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GSE134613
Mus musculus
9 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Stromal cells rapidly reorganize cell composition during would healing. Resident stromal cells secrete systemic ligands and mobilize immune cells from bone marrow. Subsequently resident cells and mobilized immune cells cooperate together for efficient wound healing.
Publication Title
Surgical Injury and Ischemia Prime the Adipose Stromal Vascular Fraction and Increase Angiogenic Capacity in a Mouse Limb Ischemia Model.
Sample Metadata Fields
Age, Specimen part
View Samples- Mus musculus
- 9 Downloadable Samples
- Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
A mouse AGM-derived cell line, AGM-s3, was shown to support the development of hematopoietic stem cells. To elucidate the molecular mechanisms regulating early hematopoiesis, we obtained subclones from AGM-s3, some of which were hematopoiesis supportive (s3-A9) and others which were non-supportive (s3-A7), and we analyzed the gene expression profiles by gene chip analysis.
Publication Title
Expression profile analysis of aorta-gonad-mesonephros region-derived stromal cells reveals genes that regulate hematopoiesis.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 1 Downloadable Sample
Illumina HumanHT-12 V4.0 expression beadchip, Illumina Genome Analyzer
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
The long noncoding RNA RMST interacts with SOX2 to regulate neurogenesis.
Sample Metadata Fields
Cell line, Treatment
View Samples- Homo sapiens
- 1 Downloadable Sample
Illumina HumanHT-12 V4.0 expression beadchip, Illumina Genome Analyzer
Description
We report that knockdown of the lncRNA RMST changes the gene expression profile of neural stem cells.
Publication Title
The long noncoding RNA RMST interacts with SOX2 to regulate neurogenesis.
Sample Metadata Fields
Cell line
View Samples- Mus musculus
- 13 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Very little is known about how intervertebral disc (IVD) is formed or maintained. Members of the TGF- superfamily are secreted signaling proteins that regulate many aspects of development including cellular differentiation. We recently showed that deletion of Tgfbr2 in Col2a expressing tissue results in alterations in development of IVD annulus fibrosus. The results suggested TGF- has an important role in regulating development of the axial skeleton, however, the mechanistic basis of TGF- action in these specialized joints is not known. One of the hurdles to understanding development of IVD is a lack of known markers. To identify genes that are enriched in the developing IVD and to begin to understand the mechanism of TGF- action in IVD development, we undertook a global analysis of gene expression comparing gene expression profiles in developing vertebrae and IVD. We also compared expression profiles in tissues from wild type and Tgfbr2 mutant mice. Lists of IVD and vertebrae enriched genes were generated. Expression patterns for several genes were verified either through in situ hybridization or literature/ database searches resulting in a list of genes that can be used as markers of IVD. Cluster analysis using genes listed under the Gene Ontology terms multicellular organism development and pattern specification indicated that mutant IVD more closely resembled vertebrae than wild type IVD. We propose TGF- has two functions in IVD development: 1) to prevent chondrocyte differentiation in the presumptive IVD and 2) to promote differentiation of annulus fibrosus from sclerotome. We have identified genes that are enriched in the IVD and regulated by TGF- that warrant further investigation as regulators of IVD development.
Publication Title
Molecular profiling of the developing mouse axial skeleton: a role for Tgfbr2 in the development of the intervertebral disc.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 9 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Very little is known about how intervertebral disc (IVD) is formed or maintained. Members of the TGF- superfamily are secreted signaling proteins that regulate many aspects of development including cellular differentiation. We recently showed that deletion of Tgfbr2 in Col2a expressing tissue results in alterations in development of IVD annulus fibrosus. The results suggested TGF- has an important role in regulating development of the axial skeleton, however, the mechanistic basis of TGF- action in these specialized joints is not known. To understand the mechanism of TGF- action in IVD development, we undertook a global analysis of gene expression comparing gene expression profiles in sclerotome cultures treated with TGF- or BMP4. As expected, treatment with BMP4 resulted in up-regulation of cartilage marker genes including Acan, Sox 5, Sox6, and Sox9. In contrast, treatment with TGF-1 did not regulate expression of cartilage markers but instead resulted in up-regulation of many IVD markers including Fmod and Adamtsl2. We propose TGF- has two functions in IVD development: 1) to prevent chondrocyte differentiation in the presumptive IVD and 2) to promote differentiation of annulus fibrosus from sclerotome. We have identified genes that are enriched in the IVD and regulated by TGF- that warrant further investigation as regulators of IVD development.
Publication Title
Molecular profiling of the developing mouse axial skeleton: a role for Tgfbr2 in the development of the intervertebral disc.
Sample Metadata Fields
No sample metadata fields
View Samples- Bos taurus
- 6 Downloadable Samples
- Affymetrix Bovine Genome Array (bovine)
Description
Bovine articular chondrocytes were grown in micromass culture and were either untreated or treated with 5 ng TGF-b1/ml for 8 hours to identify genes regulated by TGF-b.
Publication Title
Altered responsiveness to TGF-β results in reduced Papss2 expression and alterations in the biomechanical properties of mouse articular cartilage.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Saccharomyces cerevisiae
- 27 Downloadable Samples
- Illumina HiSeq 2500
Description
We performed RNAseq with Saccharomyces cerevisiae cells under both transient and steady-state conditions to study the regulation of genes by two pulsatile transcription factors, Msn2 and Mig1. The transient data allowed us to identify combinatorial targets while the steady-state data was used to study target expression dependence on the relative pulse timing between the two TFs. Overall design: For transition experiments, 18 samples (3 different strains x 3 dfferent conditions x 2 biological replicates) were analyzed. For steady-state experiments, one strain was analyzed at 9 different glucose concentrations and the other strain was analyzed at one glucose condition.
Publication Title
Combinatorial gene regulation by modulation of relative pulse timing.
Sample Metadata Fields
Cell line, Subject
View Samples- Homo sapiens
- 12 Downloadable Samples
- Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
Transcriptome analysis of mock or H1N1 IAV PR8 infected p53WT A549 and p53null A549-KO3 cells by Affymetrix GeneChip Human Transcriptome 2.0 Arrays to achieve a set of genes those are regulated by p53 and responsive to IAV infection.
Publication Title
Influenza A Virus Facilitates Its Infectivity by Activating p53 to Inhibit the Expression of Interferon-Induced Transmembrane Proteins.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 6 Downloadable Samples
- NextSeq 500
Description
We analyzed the gene expression profile of papillary thyroid cancer from central and invasive regions. Overall design: Examination of 3 different papillary thyroid cancer groups and analysis of each group between central and invasive regions.
Publication Title
Senescent tumor cells lead the collective invasion in thyroid cancer.
Sample Metadata Fields
Subject
View Samples