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DRP003241
Homo sapiens
16 Downloadable Samples
Illumina Genome Analyzer IIx
Description
Full-Parasites (http://fullmal.hgc.jp/) is a transcriptome database of apicomplexa parasites, which include Plasmodium and Toxoplasma species
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 4 Downloadable Samples
- Illumina HiSeq 2500
Description
Dengue virus (DENV) infection causes profound changes in the host cells and these changes underlie the immune response-based viral clearance and pathogenesis. There are several major cell/tissue types relevant for DENV pathogenesis in vivo, including immune cells, liver, and vascular endothelial cells. We applied a directed differentiation system that produces hepatocyte-like cells (HLCs) from pluripotent stem cells to investigate various aspects of DENV- hepatic cells interaction. Human embryonic stem cells were resistant to DENV infection while progeny hepatic cells were permissive. The transition to DENV permissiveness coincided with the upregulation of entry factors for the virus. Infection of HLCs by DENV was self-limiting due to the activation of the interferon (IFN) pathways, which protected by-stander cells from infection but failed to induce the same level of interferon-induced genes (ISGs) expression in the infected cells due to the subversion of IFN signaling by DENV. Innate immunity also protected the infected cells from virus-induced apoptosis. Furthermore, DENV infection activated the NF-?B pathway, increased production of reactive oxidative species (ROS), and led to production of inflammatory cytokines which may contribute to the cytokine storm implicated in dengue hemorrhagic fever (DHF). Finally, DENV infection of HLCs resulted several in vitro phenotypes that may have relevance for acute liver failure and vascular permeability during DHF. These include the disruption of adherens junctions and the downregulation of many liver specific genes such as albumin (ALB) and coagulation factor V (F5).
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Cell line
View Samples- Mus musculus
- 45 Downloadable Samples
- Illumina HiSeq 4000
Description
Viral and bacterial coinfections are common in nature, but infrequently studied in laboratory models of infection. We observed disease severity differences in mice infected with two of three possible respiratory viruses, depending on the order of the infection. To discover the mechanisms causing these differences, we compared gene expression responses of lung tissue at three time points following viral coinfection. Differential gene expression and immune cell counts suggest a dampening of immune responses in mice infected with rhinovirus followed by influenza A virus or pneumonia virus of mice.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part, Cell line, Treatment
View Samples- Homo sapiens
- 255 Downloadable Samples
- Illumina HiSeq 2500
Description
To understand heterogeneous behaviors of individual cancer cells, it should be important to investigate gene expression levels as well as their divergences between individual cells. Here we conducted a single cell RNA Seq analysis of a series of lung adenocarcinoma cell lines. We analyzed a total of 337 RNA Seq libraries of single cells and found gene expression diversities between individual cells are characteristic depending on genes. The genes showing highly variable expressions were enriched in particular pathways. Particularly, the EGFR pathway genes originally showed wider variations and further diversity was induced in response to an anticancer-drug stimulation. We also observed that cancer-related genes, which were identified from recent clinical cancer sequencing projects, showed potential expression variations, which firstly became apparent on the anti-cancer drug stimulation.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 122 Downloadable Samples
- IlluminaGenomeAnalyzerIIx
Description
To understand the mutual association of the transcriptomes between host humans and infecting malaria parasites, Plasmodium falciparum (Pf), in vivo, we conducted the RNA-Seq analysis of 116 Indonesian malaria patients. Using RNAs extracted from peripheral blood of the patients as the mixture of the human and Pf transcripts, we generated a total of 3 billion RNA-Seq tags. Analysis of these tags allowed us to identify genes and pathways which were associated with clinical symptoms both on human and parasite sides. Particularly, we observed characteristic expression changes in the human innate immune response pathway genes depending on severity of malaria. We also identified a group of transcription regulatory factors and signaling molecule genes which have positive or negative correlations between humans and Pfs. These genes may change their expression patterns to accommodate the respective organisms to mutually conflicting environments. Furthermore, it was possible to utilize the RNA-Seq data for genotyping of the parasites to identify possible drug resistant genetic variations. By bypassing technical difficulty in preparing samples in field, this approach should provide a practically useful mean to describe mutually interacting transcritpomes of humans and parasites, which should eventually explain diverse malaria symptoms.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 8 Downloadable Samples
- IlluminaHiSeq2500
Description
Although thousands of long noncoding RNAs(lncRNAs) are localized in the nucleus, only a fewdozen have been functionally characterized. Herewe show that nuclear enriched abundant transcript1 (NEAT1), an essential lncRNA for the formation ofnuclear body paraspeckles, is induced by influenzavirus and herpes simplex virus infection as well asby Toll-like receptor3-p38 pathway-triggered polyI:C stimulation, resulting in excess formation ofparaspeckles. We found that NEAT1 facilitates theexpression of antiviral genes including cytokinessuch as interleukin-8 (IL8). We found that splicingfactor proline/glutamine-rich (SFPQ), a NEAT1-bindingparaspeckle protein, is a repressor of IL8 transcription,and that NEAT1 induction relocates SFPQfrom the IL8 promoter to the paraspeckles, leadingto transcriptional activation of IL8. Together, ourdata show that NEAT1 plays an important role inthe innate immune response through the transcriptionalregulation of antiviral genes by the stimulusresponsivecooperative action of NEAT1 and SFPQ.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
No sample metadata fields
View Samples- Rattus norvegicus
- 2 Downloadable Samples
Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
The objective of this study is to search for calcium signal-dependent expression changes.
Publication Title
Calcium-dependent N-cadherin up-regulation mediates reactive astrogliosis and neuroprotection after brain injury.
Alternate Accession IDs
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 548 Downloadable Samples
- IlluminaHiSeq2500
Description
Single cell RNA-seq (scRNA-seq) is a powerful tool to reveal the heterogeneity in cancer cells. Cancer heterogeneity would provide crucial information to understand eventual development of drug resistant cells or metastatic disseminations in cancers. In our study, we particularly focused on transcriptomic heterogeneity in response to an anti-cancer drug in five lung adenocarcinoma-derived cell lines. We generated single-cell RNA-seq by the two different platforms, the micro-droplet based platform and the micro-chamber platform, then we attempted to combine those datasets to complete information of datasets.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
No sample metadata fields
View Samples- Zea mays
- 28 Downloadable Samples
- Illumina HiSeq 2000
Description
RNA-sequencing was used on leaf tissue from 29 diverse maize lines to characterize differences in gene expression between lines. The main goal from this study was to relate gene expression to measured traits of interest.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Age, Specimen part
View Samples- Gallus gallus
- 5 Downloadable Samples
- Illumina HiSeq 2000
Description
This project sequences the mRNA of the chorioallantoic membrane of Gallus gallus, the domestic chicken.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples