced pluripotent stem cell
  • organism-icon Mus musculus
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

We present a robust serum-free system for the rapid and efficient reprogramming of mouse somatic cells by Oct4, Sox2 and Klf4. The elimination of fetal bovine serum and oncogene c-Myc allowed reprogramming cells to be detected as early as Day 2 and reached greater than 10% of the population at Day 7 post retroviral transduction. The resulting iPS colonies were isolated with high efficiency to establish pluripotent cell lines. Based on this method, we further developed iPS-SF1 as a dedicated reprogramming medium for chemical screening and mechanistic investigations.

Publication Title

Towards an optimized culture medium for the generation of mouse induced pluripotent stem cells.

Sample Metadata Fields

Specimen part

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accession-icon GSE19378
DNA microarrays time course of a MaF pre-iPSC clone (C9) untreated or treated with Vc
  • organism-icon Mus musculus
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Treatment with vitamin C (Vc) on MaF pre-induced pluripotent stem cells (pre-iPSCs) induced a rapid conversion into full-iPSCs within a few passages. We used microarrays to identify changes induced by Vc in the MaF pre-iPSC clone.

Publication Title

Vitamin C enhances the generation of mouse and human induced pluripotent stem cells.

Sample Metadata Fields

Specimen part, 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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