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accession-icon GSE111392
Differentiation analysis of Mouse Posterior Neural tube
  • organism-icon Mus musculus
  • sample-icon 12 Downloadable Samples
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Description

Posterior embryonic axis develops from neuromesodermal progenitors which differentiate into neural tube and paraxial mesoderm

Publication Title

Recapitulating early development of mouse musculoskeletal precursors of the paraxial mesoderm <i>in vitro</i>.

Sample Metadata Fields

Treatment

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accession-icon GSE11224
Expression data from developing mouse placenta
  • organism-icon Mus musculus
  • sample-icon 54 Downloadable Samples
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Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Genomic evolution of the placenta using co-option and duplication and divergence.

Sample Metadata Fields

Specimen part

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accession-icon GSE11220
Timecourse of developing mouse placenta, with placental and decidual tissues profiled separately
  • organism-icon Mus musculus
  • sample-icon 44 Downloadable Samples
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Description

We used full genome microarrays to profile the full lifetime of the mouse placenta from embryonic day 8.5 (e8.5), at the time of chorioallantoic fusion, until postnatal day 0 (P0).

Publication Title

Genomic evolution of the placenta using co-option and duplication and divergence.

Sample Metadata Fields

Specimen part

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accession-icon GSE11222
Placental and decidual timecourse samples normalized and modeled with an undissected e17 sample
  • organism-icon Mus musculus
  • sample-icon 8 Downloadable Samples
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Description

We used full genome microarrays to profile the full lifetime of the mouse placenta from embryonic day 8.5 (e8.5), at the time of chorioallantoic fusion, until postnatal day 0 (P0). For these samples, at each stage the fetal placenta and maternal decidual tissues were dissected and profiled separately (See series 1).

Publication Title

Genomic evolution of the placenta using co-option and duplication and divergence.

Sample Metadata Fields

Specimen part

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accession-icon GSE17936
Nkx2.5 regulates Jarid2 during outflow tract morphogenesis
  • organism-icon Mus musculus
  • sample-icon 26 Downloadable Samples
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Description

The transcription factor Nkx2.5 is required for specification of pharyngeal arch second heart field (SHF) progenitors that contribute to outflow tract (OFT) and right ventricle (RV) formation. Multiple sets of microarray data were analyzed to identify genes that are candidate targets of Nkx2.5 in the second heart field. These sets are: 1) publicly available data for cardiothoracic tissue from E9.5 Nkx2.5 wild-type, heterozygous and homozygous embryos; 2) an analysis of mouse E10.5 pharyngeal arch tissue; 3) an analysis of mouse E12.5 heart tissue; and 4) a temporal analysis of the cardiogenic cell line P19CL6. This combined analysis identified 11 genes (Lrrn1, Elovl2, Safb, Slc39a6, Khdrbs1, Hoxb4, Fez1, Ccdc117, Jarid2, Nrcam, and Enpp3) expressed in SHF-containing pharyngeal arch tissue whose regulation is dependent on Nkx2.5 expression.

Publication Title

Jarid2 is among a set of genes differentially regulated by Nkx2.5 during outflow tract morphogenesis.

Sample Metadata Fields

Specimen part, Cell line

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accession-icon GSE17910
In vitro differentiation of P19CL6 cardiogenic embryonic carcinoma cells
  • organism-icon Mus musculus
  • sample-icon 16 Downloadable Samples
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Description

Pluripotent P19CL6 embryonic carcinoma cells can be differentiated to a cardiac lineage by culture in the presence of DMSO. The goal of this study was to characterize temporal gene expression patterns associated with cardiogenic differentiation. Gene expression analysis was conducted on differentiating P19CL6 cells at several time points following induction with 1% DMSO. Samples were processed for analysis by Affymetrix GeneChip.

Publication Title

Jarid2 is among a set of genes differentially regulated by Nkx2.5 during outflow tract morphogenesis.

Sample Metadata Fields

Cell line

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accession-icon GSE14997
Expression data from young and adult mice after over expression of self MHC class l protein in skeletal muscle.
  • organism-icon Mus musculus
  • sample-icon 7 Downloadable Samples
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Description

Over expression of MHC Class l protein in skeletal muscle causes myositis. Phenotype after expression in young mice is more severe.

Publication Title

Overexpression of MHC class I heavy chain protein in young skeletal muscle leads to severe myositis: implications for juvenile myositis.

Sample Metadata Fields

Sex, Specimen part, Treatment

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accession-icon GSE12536
Differentially regulated genes in control and c-myc N-myc deficient progenitors
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
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Description

Analysis of HSCs from control and c-myc N-myc deficient long-term hematopoietic stem cells. HSCs lacking both c-myc and N-myc display increased apoptosis rates. Data provide insight into the molecular changes occuring upon complete loss of Myc activity, clarifying the resulting apoptotic mechanism and the role of Myc family proteins in HSCs and commited progenitors.

Publication Title

Hematopoietic stem cell function and survival depend on c-Myc and N-Myc activity.

Sample Metadata Fields

Age, Specimen part

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accession-icon GSE12467
Differentially regulated genes in control and c-myc N-myc deficient LT-HSCs
  • organism-icon Mus musculus
  • sample-icon 5 Downloadable Samples
  • Technology Badge Icon

Description

Analysis of HSCs from control and c-myc N-myc deficient long-term hematopoietic stem cells. HSCs lacking both c-myc and N-myc display increased apoptosis rates. Data provide insight into the molecular changes occuring upon complete loss of Myc activity, clarifying the resulting apoptotic mechanism and the role of Myc family proteins in HSCs.

Publication Title

Hematopoietic stem cell function and survival depend on c-Myc and N-Myc activity.

Sample Metadata Fields

Age, Specimen part

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accession-icon GSE12538
Differentially regulated genes in control and c-myc N-myc deficient LT-HSCs and progenitors
  • organism-icon Mus musculus
  • sample-icon 1 Downloadable Sample
  • Technology Badge Icon

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Hematopoietic stem cell function and survival depend on c-Myc and N-Myc activity.

Sample Metadata Fields

Age, 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)

fund-icon Fund the CCDL

Developed by the Childhood Cancer Data Lab

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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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