• Nucleosome positioning and post-translational modifications of chromatin and histone variants can be analyzed using ChIP-seq. (news-medical.net)
  • Sources of the published scRNA-seq or snRNA-seq datasets used in this study are described in Supplementary Table 3 . (nature.com)
  • METHODS: Meta-analysis of scRNA-seq data from VSMC lineage traced cells across five experiments of murine atherosclerosis was performed. (nih.gov)
  • FACS/cell sorting, imaging, ELISA/MSD, western blot/WES, IO-related culture systems, and omics-based approaches such as scRNA-seq) to assess target modulation levels and downstream effects at cellular, protein and gene level. (nih.gov)
  • NOMePlot is a bioinformatic tool that was developed for datasets derived by NOMe-seq. (wikipedia.org)
  • 77 LSVs were confirmed using two large independent B-ALL RNA-seq datasets. (iscb.org)
  • Using multiple datasets, we find evidence of translation for 50-70% of the isoforms quantified with RNA-seq. (iscb.org)
  • In vivo expression profiles were compared to three in vitro datasets of VSMCs loaded with cholesterol and three datasets of polarized macrophages. (nih.gov)
  • They recently developed a method called Tuba-seq, which quantitatively measures the effect of different tumor suppressor gene alterations in parallel using tumor barcoding coupled with high-throughput barcode sequencing. (genomeweb.com)
  • As the cost of high-throughput sequencing technologies decreases, genome-wide chromatin accessibility profiling methods such as the assay of transposase-accessible chromatin using sequencing (ATAC-seq) are employed widely, with data accumulating at an unprecedented rate. (nih.gov)
  • In addition, the in vivo transcriptional effect of butyrate on the transcriptome of the rumen epithelium was quantified via serial biopsy sampling using high-throughput RNA-seq technology and bioinformatic tools. (usda.gov)
  • To understand the transcriptional changes that take place during the differentiation process, high-throughput RNA-Seq of newborn mouse lens epithelial cells and lens fiber cells was conducted to comprehensively compare the transcriptomes of these two cell types. (molvis.org)
  • These technologies can delineate single-cell gene expression and changes across thousands of cells in parallel, using high multiplex CRISPR screens and Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq), a method for mapping chromatin accessibility genome-wide. (nih.gov)
  • Advanced topics include single-neuron isolation and analysis, in vivo gene delivery and imaging, optogenetics, RNA interference, transgenic technologies, high-throughput analysis of gene expression (e.g. (cshlpress.com)
  • Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput. (cdc.gov)
  • To non-invasively investigate the response of the intestinal epithelium to changes in diet, we are proposing to use RNA-Seq to analyze the "exfoliome", i.e., the transcriptome of exfoliated epithelial cells excreted in feces. (nih.gov)
  • 2) to apply RNA-Seq to evaluate the feasibility of characterizing the transcriptome of exfoliated enterocytes from pigs fed control and test diet. (nih.gov)
  • Transcriptome comparisons between in vivo and in vitro states underscored that data from three in vitro cholesterol-treated VSMC experiments did not mirror cell state transitions observed in vivo. (nih.gov)
  • we capture the transcriptome of the first functional HSCs in mouse by single-cell RNA-seq, index sorting, and in vivo and in vitro haematopoietic analyses. (ed.ac.uk)
  • The transcriptome was analyzed by RNA-seq. (bvsalud.org)
  • GpC is found in all GCH trinucleotides Call for NDRs Perform Quality Analysis of methylation and NDRs identification: Visualization of methylation levels High resolution[citation needed] Identifies regulatory elements without needing to understand nucleosome modifications (in comparison to CHIP-seq)[citation needed] Greater depth regarding the position of nucleosomes (comparison to DNase-seq, FAIRE-seq, and ATAC-seq. (wikipedia.org)
  • ChIP-chip techniques cost around 400-800 USD per array, in comparison to ChIP-seq costs 1,000-2,000 USD per lane (for one such next generation platform). (news-medical.net)
  • NOMe-seq has the additional benefit of providing DNA methylation status, which also plays a crucial role in the regulation of genomic activity. (wikipedia.org)
  • Correspondingly, ChIP-Seq analysis identified unique ER-Y537S and ER-D538G genomic binding sites, and ATAC-Seq analysis showed that the mutants alter chromatin accessibility in distinct loci. (aacrjournals.org)
  • Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is the most popular assay to identify genomic regions, called ChIP-seq peaks, that are bound in vivo by transcription factors (TFs). (nih.gov)
  • We are currently using genomic approaches including RNA-seq and CUT&TAG to dissect the underlying mechanism. (nih.gov)
  • ChIP-seq, or chromatin immunoprecipitation and sequencing, is a technique that allows researchers to understand transcriptional regulation via mapping of protein-DNA interactions and epigenetic markers on a genome-wide scale. (news-medical.net)
  • Here, we present the first application of RNA-Seq to understand the transcriptional changes underlying the differentiation of epithelial cells into fiber cells in the newborn mouse lens. (molvis.org)
  • RNA-Seq analysis revealed mutant-specific transcriptional programs. (aacrjournals.org)
  • A computationally inspired in-vivo approach identifies a link between amygdalar transcriptional heterogeneity, socialization and anxiety. (harvard.edu)
  • This leads to them being obscured in ChIP-chip, but not ChIP-seq, experiments. (news-medical.net)
  • for ChIP-seq experiments, Villus epithelium were isolated by incubating dissected jejunm tissues with 15mm EDTA and then mechanical disruption with gentle vortexing. (nih.gov)
  • Our results show that despite longstanding host association, gut bacterial interactions can be recapitulated in vitro providing insights about bacterial coexistence when combined with in vivo experiments. (elifesciences.org)
  • d) Nonclinical laboratory study means in vivo or in vitro experiments in which test articles are studied prospectively in test systems under laboratory conditions to determine their safety. (nih.gov)
  • The NOMe-seq assay was subsequently developed, with the earliest mention being in 2011 and an in depth description published in 2012. (wikipedia.org)
  • Here we introduce an assay termed cross-link (XL)-DNase-seq, designed to capture chromatin interactions of dynamic TFs. (nih.gov)
  • Promoter activity was determined by chromatin immunoprecipitation-seq against Arid3a and a luciferase reporter assay. (bvsalud.org)
  • Tuba-seq combines genetically engineered mouse models of lung adenocarcinoma with CRISPR-Cas9-mediated tumor suppressor inactivation, tumor barcoding, and deep sequencing of DNA barcodes. (genomeweb.com)
  • 2013). We have led the field in development of unbiased, genome-wide strategies for profiling the specificities of CRISPR-Cas nucleases including the widely used cell-based GUIDE-seq method (Tsai et al. (massgeneral.org)
  • CRISPR/Cas9 system can cause hundreds of non-intended dsDNA breaks due to low specificity of the guide RNA, which can limit therapeutic applications of CRISPR/Cas9 by ex-vivo formats. (thno.org)
  • Performs integrative phenotyping of health and function across multiple domains in aging rodents by leveraging long-standing expertise in conducting sophisticated in vivo metabolic studies, hormonal assays, and specialized surgeries, including parabiosis, as well as newly added services, including geropathology, behavior, and cardiovascular function. (nih.gov)
  • Knowledgeable of secondary ex vivo cell-based assays across various technology platforms (e.g. (nih.gov)
  • In this time frame multiple in vivo immune assays have been developed for zebrafish larvae that possess an intact innate immune response but do not yet possess a functional adaptive immune response. (nih.gov)
  • These in vivo assays include (1) assessing the ability of larvae to recover from experimental infections, (2) quantifying the release reactive oxygen species after immune stimulation, (3) visualizing leukocyte chemotaxis and (4) quantifying NFkB activation. (nih.gov)
  • Our lab is developing methodologies for incorporating these in vivo immune assays into low- to medium-throughput immunotoxicity screens. (nih.gov)
  • The technique has since been adapted for single cell technologies, with single cell NOMe-seq (scNOMe-seq) described in 2017 and NOMe-seq using nanopore sequencing (nanoNOMe) described in 2020. (wikipedia.org)
  • 2017). We have recently shown that CIRCLE-seq can be used to identify Cas9-induced off-targets in vivo (Akcakaya & Bobbin et al. (massgeneral.org)
  • Fig. 2: snRNA-seq analysis of human imGCs across ages. (nature.com)
  • The Ped-In Vivo-TP Awardees will work closely with the Ped-In Vivo-TP Coordinating Center in the testing of agents and in the analysis and reporting of testing results. (nih.gov)
  • RNA-Seq analysis provided a comprehensive view of the relative abundance and differential expression of protein-coding and non-coding transcripts from lens epithelial cells and lens fiber cells. (molvis.org)
  • Supporting Single Cell RNA-seq Analysis at Harvard - A Community Approach. (harvard.edu)
  • Additionally, we performed differential splicing analysis between glia and glioma samples from human and mouse and found consistent changes occurring in both RNA-seq and Ribo-seq for the majority of cases, indicating that changes in the relative abundance of transcript isoforms lead to changes in the production of protein isoforms in the same direction. (iscb.org)
  • A Computational Pipeline for Cross-Species Analysis of RNA-seq Data Using R and Bioconductor. (rit.edu)
  • While it presents new opportunities for research, ChIP-Seq poses new challenges for statistical analysis that derive from the complexity of the biological systems characterized and the variability and biases in its digital sequence data. (bioconductor.org)
  • Our approach paves the path towards in vivo, quantitative, reference sequence-free analysis of mtDNA transcription in all eukaryotes. (biorxiv.org)
  • We employ a broad range of complementary experimental strategies to deeply interrogate the TME including the comprehensive analysis of patient samples (RNA-seq, proteomics, immune phenotyping, single cell analyses etc), 3D co-culture systems to mimic the TME, mouse models of cancer, multi-modal in vivo imaging platforms, and diverse computational analyses. (unil.ch)
  • The snRNA-seq data are available at the Gene Expression Omnibus database under accession numbers GSE185553 , GSE185277 and GSE198323 . (nature.com)
  • The purpose of the NCI Pediatric in Vivo Testing Program (Ped-In Vivo-TP) will be to generate, analyze, and disseminate preclinical data using genomically characterized in vivo models to help inform the development of new and more effective treatments for children with cancer. (nih.gov)
  • Because ChIP-seq makes use of antibodies in immunoprecipitation, the quality of the data relies on the quality of the antibody. (news-medical.net)
  • RNA-Seq results were compared with previously published microarray data. (molvis.org)
  • We found that RNA-Seq identified more differentially expressed genes and correlated with RT-qPCR quantification better than previously published microarray data. (molvis.org)
  • 11. Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. (nih.gov)
  • A systematic and integrative survey of RNA‑seq data from The Cancer Genome Atlas (TCGA) was performed to identify candidate lncRNAs for the prognosis of LUAD. (spandidos-publications.com)
  • To assess the quality of the exfoliome, we will compare exfoliome RNA-Seq data with RNASeq data obtained from epithelial cells collected directly from different GI organs after the animal has been sacrificed. (nih.gov)
  • 4% of the human genome, obtained by uniformly processing 1983 ChIP-seq peak data sets from the ReMap database for 232 unique TFs. (nih.gov)
  • The predictions were a posteriori assessed using protein binding microarray and ChIP-exo data, and were predominantly found in high quality ChIP-seq peaks. (nih.gov)
  • In contrast to the in vitro data, comparison between mouse and human in vivo data showed many similarities. (nih.gov)
  • We propose a method called PICS (Probabilistic Inference for ChIP-Seq) for extracting information from ChIP-Seq aligned-read data in order to identify regions bound by transcription factors. (bioconductor.org)
  • Based on the experimental data, we believe that the significant antitumor activities of TMP-A in vivo involve the MAPK and NF-κB signaling pathways because the two signaling pathways intersect. (spandidos-publications.com)
  • First, using bulk RNA-seq data, we derived novel temporal, tolerization CD4+ T cell expression and clonotype evolution signatures using differential expression and VDJ-deconvolution analyses, highlighting significant association with cell cycle and immune activation. (aacrjournals.org)
  • Then, we projected these signatures onto several recently published single-cell RNA-seq data profiling exhausted tumor-infiltrating and peripheral blood lymphocytes, finding reasonable predictive power (AUC~0.8) to classify dysfunctional T-cell states that could distinguish exhaustion from tolerance. (aacrjournals.org)
  • ChIP-seq is intrinsically immune to such sources of noise due to the direct sequencing method. (news-medical.net)
  • Hands-on experience and knowledge of humanized models, cell line-derived xenograft models, genetically engineered mouse models, adoptive immune cell transfer models, and/or in vivo genetic delivery platforms. (nih.gov)
  • We previously showed that repeated administration of recombinant tumor antigen vaccines without immunological adjuvant emulates a tolerized-like immune response that cannot be rescued even after in vivo re-challenge with adjuvant. (aacrjournals.org)
  • Our barcoded and multiplexed in vivo genome-editing approach could be easily employed to interrogate these genetic interactions' impacts on therapeutic response, cell signaling, or metastatic progression. (genomeweb.com)
  • Repetitive genome regions, such as heterochromatin or microsatellites, are usually masked out on arrays, but can be analyzed effectively using ChIP-seq. (news-medical.net)
  • We are exploiting massively parallel sequencing technologies to create genome-wide nucleosome maps (MNase-seq) and other chromatin components (ChIP-seq) in budding yeast and mouse cells. (nih.gov)
  • ChIP-Seq, which combines chromatin immunoprecipitation with massively parallel short-read sequencing, can profile in vivo genome-wide transcription factor-DNA association with higher sensitivity, specificity and spatial resolution than ChIP-chip. (bioconductor.org)
  • To benchmark in vitro-derived organoids, we developed a single-cell mRNA sequencing atlas of the human lung from 11.5 to 21 weeks of development, which revealed high degrees of similarity between the in vitro-derived and in vivo airway. (nih.gov)
  • single-cell RNA-seq. (nih.gov)
  • We used bulk and single-cell RNA-seq of purified antigen-specific CD4+ T-cells (i.e., the orchestrator of immunity) from 12 ovarian and non-small cell lung cancer patients receiving NY-ESO-1 or MAGE-A3 vaccines with or without adjuvant, over a period of 13 weeks. (aacrjournals.org)
  • Fig. 1: snRNA-seq and immunohistological analyses of imGCs in the human infant hippocampus. (nature.com)
  • In this sense, NOMe-seq consists of two independent methylation analyses that are functionally oppositional. (wikipedia.org)
  • For example, to further develop cancer treatments, it would be useful to understand the differences that arise between individual cells using the scNOMe-seq method. (wikipedia.org)
  • In the present study, in addition to conventional viability assessments, we evaluated the gene expression using RNA-seq to investigate whether the developed bioprinter influenced cell integrity in mouse embryonic stem cells. (nature.com)
  • In short, ChIP-seq involves treating cells with formaldehyde to crosslink binding proteins to DNA in vivo. (news-medical.net)
  • Butyrate is a potent inducer of histone hyper-acetylation in cells and provides an excellent in vitro/in vivo model to study the epigenomic regulation of gene expression induced by histone acetylation. (usda.gov)
  • We performed ChIP-seq on male and female mouse ES cells to determine differences in chromatin status. (springer.com)
  • And using ex vivo explant infection as well as reconstruction infection -- mucosal reconstruction infection, we have shown that HIV can penetrate by two pathway to penetrate the penile tissue, first through the foreskin where HIV target Langerhans cells trans-infect CD4 T cell. (nih.gov)
  • However, current clinical therapies are limited by the number of HSCs available for such transplantations and attempts to expand such cells ex vivo have been unsuccessful. (ed.ac.uk)
  • Cross-species Transcriptomic Comparison of In Vitro and In Vivo Mammalian Neural Cells. (rit.edu)
  • RNA‐seq revealed that treatment of GBM cells with 24OHC suppressed tumour growth through regulation of LXR and SREBP signalling. (uib.no)
  • We also measured PRDX2 expression of non-small cell lung cancer (NSCLC) cells and examined its roles in the proliferation and migration in vitro and in vivo . (hindawi.com)
  • For this study, they used Tuba-seq to systematically analyze pairwise combinations of tumor suppressor alterations in vivo . (genomeweb.com)
  • Mitochondrial DNA (mtDNA) genes are long known to be co-transcribed in polycistrones, yet it remains impossible to study nascent mtDNA transcripts quantitatively in vivo using existing tools. (biorxiv.org)
  • Nucleosome Occupancy and Methylome Sequencing (NOMe-seq) is a genomics technique used to simultaneously detect nucleosome positioning and DNA methylation. (wikipedia.org)
  • NOMe-seq relies on the methyltransferase M.CviPl, which methylates cytosines in GpC dinucleotides unbound by nucleosomes or other proteins, creating a nucleosome footprint. (wikipedia.org)
  • In addition to nucleosome foot-printing, NOMe-seq can determine locations bound by transcription factors. (wikipedia.org)
  • After its discovery, the methyltransferase was used for nucleosome foot-printing as early as 2004, but NOMe-seq was not officially described until 2012. (wikipedia.org)
  • ChIP-seq generates a more precise list of protein binding sites and targets of transcription factors, enhancers, and identification of sequence motifs. (news-medical.net)
  • In vivo , active gene promoters and enhancers are occupied by sequence-specific transcription factors and associated proteins. (nih.gov)
  • To this end we used deep sequencing (GRO-seq and PRO-seq) and analyzed nascent mtDNA-encoded RNA transcripts in diverse human cell lines and metazoan organisms. (biorxiv.org)
  • These obstacles interfered with comparative in-vivo investigation of mtDNA transcription in diverse conditions, and hampered expanding the study of mtDNA nascent transcripts to organisms lacking an mtDNA reference sequence. (biorxiv.org)
  • nanoNOMe is a method that was adapted from NOMe-seq that uses nanopore sequencing instead of bisulfite sequencing. (wikipedia.org)
  • ChIP-seq was one of the first applications of next generation sequencing, which was developed in the mid-2000s. (news-medical.net)
  • ChIP-seq, using next generation sequencing, can directly sequence the target fragments rather than hybridizing them on arrays. (news-medical.net)
  • We analyzed in vitro differential expression of genes induced by butyrate and the effect of butyrate on alternative splicing induced by butyrate in the bovine epithelial cell in vitro using deep RNA-sequencing technology (RNA-seq). (usda.gov)
  • In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes. (neurotree.org)
  • However, as mtDNA transcription was mostly studied in vitro, little remains known about the mode and tempo of in vivo OXPHOS genes' transcription residing on the mtDNA. (biorxiv.org)
  • ChIP-seq has several advantages over previous methods, such as ChIP-chip, but like all techniques, ChIP-seq has its limitations. (news-medical.net)
  • ChIP-seq has improved resolution compared to other methods. (news-medical.net)
  • Delineating the bona fide direct TF-DNA interactions within the ChIP-seq peaks remains challenging. (nih.gov)
  • We developed a dedicated software, ChIP-eat, that combines computational TF binding models and ChIP-seq peaks to automatically predict direct TF-DNA interactions. (nih.gov)
  • Although the four species engaged in negative interactions, they were able to stably coexist, both in vivo and in vitro. (elifesciences.org)
  • If it transcribes, we can sequence it: mining the complexities of host-pathogen-environment interactions using RNA-seq. (cdc.gov)
  • Both mutants enhanced endometrial cancer cell proliferation in vivo , and ER-Y537S enhanced tumor growth and metastasis in a mouse model as well. (aacrjournals.org)
  • We constructed tumor growth model using subcutaneously injection of nude mice and metastasis model by tail vein injection in vivo . (hindawi.com)
  • Silencing PRDX2 restrained tumor growth and repressed lung metastasis by EMT in vivo . (hindawi.com)
  • The Research Teams of the Ped-In Vivo-TP will determine the activity of pediatric anticancer drug candidates using preclinical models relevant to the cancer(s) on which their team focuses (supported under this FOA) and will work in concert with the Ped-In Vivo-TP Coordinating Center (supported under RFA-CA-20-041). (nih.gov)
  • With A/Prof Kim Bell-Anderson (Charles Perkins Centre), we have uncovered striking cardiac enlargement in in vivo models of pregnancy during ingestion of diets enriched with sucrose or fructose (compared to glucose and normal chow). (hri.org.au)
  • To further explore this, we are performing RNA seq in these in vivo models. (hri.org.au)
  • Further, we are generating knockout mouse models or embryo aggregation to test whether the deletion can promote PGC specification in vivo. (nih.gov)
  • This has been found to produce similar results as NOMe-seq when using bulk samples of human cell cultures. (wikipedia.org)
  • Ectopic expression of CYP46A1 suppressed cell proliferation and in vivo tumour growth by increasing 24OHC levels. (uib.no)
  • Extensive experience with T cell exhaustion, CAR-T, and in vivo targeted gene delivery. (nih.gov)
  • Approaches that use RNA marker dependent (conditional) activation of OGT agents may improve specificity but require additional validation in cell culture and in vivo . (thno.org)
  • The peaks in the profiles generated by ChIP-seq need to be compared to the same loci in a control sample to ascertain the significance of the peak. (news-medical.net)
  • oxLDL loaded macrophages showed the most similarity to in vivo states. (nih.gov)
  • Because Tuba-seq measures the size of every tumor and is compatible with multiplexing tumor genotypes in individual mice, growth effects can be measured with unprecedented precision, sensitivity, and throughput," the researchers explained. (genomeweb.com)
  • Efavirenz, an activator of CYP46A1 that is known to penetrate the blood-brain barrier, inhibited GBM growth in vivo. (uib.no)
  • RNA-Seq), and constructing and imaging fluorescent proteins. (cshlpress.com)
  • Targeting Mertk in vivo effectively reversed the protective phenotype of Arid3a deficiency in macrophages. (bvsalud.org)
  • August 31, 2020 - Pre-Application Webinar for NCI Pediatric In Vivo Testing Program and NCI Pediatric In Vivo Testing Program Coordinating Center (RFA-CA-20-034, RFA-CA-20-041). (nih.gov)
  • Bypassing the hybridization process has additional benefits for ChIP-seq. (news-medical.net)
  • Alternative DNA accessibility techniques include MNase-seq, DNase-seq, FAIRE-seq, and their successor ATAC-seq. (wikipedia.org)
  • The researchers were able to encode RNA-seq reads using 3% - 11% of the space of the sequence in raw FASTA files, which is on average more than 34% smaller than competing approaches. (rna-seqblog.com)
  • Finally, mtDNA transcription termination sites have been either mapped in-vitro, or were associated with MTERF binding sites ( Christianson and Clayton 1986 ), thus, again, limiting the capability to in-vivo map transcription terminations sites in diverse organisms. (biorxiv.org)
  • We describe a new pipeline for the quantification of individual transcript coding sequences from ribosome profiling using both RNA-seq and Ribo-seq. (iscb.org)