Full-Parasites (http://fullmal.hgc.jp/) is a transcriptome database of apicomplexa parasites, which include Plasmodium and Toxoplasma species
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Cell line
View SamplesTo 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.
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Cell line
View SamplesTo 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.
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View SamplesAlthough 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.
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View SamplesSingle 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.
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View SamplesTranscriptome sequencing was performed for the chicken B-lymphoma DT40 cell line. rRNA-depletion of total RNA was done, a standard Illumina pair-end library was prepared and sequenced on Illumina HiSeq2000 and HiScan2000.
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Cell line
View SamplesThe objective of this study is to search for calcium signal-dependent expression changes.
Calcium-dependent N-cadherin up-regulation mediates reactive astrogliosis and neuroprotection after brain injury.
Specimen part
View SamplesDuring the development of mammalian embryonic germ cells, global demethylation and de novo DNA methylation take place. In mouse embryonic germ cells, two PIWI family proteins, MILI and MIWI2, are essential for the de novo DNA methylation of retrotransposons, presumably through PIWI interacting RNAs (piRNAs). Although piRNA-associated MIWI2 has been reported to play critical roles in the process, its molecular mechanisms have remained unclear. To identify the mechanism, transgenic mice were produced; they contained a fusion protein of MIWI2 and a zinc finger (ZF) that recognized the promoter region of a type A LINE-1 gene. The ZF-MIWI2 fusion protein brought about DNA methylation, suppression of the type A LINE-1 gene and a partial rescue of the impaired spermatogenesis of MILI-null mice. In addition, ZF-MIWI2 was associated with the proteins involved in DNA methylation. These data indicate that MIWI2 functions as an effector of de novo DNA methylation of the retrotransposon.
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Specimen part
View SamplesGlobal gene expression patterns were compared among wild-type Col-0, teb, atr, teb atr of A. thaliana using shoot apices.
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Age, Specimen part, Time
View SamplesComparison of Arabidopsis wild-type developing seeds grown under sulfur-deficient condition vs Arabidopsis wild-type developing seeds grown under control condition.
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Specimen part
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