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GSE49795
Homo sapiens
3 Downloadable Samples
Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Case story. A patient with massive infiltration of the visceral adipose tissue depot by BAT in a patient with a catecholamine secreting paraganglioma. BAT tissue was identified by protein expression of UCP1 (western blotting and immunostaining)
Publication Title
Chronic adrenergic stimulation induces brown adipose tissue differentiation in visceral adipose tissue.
Sample Metadata Fields
Specimen part
View Samples- Zea mays
- 6 Downloadable Samples
Illumina HiSeq 2000
Description
Background: Maize plants developed typical gray leaf spot disease (GLS) symptoms initiating at the lower leaves and progressing to upper leaves through the season. Leaf material was collected at 77 days after planting, at which stage there were a large number of GLS disease necrotic lesions on lower leaves (8% surface area on average determined by digital image analysis), but very few lesions and only at chlorotic stage on leaves above the ear (average of 0.2% lesion surface area). Method:To collect material that reflected a difference between C.zeina infected B73 leaves and control B73 leaf material, samples were collected from two lower GLS infected leaves (second and third leaf internode below ear) , and two upper leaves with minimal GLS symptoms (second and third internode above ear), respectively. The two lower leaves from each plant were pooled prior to RNA extraction, and the two upper leaves from each plant were pooled prior to RNA extraction. Upper and lower leaf samples from three maize B73 plants were subjected to RNA sequencing individually. The three maize plants were selected randomly as one plant per row from three rows of ten B73 plants each. Result: A systems genetics strategy revealed regions on the maize genome underlying co-expression of genes in susceptible and resistance responses, including a set of 100 genes common to the susceptible response of sub-tropical and temperate maize. Overall design: To collect material that reflected a difference between C.zeina infected B73 leaves and control B73 leaf material, samples were collected from two lower GLS infected leaves (second and third leaf internode below ear) , and two upper leaves with minimal GLS symptoms (second and third internode above ear), respectively. The two lower leaves from each plant were pooled prior to RNA extraction, and the two upper leaves from each plant were pooled prior to RNA extraction. Upper and lower leaf samples from three maize B73 plants were subjected to RNA sequencing individually. The three maize plants were selected randomly as one plant per row from three rows of ten B73 plants each.
Publication Title
Systems genetics reveals a transcriptional network associated with susceptibility in the maize-grey leaf spot pathosystem.
Sample Metadata Fields
Subject
View Samples- Homo sapiens
- 5 Downloadable Samples
- Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
Complex tissues contain multiple cell types that are hierarchically organized within morphologically and functionally distinct compartments. Construction of engineered tissues with optimized tissue architecture has been limited by tissue fabrication techniques, which do not enable versatile microscale organization of multiple cell types in tissues of size adequate for physiologic studies and tissue therapies. Here, we present an Intaglio-Void/Embed-Relief Topographic (InVERT) molding method for microscale organization of many cell types, including induced pluripotent stem cell (iPS)-derived progeny, within a variety of synthetic and natural extracellular matrices and across tissues of sizes appropriate for in vitro, pre-clinical, and clinical biologic studies. We demonstrate that compartmental placement of non-parenchymal cells relative to primary or iPS-derived hepatocytes and hepatic compartment microstructure and cellular composition modulate hepatic functions. Configurations found to be optimal in vitro also result in superior survival and function after transplantation into mice, demonstrating the importance of architectural optimization prior to implantation.
Publication Title
InVERT molding for scalable control of tissue microarchitecture.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The endocytic receptor megalin constitutes the main pathway for clearance of plasma proteins from the glomerular filtrate in the proximal tubules. However, little is know about the mechanisms that control receptor activity. A widely discussed hypothesis states that the intracellular domain (ICD) of megalin, released upon ligand binding, acts as a transcription regulator to suppress receptor expression - a mechanism proposed to safeguard the proximal tubules from protein overload. Here, we have put this hypothesis to the test by generating a mouse model co-expressing the soluble ICD and the full-length receptor. Despite pronounced expression in the proximal tubules, the ICD failed to exert any effects on renal proximal tubular function such as megalin expression, protein retrieval, or renal gene transcription. Thus, our data argue that the ICD does not play a role in regulation of megalin activity in vivo in the proximal tubules.
Publication Title
The soluble intracellular domain of megalin does not affect renal proximal tubular function in vivo.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
MLL3 inactivation mutations occurs frequently in human breast cancer. To understand the function of MLL3 inactivation, we compared the gene expression profiles of the vector control (WT)
Publication Title
Mammary-Stem-Cell-Based Somatic Mouse Models Reveal Breast Cancer Drivers Causing Cell Fate Dysregulation.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 17 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The ts-p53 E285K protein is a rare p53 mutant with temperature-sensitive (ts) loss of function characteristics. In cancer cells, which express ts-p53 E285K intriniscally, endogenous wild type p53 activity is reconstituted by appropriate cultivation temperature (permissive condition). At non-appropriate cultivation temperature (restrictive condition) this p53 mutant is inactive. The present study took advantage of this mechanism and employed IPH-926 lobular breast cancer cells and BT-474 ductal breast cancer cells, which both harbor endogenous ts-p53 E285K, for the transcriptional profiling of p53-responsive genes. This new approach eliminated the need for genetic modification or cytotoxic stimulation to achive a p53 response in the cells being investigated .
Publication Title
IPH-926 lobular breast cancer cells harbor a p53 mutant with temperature-sensitive functional activity and allow for profiling of p53-responsive genes.
Sample Metadata Fields
Specimen part, Cell line, Treatment
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Human solid tumors contain rare cancer side population (SP) cells, which expel the fluorescencent dye H33342 and display cancer stem cell characteristics. Transcriptional profiling of cancer SP cells isolated by H33342 fluorescence analysis is a newly emerging approach to discover cancer stem cell markers and aberrant differentiation pathways. Using Affymetrix expression microarrays this study investigated differential gene expression between SP and non-SP (NSP) cells isolated from the CAL-51 human mammary carcinoma cell line.
Publication Title
Down-regulation of the fetal stem cell factor SOX17 by H33342: a mechanism responsible for differential gene expression in breast cancer side population cells.
Sample Metadata Fields
Specimen part
View Samples- Pseudomonas aeruginosa pao1, Pseudomonas aeruginosa
- 10 Downloadable Samples
- Affymetrix Pseudomonas aeruginosa Array (paeg1a)
Description
In the present in vitro study, interactions between P. aeruginosa (sessile biofilms as well as planktonic cells) and PMNs were analyzed by means of DNA microarray based transcriptomics. We found that the P. aeruginosa wild type biofilms, in contrast to planktonic cultures and quorum sensing (QS) deficient strains, respond to PMN exposure in a rather aggressive manner. The response does not involve protective mechanisms such as those involved in oxidative stress. Rather it is dominated by QS controlled virulence determinants such as those encoded by pqs, phz, rhlAB, all of which are designed to cripple Eukaryotic cells including PMNs and macrophages. Our comparative analysis supports the view that QS plays a major role in mechanisms by which P. aeruginosa evades host defense systems.
Publication Title
Pseudomonas aeruginosa recognizes and responds aggressively to the presence of polymorphonuclear leukocytes.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 12 Downloadable Samples
- Illumina HiSeq 2500
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Stem Cell Determinant SOX9 Promotes Lineage Plasticity and Progression in Basal-like Breast Cancer.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 6 Downloadable Samples
Affymetrix Mouse Clariom S Array (clariomsmouse)
Description
Lineage plasticity plays an important role in the development of basal-like breast cancer (BLBC), an aggressive cancer subtype. Although studies suggest BLBC is likely to originate from luminal progenitor cells, it acquires substantial basal cell features and contains a heterogenous collection of cells exhibiting basal, luminal and bipotent phenotypes. Why luminal progenitors are prone to BLBC transformation and what drives luminal-to-basal/bipotent reprogramming remains unclear. Here we show that the transcription factor SOX9 acts as a determinant for ER– luminal stem/progenitor cells (LSPCs). SOX9 controls LSPC activity in part by activating both canonical and non-canonical NF-B signaling. Inactivation of p53 and Rb in a BLBC mouse tumor model leads to upregulation of SOX9, which drives luminal-to-bipotent reprogramming in vivo. SOX9 deletion inhibits the progression of benign, neoplastic lesions to invasive carcinoma. Furthermore, SOX9 is overexpressed and correlated with shorter relapse-free survival in human BLBC. These data show that ER– LSPC determinant SOX9 acts as a lineage-specific driver for BLBC transformation.
Publication Title
Stem Cell Determinant SOX9 Promotes Lineage Plasticity and Progression in Basal-like Breast Cancer.
Sample Metadata Fields
No sample metadata fields
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