Project description:Treatment of leukemia cells with 1,25-dihydroxyvitamin D3 may overcome their differentiation block and lead to the transition from myeloblasts to monocytes. To identify microRNA-mRNA networks relevant for myeloid differentiation, we profiled the expression of mRNAs and microRNAs associated to the low- and high-density ribosomal fractions in leukemic cells and in their differentiated monocytic counterpart. Intersection between mRNAs shifted across the fractions after treatment with putative target genes of modulated microRNAs showed a series of molecular networks relevant for the monocyte cell fate determination In this dataset, we include the microRNA expression data obtained from the profiling of ribosome/polysome-associated miRNAs and mRNAs in proliferating HL60 cells and in cells induced to differentiate by 1,25-dihydroxyvitamin D3 (VitD3) treatment 18 total samples, 9 from control proliferating HL60 cells and 9 from VitD3-treated HL60 cells
Project description:Treatment of leukemia cells with 1,25-dihydroxyvitamin D3 may overcome their differentiation block and lead to the transition from myeloblasts to monocytes. To identify microRNA-mRNA networks relevant for myeloid differentiation, we profiled the expression of mRNAs and microRNAs associated to the low- and high-density ribosomal fractions in leukemic cells and in their differentiated monocytic counterpart. Intersection between mRNAs shifted across the fractions after treatment with putative target genes of modulated microRNAs showed a series of molecular networks relevant for the monocyte cell fate determination In this dataset, we include the expression data obtained from the profiling of ribosome/polysome-associated miRNAs and mRNAs in proliferating HL60 cells and in cells induced to differentiate by 1,25-dihydroxyvitamin D3 (VitD3) treatment 18 total samples, 9 from control proliferating HL60 cells and 9 from VitD3-treated HL60 cells
Project description:2D-LC/MS/MS analysis was used to examine time-dependent changes in proteome of E. coli O157:H7 strain Sakai upon an abrupt downshift in temperature (i.e., from 35°C to 14°C). Cell cultures were harvested at 30, 90, 160, and 330 min post-temperature downshift. It also should be noted that these time points were chosen with the aims to characterize the physiology of E. coli during dynamic changes in growth kinetics induced by an abrupt temperature downshift. Specifically, the samples taken at time 30 and 90 min were obtained during adaptation period, whereas the samples at time 160 and 330 min reflected the physiological state of E. coli during growth after the shift. MS/MS data obtained from each protein sample were processed by the Computational Proteomics Analysis System (CPAS), a web-based system built on the LabKey Server (v9.1, released 02.04.2009). The experimental mass spectra produced were subjected to a semi-tryptic search against the combined databases of E. coli O157:H7 Sakai (5,318 entries in total) downloaded from the National Center for Biotechnology Information (NCBI, https://www.ncbi.nlm.nih.gov/, downloaded 25.11.2008) using X!Tandem v2007.07.01. These databases included the E. coli O157:H7 Sakai database (5230 entries, NC_002695.fasta) and two E. coli O157:H7 Sakai plasmid databases, plasmid pO157 (85 entries, NC_002128.fasta) and plasmid pOSAK1 (three entries, NC_002127.fasta). The parameters for the database search were as follows: mass tolerance for precursor and fragment ions: 10 ppm and 0.5 Da, respectively; fixed modification: cysteine cabamidomethylation (+57 Da); and no variable modifications. The search results were then analyzed using the PeptideProphet and ProteinProphet algorithms from the Trans Proteomic Pipeline v3.4.2. All peptide and protein identifications were accepted at PeptideProphet and ProteinProphet of ≥0.9, corresponding to a theoretical error rate of ≤2%.
Project description:Germline mutations in CDKN2A and/or red hair colour variants in MC1R genes are associated with an increased susceptibility to develop cutaneous melanoma. To investigate the impact of germinal p.G101W CDKN2A mutation and MC1R variants on gene expression and transcription profiles associated to skin cancer and melanoma in particular, we set-up primary skin cultures from twins belonging to the melanoma prone-families with and without these genomic features. were analyzed using expression array methodology. Overall, 1535 transcripts were deregulated in CDKN2A mutated cells, finding overexpression of immunity-related genes (HLA-DPB1, CLEC2B, IFI44, IFI44L, IFI27, IFIT1, IFIT2, SP110 and IFNK) and downregulation of genes playing a role in the Notch signaling pathway. 3570 transcripts were deregulated in carriers of MC1R variants. In this case, upregulated genes were involved in oxidative stress and DNA damage pathways as well as in neurodegenerative diseases such as Parkinson’s, Alzheimer and Huntington. In contrast, downregulated genes were associated with pigmentation synthesis/transport and angiogenesis. By using a coculture system, this study identified key molecular functions and/or pathways that are deregulated due to alterations in melanoma susceptibility genes which in turn, could be involved in initiation/progression of the disease. 12 samples total. Several experimental groups: with and without genomic features (CDKN2A, MC1R).
Project description:We investigated genome-wide changes in mRNA translation in Arabidopsis thaliana T87 suspension cell cultures which thought to be one of the host materials for bioreactor. Global translational repression was observed in cells of 8 day after inoculation that is thought to be stressful condition by the nutrient deficiency and hypoxia. This suggested the negative effect of the global translational repression on transgene expression. On the other hand, previous study using heat stress showed that some mRNAs were actively translated under such stressful condition, suggesting the existence of mRNA that were actively translated in cells of 8 day after inoculations. To identify mRNAs that escape global translational repression on 8 day and its cis-elements would be the 1st step to make the system for higher transgene expression by the escaping global translational repression. To this end, we subjected polysomal RNA and non-polysomal RNA from sucrose gradient fractionated cell lysates to the co-hybridization on Agilent Arabidopsis 4 Oligo Microarrays. The ratio of signal intensities (polysomal RNA: total RNA) was used as an indicator of the translation state for each transcript. Experiment using two-fractionated mRNA, Polysomal mRNA vs. total mRNA. Biological replicates: 1
Project description:Cigarette smoke is a risk factor for inflammatory diseases, such as atherosclerosis. Tobacco smoke interacts with inflammatory cytokines to produce endothelial dysfunction and induces pro-inflammatory and pro-atherosclerotic effects in vascular tissue. Smooth muscle cells (SMCs) are present in the media of human arteries, and are considered protective against atherosclerotic plaque destabilization. Contractile SMCs are the most prominent cell type in the healthy vessel wall. SMCs are not terminally differentiated, and retain the ability to undergo a phenotypic switch from a contractile to a dedifferentiated synthetic state to express inflammatory markers and a phagocytic activity in response to environmental cues. The aim of our study was to evaluate the effects in human SMCs of lipophilic component from cigarette smoke condensate (CSC) and of hydrophilic components of Electronic-cigarette, Tobacco heating products, or cigarette smoke.
Project description:The aim of this study is to identify the differentially expressed genes in upon Akt3 over-expression after estrogen and tamoxifen treatment. RNA were extracted from three independently treated respective breast cancer cell lines and processed for further microarray experiments.
Project description:Most organisms have an endogenous circadian clock that is synchronized to environmental signals such as light and temperature. Although circadian rhythms have been described in the nematode C. elegans at the behavioral level, these rhythms appear to be relatively non-robust. Moreover, in contrast to other animal models, no circadian transcriptional rhythms have been identified. Thus, whether this simple nematode contains a bona fide circadian clock remains an open question. We used microarray experiments to identify light- and temperature-regulated transcriptional rhythms in C. elegans, and show that subsets of these transcripts are regulated in a circadian manner. In addition, we find that light and temperature also globally drive the expression of many genes, indicating that C. elegans exhibits systemic responses to these stimuli. Populations of growth-synchronized wild-type C. elegans L1 larvae were entrained for 5 days until adulthood to 12:12 hr light/dark (LD) cycles (500-1000 lux) at a constant temperature of 18°C, or for 4 days to 12:12 hr temperature cycles (25:15°C - warm/cold or WC) in constant darkness. RNA was collected every 4 hrs during the last entrainment and the subsequent free-running days and analyzed via hybridization of Affymetrix GeneChips. L4 larvae were transferred to FUDR-containing plates to inhibit embryonic development.
Project description:We descrive a joint model of transcriptional activation and mRNA accumulation, using estrogen receptor ERM-NM-1 activation in MCF-7 breast cancer cell line, which can be used for inference of transcription rate, RNA processing delay and degradation rate given data from high-throughput sequencing time course experiments. MCF-7 cells were mock treated or with 10nM 17b-E2 to nine time points (5', 10', 20', 40', 80', 160', 320', 640' and 1280'). Genome-wide identification of RNA polymerase II (RNAPII) occupancy and transcriptome profiling (RNA-seq) following E2 induction of MCF-7 cells Please note that the information in the wig.txt files is in gene-specific coordinates, not chromosomic coordinates, as this is the most sensible format for the associated project/paper.
Project description:Symptomatic glycerol kinase deficiency (GKD) is associated with episodic metabolic and central nervous system deterioration. We report here the first application of Weighted Gene Co-Expression Network Analysis (WGCNA) to investigate a knockout (KO) murine model of a human genetic disease. WGCNA identified networks and key hub transcripts from liver mRNA of glycerol kinase (Gyk) KO and wild type (WT) mice. Day of life 1 (dol1) samples from KO mice contained a network module enriched for organic acid metabolism before Gyk KO mice develop organic acidemia and die on dol3-4 and the module containing Gyk was enriched with apoptotic genes. Roles for the highly connected Acot, Psat and Plk3 transcripts were confirmed in cell cultures and subsequently validated by causality testing. We provide evidence that GK may have an apoptotic moonlighting role that is lost in GKD. This systems biology strategy has improved our understanding of GKD pathogenesis and suggests possible treatments. Male WT and KO mouse pups were sacrificed on day of life (dol) 1 and each liver was harvested. Total RNA from 4 KO and 3 WT livers was isolated individually. Affymetrix mus 430 2.0 GeneChips were used to analyze differences in liver gene expression between KO and WT mice. Dol1 and 3 Gyk KO mice represent different disease states. Dol 1 was chosen because mice are phenotypically asymptomatic with respect to Glycerol Kinase Deficiency (GKD) and allowed us to look at alterations that occur before the overt disease state. Dol 3 mice are phenotypically symptomatic with respect to GKD.