Ontology highlight
ABSTRACT:
PROVIDER: PRJNA983533 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24912700_1.fastq.gz | Fastqsanger.gz | |||
| SRR24912700_2.fastq.gz | Fastqsanger.gz | |||
| SRR24912800_1.fastq.gz | Fastqsanger.gz | |||
| SRR24912800_2.fastq.gz | Fastqsanger.gz | |||
| SRR24912900_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 459 |
Similar Datasets
Project description:The complex life cycle of the malaria parasite Plasmodium falciparum (Pf) involves the differentiation into multiple distinct forms, requiring a tight and dynamic control of gene expression at each stage. However, the full range of variation cannot solely be explained by stage-specific transcription factors, such as ApiAP2-family members, as they are strongly under-represented in Pf. Huge changes in chromatin structure and epigenetic modifications during life cycle progression suggest a central role of these mechanisms in regulating the transcriptional program for parasite development. Pf chromatin is distinct from other eukaryotes with an extraordinarily high AT-content (>80 %) and highly divergent histones lacking typical DNA packaging properties. In addition, the chromatin remodelers, key in shaping chromatin structure, are not conserved and unexplored in Pf. We identified PfSnf2L (PF3D7_1104200) as ISWI-related ATPase actively repositioning Pf nucleosomes in vitro. Knockout studies demonstrate that PfSnf2L is essential, regulating asexual development and sexual differentiation. It globally controls just-in-time transcription by spatiotemporally determining nucleosome positioning at promoters of stage-specific genes. The unique sequence and functional properties of PfSnf2L allows the identification of an inhibitor that specifically kills Plasmodium falciparum, phenocopies the loss of correct gene expression timing, and inhibits the formation of gametocytes.
2024-10-17 | GSE237217 | GEO
Project description:Pulmonary fibrosis (PF) is a form of chronic lung disease characterized by progressive destruction of normal alveolar gas-exchange surfaces and accumulation of extracellular matrix (ECM). In order to comprehensively define the cell types, mechanisms and mediators driving ECM deposition and fibrotic remodeling in lungs with pulmonary fibrosis, we performed single-cell RNA-sequencing (scRNA-seq) of single-cell suspensions generated from non-fibrotic control and PF lungs. Analysis of over 114,000 cells from 20 PF and 10 control lungs identified 31 distinct cell types. We identified multiple distinct lineages directly contribute to ECM expansion, including a novel HAS1hi fibroblast subtype and a previously undescribed KRT5-/KRT17+, collagen and ECM-producing epithelial cell population that was highly enriched in PF lungs. Together these data provide high-resolution insights into the basic mechanisms of pulmonary fibrosis, and indicate a direct profibrotic role of the lung epithelium in PF pathogenesis.
2019-09-05 | GSE135893 | GEO
Project description:Transcriptome profiling of pyrethroid resistant field populations of Anopheles funestus across Uganda and neighboring Kenya from Uganda and Kenya compared to a susceptible lab strain FANG
2020-10-19 | E-MTAB-9529 | biostudies-arrayexpress
Project description:22q11.2 deletion syndrome (22q11DS) substantially increases the risk of cognitive decline and psychiatric disease. However, neuroanatomic changes in 22q11DS are of a subtle-to-moderate degree and their connection to brain function is not clear. Here we report a severe (~70%) and specific reduction (dysplasia) of two cerebellar lobules, paraflocculus and flocculus (PF/F) and associated deficits in vestibulo-ocular reflex (VOR) in mouse models of 22q11DS (22q11DS mice). A specific but less severe PF/F dysplasia was confirmed in humans with 22q11DS. Tbx1 haploinsufficiency recapitulated the PF/F and VOR deficits in 22q11DS mice. The 22q11DS-associated PF/F dysplasia was not due to altered neural composition or neurogenesis. Rather, a part of temporal bone called subarcuate fossa (SF), which encapsulates the PF/F, and semicircular canals of the inner ear, which connects to the SF were malformed in 22q11DS and Tbx1-deficientmice. Our single-nuclei RNA Sequencing and immunohistochemistry data revealed that Tbx1 haploinsufficiency caused precocious differentiation of chondrocyte to osteoblasts in the petrous bone, but no changes in cell type compositions in the PF/F. These data suggest a novel structure-function pathogenic interrelationship in 22q11DS, where Tbx1 haploinsufficiency causes a skeletal deformity occluding cerebellar development and resulting in motor learning deficiency.
2024-09-19 | GSE254044 | GEO
Project description:Bruton’s tyrosine kinase (BTK) inhibitors such as ibrutinib represent an effective strategy for treatment of chronic lymphocytic leukemia (CLL), although ~30% of patients eventually undergo disease progression. Here we investigated the long-term modulation of the CXCR4dim/CD5bright proliferative fraction (PF) and the CXCR4bright/CD5dim resting fraction (RF) in CLL samples, and their correlation with therapeutic outcome and emergence of ibrutinib resistance. Longitudinal tracking by flow cytometry revealed that PF, initially suppressed by ibrutinib, reappeared upon early disease progression suggesting that PF evaluation could represent a sensitive and specific marker of CLL progression upon ibrutinib treatment. Transcriptomic analyses of PF at progression revealed similar proliferation signatures between pre- and post-treatment PF, demonstrating the emergence upon progression of a newly proliferating cell population.
2024-04-02 | GSE249956 | GEO
Project description:Janthinobacterium rivuli strain:MSP1 Genome sequencing
| PRJNA1171188 | ENA
Project description:Magnaporthe oryzae snodprot1 homolog (MSP1), a recently identified PAMP, is known to trigger defense responses in rice. However, the receptor(s) and downstream interacting components of MSP1 in rice have not been identified so far. Using multiple immunoprecipitation-mass spectrometry (IP-MS) analyses in transgenic rice expressing MSP1-YFP, we identified several heat shock proteins (HSPs) as MSP1 interacting partners. Heat stress treatment suppressed MSP1-induced cell death in tobacco plants transiently expressing MSP1. Subsequent IP-MS analysis on these tobacco plants, exposed to heat stress, resulted in the identification of a HSP having a highly conserved sequence to the OsHSP70 of rice. Co-expression of MSP1 with OsHSP70 failed to induce cell death in tobacco, confirming the involvement of the OsHSP70 in the MSP1 immune response. Rice protoplasts, co-expressing MSP1 and OsHSP70, showed a direct interaction between these two proteins in planta. Taken together, the results reported here highlight the pivotal role of OsHSP70 in MSP1-induced signaling and enhance our understanding of rice-M. oryzae interaction.
2025-04-23 | PXD057048 | Pride
Project description:To better understand mutations that can contribute to Zika pathogenesis, we allow the H/PF/2013 wild-type strain to replicate in HuH-7 cells to analyze the population of viral variants.
2021-05-24 | E-MTAB-10474 | biostudies-arrayexpress
Project description:Large-scale changes in the structure and cellular makeup of the distal lung are a hallmark of pulmonary fibrosis (PF), but the spatial contexts that contribute to disease pathogenesis have remained uncertain. Using image-based spatial transcriptomics, we analyzed the gene expression of 1.6 million cells from 35 unique lungs. Through complementary cell-based and innovative cell-agnostic analyses, we characterized the localization of PF-emergent cell types, established the cellular and molecular basis of classical PF histopathologic features and identified a diversity of distinct molecularly defined spatial niches in control and PF lungs. Using machine learning and trajectory analysis to segment and rank airspaces on a gradient of remodeling severity, we identified compositional and molecular changes associated with progressive distal lung pathology, beginning with alveolar epithelial dysregulation and culminating with changes in macrophage polarization. Together, these results provide a unique, spatially resolved view of PF and establish methods that could be applied to other spatial transcriptomic studies.
2024-06-04 | GSE250346 | GEO