keyword
MENU ▼
Read by QxMD icon Read
search

Transcriptomics

keyword
https://www.readbyqxmd.com/read/27933531/using-baseline-transcriptional-connectomes-in-rat-to-identify-genetic-pathways-associated-with-predisposition-to-complex-traits
#1
Laura Saba, Paula Hoffman, Boris Tabakoff
Although rat is a critical model organism in preclinical medications development, its use in systems genetics studies remains sparse. The PhenoGen database and website contain detailed information on the qualitative and quantitative aspects of the rat brain, liver, heart, and brown adipose transcriptome. This database has been generated using the HXB/BXH recombinant inbred panel and is being expanded to a hybrid rat diversity panel that includes many common inbred strains as well. By using such a panel, the PhenoGen project has created a renewable and cumulative resource for the rat genomics community...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933528/rna-seq-in-the-collaborative-cross
#2
Richard Green, Courtney Wilkins, Martin T Ferris, Michael Gale
The Collaborative Cross (CC) is a large panel of inbred mouse strains currently being developed for multiple areas of research. Scientists are taking integrated omics-style approaches to collecting data in order to obtain a deeper understanding of the biological mechanisms underlying a number of diverse disease phenotypes. As the cost of the next generation sequencing (NGS) decreases, RNA-sequencing (RNA-seq) has become the favored approach to transcriptomic analyses versus microarrays due to increases in sensitivity and resolution...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933527/integrating-multidimensional-data-sources-to-identify-genes-regulating-complex-phenotypes
#3
Rupert W Overall
Phenotypes collected with a view to quantitative trait locus mapping can be augmented with compatible whole-transcriptome expression data and information from several other sources. These different data sources can be assembled into multidimensional network models which allow the identification of key genes potentially driving the phenotype of interest. The following chapter describes this approach using an example workflow. Several alternatives and potential limitations are discussed to aid the researcher when applying these techniques to their own work...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933524/a-suite-of-tools-for-biologists-that-improve-accessibility-and-visualization-of-large-systems-genetics-datasets-applications-to-the-hybrid-mouse-diversity-panel
#4
Christoph D Rau, Mete Civelek, Calvin Pan, Aldons J Lusis
In this chapter we address the recent explosion in large multilevel population studies such as the METSIM study in humans as well as large panels of animal models such as the Hybrid Mouse Diversity Panel or the BXD set of recombinant inbred strains. These studies have harnessed the increasing affordability of large-scale high-throughput profiling to gather massive quantities of data. These datasets, spread across different -omics levels (genome, transcriptome, etc.), different tissues (e.g. heart, plasma, bone) and different environmental factors (e...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933319/a-metabolic-widget-adjusts-the-phosphoenolpyruvate-dependent-fructose-influx-in-pseudomonas-putida
#5
Max Chavarría, Ángel Goñi-Moreno, Víctor de Lorenzo, Pablo I Nikel
Fructose uptake in the soil bacterium Pseudomonas putida occurs through a canonical phosphoenolpyruvate (PEP)-dependent sugar transport system (PTS(Fru)). The logic of the genetic circuit that rules its functioning is puzzling: the transcription of the fruBKA operon, encoding all the components of PTS(Fru), can escape the repression exerted by the catabolite repressor/activator protein Cra solely in the presence of intracellular fructose-1-P, an agonist formed only when fructose has been already transported...
November 2016: MSystems
https://www.readbyqxmd.com/read/27933318/global-analysis-and-comparison-of-the-transcriptomes-and-proteomes-of-group-a-streptococcus-biofilms
#6
Jeffrey A Freiberg, Yoann Le Breton, Bao Q Tran, Alison J Scott, Janette M Harro, Robert K Ernst, Young Ah Goo, Emmanuel F Mongodin, David R Goodlett, Kevin S McIver, Mark E Shirtliff
To gain a better understanding of the genes and proteins involved in group A Streptococcus (GAS; Streptococcus pyogenes) biofilm growth, we analyzed the transcriptome, cellular proteome, and cell wall proteome from biofilms at different stages and compared them to those of plankton-stage GAS. Using high-throughput RNA sequencing (RNA-seq) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) shotgun proteomics, we found distinct expression profiles in the transcriptome and proteome. A total of 46 genes and 41 proteins showed expression across the majority of biofilm time points that was consistently higher or consistently lower than that seen across the majority of planktonic time points...
November 2016: MSystems
https://www.readbyqxmd.com/read/27933111/aberrant-dna-hypermethylation-silenced-sox21-as1-gene-expression-and-its-clinical-importance-in-oral-cancer
#7
Cheng-Mei Yang, Tsung-Han Wang, Hung-Chih Chen, Sung-Chou Li, Ming-Chien Lee, Huei-Han Liou, Pei-Feng Liu, Yu-Kai Tseng, Yow-Ling Shiue, Luo-Ping Ger, Kuo-Wang Tsai
BACKGROUND: Long noncoding RNAs (lncRNAs) are more than 200 nucleotides in length and lack transcriptional ability. The biological function of lncRNAs in oral squamous cell carcinoma (OSCC) remains unclear. The aim of this study was to identify the dysfunction of lncRNA in OSCC. RESULTS: We analyzed the transcriptome profiles of human OSCC tissues and paired adjacent normal tissues from two patients through a next-generation sequencing approach. A total of 14 lncRNAs were upregulated (fold change ≥3) and 13 were downregulated (fold change ≤-3) in OSCC tissues compared with the adjacent normal tissues...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27933082/rna-seq-transcriptome-response-of-flax-linum-usitatissimum-l-to-the-pathogenic-fungus-fusarium-oxysporum-f-sp-lini
#8
Leonardo Galindo-González, Michael K Deyholos
Fusarium oxysporum f. sp. lini is a hemibiotrophic fungus that causes wilt in flax. Along with rust, fusarium wilt has become an important factor in flax production worldwide. Resistant flax cultivars have been used to manage the disease, but the resistance varies, depending on the interactions between specific cultivars and isolates of the pathogen. This interaction has a strong molecular basis, but no genomic information is available on how the plant responds to attempted infection, to inform breeding programs on potential candidate genes to evaluate or improve resistance across cultivars...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27933070/transcriptional-responses-in-root-and-leaf-of-prunus-persica-under-drought-stress-using-rna-sequencing
#9
Najla Ksouri, Sergio Jiménez, Christina E Wells, Bruno Contreras-Moreira, Yolanda Gogorcena
Prunus persica L. Batsch, or peach, is one of the most important crops and it is widely established in irrigated arid and semi-arid regions. However, due to variations in the climate and the increased aridity, drought has become a major constraint, causing crop losses worldwide. The use of drought-tolerant rootstocks in modern fruit production appears to be a useful method of alleviating water deficit problems. However, the transcriptomic variation and the major molecular mechanisms that underlie the adaptation of drought-tolerant rootstocks to water shortage remain unclear...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27932622/inflammasome-activation-underlies-central-nervous-system-deterioration-in-hiv-associated-tuberculosis
#10
Suzaan Marais, Rachel P J Lai, Katalin A Wilkinson, Graeme Meintjes, Anne O'Garra, Robert J Wilkinson
Tuberculosis meningitis (TBM) is a frequent cause of meningitis in HIV-infected individuals, resulting in death in ~ 40% of affected patients. A severe complication of antiretroviral therapy (ART) in these patients is neurological TB-immune reconstitution inflammatory syndrome (IRIS), but its underlying cause remains poorly understood. To investigate the pathogenesis of TBM-IRIS, we performed longitudinal whole blood microarray analysis of HIV-infected TBM patients and reflected the findings at the protein level...
December 8, 2016: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/27932543/members-of-the-zinc-cluster-factor-family-alters-virulence-in-candida-albicans
#11
Luca Issi, Rhys A Farrer, Kelly Pastor, Benjamin Landry, Toni Delorey, George W Bell, Dawn A Thompson, Christina A Cuomo, Reeta P Rao
Virtually all humans are colonized with Candida albicans However, in immunocompromised individuals this benign commensal organism becomes a serious, life-threatening pathogen. Here, we describe and analyze the regulatory networks that modulate innate responses in the host niches. We identified Zcf15 and Zcf29, two Zinc Cluster transcription Factors (ZCF) that are required for C. albicans virulence. Previous sequence analysis of clinical C. albicans isolates from immunocompromised patients indicates that both ZCF genes diverged during clonal evolution...
December 7, 2016: Genetics
https://www.readbyqxmd.com/read/27932419/jasmonic-acid-enhances-al-induced-root-growth-inhibition
#12
Zhong-Bao Yang, Chunmei He, Yanqi Ma, Marco Herde, Zhaojun Ding
Phytohormones such as ethylene and auxin are involved in the regulation of the aluminum (Al)-induced root-growth inhibition. Although jasmonate (JA) has been reported to play a crucial role in the regulation of root growth and development in response to environmental stresses through interplay with ethylene and auxin, its role in the regulation of root-growth response to Al stress is not yet known. In an attempt to elucidate the role of JA, we found that exogenous application of JA enhanced the Al-induced root-growth inhibition...
December 8, 2016: Plant Physiology
https://www.readbyqxmd.com/read/27932387/the-long-non-coding-rna-transcriptome-of-dictyostelium-discoideum-development
#13
Rafael D Rosengarten, Balaji Santhanam, Janez Kokosar, Gad Shaulsky
Dictyostelium discoideum live in the soil as single cells, engulfing bacteria and growing vegetatively. Upon starvation, tens of thousands of amoebae enter a developmental program that includes aggregation, multicellular differentiation, and sporulation. Major shifts across the protein-coding transcriptome accompany these developmental changes. However, no study has presented a global survey of long non-coding RNAs in D. discoideum To characterize the antisense and long intergenic non-coding RNA transcriptome, we analyzed previously published developmental time course samples using an RNA-sequencing library preparation method that selectively depletes ribosomal RNAs...
December 7, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27931240/skeletal-muscle-characteristics-are-preserved-in-htert-cdk4-human-myogenic-cell-lines
#14
Matthew Thorley, Stéphanie Duguez, Emilia Maria Cristina Mazza, Sara Valsoni, Anne Bigot, Kamel Mamchaoui, Brennan Harmon, Thomas Voit, Vincent Mouly, William Duddy
BACKGROUND: hTERT/cdk4 immortalized myogenic human cell lines represent an important tool for skeletal muscle research, being used as therapeutically pertinent models of various neuromuscular disorders and in numerous fundamental studies of muscle cell function. However, the cell cycle is linked to other cellular processes such as integrin regulation, the PI3K/Akt pathway, and microtubule stability, raising the question as to whether genetic modification related to the cell cycle results in secondary effects that could undermine the validity of these cell models...
December 8, 2016: Skeletal Muscle
https://www.readbyqxmd.com/read/27931186/transcriptome-profiling-reveals-differential-gene-expression-of-detoxification-enzymes-in-a-hemimetabolous-tobacco-pest-after-feeding-on-jasmonate-silenced-nicotiana-attenuata-plants
#15
Cristina M Crava, Christoph Brütting, Ian T Baldwin
BACKGROUND: The evolutionary arms race between plants and insects has driven the co-evolution of sophisticated defense mechanisms used by plants to deter herbivores and equally sophisticated strategies that enable phytophagous insects to rapidly detoxify the plant's defense metabolites. In this study, we identify the genetic determinants that enable the mirid, Tupiocoris notatus, to feed on its well-defended host plant, Nicotiana attenuata, an outstanding model for plant-insect interaction studies...
December 8, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27931185/characterization-of-the-cytokinin-responsive-transcriptome-in-rice
#16
Tracy Raines, Ivory C Blakley, Yu-Chang Tsai, Jennifer M Worthen, José Manuel Franco-Zorrilla, Roberto Solano, G Eric Schaller, Ann E Loraine, Joseph J Kieber
BACKGROUND: Cytokinin activates transcriptional cascades important for development and the responses to biotic and abiotic stresses. Most of what is known regarding cytokinin-regulated gene expression comes from studies of the dicotyledonous plant Arabidopsis thaliana. To expand the understanding of the cytokinin-regulated transcriptome, we employed RNA-Seq to analyze gene expression in response to cytokinin in roots and shoots of the monocotyledonous plant rice. RESULTS: We identified over 4,600 and approximately 2,400 genes differentially expressed in response to cytokinin in roots and shoots respectively...
December 8, 2016: BMC Plant Biology
https://www.readbyqxmd.com/read/27931182/exposure-of-bovine-oocytes-and-embryos-to-elevated-non-esterified-fatty-acid-concentrations-integration-of-epigenetic-and-transcriptomic-signatures-in-resultant-blastocysts
#17
K L J Desmet, V Van Hoeck, D Gagné, E Fournier, A Thakur, A M O'Doherty, C P Walsh, M A Sirard, P E J Bols, J L M R Leroy
BACKGROUND: Metabolic stress associated with negative energy balance in high producing dairy cattle and obesity in women is a risk factor for decreased fertility. Non-esterified fatty acids (NEFA) are involved in this pathogenesis as they jeopardize oocyte and embryo development. Growing evidence indicates that maternal metabolic disorders can disturb epigenetic programming, such as DNA methylation, in the offspring. Oocyte maturation and early embryo development coincide with methylation changes and both are sensitive to adverse environments...
December 8, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27931000/thorium-impact-on-tobacco-root-transcriptome
#18
Kateřina Mazari, Přemysl Landa, Sylva Přerostová, Karel Müller, Radomíra Vaňková, Petr Soudek, Tomáš Vaněk
Thorium is natural actinide metal with potential use in nuclear energetics. Contamination by thorium, originated from mining activities or spills, represents environmental risk due to its radioactivity and chemical toxicity. A promising approach for cleaning of contaminated areas is phytoremediation, which need to be based, however, on detail understanding of the thorium effects on plants. In this study we investigated transcriptomic response of tobacco roots exposed to 200μM thorium for one week. Thorium application resulted in up-regulation of 152 and down-regulation of 100 genes (p-value <0...
November 30, 2016: Journal of Hazardous Materials
https://www.readbyqxmd.com/read/27930681/transcriptomic-changes-in-liver-of-young-bulls-caused-by-diets-low-in-mineral-and-protein-contents-and-supplemented-with-n-3-fatty-acids-and-conjugated-linoleic-acid
#19
Sara Pegolo, Alessio Cecchinato, Núria Mach, Massimiliano Babbucci, Marianna Pauletto, Luca Bargelloni, Stefano Schiavon, Giovanni Bittante
The aim of the present study was to identify transcriptional modifications and regulatory networks accounting for physiological and metabolic responses to specific nutrients in the liver of young Belgian Blue × Holstein bulls using RNA-sequencing. A larger trial has been carried out in which animals were fed with different diets: 1] a conventional diet; 2] a low-protein/low-mineral diet (low-impact diet) and 3] a diet enriched in n-3 fatty acids (FAs), conjugated linoleic acid (CLA) and vitamin E (nutraceutical diet)...
2016: PloS One
https://www.readbyqxmd.com/read/27930677/de-novo-sequencing-and-comparative-analysis-of-schima-superba-seedlings-to-explore-the-response-to-drought-stress
#20
Bao-Cai Han, Wei Wei, Xiang-Cheng Mi, Ke-Ping Ma
Schima superba is an important dominant species in subtropical evergreen broadleaved forests of China, and plays a vital role in community structure and dynamics. However, the survival rate of its seedlings in the field is low, and water shortage could be a factor that limits its regeneration. In order to better understand the response of its seedlings to drought stress on a functional genomics scale, RNA-seq technology was utilized in this study to perform a large-scale transcriptome sequencing of the S. superba seedlings under drought stress...
2016: PloS One
keyword
keyword
55307
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"