Similar Datasets
Project description:Methanomicrobium mobile BP strain:BP Genome sequencing and assembly
| PRJNA223456 | ENA
Project description:Bromodomain and extraterminal domain (BET) proteins have emerged as therapeutic targets in multiple cancers, including the most common primary adult brain tumor glioblastoma (GBM). Although several bet inhibitors have entered clinical trials, few are brain penetrant. We have generated UM-002, a novel brain penetrant BET inhibitor that reduces GBM cell proliferation in vitro and in a human cerebral brain organoid model. Since UM-002 is more potent than other BET inhibitors, it could potentially be developed for GBM treatment. Furthermore, UM-002 treatment reduces the expression of cell-cycle related genes in vivo, and reduces the expression of invasion related genes within the non-proliferative cells present in tumors as measured by single cell RNAsequencing. These studies suggest that BET inhibition alters the transcriptional landscape of GBM tumors, which has implications for designing combination therapies. Importantly, they also provide an integrated dataset that combines in vitro and ex vivo studies with in vivo single-cell RNA-sequencing to characterize a novel BET inhibitor in GBM.
2021-12-01 | GSE173146 | GEO
Project description:BP and ER encode proteins that act synergistically to regulate Arabidopsis inflorescence architecture. To search for genes/proteins that influence the BP/ER signaling pathways, we conducted mutagenesis of the bp er double mutant and found that a mutation in FILAMENTOUS FLOWER (FIL) suppresses many of the morphological/developmental defects in bp er. Given that FIL encodes a Zn-finger containing transcription factor, microarray analysis was conducted on bp er vs. the bp er fil line to identify genes that are misregulated and which might implicate specific genes/proteins/pathways that are involved in regulating inflorescence development.
2016-09-10 | GSE86643 | GEO
Project description:This is a Phase 1/2 study to assess the safety and efficacy of ELI-002 7P immunotherapy (a lipid-conjugated immune-stimulatory oligonucleotide [Amph-CpG-7909] plus a mixture of lipid-conjugated peptide-based antigens [Amph-Peptides 7P]) as adjuvant treatment in subjects with solid tumors with mutated KRAS/NRAS. This study builds on the experience obtained with related product ELI-002 2P, which was studied in protocol ELI-002-001 under IND 26909.
| 8247 | ecrin-mdr-crc
Project description:Cytophagales bacterium TFI 002 Genome sequencing
| PRJNA370767 | ENA
Project description:Natural isolates of Burkholderia pseudomallei (Bp), the causative agent of melioidosis, are known to exhibit diverse phenotypic traits, suggesting significant intraspecies genetic heterogeneity. Using whole-genome Bp microarrays, we experimentally mapped patterns of large-scale genomic variation in 93 South East Asian clinical, environmental, and animal Bp isolates. 14% of the reference Bp K96243 genome was variably present across the strain panel, more than double previous estimates, and both hypothetical proteins and paralogous gene pairs (PGPs) were significantly over-represented in the set of strain-variable genes. Examining patterns of PGP retention and loss, we successfully sub-categorized the PGPs into non-redundant, functionally biased, and completely redundant classes. We then identified 20 novel regions (“islands”) variably present between strains previously missed by computational analysis. Three of these novel islands contained lipopolysaccharide (LPS) biosynthesis genes, and strains lacking one such LPS island demonstrated reduced virulence in mouse infection assays. Clinical isolates associated with human melioidosis were strongly associated with the presence of specific genomic islands, but a common set of virulence-related genes was present in all strains. Our results suggest that most Bp strains possess a core virulence machinery capable of causing disease, but accessory functions provided by mobile elements may predispose distinct host species and ecological niches to specific individual strains. This hierarchical model of Bp virulence reconciles previous conflicting studies comparing Bp environmental and clinical isolates, and suggests novel molecular strategies for disease surveillance and outbreak detection efforts in melioidosis. Keywords: aCGH of 93 Bp strains
2008-12-26 | GSE9491 | GEO
Project description:We investigated the effects of the TLR8 agonist 3M-002 on latently HIV infected U1 cells. We found a prominent upregulation of TLR-dependent genes. Notably, the TLR8 agonist resulted in a marked activation of HIV.
2011-01-11 | GSE26469 | GEO
Project description:Procambarus clarkii strain:002 Raw sequence reads
| PRJNA754693 | ENA
Project description:The E. histolytica transcription factor URE3-BP is a calcium-responsive regulator of two E. histolytica virulence genes, hgl5 and fdx1. URE3-BP was previously identified by a yeast one-hybrid screen of E. histolytica proteins capable of binding to the sequence TATTCTATT (URE3) in the promoter regions of hgl5 and fdx1. In this work precise definition of the consensus URE3 element was performed by electrophoretic mobility shift assays (EMSA) using base-substituted oligonucleotides, and the consensus motif validated using episomal reporter constructs. Transcriptome profiling of a strain induced to produce a dominant-positive URE3-BP was then used to identify additional genes regulated by URE3-BP. Fifty modulated transcripts were identified, and of these the EMSA defined motif T[atg]T[tc][cg]T[at][tgc][tg] was found in over half of the promoters (54% p<0.0001). Fifteen of the URE3-BP regulated genes were potential membrane proteins suggesting that one function of URE3-BP is to remodel the surface of E. histolytica in response to a calcium signal. Induction of URE3-BP lead to an increase in tranwell migration suggesting a possible role in the regulation of cellular motility.
2008-10-14 | GSE12188 | GEO
Project description:We investigated the effects of the TLR8 agonist 3M-002 on latently HIV infected U1 cells. We found a prominent upregulation of TLR-dependent genes. Notably, the TLR8 agonist resulted in a marked activation of HIV. We stimulated U1 cells for 6 or 10 hours with 3M-002 and subsequently harvested the cells, extracted total RNA. RNA was then used for quantifiying TLR-dependent gene upregulation using a commercial PCR array pathway
2011-01-11 | E-GEOD-26469 | biostudies-arrayexpress