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SRP083755
Mus musculus
463 Downloadable Samples
Illumina HiSeq 2500, Illumina HiSeq 2000
Description
The pancreas of vertebrates is separately derived from both the dorsal and ventral endodermal domains. However, the difference between these two programs has been unclear. Here, using a pancreatic determination gene, Pdx1, driven GFP transgenic mouse strain, we identified Pdx1-GFP highly expressing cells (Pdx1high) and Pdx1-GFP lowly expressing cells (Pdx1low) in both embryonic dorsal Pdx1-expressing region (DPR) and ventral Pdx1-expressing region (VPR). We analyzed the transcriptomes of single Pdx1low and Pdx1high cells from the DPR and VPR. In the VPR, Pdx1low cells have an intermediate progenitor identity and can generate hepatoblasts, extrahepatobiliary cells, and Pdx1high pancreatic progenitor cells. In the DPR, Pdx1high cells are directly specified as pancreatic progenitors, whereas Pdx1low cells are precocious endocrine cells. Therefore, our study defines distinct road maps for dorsal and ventral pancreatic progenitor specification. The findings provide guidance for optimization of current ß-cell induction protocols by following the in vivo dorsal pancreatic specification program. Overall design: The overall goal of this study was understanding the programs of ventral and dorsal pancreatic progenitor development. Specifically, to get an overall gene expression profiles during ventral and dorsal pancreas development, we performed bulk cell RNA-seq in E10.5 ventral and dorsal pancreatic progenitor cells purified from Pdx1-GFP transgene embryos; E14.5 ventral and dorsal endocrine progenitor cells from Ngn3-GFP transgene embryos; and E17.5 ventral and dorsal beta cells from Insulin-RFP transgene embryos. To determine the progress and cell type components during the specification of pancreatic progenitor in ventral and dorsal domains, we performed single-cell transcriptomic analysis in sorted Pdx1-GFP+ cells from ventral and dorsal pancreatic buds.
Publication Title
Single-cell transcriptomic analyses reveal distinct dorsal/ventral pancreatic programs.
Alternate Accession IDs
Sample Metadata Fields
Treatment, Subject
View Samples- Saccharomyces cerevisiae
- 12 Downloadable Samples
Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
Ixr1 is a transcriptional factor from Saccharomyces cerevisae with high affinity to cisplatin-DNA adducts through their two HMG-box DNA binding domains. Its transcriptional regulation is essential in the cytotoxicity caused by cisplatin, although the molecular mechanisms supporting this function are not understood. We present a transcriptome analysis discriminating between RNA changes induced by cisplatin which are dependent or independent of the Ixr1 function.
Publication Title
Ixr1 Regulates Ribosomal Gene Transcription and Yeast Response to Cisplatin.
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Endothelin-1 (ET-1) plays a critical role in connective tissue remodeling by fibroblasts during tissue repair and fibrosis. We investigated the molecular pathways in the transmission of ET-1 signals that lead to features of connective tissue remodeling, in particular the role of FAK (focal adhesion kinase).
Publication Title
Inhibition of focal adhesion kinase prevents experimental lung fibrosis and myofibroblast formation.
Alternate Accession IDs
Sample Metadata Fields
Specimen part, Treatment
View Samples- Homo sapiens
- 48 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
The objective is to quantify the contribution of genetic and common environmental effects in the familial resemblances of whole blood genome-wide gene expression levels. We also make comparisons with familial resemblances in blood leukocytes genome-wide DNA methylation levels in the same cohort in order to further investigate biological mechanims.
Publication Title
Familial resemblances in human whole blood transcriptome.
Alternate Accession IDs
Sample Metadata Fields
Sex, Specimen part
View Samples- Escherichia coli
- 8 Downloadable Samples
- Affymetrix E. coli Genome 2.0 Array (ecoli2)
Description
Many reports show an association between the Pst system, the Pho regulon related genes and bacterial virulence. Our previous results showed that a functional Pst system is required for full virulence, resistance to serum, polymyxin B and acid shock. However, the interplay between the Pst system and virulence has an unknown molecular basis. To understand global APEC virulent strain responses to Pho regulon activation, we conducted transcriptome profiling experiments comparing the APEC chi7122 strain and its isogenic Pst mutant grown in rich phosphate medium using the Affymetrix GeneChip E. coli Genome 2.0 Array. The Affymetrix GeneChip E. coli Genome 2.0 Array contains the genome of the E. coli MG1655 and three pathogenic E. coli strain (EDL933, Sakai and CFT073) representing 20,366 genes. While comparing genes expression between Pst mutant and the wild type chi7122 strain, 471 genes are either up- (254) or down-regulated (217) of at least 1.5-fold, with a p-value inferior or equal to 0.05 and a false discovery rate of 2.71%.
Publication Title
Genome-wide transcriptional response of an avian pathogenic Escherichia coli (APEC) pst mutant.
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)
Description
Extracellular matrix interactions play essential roles in normal physiology and many pathological processes. Here, we report a novel screening platform capable of measuring phenotypic responses to combinations of ECM molecules. While the importance of ECM interactions in metastasis is well documented, systematic approaches to identify their roles in distinct stages of tumorigenesis have not been described. Using a genetic mouse model of lung adenocarcinoma, we measured the ECM-dependent adhesion of tumor-derived cells. Hierarchical clustering of adhesion profiles generated using this platform differentially segregated metastatic cell lines from primary tumor lines. Furthermore, we uncovered that metastatic cells selectively associate with fibronectin when in combination with galectin-3, galectin-8, or laminin. These interactions appear to be mediated in part by 31 integrin both in vitro and in vivo. We show that these galectins also correlate with human disease at both a transcriptional and histological level. Thus, our in vitro platform allowed us to interrogate the interactions of metastatic cells with their surrounding environment, and identified ECM and integrin interactions that could lead to therapeutic targets for metastasis prevention.
Publication Title
A combinatorial extracellular matrix platform identifies cell-extracellular matrix interactions that correlate with metastasis.
Alternate Accession IDs
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Expression 430A Array (moe430a)
Description
The aim of this experiment was to get a comparison of the signatures between a non-transformed cell (NIH3T3 + vector) and a transformed cell (NIH3T3 + Fbxo7). NIH3T3 cells become transformed after the stable integration of the Fbxo7 gene. Fbxo7 potentiates cyclin D/cdk6 activity.
Publication Title
Transforming activity of Fbxo7 is mediated specifically through regulation of cyclin D/cdk6.
Alternate Accession IDs
None
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 4 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Gene expression profiles were assessed for vincristine-sensitive parental ovarian tumor cell line (SKOV3) and its highly vincristine-resistant derivative (SKVCR 2.0)
Publication Title
Genetic changes in the evolution of multidrug resistance for cultured human ovarian cancer cells.
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 162 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
These arrays are used for various projects
Publication Title
DNA amplification is a ubiquitous mechanism of oncogene activation in lung and other cancers.
Alternate Accession IDs
Sample Metadata Fields
Sex, Age, Race
View Samples- Homo sapiens
- 30 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
An antagonistic interplay between YAP and RUNX where RUNX proteins abrogate YAP-mediated transcription of EMT and Stemness associated genes in mammary epithelial cells in an interaction dependent manner.
Publication Title
RUNX1 and RUNX3 protect against YAP-mediated EMT, stem-ness and shorter survival outcomes in breast cancer.
Alternate Accession IDs
Sample Metadata Fields
Cell line
View Samples