keyword
MENU ▼
Read by QxMD icon Read
search

Atac

keyword
https://www.readbyqxmd.com/read/28075484/assay-for-transposase-accessible-chromatin-using-sequencing-atac-seq-data-analysis
#1
Kristy L S Miskimen, E Ricky Chan, Jonathan L Haines
The study of epigenetic properties of the human genome, including structural modifications of DNA and chromatin, has increased tremendously as mounting evidence has demonstrated how much epigenetics affects human gene expression. Buenrostro et al. have developed a rapid method, requiring low numbers of living cells as input, for examining chromatin accessibility across the epigenome, known as the assay for transposase-accessible chromatin using sequencing (ATAC-seq). The overall goal of this unit is to provide a thorough ATAC-seq data analysis plan, as well as describe how primary human blood samples can be processed for use in ATAC-seq...
January 11, 2017: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/28045414/evaluation-of-left-atrial-mechanical-function-and-atrial-conduction-abnormalities-in-patients-with-isolated-bicuspid-aortic-valve
#2
Arif Arısoy, Kadriye Memiç, Selami Demirelli, Kayıhan Karaman, Fatih Altunkaş, Metin Karayakalı, Yusuf Karavelioğlu, Ataç Çelik
OBJECTIVE: Present study is an evaluation of left atrial (LA) mechanical and conduction function in patients with bicuspid aortic valve (BAV) without significant valve dysfunction, and an investigation of relationship between LA function and aortic elasticity. METHODS: Study population consisted of 34 isolated BAV patients (mean age: 34±13 years) and 29 healthy, age- and sex-matched volunteers (mean age: 30±10 years). LA volume was measured using biplane area-length method and LA active and passive emptying volume and fraction was calculated...
December 2016: Türk Kardiyoloji Derneği Arşivi: Türk Kardiyoloji Derneğinin Yayın Organıdır
https://www.readbyqxmd.com/read/28012628/syneresis-and-rheological-behaviors-of-set-yogurt-containing-green-tea-and-green-coffee-powders
#3
Özge Dönmez, Burçe Ataç Mogol, Vural Gökmen
This study aimed to investigate the effect of added green coffee powder (GCP) and green tea powder (GTP) on syneresis behavior and consistency of set yogurts. Adding GCP (1 or 2%) decreased syneresis rate. It was confirmed that the effect of GTP on the syneresis rate was concentration dependent. In comparison to the control, GTP decreased syneresis rate when it was added at 0.02%, but it caused an increase when added at 2%. No significant difference was observed in the syneresis rates when GTP was added at amounts of 1 and 0...
December 21, 2016: Journal of Dairy Science
https://www.readbyqxmd.com/read/28011773/altre-workflow-for-defining-altered-regulatory-elements-using-chromatin-accessibility-data
#4
Elizabeth Baskin, Rick Farouni, Ewy A Mathé
: : Regulatory elements regulate gene transcription, and their location and accessibility is cell-type specific, particularly for enhancers. Mapping and comparing chromatin accessibility between different cell types may identify mechanisms involved in cellular development and disease progression. To streamline and simplify differential analysis of regulatory elements genome-wide using chromatin accessibility data, such as DNase-seq, ATAC-seq, we developed ALTRE (ALTered Regulatory Elements), an R package and associated R Shiny web app...
December 22, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27996962/an-atlas-of-transcriptional-chromatin-accessibility-and-surface-marker-changes-in-human-mesoderm-development
#5
Pang Wei Koh, Rahul Sinha, Amira A Barkal, Rachel M Morganti, Angela Chen, Irving L Weissman, Lay Teng Ang, Anshul Kundaje, Kyle M Loh
Mesoderm is the developmental precursor to myriad human tissues including bone, heart, and skeletal muscle. Unravelling the molecular events through which these lineages become diversified from one another is integral to developmental biology and understanding changes in cellular fate. To this end, we developed an in vitro system to differentiate human pluripotent stem cells through primitive streak intermediates into paraxial mesoderm and its derivatives (somites, sclerotome, dermomyotome) and separately, into lateral mesoderm and its derivatives (cardiac mesoderm)...
December 20, 2016: Scientific Data
https://www.readbyqxmd.com/read/27993786/defcom-analysis-and-modeling-of-transcription-factor-binding-sites-using-a-motif-centric-genomic-footprinter
#6
Bryan Quach, Terrence S Furey
MOTIVATION: Identifying the locations of transcription factor binding sites is critical for understanding how gene transcription is regulated across different cell types and conditions. Chromatin accessibility experiments such as DNaseI sequencing (DNase-seq) and Assay for Transposase Accessible Chromatin sequencing (ATAC-seq) produce genome-wide data that include distinct "footprint" patterns at binding sites. Nearly all existing computational methods to detect footprints from these data assume that footprint signals are highly homogeneous across footprint sites...
December 19, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27989964/histone-acetylation-of-glucose-induced-thioredoxin-interacting-protein-gene-expression-in-pancreatic-islets
#7
Pradeep Bompada, David Atac, Cheng Luan, Robin Andersson, Judit Domènech Omella, Emilia Ottosson Laakso, Jason Wright, Leif Groop, Yang De Marinis
Thioredoxin-interacting protein (TXNIP) has been shown to be associated with glucose-induced deterioration of pancreatic beta cell function in diabetes. However, whether epigenetic mechanisms contribute to the regulation of TXNIP gene expression by glucose is not clear. Here we studied how glucose exerts its effect on TXNIP gene expression via modulation of histone acetylation marks. To achieve this, we applied clustered regularly interspaced short palindromic repeats/Cas9 (CRISPR/Cas9) to knock out histone acetyltransferase (HAT) p300 in a rat pancreatic beta cell line INS1 832/13...
October 29, 2016: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/27968730/the-functionality-and-evolution-of-eukaryotic-transcriptional-enhancers
#8
A D Buffry, C C Mendes, A P McGregor
Enhancers regulate precise spatial and temporal patterns of gene expression in eukaryotes and, moreover, evolutionary changes in these modular cis-regulatory elements may represent the predominant genetic basis for phenotypic evolution. Here, we review approaches to identify and functionally analyze enhancers and their transcription factor binding sites, including assay for transposable-accessible chromatin-sequencing (ATAC-Seq) and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9, respectively...
2016: Advances in Genetics
https://www.readbyqxmd.com/read/27939672/dynamic-changes-in-chromatin-accessibility-occur-in-cd8-t-cells-responding-to-viral-infection
#9
James P Scott-Browne, Isaac F López-Moyado, Sara Trifari, Victor Wong, Lukas Chavez, Anjana Rao, Renata M Pereira
In response to acute infection, naive CD8(+) T cells expand, differentiate into effector cells, and then contract to a long-lived pool of memory cells after pathogen clearance. During chronic infections or in tumors, CD8(+) T cells acquire an "exhausted" phenotype. Here we present genome-wide comparisons of chromatin accessibility and gene expression from endogenous CD8(+) T cells responding to acute and chronic viral infection using ATAC-seq and RNA-seq techniques. Acquisition of effector, memory, or exhausted phenotypes was associated with stable changes in chromatin accessibility away from the naive T cell state...
December 20, 2016: Immunity
https://www.readbyqxmd.com/read/27936378/genome-wide-identification-of-neuronal-activity-regulated-genes-in-drosophila
#10
Xiao Chen, Reazur Rahman, Fang Guo, Michael Rosbash
Activity-regulated genes (ARGs) are important for neuronal functions like long-term memory and are well-characterized in mammals but poorly studied in other model organisms like Drosophila. Here we stimulated fly neurons with different paradigms and identified ARGs using high-throughput sequencing from brains as well as from sorted neurons: they included a narrow set of circadian neurons as well as dopaminergic neurons. Surprisingly, many ARGs are specific to the stimulation paradigm and very specific to neuron type...
December 9, 2016: ELife
https://www.readbyqxmd.com/read/27911843/impact-of-the-gut-microbiota-on-enhancer-accessibility-in-gut-intraepithelial-lymphocytes
#11
Nicholas P Semenkovich, Joseph D Planer, Philip P Ahern, Nicholas W Griffin, Charles Y Lin, Jeffrey I Gordon
The gut microbiota impacts many aspects of host biology including immune function. One hypothesis is that microbial communities induce epigenetic changes with accompanying alterations in chromatin accessibility, providing a mechanism that allows a community to have sustained host effects even in the face of its structural or functional variation. We used Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) to define chromatin accessibility in predicted enhancer regions of intestinal αβ(+) and γδ(+) intraepithelial lymphocytes purified from germ-free mice, their conventionally raised (CONV-R) counterparts, and mice reared germ free and then colonized with CONV-R gut microbiota at the end of the suckling-weaning transition...
December 20, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27903897/combining-atac-seq-with-nuclei-sorting-for-discovery-of-cis-regulatory-regions-in-plant-genomes
#12
Zefu Lu, Brigitte T Hofmeister, Christopher Vollmers, Rebecca M DuBois, Robert J Schmitz
: Chromatin structure plays a pivotal role in facilitating proper control of gene expression. Transcription factor (TF) binding of cis-elements is often associated with accessible chromatin regions. Therefore, the ability to identify these accessible regions throughout plant genomes will advance understanding of the relationship between TF binding, chromatin status and the regulation of gene expression. Assay for Transposase Accessible Chromatin sequencing (ATAC-seq) is a recently developed technique used to map open chromatin zones in animal genomes...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27900529/effectiveness-of-pit-and-fissure-sealants-bonded-with-different-adhesive-systems-a-prospective-randomized-controlled-trial
#13
Gizem Erbas Unverdi, Stephan Atilla Atac, Zafer Cavit Cehreli
OBJECTIVES: To evaluate and compare the clinical retention of a resin-based fissure sealant placed with an intermediate layer of etch-and-rinse (ER) or self-etch (SE) adhesives. MATERIALS AND METHODS: Two hundred twenty-eight sealants were placed in 57 children with previously unsealed, caries-free permanent first molars, employing a split-mouth design. The teeth were randomized into four groups (n = 57 teeth/groups) according to the adhesive system placed under the tested sealant (Delton FS+; Dentsply)...
November 30, 2016: Clinical Oral Investigations
https://www.readbyqxmd.com/read/27900485/serum-glutathione-peroxidase-xanthine-oxidase-and-superoxide-dismutase-activities-and-malondialdehyde-levels-in-patients-with-parkinson-s-disease
#14
Burcu Gökçe Çokal, Mustafa Yurtdaş, Selda Keskin Güler, Hafize Nalan Güneş, Ceyla Ataç Uçar, Bilal Aytaç, Zahide Esra Durak, Tahir Kurtuluş Yoldaş, İlker Durak, Hikmet Can Çubukçu
Parkinson's disease (PD) is a progressive neurodegenerative disorder characterized by loss of dopaminergic (DA) neurons in the substantia nigra pars compacta (SNpc). Oxidative stress has been hypothesized to play a major role in the development of PD in various studies. This study assessed to investigate oxidative and anti-oxidative status in PD patients. We evaluated oxidant/antioxidant status by measuring serum malondialdehyde (MDA) levels, xanthine oxidase (XO) activities, and activities of antioxidant enzymes, namely, glutathione peroxidase (GSH-Px) and superoxide dismutase (SOD)...
November 30, 2016: Neurological Sciences
https://www.readbyqxmd.com/read/27896813/transcriptional-and-post-transcriptional-regulation-of-histone-variant-h2a-z-during-sea-urchin-development
#15
Mihai Hajdu, Jasmine Calle, Andrea Puno, Aminat Haruna, César Arenas-Mena
Histone variant H2A.Z promotes chromatin accessibility at transcriptional regulatory elements and is developmentally regulated in metazoans. We characterize the transcriptional and post-transcriptional regulation of H2A.Z in the purple sea urchin Strongylocentrotus purpuratus. H2A.Z depletion by antisense translation-blocking morpholino oligonucleotides during early development causes developmental collapse, in agreement with its previously demonstrated general role in transcriptional multipotency. During H2A...
December 2016: Development, Growth & Differentiation
https://www.readbyqxmd.com/read/27895806/genome-wide-epigenomic-profiling-for-biomarker-discovery
#16
REVIEW
René A M Dirks, Hendrik G Stunnenberg, Hendrik Marks
A myriad of diseases is caused or characterized by alteration of epigenetic patterns, including changes in DNA methylation, post-translational histone modifications, or chromatin structure. These changes of the epigenome represent a highly interesting layer of information for disease stratification and for personalized medicine. Traditionally, epigenomic profiling required large amounts of cells, which are rarely available with clinical samples. Also, the cellular heterogeneity complicates analysis when profiling clinical samples for unbiased genome-wide biomarker discovery...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27888827/excision-of-recurrent-synovial-sarcoma-of-the-infratemporal-fossa
#17
Fakih Cihat Eravcı, Mehmet Düzlü, Mehmet Ekrem Zorlu, Metin Yılmaz, Mustafa Sancar Ataç
Synovial sarcoma is a soft tissue sarcoma especially encountered in the lower extremities. The infratemporal fossa is quite a rare location. Since it is a closed location, combined approaches and multidisciplinary planning always need to be considered. This case emphasizes the high-grade character of synovial sarcoma, which causes it to recur often. The difficulty of clear surgical margins in the infratemporal fossa adds to synovial sarcoma a second challenging issue. Therefore, the need of complementary therapy is essential...
September 2016: Kulak Burun Boğaz Ihtisas Dergisi: KBB, Journal of Ear, Nose, and Throat
https://www.readbyqxmd.com/read/27846204/epigenomics-massive-atac
#18
Joshua M Finkelstein
No abstract text is available yet for this article.
November 15, 2016: Nature Chemical Biology
https://www.readbyqxmd.com/read/27837368/comparison-of-neutrophil-lymphocyte-ratio-nlr-in-parkinson-s-disease-subtypes
#19
Ceyla Ataç Uçar, Burcu Gökçe Çokal, Hanzade Aybüke Ünal Artık, Levent Ertuğrul İnan, Tahir Kurtuluş Yoldaş
It has been hypothesized that chronic inflammation may play an important role in the development and progression of the neurodegeneration of Idiopathic Parkinson's disease (IPD). Neutrophil-lymphocyte ratio (NLR) is a marker that indicates the peripheral inflammation. There is only one study regarding NLR and IPD. In this study, we assessed to investigate NLR in patients with IPD, comparing the results with controls and to determine whether there is a difference in NLR levels in subgroups of IPD (akinetic-rigid and tremor-dominant) differ in their levels of NLR...
November 11, 2016: Neurological Sciences
https://www.readbyqxmd.com/read/27832532/assay-for-transposase-accessible-chromatin-with-high-throughput-sequencing-atac-seq-protocol-for-zebrafish-embryos
#20
Canan Doganli, Melissa Sandoval, Sean Thomas, Daniel Hart
Assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) is a useful method to map genome-wide chromatin accessibility and nucleosome positioning. Genome-wide sequencing is performed utilizing adapter sequences inserted by a prokaryotic transposase, Tn5, into the accessible regions of chromatin. Here we describe the use of ATAC-seq in the zebrafish embryo and thereby the applicability of this approach in whole vertebrate embryos.
2017: Methods in Molecular Biology
keyword
keyword
103503
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"