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https://www.readbyqxmd.com/read/28726847/mapping-genome-wide-transcription-factor-binding-sites-using-dap-seq
#1
Anna Bartlett, Ronan C O'Malley, Shao-Shan Carol Huang, Mary Galli, Joseph R Nery, Andrea Gallavotti, Joseph R Ecker
To enable low-cost, high-throughput generation of cistrome and epicistrome maps for any organism, we developed DNA affinity purification sequencing (DAP-seq), a transcription factor (TF)-binding site (TFBS) discovery assay that couples affinity-purified TFs with next-generation sequencing of a genomic DNA library. The method is fast, inexpensive, and more easily scaled than chromatin immunoprecipitation sequencing (ChIP-seq). DNA libraries are constructed using native genomic DNA from any source of interest, preserving cell- and tissue-specific chemical modifications that are known to affect TF binding (such as DNA methylation) and providing increased specificity as compared with in silico predictions based on motifs from methods such as protein-binding microarrays (PBMs) and systematic evolution of ligands by exponential enrichment (SELEX)...
August 2017: Nature Protocols
https://www.readbyqxmd.com/read/28723146/generalized-noise-study-of-solid-state-nanopores-at-low-frequencies
#2
Chenyu Wen, Shuangshuang Zeng, Kai Arstila, Timo Sajavaara, Yu Zhu, Zhen Zhang, Shi-Li Zhang
Nanopore technology has been extensively investigated for analysis of biomolecules, and a success story in this field concerns DNA sequencing using a nanopore chip featuring an array of hundreds of biological nanopores (BioNs). Solid-state nanopores (SSNs) have been explored to attain longer lifetime and higher integration density than what BioNs can offer, but SSNs are generally considered to generate higher noise whose origin remains to be confirmed. Here, we systematically study low-frequency (including thermal and flicker) noise characteristics of SSNs measuring 7 to 200 nm in diameter drilled through a 20-nm-thick SiNx membrane by focused ion milling...
February 24, 2017: ACS Sensors
https://www.readbyqxmd.com/read/28718849/an-efficient-method-to-transcription-factor-binding-sites-imputation-via-simultaneous-completion-of-multiple-matrices-with-positional-consistency
#3
Wei-Li Guo, De-Shuang Huang
Transcription factors (TFs) are DNA-binding proteins that have a central role in regulating gene expression. Identification of DNA-binding sites of TFs is a key task in understanding transcriptional regulation, cellular processes and disease. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) enables genome-wide identification of in vivo TF binding sites. However, it is still difficult to map every TF in every cell line owing to cost and biological material availability, which poses an enormous obstacle for integrated analysis of gene regulation...
July 18, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28715808/retinoic-acid-facilitates-toll-like-receptor-4-expression-to-improve-intestinal-barrier-function-through-retinoic-acid-receptor-beta
#4
Yingying Li, Yuan Gao, Ting Cui, Ting Yang, Lan Liu, Tingyu Li, Jie Chen
BACKGROUND/AIMS: Vitamin A (VA) protects the intestinal epithelial barrier by improving cell migration and proliferation. Our previous studies demonstrated that VA deficiency (VAD) during pregnancy suppresses the systemic and mucosal immune responses in the intestines of offspring and that VA supplementation (VAS) during early life can increase immune cell counts. However, little is known about the mechanisms by which VA regulates intestinal epithelial barrier function. METHODS: Caco-2 cells were treated with all-trans retinoic acid (ATRA) for 24 hours to determine the optimum ATRA concentration to which the cells in question respond...
July 17, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28715394/a-filtration-based-method-of-preparing-high-quality-nuclei-from-cross-linked-skeletal-muscle-for-chromatin-immunoprecipitation
#5
Kazunari Nohara, Zheng Chen, Seung-Hee Yoo
Chromatin immunoprecipitation (ChIP) is a powerful method to determine protein binding to chromatin DNA. Fiber-rich skeletal muscle, however, has been a challenge for ChIP due to technical difficulty in isolation of high-quality nuclei with minimal contamination of myofibrils. Previous protocols have attempted to purify nuclei before cross-linking, which incurs the risk of altered DNA-protein interaction during the prolonged nuclei preparation process. In the current protocol, we first cross-linked the skeletal muscle tissue collected from mice, and the tissues were minced and sonicated...
July 6, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28714133/tilted-pillar-array-fabrication-by-the-combination-of-proton-beam-writing-and-soft-lithography-for-microfluidic-cell-capture-part-2-image-sequence-analysis-based-evaluation-and-biological-application
#6
Gabor Járvás, Tamas Varga, Marton G Szigeti, Laszlo Hajba, Peter Fürjes, Istvan Rajta, Andras Guttman
As a continuation of our previously published work, this paper presents a detailed evaluation of a microfabricated cell capture device utilizing a doubly tilted micropillar array. The device was fabricated using a novel hybrid technology based on the combination of proton beam writing and conventional lithography techniques. Tilted pillars offer unique flow characteristics and support enhanced fluidic interaction for improved immuno-affinity based cell capture. The performance of the microdevice was evaluated by an image sequence analysis based in-house developed single cell tracking system...
July 17, 2017: Electrophoresis
https://www.readbyqxmd.com/read/28714006/aldh1l1-variant-rs2276724-and-mrna-expression-predict-post-operative-clinical-outcomes-and-are-associated-with-tp53-expression-in-hbv-related-hepatocellular-carcinoma
#7
Guangzhi Zhu, Xiwen Liao, Chuangye Han, Xiaoguang Liu, Long Yu, Wei Qin, Sicong Lu, Hao Su, Zhiwei Chen, Zhengtao Liu, Yu Liang, Jianlu Huang, Tingdong Yu, Chengkun Yang, Ketuan Huang, Liming Shang, Xinping Ye, Lequn Li, Xue Qin, Kaiyin Xiao, Minhao Peng, Tao Peng
Aldehyde dehydrogenase 1 family member L1 (ALDH1L1) is downregulated in hepatocellular carcinoma (HCC) tumors, and its decreased expression is associated with the poor prognosis of HCC patients. We, therefore, evaluated the effect of single nucleotide polymorphisms (SNPs) of ALDH1L1, and its mRNA expression on the survival of hepatitis B virus (HBV)‑related HCC patients and the association with tumor protein p53 (TP53) expression. ALDH1L1 SNPs in 415 HBV-related HCC patients were genotyped via direct sequencing...
July 14, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28713645/effects-of-a-novel-disc-formulation-on-dry-mouth-symptoms-and-enamel-remineralization-in-patients-with-hyposalivation-an-in-vivo-study
#8
Jessica Ho, Miracle Vania Firmalino, Afarin Golabgir Anbarani, Thair Takesh, Joel Epstein, Petra Wilder-Smith
BACKGROUND: The goal of this study was to identify the in vivo effects in patients with hyposalivation of a novel slowly dissolving adhering test disc upon on enamel remineralization, oral biofilm, salivary production, pH and buffering, gingival health, and on self-evaluation of oral well-being. METHODS: Five subjects with xerostomia wore custom made retainers carrying 5 demineralized enamel chips for periods of 1 week each. In 1 study arm, subjects used the test agent plus oral hygiene self-care; in the other they used oral hygiene self-care only, with a 1 week washout in between arms...
February 2017: Dentistry: Current Research
https://www.readbyqxmd.com/read/28707250/genomic-prediction-of-starch-content-and-chipping-quality-in-tetraploid-potato-using-genotyping-by-sequencing
#9
Elsa Sverrisdóttir, Stephen Byrne, Ea Høegh Riis Sundmark, Heidi Øllegaard Johnsen, Hanne Grethe Kirk, Torben Asp, Luc Janss, Kåre L Nielsen
Genomic prediction models for starch content and chipping quality show promising results, suggesting that genomic selection is a feasible breeding strategy in tetraploid potato. Genomic selection uses genome-wide molecular markers to predict performance of individuals and allows selections in the absence of direct phenotyping. It is regarded as a useful tool to accelerate genetic gain in breeding programs, and is becoming increasingly viable for crops as genotyping costs continue to fall. In this study, we have generated genomic prediction models for starch content and chipping quality in tetraploid potato to facilitate varietal development...
July 13, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28706572/a-microwell-printing-fabrication-strategy-for-the-on-chip-templated-biosynthesis-of-protein-microarrays-for-surface-plasmon-resonance-imaging
#10
Gerald Manuel, Andrej Lupták, Robert M Corn
A two-step templated, ribosomal biosynthesis/printing method for the fabrication of protein microarrays for surface plasmon resonance imaging (SPRI) measurements is demonstrated. In the first step, a sixteen component microarray of proteins is created in microwells by cell free on chip protein synthesis; each microwell contains both an in vitro transcription and translation (IVTT) solution and 350 femtomoles of a specific DNA template sequence that together are used to create approximately 40 picomoles of a specific hexahistidine-tagged protein...
September 22, 2016: Journal of Physical Chemistry. C, Nanomaterials and Interfaces
https://www.readbyqxmd.com/read/28704393/whole-exome-sequence-based-association-analyses-of-plasma-amyloid-%C3%AE-in-african-and-european-americans-the-atherosclerosis-risk-in-communities-neurocognitive-study
#11
Jeannette Simino, Zhiying Wang, Jan Bressler, Vincent Chouraki, Qiong Yang, Steven G Younkin, Sudha Seshadri, Myriam Fornage, Eric Boerwinkle, Thomas H Mosley
OBJECTIVE: We performed single-variant and gene-based association analyses of plasma amyloid-β (aβ) concentrations using whole exome sequence from 1,414 African and European Americans. Our goal was to identify genes that influence plasma aβ42 concentrations and aβ42:aβ40 ratios in late middle age (mean = 59 years), old age (mean = 77 years), or change over time (mean = 18 years). METHODS: Plasma aβ measures were linearly regressed onto age, gender, APOE ε4 carrier status, and time elapsed between visits (fold-changes only) separately by race...
2017: PloS One
https://www.readbyqxmd.com/read/28700938/golgi-outpost-synthesis-impaired-by-toxic-polyglutamine-proteins-contributes-to-dendritic-pathology-in-neurons
#12
Chang Geon Chung, Min Jee Kwon, Keun Hye Jeon, Do Young Hyeon, Myeong Hoon Han, Jeong Hyang Park, In Jun Cha, Jae Ho Cho, Kunhyung Kim, Sangchul Rho, Gyu Ree Kim, Hyobin Jeong, Jae Won Lee, TaeSoo Kim, Keetae Kim, Kwang Pyo Kim, Michael D Ehlers, Daehee Hwang, Sung Bae Lee
Dendrite aberration is a common feature of neurodegenerative diseases caused by protein toxicity, but the underlying mechanisms remain largely elusive. Here, we show that nuclear polyglutamine (polyQ) toxicity resulted in defective terminal dendrite elongation accompanied by a loss of Golgi outposts (GOPs) and a decreased supply of plasma membrane (PM) in Drosophila class IV dendritic arborization (da) (C4 da) neurons. mRNA sequencing revealed that genes downregulated by polyQ proteins included many secretory pathway-related genes, including COPII genes regulating GOP synthesis...
July 11, 2017: Cell Reports
https://www.readbyqxmd.com/read/28700586/systematic-identification-and-characterization-of-regulatory-elements-derived-from-human-endogenous-retroviruses
#13
Jumpei Ito, Ryota Sugimoto, Hirofumi Nakaoka, Shiro Yamada, Tetsuaki Kimura, Takahide Hayano, Ituro Inoue
Human endogenous retroviruses (HERVs) and other long terminal repeat (LTR)-type retrotransposons (HERV/LTRs) have regulatory elements that possibly influence the transcription of host genes. We systematically identified and characterized these regulatory elements based on publicly available datasets of ChIP-Seq of 97 transcription factors (TFs) provided by ENCODE and Roadmap Epigenomics projects. We determined transcription factor-binding sites (TFBSs) using the ChIP-Seq datasets and identified TFBSs observed on HERV/LTR sequences (HERV-TFBSs)...
July 12, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28698299/neat1-is-a-p53-inducible-lincrna-essential-for-transformation-suppression
#14
Stephano S Mello, Carolyn Sinow, Nitin Raj, Pawel K Mazur, Kathryn Bieging-Rolett, Daniela Kenzelmann Broz, Jamie F Conklin Imam, Hannes Vogel, Laura D Wood, Julien Sage, Tetsuro Hirose, Shinichi Nakagawa, John Rinn, Laura D Attardi
The p53 gene is mutated in over half of all cancers, reflecting its critical role as a tumor suppressor. Although p53 is a transcriptional activator that induces myriad target genes, those p53-inducible genes most critical for tumor suppression remain elusive. Here, we leveraged p53 ChIP-seq (chromatin immunoprecipitation [ChIP] combined with high-throughput sequencing) and RNA-seq (RNA sequencing) data sets to identify new p53 target genes, focusing on the noncoding genome. We identify Neat1, a noncoding RNA (ncRNA) constituent of paraspeckles, as a p53 target gene broadly induced by mouse and human p53 in different cell types and by diverse stress signals...
July 11, 2017: Genes & Development
https://www.readbyqxmd.com/read/28697761/hla-check-evaluating-hla-data-from-snp-information
#15
Marc Jeanmougin, Josselin Noirel, Cédric Coulonges, Jean-François Zagury
BACKGROUND: The major histocompatibility complex (MHC) region of the human genome, and specifically the human leukocyte antigen (HLA) genes, play a major role in numerous human diseases. With the recent progress of sequencing methods (eg, Next-Generation Sequencing, NGS), the accurate genotyping of this region has become possible but remains relatively costly. In order to obtain the HLA information for the millions of samples already genotyped by chips in the past ten years, efficient bioinformatics tools, such as SNP2HLA or HIBAG, have been developed that infer HLA information from the linkage disequilibrium existing between HLA alleles and SNP markers in the MHC region...
July 11, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28690234/-pcdh19-gene-mutations-lead-to-epilepsy-with-mental-retardation-limited-to-females-in-2-cases-and-literature-review
#16
Li Yang, Ahmed Arafat, Jing Peng, Chen Chen, Yuping Ma, Fei Yin
Epilepsy with mental retardation limited to females (EFMR) is a syndrome characterized by early onset heat-sensitive epilepsy of infancy or early childhood and generally limited to females, which previously reported that the cadherin gene superfamily subtype protocadherin 19 (PCDH19) gene is its pathogenic gene. We retrospectively analyzed the clinical data for 2 cases of EFMR patients with PCDH19 mutation diagnosed by Department of Pediatric Neurology of Xiangya Hospital, Central South University in 2015. Literature on PubMed, OMIM and HGMD relevant to this syndrome was reviewed, and the clinical characteristics were summarized accordingly...
June 28, 2017: Zhong Nan da Xue Xue Bao. Yi Xue Ban, Journal of Central South University. Medical Sciences
https://www.readbyqxmd.com/read/28688207/the-application-of-a-microfluidic-reactor-including-spontaneously-adsorbed-trypsin-for-rapid-protein-digestion-of-human-tear-samples
#17
Adam Kecskemeti, Cynthia Nora Nagy, Eva Csosz, Gergo Kallo, Attila Gaspar
In this study the application of a newly developed microfluidic immobilized enzymatic reactor (IMER) designed to accelerate protein digestion in clinical samples is presented. The IMER contains trypsin adsorbed on the porous surface of a PDMS microfluidic chip. Human tear with its relatively low volume and high protein content was collected and used for testing the digestion efficiency of the IMER. With the use of CZE peptide mapping, the efficiency and reproducibility of the reactor were investigated. No significant difference was observed in the CZE peptide profiles of the same tear sample digested in-solution or via microfluidic IMER...
July 8, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28684636/foxc1-regulates-fgfr1-isoform-switching-to-promote-invasion-following-tgf%C3%AE-induced-emt
#18
Alexander Hopkins, Mackenzie L Coatham, Fred B Berry
Epithelial-to-mesenchymal transition (EMT) is an important physiological process that drives tissue formation during development, but also contributes to disease pathogenesis including fibrosis and cancer metastasis. Elevated expression of the FOXC1 transcription factor has been detected in several metastatic cancers that have undergone EMT. Therefore, mechanistic insight into the role of FOXC1 in the initiation of the EMT process was sought. It was determined that although Foxc1 transcript expression was elevated following TGF-β1 induced EMT of NMuMG cells, FOXC1 was not required for this induction...
July 6, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/28684635/a-type-2-diabetes-associated-functional-regulatory-variant-in-a-pancreatic-islet-enhancer-at-the-adcy5-locus
#19
Tamara S Roman, Maren E Cannon, Swarooparani Vadlamudi, Martin L Buchkovich, Brooke N Wolford, Ryan P Welch, Mario A Morken, Grace J Kwon, Arushi Varshney, Romy Kursawe, Ying Wu, Anne U Jackson, Michael R Erdos, Johanna Kuusisto, Markku Laakso, Laura J Scott, Michael Boehnke, Francis S Collins, Stephen C J Parker, Michael L Stitzel, Karen L Mohlke
Molecular mechanisms remain unknown for most type 2 diabetes genome-wide association study (GWAS) identified loci. Variants associated with type 2 diabetes and fasting glucose levels reside in introns of ADCY5, a gene that encodes adenylate cyclase 5. Adenylate cyclase 5 catalyzes the production of cyclic AMP, which is a second messenger molecule involved in cell signaling and pancreatic beta cell insulin secretion. We demonstrated that type 2 diabetes risk alleles are associated with decreased ADCY5 expression in human islets and examined candidate variants for regulatory function...
July 6, 2017: Diabetes
https://www.readbyqxmd.com/read/28683716/putative-enhancer-sites-in-the-bovine-genome-are-enriched-with-variants-affecting-complex-traits
#20
Min Wang, Timothy P Hancock, Iona M MacLeod, Jennie E Pryce, Benjamin G Cocks, Benjamin J Hayes
BACKGROUND: Enhancers are non-coding DNA sequences, which when they are bound by specific proteins increase the level of gene transcription. Enhancers activate unique gene expression patterns within cells of different types or under different conditions. Enhancers are key contributors to gene regulation, and causative variants that affect quantitative traits in humans and mice have been located in enhancer regions. However, in the bovine genome, enhancers as well as other regulatory elements are not yet well defined...
July 6, 2017: Genetics, Selection, Evolution: GSE
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