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SRP061931
Mus musculus
8 Downloadable Samples
Illumina HiSeq 2000
Description
We use RNA-sequencing to generate gene expression profiles of fetal mammary cells that have been induced to overexpress Sox10. These data highlight multiple important molecular mechanisms that are altered in response to this perturbation, and offer a resource to probe the basis of the stem/progenitor and EMT-like functions that are mediated by Sox10 in mammary cells. Overall design: Expression profiling of fetal mammary cells that express ectopic levels of Sox10
Publication Title
Sox10 Regulates Stem/Progenitor and Mesenchymal Cell States in Mammary Epithelial Cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 7 Downloadable Samples
- Illumina HiSeq 2000
Description
We use RNA-sequencing to generate gene expression profiles of fetal mammary cells with unique sorting strategies. These analyses reveal that sorting fetal mammary cells with Sox10 and EpCAM sorting markers provides a stroma-free fMaSC-enriched cell population. The gene expression profiling of these cells offers a resources to probe the molecular mechanisms that specify this unique cell state. Overall design: Examination of 2 different sorting strategies for fetal mammary cells
Publication Title
Sox10 Regulates Stem/Progenitor and Mesenchymal Cell States in Mammary Epithelial Cells.
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- Homo sapiens
- 4 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Our understanding of how mesodermal tissue is formed, has been limited by the absence of specific and reliable markers of early mesoderm commitment. We report that mesoderm commitment from human embryonic stem cells (hESC) is initiated by Epithelial to Mesenchymal transition (EMT) as shown by gene expression profiling and by reciprocal changes in expression of the cell surface proteins, EpCAM/CD326 and NCAM/CD56. Molecular and functional assays reveal that CD326negCD56+ cells, generated from hESC in the presence of activin A, BMP4, VEGF and FGF2, represent a novel, multi-potent mesoderm-committed progenitor population. CD326negCD56+ progenitors are unique in their ability to generate all mesodermal lineages including hematopoietic, endothelial, mesenchymal (bone, cartilage, fat, fibroblast), smooth muscle and cardiomyocytes, while lacking the pluripotency of hESC. CD326negCD56+ cells are the precursors of previously reported, more lineage-restricted mesodermal progenitors. These findings present a novel approach to study how germ layer specification is regulated, and offer a unique target for tissue engineering.
Publication Title
Mapping the first stages of mesoderm commitment during differentiation of human embryonic stem cells.
Sample Metadata Fields
Cell line
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
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-KB 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
Specimen part
View Samples- Sus scrofa
- 79 Downloadable Samples
- Illumina HiSeq 2500
Description
Boar taint (BT) is an offensive odour or taste observed in pork from a proportion of non-castrated male pigs. Surgical castration is effective in avoiding BT, but animal welfare issues have created an incentive for alternatives such as genomic selection. In order to find candidate biomarkers, gene expression profiles were analysed from tissues of non-castrated pigs grouped by their genetic merit of BT. Differential expression analysis revealed substantial changes with log-transformed fold changes of liver and testis from -3.39 to 2.96 and -7.51 to 3.53, respectively. Co-expression network analysis revealed one module with a correlation of -0.27 in liver and three modules with correlations of 0.31, -0.44 and -0.49 in testis. Differential expression and co-expression analysis revealed candidate biomarkers with varying biological functions: phase I (COQ3, COX6C, CYP2J2, CYP2B6, ACOX2) and phase II metabolism (GSTO1, GSR, FMO3) of skatole and androstenone in liver to steroidgenesis (HSD17B7, HSD17B8, CYP27A1), regulation of steroidgenesis (STARD10, CYB5R3) and GnRH signalling (MAPK3, MAP2K2, MAP3K2) in testis. Overrepresented pathways included “Ribosome”, “Protein export” and “Oxidative phosphorylation” in liver and “Steroid hormone biosynthesis” and “Gap junction” in testis. Future work should evaluate the biomarkers in large populations to ensure their usefulness in genomic selection programs. Overall design: Total RNA was extracted from liver and testis of 48 Danish Landrace pigs with low- medium and high genetic merit of boar taint and sequenced by Illumina HiSeq 2500.
Publication Title
Systems genomics study reveals expression quantitative trait loci, regulator genes and pathways associated with boar taint in pigs.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 30 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Numerous studies have established a critical role for BMP signaling in skeletal development. In the developing axial skeleton, sequential SHH and BMP signals are required for specification of a chondrogenic fate in somitic tissue. A similar paradigm is thought to operate in the limb, but the signals involved are unclear. To investigate the nature of these signals we examined BMP action in mesenchymal populations derived from the early murine limb bud (~ E10.5). These populations exhibited a graded response to BMPs, in which early limb mesenchymal (EL) cells (from the distal hind limb) displayed an anti-chondrogenic response, whereas BMPs promoted chondrogenesis in older cell populations. To better understand the molecular basis of disparate BMP action in these various populations, gene expression profiling with Affymetrix microarrays was employed to identify BMP-regulated genes. These analyses showed that BMPs induced a distinct gene expression pattern in the EL cultures versus later mesenchymal limb populations (IM and LT).
Publication Title
Regulation of BMP-dependent chondrogenesis in early limb mesenchyme by TGFbeta signals.
Sample Metadata Fields
Specimen part
View Samples- Bos taurus
- 40 Downloadable Samples
- Illumina Genome Analyzer II
Description
Rift Valley Fever Virus (RVFV), a negative-stranded RNA virus, is the etiological agent of the vector-borne zoonotic disease, Rift Valley Fever (RVF). In both humans and livestock, protective immunity can be achieved through vaccination. Earlier and more recent vaccine trials in cattle and sheep demonstrated a strong neutralizing antibody and total IgG response induced by the RVFV vaccine, MP-12. From previous work, protective immunity in sheep and cattle vaccinates normally occurs from 7 to 21 days after inoculation with MP-12. While the serology and protective response induced by MP-12 has been studied, little attention has been paid to the underlying molecular and genetic events occurring prior to the serologic immune response. To address this, we isolated RNA from whole blood from vaccinates over a time course of 21 days before and after inoculation during a recent vaccine trial with MP-12. This RNA time course was deeply sequenced by RNASeq and bioinformatically analyzed. Our results revealed time-dependent activation or repression of numerous gene ontologies and pathways related to immune response and regulation. Additional analyses identified a correlative relationship between specific genes related to immune activity and protective immunity prior to serologic detection of antibody response. These data provide an important proof of concept for identifying molecular and genetic components underlying the immune response to vaccination and protection prior to serologic detection. Overall design: Experimental Animals: Healthy, 4 – 6 month old Bos taurus heifer and steer calves were used in the present study. The calves were seronegative to both bovine viral diarrhea and bovine leukemia virus by antigen capture enzyme-linked immunosorbent assay (ELISA) analyses done at the Texas Veterinary Medical Diagnostic Laboratory, College Station, Texas and had no detectable neutralizing antibodies to RVFV by PRNT80 at the time of vaccination. The animal experiments were performed under an Institutional Animal Care and Use Committee approved protocol #2010-192. Vaccines: The authentic recombinant MP-12 (MP12) is an attenuated RVFV vaccine prepared for use in humans by the U. S. Army Medical Research Institute of Infectious Diseases. Vaccines were propagated and prepared at University of Texas Medical Branch in Galveston, TX. Experimental Design: The calves were housed in an ABSL2 Ag biocontainment facility where they were randomized into test groups and acclimated to the facility for 14 days. Animals were inoculated either subcutaneously (s.c.) or intramuscularly (i.m.) with 1x105 PFU of MP-12 (3 animals in each group). Whole blood was collected prior to inoculation on Days 0 through 7, 10, 14, 21 and preserved for serum neutralization studies (PRNT) or total RNA purification for RNASeq analysis. Experimentally determined PRNT values were used to determine the “serologic response status” for animals “unvaccinated”, “vaccinated, not protected”, or “vaccinated, protected” with animals having a serum dilution ration of >1:80 being considered protected. Only RNA samples that met the minimum quality and quantity thresholds were used for the sequencing analysis. Rectal temperatures were recorded each time blood was collected and their health status was documented daily. At the end of the respective studies, the calves were euthanized with pentobarbital sodium (120 mg/kg i.v.). All calves were healthy and clinically normal at the termination of the respective studies. Morrill, John C., Richard C. Laughlin, Nandadeva Lokugamage, Jing Wu, Roberta Pugh, Pooja Kanani, L. Garry Adams, Shinji Makino, C. J. Peters. Immunogenicity of a Recombinant Rift Valley Fever MP-12 Vaccine Candidate in Calves. Vaccine. 2013. doi:10.1016/j.vaccine.2013.08.003. 238. Morrill, John C., Richard C. Laughlin, Nandadeva Lokugamage, Roberta Pugh, Elena Sbrana, William J. Weise, L. Garry Adams, Shinji Makino and C. J. Peters.. Safety and Immunogenicity of Recombinant Rift Valley Fever MP-12 Vaccine Candidates in Sheep. Vaccine 10.1016/j.vaccine.2012.10.118, 2012.
Publication Title
Correlative Gene Expression to Protective Seroconversion in Rift Valley Fever Vaccinates.
Sample Metadata Fields
Specimen part, Subject, Time
View Samples- Mus musculus
- 18 Downloadable Samples
- Illumina HiSeq 2500
Description
We characterize the gene expression changes which occur in the mouse glomerular podocyte, mesangial, and endothelial cells between control mice and mutant mice which are missing two copies of Fyn-proto oncogene (Fyn) and one copy of CD2-associated protein (CD2AP) in a mouse model of FSGS. Overall design: The glomeruli are purified by digestion with Collagenase A and sieving, a single cell suspension is generated via enzymatic dissociation; the single cell suspension is then FACS sorted based on GFP-fluorescence (targeting the glomerular endothelial, mesangial, and podocyte cells). Total RNA was purified using a column-based system. RNA was then quantitatively and qualitatively analyzed using an agilent bioanalynzer, cDNA libraries were generated using Nugen Ovation RNA-Seq V2, and the resulting libraries were ran on an Illumina HiSeq 2500. Data was analyzed using Strand NGS version 2.6.
Publication Title
A bigenic mouse model of FSGS reveals perturbed pathways in podocytes, mesangial cells and endothelial cells.
Sample Metadata Fields
Specimen part, Subject
View Samples