Filters
Technology
Platform
Drosophila melanogaster
14 Downloadable Samples
Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
Wound healing is an essential homeostatic mechanism that maintains the epithelial barrier integrity after tissue damage. Although we know the main events participating in the healing of a wound, many of the underlying molecular mechanisms remain unclear. Genetically amenable systems, such as wound healing in Drosophila imaginal discs, do not model all aspects of the repair process, but allow exploring many unanswered features of the healing response; e.g., which are the signal(s) responsible for initiating tissue remodeling? How is the sealing of the epithelia achieved? Or which are the inhibitory cues that cancel the healing machinery upon completion? Answering these and other questions demands in first place the identification and functional analysis of wound-specific genes. A variety of different microarray analyses of murine and humans have identified characteristic profiles of gene expression at the wound site, however, very few functional studies in healing regulation have been carried out. We developed an experimentally controlled method to culture imaginal discs that allows live imaging and biochemical analysis and is healing-permissive. Employing this approach, we performed a comparative genome-wide profiling between those Drosophila imaginal cells actively involved in healing versus their non-engaged siblings. This lets us identify a set of potential wound-specific genes. Importantly, besides identifying and categorizing new genes, we functionally tested many of their gene products by genetic interference and overexpression in a healing assay. This non-saturated analysis defines a relevant set of new genes whose changes in expression levels are functionally significant for proper tissue repair. There is promise that our newly identified wound-healing genes will guide future work in the more complex mammalian wound response.
Publication Title
Identification and functional analysis of healing regulators in Drosophila.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Identification of TLR4 as one of the most abundant RNA species in pericytes with respect to MSC, and corroboration of TLR4 expression on the cell surface, led us to obtain a comprehensive overview of the expression program of lipopolysaccharide (LPS) stimulated pericytes. Microarray analyisis demonstrated the significant upregulation of 76 annotated genes including transcripts for adhesion molecules, inflammation mediators, pro-angiogenic factors, transcription factors and anti-apoptotic proteins.
Publication Title
Lipopolysaccharide activates Toll-like receptor 4 (TLR4)-mediated NF-κB signaling pathway and proinflammatory response in human pericytes.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Pericytes and mesenchymal stem cells (MSC) are ontogenically related, and in fact no phenotypic differences were observed by flow cytometry using a panel of surface antigen markers. Global gene expression profiles of human pericytes and MSC revealed that 43 genes were expressed more than 10 fold in pericytes as compared to MSC.
Publication Title
Lipopolysaccharide activates Toll-like receptor 4 (TLR4)-mediated NF-κB signaling pathway and proinflammatory response in human pericytes.
Sample Metadata Fields
Specimen part
View Samples
SRP106343- Mus musculus
- 18 Downloadable Samples
Illumina HiSeq 2500
Description
Role of CTCF in activated B cells. Overall design: Transcriptome profiling of CTCF deficient and proficient activated in vitro B cells.
Publication Title
CTCF orchestrates the germinal centre transcriptional program and prevents premature plasma cell differentiation.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina HiSeq 2500
Description
Germinal center (CD19+Fas+GL7+) and naive (CD19+Fas-GL7-) B cells were sorted from Peyer''s patches of littermate 12 weeks old WT C57BL/6 mice. Three biological replicates were analyzed, each composed of a pool of 5 female mice. RNA was purified from pellets of 2-2.5x10^4 cells and sequencing libraries were prepared from 100ng of total RNA per replicate. Overall design: Transcriptional profiling of germinal center and naive B cells from Peyer's patches of WT mice.
Publication Title
A broad atlas of somatic hypermutation allows prediction of activation-induced deaminase targets.
Sample Metadata Fields
Sex, Age, Specimen part, Cell line, Subject
View Samples- Arabidopsis thaliana
- 6 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Cysteine occupies a central position in plant metabolism due to its biochemical functions. Arabidopsis thaliana cells contain different O-acetylserine(thiol)lyase (OASTL) enzymes that catalyze the biosynthesis of cysteine. Because they are localized in the cytosol, plastids and mitochondria, this results in multiple subcellular cysteine pools. Much progress has been made on the most abundant OASTL enzymes; however, information on the less abundant OASTL-like proteins has been scarce. To unequivocally establish the enzymatic reaction catalyzed by the minor cytosolic OASTL isoform CS-LIKE (AT5G28030), we expressed this enzyme in bacteria and characterized the purified recombinant protein. Our results demonstrate that CS-LIKE catalyzes the desulfuration of L-cysteine to sulfide plus ammonia and pyruvate. Thus, CS-LIKE is a novel L-cysteine desulfhydrase (EC 4.4.1.1), and we propose to designate it DES1. The impact and functionality of DES1 in cysteine metabolism was revealed by the phenotype of the T-DNA insertion mutants des1-1 and des1-2. Mutation of the DES1 gene leads to premature leaf senescence, as demonstrated by the increased expression of senescence-associated genes and transcription factors. Also, the absence of DES1 significantly reduces the total cysteine desulfuration activity in leaves, and there is a concomitant increase in the total cysteine content. As a consequence, the expression levels of sulfur-responsive genes are de-regulated, and the mutant plants show enhanced antioxidant defenses and tolerance to conditions that promote oxidative stress. Our results suggest that DES1 from Arabidopsis is an L-cysteine desulfhydrase involved in maintaining cysteine homeostasis, mainly at late developmental stages or under environmental perturbations.
Publication Title
Cysteine homeostasis plays an essential role in plant immunity.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 12 Downloadable Samples
- Illumina HiSeq 2500
Description
Our studies identify the role of mIR-28 in germinal center response and its therapeutic potential for the treatment of non-Hodgkin lymphomas Overall design: The effect of miR-28 expression in the transcriptome was analyzed in Ramos Burkitt B cells by RNASeq.
Publication Title
miR-28 regulates the germinal center reaction and blocks tumor growth in preclinical models of non-Hodgkin lymphoma.
Sample Metadata Fields
Treatment, Subject
View Samples- Arabidopsis thaliana
- 12 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Arabidopsis thaliana cells contain different O-acetylserine(thiol)lyase (OASTL) enzymes that catalyze the biosynthesis of cysteine. Recently, we have deeply investigated about one of the minor OASTL-like protein located in the cytosol, named DES1, highlighting some important clues about its metabolic function. We have demonstrated that DES1 catalyzes the desulfuration of L-cysteine to sulfide plus ammonia and pyruvate, instead of the biosynthesis of Cys, and thus, is a novel L-cysteine desulfhydrase (EC 4.4.1.1). The functionality of DES1 is being revealed by the phenotype of the T-DNA insertion mutants des1-1 and des1-2. We have performed a comparative transcriptomic analysis on leaves of the des1-1 and Col-0 wild type plants grown for 30 days under long-day conditions. The normalized data from the replicates showed differential expression of 1614 genes in the des1-1 mutant, with 701 genes down-regulated and 913 genes up-regulated by more than twofold, with a False Discovery Rate (FDR) of < 0.05 and an intensity signal restriction of lgSignal >7. This des1-1 transcriptional profile show a strong alteration when compared to a previous comparative transcriptomic analysis performed on leaves of the des1-1 and Col-0 wild type plants grown for 20 days under identical long-day conditions (GSE 19244). We have also performed a comparative transcriptomic analysis on leaves of the des1-1 and Col-0 wild type plants grown for 20 days and treated with sodium sulfide for 10 additional days. The comparison of the transcriptional profile of des1-1+Na2S versus Col-0+Na2S clearly shows that exogenous sulfide reversed the transcriptional level differences between the mutant and the wild type to reach similar transcriptional patterns as the array GSE19244. Our results suggest a role of sulfide as transcriptional regulator in the des1-1 mutant background.
Publication Title
Cysteine-generated sulfide in the cytosol negatively regulates autophagy and modulates the transcriptional profile in Arabidopsis.
Sample Metadata Fields
Age, Specimen part, Treatment
View Samples- Homo sapiens
- 31 Downloadable Samples
- Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
Objectives: Phosphatidylinositol 3-kinase catalytic subunit alpha (PIK3CA) is commonly altered in many human tumors, leading to the activation of p110 enzymatic activity that stimulates growth factor-independent cell growth. PIK3CA alterations such as mutation, gene amplification and overexpression are common in head and neck squamous cell carcinoma (HNSCC) and. We aim to explore how these alterations and clinical outcome are associated, as well as the molecular mechanisms involved.
Publication Title
Overexpression of PIK3CA in head and neck squamous cell carcinoma is associated with poor outcome and activation of the YAP pathway.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 4 Downloadable Samples
- Illumina HiSeq 2500
Description
Purpose: Here we demonstrate ALK3Bright/PDX1+ cells residing within the human pancreatic ducts have progenitor like characteristics. Using flow cytometery, live-cell sorting of ALK3bright/PDX1+ cells is possible using a surrogate surface marker for PDX1 (P2RY1). Treating ALK3bright/P2RY1+ cells with BMP7 results in their expansion. Later removal of BMP7 results in the differentiation of these cells to ß-like cells. Here we compare the mRNA expression profiles of these three different cell types (in triplicate). Methods: mRNA profiles of ALK3Bright/P2RY1+ cells isolated from human non-endocrine pancreatic tissue, ALK3Bright/P2RY1+ cells treated with BMP7 and ALK3Bright/P2RY1+ cells differentiated to ß-like cells after BMP7 removal were generated by deep sequencing, in triplicate, using Illumina HiSeq PE Cluster Kit v4 and Illumina HiSeq Flow Cell v4 with 50 nt paired end reads plus dual index reads using the Illumina HiSeq SBS kit v4. Sequence reads that passed quality filters were analyzed at the transcript isoform level following alignment using TopHat v2.1.0 followed by exon and gene level counting using Bioconductor easyRNASeq v 2.4.7. Conclusions: Our study represents the first detailed analysis of ALK3Bright/P2RY1+ sorted cells with biological replicates. We demonstrate ALK3Bright/P2RY1+ cells were shown to form progenitor-like epithelial colonies characterized by NKX6.1 and PDX1 expression. Unlike the negative fraction controls, these colonies responded to BMP-7 by generating new ß-like cells as well as cells from other pancreatic lineages. The transcriptional profile of these cells and their BMP7 treated counterparts suggest a mitotic and progenitor like state. Our studies confirm the progenitor-like nature of ALK3Bright/PDX1+ cells within the human pancreas and suggest a specific anatomical location within the ductal network. Overall design: Comparison of transcriptional expression in Alk3Bright/P2RY1+ cells, Alk3Bright/P2RY1+ cells treated with BMP7 and Alk3Bright/P2RY1+ cells allowed to differentiate after BMP7 removal. Human islets, isolated from the same donors were included as a control.
Publication Title
P2RY1/ALK3-Expressing Cells within the Adult Human Exocrine Pancreas Are BMP-7 Expandable and Exhibit Progenitor-like Characteristics.
Sample Metadata Fields
Specimen part, Subject
View Samples