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Tytuł:
Titration-based normalization of antibody amount improves consistency of ChIP-seq experiments.
Autorzy:
Caride A; Epigenomics Development Laboratory, Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Stabile Building 12-04, 200 First Street SW, Rochester, MN, USA.
Jang JS; Medical Genome Facility, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.
Shi GX; Epigenomics Development Laboratory, Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Stabile Building 12-04, 200 First Street SW, Rochester, MN, USA.
Lenz S; Epigenomics Development Laboratory, Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Stabile Building 12-04, 200 First Street SW, Rochester, MN, USA.
Zhong J; Epigenomics Development Laboratory, Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Stabile Building 12-04, 200 First Street SW, Rochester, MN, USA.
Kim KH; Epigenomics Development Laboratory, Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Stabile Building 12-04, 200 First Street SW, Rochester, MN, USA.
Allen M; Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.
Robertson KD; Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA.
Farrugia G; Enteric Neuroscience Program, Mayo Clinic, Rochester, MN, USA.
Ordog T; Epigenomics Development Laboratory, Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Stabile Building 12-04, 200 First Street SW, Rochester, MN, USA.; Enteric Neuroscience Program, Mayo Clinic, Rochester, MN, USA.; Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA.; Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN, USA.
Ertekin-Taner N; Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.; Department of Neurology, Mayo Clinic, Jacksonville, FL, USA.
Lee JH; Epigenomics Development Laboratory, Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Stabile Building 12-04, 200 First Street SW, Rochester, MN, USA. .; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA. .; Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA. .
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Źródło:
BMC genomics [BMC Genomics] 2023 Apr 04; Vol. 24 (1), pp. 171. Date of Electronic Publication: 2023 Apr 04.
Typ publikacji:
Journal Article
MeSH Terms:
Chromatin Immunoprecipitation Sequencing*/methods
Histones*/genetics
Chromatin Immunoprecipitation/methods ; Chromatin ; Antibodies
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
xcore: an R package for inference of gene expression regulators.
Autorzy:
Migdał M; Laboratory of Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.
Arakawa T; RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan.
Takizawa S; RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan.
Furuno M; RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan.
Suzuki H; RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan.
Arner E; RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan.; GSK, Gunnels Wood Rd, Stevenage, SG1 2NY, UK.
Winata CL; Laboratory of Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland. .
Kaczkowski B; RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan. .; Data Sciences and Quantitative Biology, Discovery Sciences, AstraZeneca R&D, Cambridge, UK. .
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Źródło:
BMC bioinformatics [BMC Bioinformatics] 2023 Jan 11; Vol. 24 (1), pp. 14. Date of Electronic Publication: 2023 Jan 11.
Typ publikacji:
Journal Article
MeSH Terms:
Transcription Factors*/genetics
Transcription Factors*/metabolism
Chromatin Immunoprecipitation Sequencing*
Animals ; Chromatin Immunoprecipitation/methods ; Protein Binding ; Gene Expression ; Binding Sites
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Web-MCOT Server for Motif Co-Occurrence Search in ChIP-Seq Data.
Autorzy:
Levitsky VG; Department of System Biology, Institute of Cytology and Genetics, 630090 Novosibirsk, Russia.; Department of Natural Science, Novosibirsk State University, 630090 Novosibirsk, Russia.
Mukhin AM; Department of System Biology, Institute of Cytology and Genetics, 630090 Novosibirsk, Russia.
Oshchepkov DY; Department of System Biology, Institute of Cytology and Genetics, 630090 Novosibirsk, Russia.
Zemlyanskaya EV; Department of System Biology, Institute of Cytology and Genetics, 630090 Novosibirsk, Russia.; Department of Natural Science, Novosibirsk State University, 630090 Novosibirsk, Russia.
Lashin SA; Department of System Biology, Institute of Cytology and Genetics, 630090 Novosibirsk, Russia.; Department of Natural Science, Novosibirsk State University, 630090 Novosibirsk, Russia.
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Źródło:
International journal of molecular sciences [Int J Mol Sci] 2022 Aug 11; Vol. 23 (16). Date of Electronic Publication: 2022 Aug 11.
Typ publikacji:
Journal Article
MeSH Terms:
Chromatin Immunoprecipitation Sequencing*
Transcription Factors*/genetics
Binding Sites ; Chromatin Immunoprecipitation/methods
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Virtual ChIP-seq: predicting transcription factor binding by learning from the transcriptome.
Autorzy:
Karimzadeh M; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.; Princess Margaret Cancer Centre, Toronto, ON, Canada.; Vector Institute, Toronto, ON, Canada.
Hoffman MM; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada. .; Princess Margaret Cancer Centre, Toronto, ON, Canada. .; Vector Institute, Toronto, ON, Canada. .; Department of Computer Science, University of Toronto, Toronto, ON, Canada. .
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Źródło:
Genome biology [Genome Biol] 2022 Jun 10; Vol. 23 (1), pp. 126. Date of Electronic Publication: 2022 Jun 10.
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:
Chromatin Immunoprecipitation Sequencing*
Transcriptome*
Binding Sites ; Chromatin Immunoprecipitation ; Protein Binding ; Transcription Factors/metabolism
Czasopismo naukowe
Szczegóły
Tytuł:
Comprehensive assessment of differential ChIP-seq tools guides optimal algorithm selection.
Autorzy:
Eder T; Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria.
Grebien F; Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria. .
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Źródło:
Genome biology [Genome Biol] 2022 May 24; Vol. 23 (1), pp. 119. Date of Electronic Publication: 2022 May 24.
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:
Algorithms*
Chromatin Immunoprecipitation Sequencing*
Chromatin Immunoprecipitation ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; Software
Czasopismo naukowe
Szczegóły
Tytuł:
Novel ZNF414 activity characterized by integrative analysis of ChIP-exo, ATAC-seq and RNA-seq data.
Autorzy:
Rodriguez-Martinez A; Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Tays Cancer Center, Tampere University Hospital, Tampere, Finland; BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland. Electronic address: .
Vuorinen EM; Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Tays Cancer Center, Tampere University Hospital, Tampere, Finland; BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
Shcherban A; Tays Cancer Center, Tampere University Hospital, Tampere, Finland; BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.
Uusi-Mäkelä J; Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Tays Cancer Center, Tampere University Hospital, Tampere, Finland; BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
Rajala NKM; BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
Nykter M; Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Tays Cancer Center, Tampere University Hospital, Tampere, Finland; BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
Kallioniemi A; Tays Cancer Center, Tampere University Hospital, Tampere, Finland; BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Fimlab Laboratories, Tampere, Finland.
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Źródło:
Biochimica et biophysica acta. Gene regulatory mechanisms [Biochim Biophys Acta Gene Regul Mech] 2022 Apr; Vol. 1865 (3), pp. 194811. Date of Electronic Publication: 2022 Mar 19.
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:
Chromatin*/genetics
Chromatin Immunoprecipitation Sequencing*
Chromatin Immunoprecipitation ; DNA ; RNA-Seq
Czasopismo naukowe
Szczegóły
Tytuł:
A cell-sorting-based protocol for cell cycle small-scale ChIP sequencing.
Autorzy:
Whetstine JR; Cancer Signaling and Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.; Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
Van Rechem C; Stanford Medicine Department of Pathology, Stanford, CA 94305, USA.
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Źródło:
STAR protocols [STAR Protoc] 2022 Mar 15; Vol. 3 (2), pp. 101243. Date of Electronic Publication: 2022 Mar 15 (Print Publication: 2022).
Typ publikacji:
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
MeSH Terms:
Chromatin*/genetics
Chromatin Immunoprecipitation Sequencing*
Cell Cycle/genetics ; Chromatin Immunoprecipitation/methods ; Histone Code
Czasopismo naukowe
Szczegóły
Tytuł:
ChIP-AP: an integrated analysis pipeline for unbiased ChIP-seq analysis.
Autorzy:
Suryatenggara J; Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.
Yong KJ; Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.
Tenen DE; Broad Institute of MIT and Harvard, Boston, 02142, USA.
Tenen DG; Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.; Harvard Stem Cell Institute, Boston, 02138, USA.
Bassal MA; Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.; Harvard Stem Cell Institute, Boston, 02138, USA.
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Źródło:
Briefings in bioinformatics [Brief Bioinform] 2022 Jan 17; Vol. 23 (1).
Typ publikacji:
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
MeSH Terms:
Chromatin Immunoprecipitation Sequencing*
Oligonucleotide Array Sequence Analysis/*methods
Sequence Analysis, DNA/*methods
Algorithms ; Benchmarking ; Cell Line ; Chromatin Immunoprecipitation ; Software ; Transcription Factors
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Optimization of ATAC-seq in wheat seedling roots using INTACT-isolated nuclei.
Autorzy:
Debernardi JM; University of California, Davis, CA, 95616, USA. .; Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA. .
Burguener G; University of California, Davis, CA, 95616, USA.; Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
Bubb K; Dept. of Biology, University of Washington, Seattle, WA, 98195, USA.
Liu Q; University of California, Davis, CA, 95616, USA.; Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
Queitsch C; Dept. of Biology, University of Washington, Seattle, WA, 98195, USA.
Dubcovsky J; University of California, Davis, CA, 95616, USA. .; Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA. .
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Źródło:
BMC plant biology [BMC Plant Biol] 2023 May 22; Vol. 23 (1), pp. 270. Date of Electronic Publication: 2023 May 22.
Typ publikacji:
Journal Article
MeSH Terms:
Chromatin Immunoprecipitation Sequencing*
Seedlings*/genetics
Triticum/genetics ; Reproducibility of Results ; Tetraploidy ; Chromatin/genetics ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Integration of ATAC-Seq and RNA-Seq reveals FOSL2 drives human liver progenitor-like cell aging by regulating inflammatory factors.
Autorzy:
Ding M; Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.; Department of Interventional Oncology, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, China.
Huang W; Department of Anesthesiology and Critical Care Medicine, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, China.
Liu G; Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
Zhai B; Department of Interventional Oncology, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, China. .; State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China. .
Yan H; Department of Interventional Oncology, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, China. .; Department of Anesthesiology and Critical Care Medicine, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, China. .; Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, China. .
Zhang Y; Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China. .
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Źródło:
BMC genomics [BMC Genomics] 2023 May 13; Vol. 24 (1), pp. 260. Date of Electronic Publication: 2023 May 13.
Typ publikacji:
Journal Article
MeSH Terms:
Cellular Senescence*/genetics
Chromatin*/genetics
Chromatin Immunoprecipitation Sequencing*
Fos-Related Antigen-2*/genetics
Humans ; High-Throughput Nucleotide Sequencing/methods ; Liver ; RNA-Seq
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
An optimized approach for multiplexing single-nuclear ATAC-seq using oligonucleotide-conjugated antibodies.
Autorzy:
Bera BS; Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.; Center for Genetic Medicine, Children's National Medical Center, Washington, DC, USA.
Thompson TV; Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.
Sosa E; Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.
Nomaru H; Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.; Thinkcyte Inc., Tokyo, Japan.
Reynolds D; Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.
Dubin RA; Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.
Maqbool SB; Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.
Zheng D; Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.; Departments of Neurology and Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA.
Morrow BE; Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.
Greally JM; Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.
Suzuki M; Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA. .; Department of Nutrition, Texas A&M University, College Station, TX, USA. .
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Źródło:
Epigenetics & chromatin [Epigenetics Chromatin] 2023 Apr 28; Vol. 16 (1), pp. 14. Date of Electronic Publication: 2023 Apr 28.
Typ publikacji:
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
MeSH Terms:
Chromatin Immunoprecipitation Sequencing*
Cell Nucleus*/genetics
Cell Nucleus*/metabolism
Male ; Female ; Humans ; Animals ; Mice ; Sequence Analysis, DNA/methods ; Chromatin/genetics ; Chromatin/metabolism ; Oligonucleotides/metabolism
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Cellcano: supervised cell type identification for single cell ATAC-seq data.
Autorzy:
Ma W; Department of Computer Science, Emory University, 400 Dowman Drive, Atlanta, GA, 30322, USA.
Lu J; Department of Computer Science, Emory University, 400 Dowman Drive, Atlanta, GA, 30322, USA.
Wu H; Faculty of Computer Science and Control Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen University Town, Shenzhen, 518055, P. R. China. .; Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, 1518 Clifton Road NE, Atlanta, GA, 30322, USA. .
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Źródło:
Nature communications [Nat Commun] 2023 Apr 03; Vol. 14 (1), pp. 1864. Date of Electronic Publication: 2023 Apr 03.
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't; Research Support, N.I.H., Extramural
MeSH Terms:
Chromatin Immunoprecipitation Sequencing*/methods
Chromatin*/genetics
Algorithms ; Epigenomics ; Single-Cell Analysis/methods
Czasopismo naukowe
Szczegóły
Tytuł:
Statistical estimates of multiple transcription factors binding in the model plant genomes based on ChIP-seq data.
Autorzy:
Dergilev AI; Novosibirsk State University, 630090 Novosibirsk, Russia.; Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.
Orlova NG; Financial University under the Government of the Russian Federation, 125993 Moscow, Russia.; Moscow State Technical University of Civil Aviation, 125993 Moscow, Russia.
Dobrovolskaya OB; Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.; Agrarian and Technological Institute, Peoples' Friendship University of Russia, 117198 Moscow, Russia.
Orlov YL; Novosibirsk State University, 630090 Novosibirsk, Russia.; Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.; Agrarian and Technological Institute, Peoples' Friendship University of Russia, 117198 Moscow, Russia.; The Digital Health Institute, I.M.Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia.
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Źródło:
Journal of integrative bioinformatics [J Integr Bioinform] 2021 Dec 21; Vol. 19 (1). Date of Electronic Publication: 2021 Dec 21.
Typ publikacji:
Journal Article
MeSH Terms:
Chromatin Immunoprecipitation Sequencing*
Transcription Factors*/genetics
Transcription Factors*/metabolism
Animals ; Binding Sites/genetics ; Chromatin Immunoprecipitation ; Genome, Plant ; Mammals/genetics ; Mammals/metabolism
Czasopismo naukowe
Szczegóły
Tytuł:
CHIPIN: ChIP-seq inter-sample normalization based on signal invariance across transcriptionally constant genes.
Autorzy:
Polit L; Institut Cochin, Inserm U1016, CNRS UMR 8104, Paris Descartes University UMR-S1016, 75014, Paris, France.
Kerdivel G; Institut Cochin, Inserm U1016, CNRS UMR 8104, Paris Descartes University UMR-S1016, 75014, Paris, France.
Gregoricchio S; INSERM UMR1170, Equipe Labellisée Ligue Nationale Contre Le Cancer, Gustave Roussy, Paris-Saclay University, 94800, Villejuif, France.
Esposito M; INSERM UMR1170, Equipe Labellisée Ligue Nationale Contre Le Cancer, Gustave Roussy, Paris-Saclay University, 94800, Villejuif, France.
Guillouf C; INSERM UMR1170, Equipe Labellisée Ligue Nationale Contre Le Cancer, Gustave Roussy, Paris-Saclay University, 94800, Villejuif, France.
Boeva V; Institut Cochin, Inserm U1016, CNRS UMR 8104, Paris Descartes University UMR-S1016, 75014, Paris, France. .; Department of Computer Science, Institute for Machine Learning, ETH Zurich, 8092, Zurich, Switzerland. .; Swiss Institute for Bioinformatics (SIB), Zürich, Switzerland. .
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Źródło:
BMC bioinformatics [BMC Bioinformatics] 2021 Aug 17; Vol. 22 (1), pp. 407. Date of Electronic Publication: 2021 Aug 17.
Typ publikacji:
Journal Article
MeSH Terms:
Chromatin*
Chromatin Immunoprecipitation Sequencing*
Chromatin Immunoprecipitation ; Protein Binding ; Sequence Analysis, DNA
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
ChIP-R: Assembling reproducible sets of ChIP-seq and ATAC-seq peaks from multiple replicates.
Autorzy:
Newell R; School of Chemistry and Molecular Biosciences, The University of Queensland, Cooper Road, QLD 4072, Australia.
Pienaar R; School of Chemistry and Molecular Biosciences, The University of Queensland, Cooper Road, QLD 4072, Australia.
Balderson B; School of Chemistry and Molecular Biosciences, The University of Queensland, Cooper Road, QLD 4072, Australia.
Piper M; School of Biomedical Science, The University of Queensland, QLD, Australia.
Essebier A; School of Chemistry and Molecular Biosciences, The University of Queensland, Cooper Road, QLD 4072, Australia.
Bodén M; School of Chemistry and Molecular Biosciences, The University of Queensland, Cooper Road, QLD 4072, Australia. Electronic address: .
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Źródło:
Genomics [Genomics] 2021 Jul; Vol. 113 (4), pp. 1855-1866. Date of Electronic Publication: 2021 Apr 18.
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:
Algorithms*
Chromatin Immunoprecipitation Sequencing*
Binding Sites ; Chromatin Immunoprecipitation/methods ; High-Throughput Nucleotide Sequencing/methods ; Reproducibility of Results ; Sequence Analysis, DNA/methods
Czasopismo naukowe
Szczegóły
Tytuł:
In vivo RNA-seq and ChIP-seq analyses show an obligatory role for the C terminus of p53 in conferring tissue-specific radiation sensitivity.
Autorzy:
Resnick-Silverman L; Department of Oncological Sciences and Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Zhou R; Department of Oncological Sciences and Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Campbell MJ; Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy at The Ohio State University, Columbus, OH 43210, USA.
Leibling I; Department of Oncological Sciences and Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Parsons R; Department of Oncological Sciences and Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Manfredi JJ; Department of Oncological Sciences and Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Electronic address: .
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Źródło:
Cell reports [Cell Rep] 2023 Mar 28; Vol. 42 (3), pp. 112216. Date of Electronic Publication: 2023 Mar 15.
Typ publikacji:
Journal Article; Research Support, N.I.H., Extramural
MeSH Terms:
Tumor Suppressor Protein p53*/metabolism
Chromatin Immunoprecipitation Sequencing*
Animals ; Mice ; RNA-Seq ; Transcriptional Activation ; Radiation Tolerance
Czasopismo naukowe
Szczegóły
Tytuł:
Epi-Impute: Single-Cell RNA-seq Imputation via Integration with Single-Cell ATAC-seq.
Autorzy:
Raevskiy M; Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, 141701 Moscow, Russia.; Skolkovo Institute of Science and Technology, 121205 Moscow, Russia.
Yanvarev V; Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, 141701 Moscow, Russia.
Jung S; Computational Biology Laboratory, Center for Cooperative Research in Biosciences, 48160 Derio, Bizkaia, Spain.; Centre for Systems Biomedicine, The University of Luxembourg, 4365 Luxembourg, Luxembourg.
Del Sol A; Computational Biology Laboratory, Center for Cooperative Research in Biosciences, 48160 Derio, Bizkaia, Spain.; Centre for Systems Biomedicine, The University of Luxembourg, 4365 Luxembourg, Luxembourg.
Medvedeva YA; Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, 141701 Moscow, Russia.; Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia.; The National Medical Research Center for Endocrinology, 117036 Moscow, Russia.
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Źródło:
International journal of molecular sciences [Int J Mol Sci] 2023 Mar 25; Vol. 24 (7). Date of Electronic Publication: 2023 Mar 25.
Typ publikacji:
Journal Article
MeSH Terms:
Software*
Chromatin Immunoprecipitation Sequencing*
Sequence Analysis, RNA/methods ; Single-Cell Gene Expression Analysis ; Single-Cell Analysis/methods ; Gene Expression Profiling
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
A Unified Deep Learning Framework for Single-Cell ATAC-Seq Analysis Based on ProdDep Transformer Encoder.
Autorzy:
Wang Z; School of Computer Science, Chengdu University of Information Technology, Chengdu 610225, China.
Zhang Y; School of Computer Science, Chengdu University of Information Technology, Chengdu 610225, China.
Yu Y; School of Computer Science, Chengdu University of Information Technology, Chengdu 610225, China.
Zhang J; School of Computer Science, Chengdu University of Information Technology, Chengdu 610225, China.
Liu Y; School of Computer Science, Chengdu University of Information Technology, Chengdu 610225, China.
Zou Q; Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China.
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Źródło:
International journal of molecular sciences [Int J Mol Sci] 2023 Mar 01; Vol. 24 (5). Date of Electronic Publication: 2023 Mar 01.
Typ publikacji:
Journal Article
MeSH Terms:
Chromatin Immunoprecipitation Sequencing*/methods
Deep Learning*
Chromatin ; Gene Expression Regulation ; Transcription Factors/metabolism ; Single-Cell Analysis/methods
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Integrated analysis of ATAC-seq and RNA-seq reveals the transcriptional regulation network in SLE.
Autorzy:
Wu J; Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, China; Research Unit of Key Technologies of Immune-Related Skin Diseases Diagnosis and Treatment, Chinese Academy of Medical Sciences, Changsha, China.
Li Y; Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, China; Research Unit of Key Technologies of Immune-Related Skin Diseases Diagnosis and Treatment, Chinese Academy of Medical Sciences, Changsha, China.
Feng D; Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, China; Research Unit of Key Technologies of Immune-Related Skin Diseases Diagnosis and Treatment, Chinese Academy of Medical Sciences, Changsha, China.
Yu Y; Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, China; Research Unit of Key Technologies of Immune-Related Skin Diseases Diagnosis and Treatment, Chinese Academy of Medical Sciences, Changsha, China.
Long H; Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, China; Research Unit of Key Technologies of Immune-Related Skin Diseases Diagnosis and Treatment, Chinese Academy of Medical Sciences, Changsha, China.
Hu Z; Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, China; Research Unit of Key Technologies of Immune-Related Skin Diseases Diagnosis and Treatment, Chinese Academy of Medical Sciences, Changsha, China.
Lu Q; Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, China; Research Unit of Key Technologies of Immune-Related Skin Diseases Diagnosis and Treatment, Chinese Academy of Medical Sciences, Changsha, China; Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China.
Zhao M; Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, China; Research Unit of Key Technologies of Immune-Related Skin Diseases Diagnosis and Treatment, Chinese Academy of Medical Sciences, Changsha, China. Electronic address: .
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Źródło:
International immunopharmacology [Int Immunopharmacol] 2023 Mar; Vol. 116, pp. 109803. Date of Electronic Publication: 2023 Feb 02.
Typ publikacji:
Journal Article
MeSH Terms:
Chromatin Immunoprecipitation Sequencing*
Lupus Erythematosus, Systemic*/metabolism
Humans ; RNA-Seq ; Gene Expression Regulation ; Chromatin ; Membrane Proteins/metabolism ; RNA-Binding Proteins/genetics ; Repressor Proteins/genetics
Czasopismo naukowe
Szczegóły
Tytuł:
Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Mouse Corneal Epithelial Cells.
Autorzy:
Lu ZJ; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China.; Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China.; Research Unit of Ocular Development and Regeneration, Chinese Academy of Medical Sciences, China.
Ye JG; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China.
Wang DL; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China.
Li MK; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China.
Zhang QK; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China.
Liu Z; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China.
Huang YJ; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China.
Pan CN; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China.
Lin YH; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China.
Shi ZX; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China.
Zheng YF; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China.; Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China.; Research Unit of Ocular Development and Regeneration, Chinese Academy of Medical Sciences, China.
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Źródło:
Investigative ophthalmology & visual science [Invest Ophthalmol Vis Sci] 2023 Mar 01; Vol. 64 (3), pp. 30.
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:
Chromatin Immunoprecipitation Sequencing*
Single-Cell Gene Expression Analysis*
Animals ; Mice ; Chromatin ; Gene Expression Regulation ; Epithelial Cells
Czasopismo naukowe
Szczegóły
Wyświetlanie 1-20 z 26927

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