Filters
Technology
Platform
Danio rerio
2 Downloadable Samples
IlluminaHiSeq2000
Description
Most ribosomal proteins (RP) are regarded as essential, static components that only contribute to ribosome biogenesis and protein synthesis. However, emerging evidence suggests that RNA-binding RP are dynamic and can influence cellular processes by performing “extraribosomal”, regulatory functions involving binding to select, critical target mRNAs. We report here that the RP, Rpl22, and its highly homologous paralog, Rpl22-Like1 (Rpl22l1 or Like1), play critical, extraribosomal roles in embryogenesis. Indeed, they antagonistically control morphogenesis through developmentally-regulated localization to the nucleus where they modulate splicing of the pre-mRNA encoding smad2, an essential transcriptional effector of Nodal/TGF-ß signaling. During gastrulation, Rpl22 binds to intronic sequences of smad2 pre-mRNA and induces exon 9 skipping in cooperation with hnRNP-A1. This action is opposed by its paralog, Like1, which promotes exon 9 inclusion in the mature transcript. The nuclear roles of these RP in controlling morphogenesis represent a fundamentally different and paradigm-shifting mode of action for RP.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples
SRP063416- Homo sapiens
- 7 Downloadable Samples
- IlluminaHiSeq2000
Description
In the present study, the autologous cell based therapy for the compromised liver disease due to hepatitis B infection has been investigated. To perform this research, the HBsAg positive and nucleic acid test (NAT) positive blood samples along with healthy blood samples were utilized to generate hepatocyte-like cells (NeoHeps) from monocytes. The monocytes were sorted by MACS technology from the PBMCs so that the abundant non-monocyte cells were depleted.The isolated monocytes were cultured in two steps for 21 days. In the first step monocytes were incubated with serum supplemented IMDM medium containing cytokines like IL-3, MCSF and 2-ME for a period of six days for priming to induce plasticity in them. After six day in culture, the primed monocytes were termed as reprogrammed monocytes (RM). The reprogrammed monocytes were then differentiated for 15 days in serum supplemented IMDM medium containing mitogenic reagents like EGF, HGF and FGF-4 to generate NeoHeps.The RNA sequencing (RNASeq) of the Monocytes, RM and NeoHeps generated from both healthy and HBsAg positive blood samples were performed to analyse the kinetics of this differentiation process at the transcript level.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 18 Downloadable Samples
- Illumina HiSeq 4000
Description
Mice expressing luciferase and GFP under control of the FoxP3 promoter were treated with either the DR3 agonist antibody 4C12 or the DR3 agonist fusion protein TL1A-Ig with low-dose IL-2 (or isotype control antibody), regulatory T cells were sorted from spleens on day 7, and bulk RNA sequencing was performed.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line, Treatment
View Samples ERP000573- Homo sapiens
- 10 Downloadable Samples
- IlluminaGenomeAnalyzerII
Description
No description.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 535 Downloadable Samples
Description
Prediction of human response to chemical exposures is a major challenge in both pharmaceutical and toxicological research. Transcriptomics has been a powerful tool to explore chemical-biological interactions. However, limited throughput, high-costs and complexity of transcriptomic interpretations have yielded numerous studies lacking sufficient experimental context for predictive application. We utilized a novel high-throughput transcriptomics platform to explore a broad range of exposures to 24 reference compounds in both differentiated and undifferentiated human HepaRG cultures. Our goals were to 1) explore transcriptomic characteristics distinguishing liver injury compounds, 2) assess impacts of differentiation state on baseline and compound-induced responses (e.g., metabolically-activated), and 3) identify and resolve reference biological-response pathways and their quantitative translation to human exposures. Study data revealed the predictive utility of transcriptomic concentration-response modeling to quantitatively identify human liver injury compounds by their respective benchmark concentrations (BMCs), and model hepatic responses to classical reference compounds yielding plausibly-relevant estimations of human potency.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 11 Downloadable Samples
- IonTorrentProton
Description
The study was undertaken to compare the gene expression profile in mesenchymal stem/stromal cells from bone marrow of healthy donors and patients with newly diagnosed acute acute myeloid leukemia
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 3 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
In tumor microenvironment, tumor-associated macrophages (TAMs) have been characterized as M1-like or M2-like phenotype. In this study, we investigated the characteristics and functional roles of different TAMs on cancer metastasis. We isolated TAMs from primary tumor and metastatic lung and performed microarrays to identify the gene expression in distinct TAMs populations.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Drosophila melanogaster
- 9 Downloadable Samples
- Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
Cardiogenesis involves multiple biological processes acting in concert during development, a coordination achieved by the regulation of diverse cardiac genes by a finite set of transcription factors (TFs). Previous work from our laboratory identified the roles of two Forkhead TFs, Checkpoint suppressor homologue (CHES-1-like) and Jumeau (Jumu) in governing cardiac progenitor cell divisions by regulating Polo kinase activity. These TFs were also implicated in the regulation of numerous other cardiac genes. Here we show that these two Forkhead TFs play an additional and mutually redundant role in specifying the cardiac mesoderm (CM): eliminating the functions of both CHES-1-like and jumu in the same embryo results in defective hearts with missing hemisegments. Our observations indicate that this process is mediated by the Forkhead TFs regulating the fibroblast growth factor receptor Heartless (Htl) and the Wnt receptor Frizzled (Fz), both previously known to function in cardiac progenitor specification: CHES-1-like and jumu exhibit synergistic genetic interactions with htl and fz in CM specification, thereby implying function through the same genetic pathways, and transcriptionally activate the expression of both receptor-encoding genes. Furthermore, ectopic overexpression of either htl or fz in the mesoderm partially rescues the defective CM specification phenotype seen in embryos doubly homozygous for mutations in jumu and CHES-1-like. Together, these data emphasize the functional redundancy that leads to robustness in the cardiac progenitor specification process mediated by Forkhead TFs regulating the expression of signaling pathway receptors, and illustrate the pleiotropic functions of this class of TFs in different aspects of cardiogenesis.
Publication Title
Two forkhead transcription factors regulate the division of cardiac progenitor cells by a Polo-dependent pathway.
Sample Metadata Fields
Specimen part
View Samples- Drosophila melanogaster
- 5 Downloadable Samples
- Affymetrix Drosophila Genome Array (drosgenome1)
Description
The development of a complex organ requires the specification of appropriate numbers of each of its constituent cell types, as well as their proper differentiation and correct positioning relative to each other. During Drosophila cardiogenesis, all three of these processes are controlled by jumeau (jumu) and Checkpoint suppressor homologue (CHES-1-like), two genes encoding forkhead transcription factors that we discovered utilizing an integrated genetic, genomic and computational strategy for identifying novel genes expressed in the developing Drosophila heart. Both jumu and CHES-1-like are required during asymmetric cell division for the derivation of two distinct cardiac cell types from their mutual precursor, and in symmetric cell divisions that produce yet a third type of heart cell. jumu and CHES-1-like control the division of cardiac progenitors by regulating the activity of Polo, a kinase involved in multiple steps of mitosis. This pathway demonstrates how transcription factors integrate diverse developmental processes during organogenesis.
Publication Title
Two forkhead transcription factors regulate the division of cardiac progenitor cells by a Polo-dependent pathway.
Sample Metadata Fields
Specimen part
View Samples- Drosophila melanogaster
- 6 Downloadable Samples
- Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
The development of a complex organ requires the specification of appropriate numbers of each of its constituent cell types, as well as their proper differentiation and correct positioning relative to each other. During Drosophila cardiogenesis, all three of these processes are controlled by jumeau (jumu) and Checkpoint suppressor homologue (CHES-1-like), two genes encoding forkhead transcription factors that we discovered utilizing an integrated genetic, genomic and computational strategy for identifying novel genes expressed in the developing Drosophila heart. Both jumu and CHES-1-like are required during asymmetric cell division for the derivation of two distinct cardiac cell types from their mutual precursor, and in symmetric cell divisions that produce yet a third type of heart cell. jumu and CHES-1-like control the division of cardiac progenitors by regulating the activity of Polo, a kinase involved in multiple steps of mitosis. This pathway demonstrates how transcription factors integrate diverse developmental processes during organogenesis.
Publication Title
Two forkhead transcription factors regulate the division of cardiac progenitor cells by a Polo-dependent pathway.
Sample Metadata Fields
Specimen part
View Samples