Cusanovich et al. 2015

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August undefined, 2024

WebReading Cusanovich et al. (2015) I encountered the sentence: We mixed pairs of cell lines (HEK293T or HL-60 versus GM12878), performed combinatorial cellular indexing, and sequenced the resulting ... Cusanovich, D. A. et al. Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing. Science 348, 910–914 ... WebJun 30, 2015 · Cusanovich, D.A. et al. Science 348 , 910–914 (2015). The accessibility of chromatin to regulatory proteins provides an important layer of gene expression control, …

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WebJul 22, 2024 · seq (Chen et al., 2024; Cusanovich et al., 2015; Lareau et al., 2024) which assesses regions of open chromatin. There are existing tools publicly available to analyze scATAC-seq such as chromVar (Schep et al., 2024), Cicero (Pliner et al., 2024) or Scasat (Baker et al., 2024). However these tools are dedicated to scATAC-seq and are not … Web2015), and ChIP-seq (Rotem et al., 2015). Interpretation of these data in single cells is complicated because of the near binary and extremely sparse signal (Cusanovich et al., 2015; Buenrostro et ... guildford to redhill train

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Web2012; Buenrostro et al, 2015; Cusanovich et al, 2015). Early scRNA/ snATAC-seq workflows were limited to analyzing tens to hundreds of individual cells at a time. With the latest development of single-cell sequencing technologies based on microwells (Gierahn et al, 2024), combinatorial indexing (Cusanovich et al, 2015; Cao et al, WebJan 1, 2024 · To reduce dimension, the resulting feature-by-cell matrix is processed by singular value decomposition, which generates a Latent Semantic Indexing (LSI) score … WebFrom a single tagmentation event, adapters are incorporated in an outward-facing manner; thus, in order to form a viable sequencing library molecule, a second tagmentation event must have been completed successfully nearby (i.e., within a length suitable for PCR and sequencing, typically <1000 bp). guildford to pagham

A Single-Cell Atlas of In Vivo Mammalian Chromatin …

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WebApr 6, 2024 · Combinatorial sample indexing allows more samples to be indexed with limited number of barcodes and, therefore, to increase indexing capacity in a cost-effective way (Cusanovich et al, 2015; Cao et al, 2024; Cao et al, 2024; Cao et al, 2024). Commonly used strategies include simultaneous combinatorial indexing and sequential split-pool … WebDec 5, 2024 · Single-cell transcriptomic technologies have emerged as powerful tools to explore cellular heterogeneity at the resolution of individual cells. Srivatsan et al. now … bourla bookWebTo generate these data we have used a technique we developed called sci-ATAC-seq (Cusanovich et al., Science 2015). sci-ATAC-seq uses a paradigm called combinatorial … bourla last name origin

"WebAug 21, 2015 · Overall Cusanovich et al. obtained scATAC-seq data from over 15,000 individual cells from mixtures of GM12878 lymphoblastoid cells with HEK293, HL-60, or … " - Cusanovich et al. 2015

Cusanovich et al. 2015

WebWelcome RNA Journal Club WebAug 30, 2024 · Cusanovich DA et al., Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing. Science. 348, 910–914 (2015). [Europe PMC free article] [Google Scholar] 9. Ramani V ... 31, 166–169 (2015). [Europe PMC free article] [Google Scholar] 35.

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WebNov 3, 2015 · Genome-Wide Association Studies of the Human Gut Microbiota The bacterial composition of the human fecal microbiome is influenced by many lifestyle factors, notably diet. It is less clear, however, what role host genetics plays in dictating the composition of bacteria living in the gut. WebJun 6, 2024 · In 2015, Cusanovich et al. developed sci-ATAC-seq based on the SCI strategy ( Cusanovich et al., 2015 ). The initial version of sci-ATAC-seq analyzed hundreds of cells, and the median reads per cell were only 2.5 × 10 3. However, the theoretical barcode combination of sci-ATAC-seq is sufficient for tens of thousands of single nuclei.

WebMay 7, 2015 · Cusanovitch et al. skirted previously identified technological limitations to identify regions of accessible chromatin at single-cell resolution. Combinatorial cellular … WebPLoS Genetics (2015) PMID: 26230489 ... Cusanovich et al. Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing. Science (2015) PMID: 25953818 (with Trapnell Lab) PDF. O'Roak, Stessman et al. Recurrent de novo mutations implicate novel genes underlying simplex autism risk. Nature Communications (2014)

WebApr 20, 2015 · 2015 Apr 20;9:129. doi: 10.3389/fnins.2015.00129. eCollection 2015. Authors Rosario Pivonello 1 , Chiara Simeoli 1 , Maria Cristina De Martino 1 , Alessia Cozzolino 1 …

WebAug 23, 2024 · Cusanovich et al., 2015). The total number of cells profiled per tissue (after further filtering detailed below) ranged from 2,278 for cerebellum to 9,996 for lung (Figure …

WebNov 10, 2024 · Signac enables an end-to-end analysis of single-cell chromatin data, including peak calling, quantification, quality control, dimension reduction, clustering, integration with single-cell gene... bourla antwerpen brunchWebMar 28, 2024 · These experimental factors make it challenging to analyze single-cell genomic data, and they can impact the result and interpretation of unsupervised learning methods, including dimension reduc- tion and clustering (Jaitin et al., 2014; Usoskin et al., 2015; Lafon and Lee, 2006; Vandermaaten, 2008). guildford to redhill busWebFeb 7, 2024 · technology has advanced and has become commercially available (Cusanovich et al. 2015), opening a window to understand the dynamics of chromatin at … bourla foyerWebJul 10, 2024 · ATAC-seq methods have also been used for single cells ( Buenrostro et al., 2015, Cusanovich et al., 2015 ). Using the genome-wide approaches, dynamic changes in chromatin accessibility have been investigated when transcription patterns of somatic cells are reprogrammed in induced pluripotent stem (iPS) cells. guildford to redruthWebMay 5, 2024 · single-cell ATAC-seq (Buenrostro et al., 2024; Cusanovich et al., 2015). The established ATAC-seq protocol was developed using peripheral blood samples (Buenrostro et al., 2013), and many studies using ATAC-seq focus on mammalian or human-derived tissues (Bysani et al., 2024; Davie et al., 2015; Liu et al., 2024). Recent bourland airparkWebAug 2, 2024 · With ~3.9 billion read pairs, we identified 104,039 cells, with ~12% of these being likely doublets or ‘collisions’ ( Cusanovich et al., 2015 ). The total number of cells profiled per tissue (after further filtering detailed below) ranged from 2,278 for cerebellum to 9,996 for lung ( Fig. 1C ). bourla biontechWebFeb 1, 2024 · In one study, a sciATAC-seq (single-cell combinatorial indexed ATAC-seq) assay was used in a combinatorial tagging strategy ( Cusanovich et al., 2015 ). Here, thousands of nuclei were first separated into a 96-well plate in which ATAC-seq was performed with barcoded transposase complexes. guildford to reading