Single-cell ATAC sequencing analysis: From data preprocessing to hypothesis generation
Computational and Structural Biotechnology Journal, 2020 Most genetic variations associated with human complex traits are located in non-coding genomic regions. Therefore, understanding the genotype-to-phenotype axis requires a comprehensive catalog of functional non-coding genomic elements, most of which are ...
Seungbyn Baek, Insuk Lee
doaj +1 more source
One read per cell per gene is optimal for single-cell RNA-Seq [PDF]
, 2018 An underlying question for virtually all single-cell RNA sequencing experiments is how to allocate the limited sequencing budget: deep sequencing of a few cells or shallow sequencing of many cells?
Ntranos, V., Tse, D., Zhang, M. J.
core
Transgene silencing and transgene-derived siRNA production in tobacco plants homozygous for an introduced AtMYB90 construct [PDF]
, 2015 Transgenic tobacco (Nicotiana tabacum) lines were engineered to ectopically over-express AtMYB90 (PAP2), an R2-R3 Myb gene associated with regulation of anthocyanin production in Arabidopsis thaliana. Independently transformed transgenic lines, Myb27 and
Cakir, Cahid +4 more
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Molecular Oncology, EarlyView.Combining PTEN protein assessment and transcriptomic profiling of prostate tumors, we uncovered a network enriched in senescence and extracellular matrix (ECM) programs associated with PTEN loss and conserved in a mouse model. We show that PTEN‐deficient cells trigger paracrine remodeling of the surrounding stroma and this information could help ...
Ivana Rondon‐Lorefice +16 more
wiley +1 more source
, 2016 Cataloging the neuronal cell types that comprise circuitry of individual brain regions is a major goal of modern neuroscience and the BRAIN initiative.
Anandkumar, Animashree +8 more
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Transcriptome analyses reveal reduced hepatic lipid synthesis and accumulation in more feed efficient beef cattle [PDF]
, 2018 peer-reviewedThe genetic mechanisms controlling residual feed intake (RFI) in beef cattle are still largely unknown. Here we performed whole transcriptome analyses to identify differentially expressed (DE) genes and their functional roles in liver ...
Fitzsimmons, Carolyn +6 more
core +3 more sources
Cell surface interactome analysis identifies TSPAN4 as a negative regulator of PD‐L1 in melanoma
Molecular Oncology, EarlyView.Using cell surface proximity biotinylation, we identified tetraspanin TSPAN4 within the PD‐L1 interactome of melanoma cells. TSPAN4 negatively regulates PD‐L1 expression and lateral mobility by limiting its interaction with CMTM6 and promoting PD‐L1 degradation.
Guus A. Franken +7 more
wiley +1 more source
Plecstatin inhibits hepatocellular carcinoma tumorigenesis and invasion through cytolinker plectin
Molecular Oncology, EarlyView.The ruthenium‐based metallodrug plecstatin exerts its anticancer effect in hepatocellular carcinoma (HCC) primarily through selective targeting of plectin. By disrupting plectin‐mediated cytoskeletal organization, plecstatin inhibits anchorage‐dependent growth, cell polarization, and tumor cell dissemination.
Zuzana Outla +10 more
wiley +1 more source
Extracellular RNA in a single droplet of human serum reflects physiologic and disease states. [PDF]
, 2019 Extracellular RNAs (exRNAs) are present in human serum. It remains unclear to what extent these circulating exRNAs may reflect human physiologic and disease states. Here, we developed SILVER-seq (Small Input Liquid Volume Extracellular RNA Sequencing) to
Calandrelli, Riccardo +11 more
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A computational method for estimating the PCR duplication rate in DNA and RNA-seq experiments. [PDF]
, 2017 BackgroundPCR amplification is an important step in the preparation of DNA sequencing libraries prior to high-throughput sequencing. PCR amplification introduces redundant reads in the sequence data and estimating the PCR duplication rate is important to
Bansal, Vikas
core +2 more sources