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accession-icon GSE30028
Expression data from control and Pbx1-null CMPs and GMPs
  • organism-icon Mus musculus
  • sample-icon 17 Downloadable Samples
  • Technology Badge Icon

Description

The capacity of the hematopoietic system to promptly respond to peripheral demands relies on adequate pools of progenitors able to transiently proliferate and differentiate in a regulated manner. However, little is known about factors that may restrain progenitor maturation to maintain their reservoirs. In addition to a profound defect in hematopoietic stem cell (HSC) self-renewal, conditional knockout mice for the Pbx1 proto-oncogene have a significant reduction in lineage-restricted progenitors, including common myeloid progenitors (CMPs) and, to a lesser extent, granulocyte-monocyte progenitors (GMPs).

Publication Title

Pbx1 restrains myeloid maturation while preserving lymphoid potential in hematopoietic progenitors.

Sample Metadata Fields

Age, Specimen part

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accession-icon GSE13690
Gene expression profiling of murine MLL leukemias (whole BM)
  • organism-icon Mus musculus
  • sample-icon 38 Downloadable Samples
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Description

The genetic programs that promote retention of self-renewing leukemia stem cells (LSCs) at the apex of cellular hierarchies in acute myeloid leukemia (AML) are not known. In a mouse model of human AML, LSCs exhibit variable frequencies that correlate with the initiating MLL oncogene and are maintained in a self-renewing state by a transcriptional sub-program more akin to that of embryonic stem cells (ESCs) than adult stem cells. The transcription/chromatin regulatory factors Myb, Hmgb3 and Cbx5 are critical components of the program and suffice for Hoxa/Meis-independent immortalization of myeloid progenitors when co-expressed, establishing the cooperative and essential role of an ESC-like LSC maintenance program ancillary to the leukemia initiating MLL/Hox/Meis program. Enriched expression of LSC maintenance and ESC-like program genes in normal myeloid progenitors and poor prognosis human malignancies links the frequency of aberrantly self-renewing progenitor-like cancer stem cells to prognosis in human cancer.

Publication Title

Hierarchical maintenance of MLL myeloid leukemia stem cells employs a transcriptional program shared with embryonic rather than adult stem cells.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE13693
Gene expression profiling of normal mouse myeloid cell populations
  • organism-icon Mus musculus
  • sample-icon 9 Downloadable Samples
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Description

Normal myeloid lineage cell populations (C57BL/6 mice, aged 4-10 weeks, male or female) with three distinct immunophenotypes were prospectively isolated and characterized. In preparation for FACS sorting, bone marrow cells were separated into c-kit+ and c-kit- fractions using an AutoMACS device. C-kit+ cells were further fractionated based on Gr1 and Mac1 expression, and absence of lineage antigen expression (B220, TER119, CD3, CD4, CD8 and IL7R), by cell sorting. C-kit+ Gr1+ Mac1lo/- and c-kit+ Gr1+ Mac1+ displayed cytologic features of undifferentiated hematopoietic cells or myeloblasts, whereas c-kit- Gr1+ Mac1+ cells were mature neutrophils.

Publication Title

Hierarchical maintenance of MLL myeloid leukemia stem cells employs a transcriptional program shared with embryonic rather than adult stem cells.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE13692
Expression profiling of MLL-AF10 myeloid leukemia cellular subsets
  • organism-icon Mus musculus
  • sample-icon 8 Downloadable Samples
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Description

Leukemia cells from mice with MLL-AF10 AML were fractionated into separate sub-populations on the basis of c-kit expression, which correlates with MLL LSC frequency (Somervaille and Cleary, 2006). The sorted AML sub-populations exhibited substantial differences in their frequencies of AML CFCs/LSCs (mean 14-fold) and morphologic features, consistent with a leukemia cell hierarchy with maturation through to terminally differentiated neutrophils.

Publication Title

Hierarchical maintenance of MLL myeloid leukemia stem cells employs a transcriptional program shared with embryonic rather than adult stem cells.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE109583
Epidermal fatty acid binding protein prevents chemical-induced skin tumorigenesis by inhibition of SOX2 expression in keratinocytes
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
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Description

E-FABP expression in keratinocytes increase interferons, in particualur IFNlamda, expression, which activate P53, a critical tumor suppessor, to inhibit or prevent chemical-induced skin tumorigenesis.

Publication Title

Epidermal FABP Prevents Chemical-Induced Skin Tumorigenesis by Regulation of TPA-Induced IFN/p53/SOX2 Pathway in Keratinocytes.

Sample Metadata Fields

Specimen part

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accession-icon GSE32199
BMP and Activin treatment of mouse extraembryonic endoderm (XEN) cells
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
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Description

XEN cells are derived from the primitive endoderm of mouse blastocysts. In culture and in chimeras they exhibit properties of parietal endoderm. However, BMP signaling promotes XEN cells to form an epithelium and differentiate into visceral endoderm (VE). Of the several different subtypes of VE described, BMP induces a subtype that is most similar to the VE adjacent to the trophoblast-derived extraembryonic ectoderm.

Publication Title

BMP signaling induces visceral endoderm differentiation of XEN cells and parietal endoderm.

Sample Metadata Fields

Treatment

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accession-icon GSE87081
Functional Roles of Acetylated Histone Marks at Mouse Meiotic Recombination Hotspots
  • organism-icon Mus musculus
  • sample-icon 23 Downloadable Samples
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Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Functional Roles of Acetylated Histone Marks at Mouse Meiotic Recombination Hot Spots.

Sample Metadata Fields

Sex, Age, Specimen part

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accession-icon GSE21710
Insulin receptor signaling in osteoblasts regulates postnatal bone acquisition and body composition
  • organism-icon Mus musculus
  • sample-icon 4 Downloadable Samples
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Description

Global energy balance in mammals is controlled by the actions of circulating hormones that coordinate fuel production and utilization in metabolically active tissues. Bone-derived osteocalcin, in its undercarboxylated, hormonal form, regulates fat deposition and is a potent insulin secretagogue. Here, we show that insulin receptor (IR) signaling in osteoblasts controls osteoblast development and osteocalcin expression by suppressing the Runx2 inhibitor Twist-2. Mice lacking IR in osteoblasts have low circulating undercarboxylated osteocalcin and reduced bone acquisition due to decreased bone formation and deficient numbers of osteoblasts. With age, these mice develop marked peripheral adiposity and hyperglycemia accompanied by severe glucose intolerance and insulin resistance. The metabolic abnormalities in these mice are improved by infusion of exogenous under-carboxylated osteocalcin. These results indicate the existence of a bone-pancreas endocrine loop through which insulin signaling in the osteoblast ensures osteoblast differentiation and stimulates osteocalcin production, which in turn regulates insulin sensitivity and pancreatic insulin secretion to control glucose homeostasis.

Publication Title

Insulin receptor signaling in osteoblasts regulates postnatal bone acquisition and body composition.

Sample Metadata Fields

Specimen part, Time

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accession-icon GSE63188
An EphB-Abl signaling pathway important for intestinal tumor initiation and growth
  • organism-icon Mus musculus
  • sample-icon 10 Downloadable Samples
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Description

EphB receptors regulate the proliferation and positioning of intestinal stem and progenitor cells. In addition, they can act as tumor promoters for adenoma development, but suppress progression to invasive carcinoma. Here we used imatinib to abrogate Abl kinase activity in ApcMin/+ mice and in mice with LGR5+ stem cells genetically targeted for APC. This treatment inhibited the tumor-promoting effects of EphB signaling without attenuating EphB-mediated tumor suppression, demonstrating the role of EphB signaling in intestinal tumor initiation. The investigated treatment regimen extended the lifespan of ApcMin/+ mice, and reduced cell proliferation in cultured slices of adenomas from FAP patients. These findings connect the EphB signaling pathway to the regulation of intestinal adenoma initiation via Abl kinase. Our findings may have clinical implications for pharmacological therapy against adenoma formation and cancer progression in patients predisposed to develop colon cancer.

Publication Title

An EphB-Abl signaling pathway is associated with intestinal tumor initiation and growth.

Sample Metadata Fields

Specimen part

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accession-icon GSE27605
The intestinal stem cell signature identifies colorectal cancer stem cells and predicts disease relapse
  • organism-icon Mus musculus
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon

Description

Using EphB2 or the ISC marker Lgr5, we have FACS-purified and profiled intestinal stem cells (ISCs), crypt proliferative progenitors and late transient amplifying cells to define a gene expression program specific for normal ISCs.

Publication Title

The intestinal stem cell signature identifies colorectal cancer stem cells and predicts disease relapse.

Sample Metadata Fields

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)

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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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