The impact of cell source, culture methodology, culture location and individual donors on gene expression profiles of bone marrow-derived and adipose-derived stromal cells.
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE42245 | GEO | 2013/01/01
SECONDARY ACCESSION(S): PRJNA179401
REPOSITORIES: GEO
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Project description:Gene expression was influenced most by the tissue source, followed by culture methodology, next by location where the cells were cultured and lastly the donor variability. On the normalized log2 expression values per gene a multifactorial Analyses of Variance (ANOVA) was conducted. Factors CELL CULTURES (cell source), MEDIUM (culture methodology), LOCATION (culture location), and SCAN DATE (hybridization batch) were included in the ANOVA model as independent factors. The following pairwise comparisons were made; Fetal calf serum vs. Human platelet lysate, Bone marrow vs. Adipose tissue, Utrecht vs. Leiden, Utrecht vs Nijmegen, and Leiden vs Nijmegen. Changes ≥2 and Benjamini Hochberg corrected p-values <0.05 were considered significant.
2013-01-01 | E-GEOD-42245 | biostudies-arrayexpress
Project description:Bone marrow (BM) stromal cells (MSCs), also known as mesenchymal stem cells, display a high degree of heterogeneity. To shed light on the causes of this heterogeneity, MSCs were collected from either human BM (n=5) or adipose tissue (AT) (n=5), and expanded using 2 different culture methods: one based on fetal calf serum, and one based on human platelet lysate. After initial expansion, MSCs were frozen, and the vials were transported to 3 different laboratories and grown for 1 passage using the same brand of culture plastic, medium, and supplements. Subsequently, the cells were harvested and assayed for their gene expression profile using the Affymetrix exon microarray platform. Based on gene expression profiles, the most discriminative feature was the anatomical harvesting site, followed by culture methodology. Remarkably, genes in the WNT pathway were expressed at higher levels in BM-derived MSCs than in AT-derived MSCs. Although differences were found between laboratories, cell culture location only slightly affects heterogeneity. Furthermore, individual donors contributed marginally to the observed differences in transcriptomes. Finally, BM-derived MSCs displayed the highest level of similarity, irrespective their culture conditions, when compared to AT-derived cells.
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Project description:A fundamental question in biology is how gene expression is regulated to give rise to a phenotype. However, transcriptional variability is rarely considered and could influence the relationship between genotype and phenotype. It is known in unicellular organisms that gene expression is often noisy rather than uniform and has been proposed to be beneficial when environmental conditions are unpredictable. However, little is known about transcriptional variability in multicellular organisms. Using transcriptomic approaches, we analysed gene expression variability over a 24 hours time-course between individual Arabidopsis thaliana plants growing in stable conditions. We identified hundreds of genes that exhibit high inter-individual variability and found that many are involved in environmental responses. We also identified factors that might facilitate gene expression variability, such as gene size, the number of transcription factors regulating a gene and the chromatin environment. These results will bring a new light into the impact of transcriptional variability in gene expression regulation in plants.
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Project description:R-loops serve as key modulators in various biological processes in humans and plants.Current high-throughput methodologies for R-loop profiling have their own intrinsic pros and cons. Therefore, any robust, sensitive, and amenable methods, complementary and/or advantageous to existing methodologies, are much needed for advancing R-loop biology. We here present an RNase H based cleavage combined with DNA polymerase-mediated in situ biotin-dATP/dCTP labeling of newly synthesized DNA for sequencing, termed ISRH-seq, an antibody-independent approach for strand-specific mapping of R-loops. After conducting a parallel comparison with DRIP-seq, we found that ISRH-seq can identify more R-loop peaks with the same sequencing depth. Moreover, ISRH- and DRIP-specific R-loops had distinct genomic and epigenetic features, exhibited distinct relationships with expression of overlapping genes, and functional divergence. Importantly, we found that ISRH-seq can be scalable down to 250-100ng DNA input, indicative of a robust and sensitive high-throughput methodology. In addition, it can be applied for R-loop profiling under stress conditions. Thus, our study provides a valuable orthogonal methodology for comprehensive profiling of R-loops in plants. It could be easily adapted to other non-plant systems, especially for these biologically important tissues or cell types with limited cell numbers, thereby advancing understanding of R-loop biology.
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Project description:DNA methylation is an important component of epigenetic modifications that influences the transcriptional machinery and is aberrant in many human diseases. Several methods have been developed to map DNA methylation for either limited regions or genome-wide. In particular, antibodies specific for methylated CpG have been successfully applied in genome-wide studies. However, despite the relevance of the obtained results, the interpretation of antibody enrichment is not trivial. Of greatest importance, the coupling of antibody-enriched methylated fragments with microarrays generates DNA methylation estimates that are not linearly related to the true methylation level. Here, we present an experimental and analytical methodology to obtain enhanced estimates which better describe the true values of DNA methylation level throughout the genome. We propose an experimental scenario for evaluating the true relationship in a high-throughput setting and a model-based analysis to predict the absolute and relative DNA methylation levels. We successfully applied this model to evaluate DNA methylation status of normal human melanocytes compared to a melanoma cell strain. Despite the low resolution typical of methods based on immunoprecipitation, we show that model-derived estimates of DNA methylation provide relatively high correlation with measured absolute and relative levels, as validated by bisulfite genomic DNA sequencing. Importantly, the model-derived DNA methylation estimates simplify the interpretation of the results both at single-loci and at chromosome-wide levels. The MEDME R library as well as installation instructions and a PDF tutorial are available online at the website below.
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2016-09-21 | GSE59549 | GEO
Project description:Single-electron transfer is an important process in organic chemistry, in which a single-electron reductant (electron donor) acts as a key component. Compared with metal-based electron donors, organic electron donors have some unique advantages, such as tunable reduction ability and mild reaction conditions. The development of novel organic electron donors with good reduction ability together with ease of preparation is in high demand. Based on the pyridine-catalyzed radical borylation reaction developed in our laboratory, we have discovered that, the reaction system consisting of a diboron(4) compound, methoxide and a pyridine derivative could smoothly produce super electron donors in situ. Two boryl-pyridine based species, the major one being a trans-2H,2'H-[2,2'-bipyridine]-1,1'-diide borate complex and the minor one being a pyridine radical anion-borate complex, were observed and carefully characterized. These complexes were found to be organic super electron donors unprecedented in literature, and their formation mechanisms were studied by DFT calculations. The diboron/methoxide/pyridine system enables the preparation of organic super electron donors from easily accessible starting materials under mild conditions, which has the potential to be a general and practical single-electron reducing agent in organic synthesis.
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Project description:A key function of the auditory system is to provide reliable information about the location of sound sources. Here, we describe how sound location is represented by synaptic input arriving onto pyramidal cells within auditory cortex by combining free-field acoustic stimulation in the frontal azimuthal plane with in vivo whole-cell recordings. We found that subthreshold activity was panoramic in that EPSPs could be evoked from all locations in all cells. Regardless of the sound location that evoked the largest EPSP, we observed a slowing in the EPSP slope along the contralateral-ipsilateral plane that was reflected in a temporal sequence of peak EPSP times. Contralateral sounds evoked EPSPs with earlier peak times and consequently generated action potential firing with shorter latencies than ipsilateral sounds. Thus, whereas spiking probability reflected the region of space evoking the largest EPSP, across the population, synaptic inputs enforced a gradient of spike latency and precision along the horizontal axis. Therefore, within auditory cortex and regardless of preferred location, the time window of synaptic integration reflects sound source location and ensures that spatial acoustic information is represented by relative timings of pyramidal cell output.
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Project description:BackgroundThe ageing population and recent migration flows may negatively affect the blood supply in the long term, increasing the importance of targeted recruitment and retention strategies to address donors. This review sought to identify individual, network and contextual characteristics related to blood donor status and behaviour, to systematically discuss differences between study results, and to identify possible factors to target in recruitment and retention efforts.MethodsThe systematic review was conducted in accordance with a predefined PROSPERO protocol (CRD42016039591). After quality assessments by multiple independent raters, a final set of 66 peer-reviewed papers, published between October 2009 and January 2017, were included for review.ResultsIndividual and contextual characteristics of blood donor status and behaviour were categorised into five main lines of research: donor demographics, motivations and barriers, adverse reactions and deferral, contextual factors, and blood centre factors. Results on donor demographics, motivations and barriers, and contextual factors were inconclusive, differing between studies, countries, and sample characteristics. Adverse reactions and deferral were negatively related to blood donor behaviour. Blood centre factors play an important role in donor management, e.g., providing information, reminders, and (non-)monetary rewards. No studies were found on network characteristics of (non-)donors.DiscussionAlthough individual and contextual characteristics strongly relate to blood donor status and behaviour, mechanisms underlying these relations have not been studied sufficiently. We want to stress the importance of longitudinal studies in donor behaviour, exploring the role of life events and network characteristics within blood donor careers. Increased understanding of donor behaviour will assist policy makers of blood collection agencies, with the ultimate goal of safeguarding a sufficient and matching blood supply.
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