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  1. Article ; Online: Standing on the shoulders of microbes: How cancer biologists are expanding their view of hard-to-kill persister cells.

    Oren, Yaara

    Molecular systems biology

    2022  Volume 18, Issue 7, Page(s) e11168

    Abstract: Similar to persister bacterial cells that survive antibiotic treatments, some cancer cells can evade drug treatments. This Commentary discusses the different classes of persister cells and their implications for developing more efficient cancer ... ...

    Abstract Similar to persister bacterial cells that survive antibiotic treatments, some cancer cells can evade drug treatments. This Commentary discusses the different classes of persister cells and their implications for developing more efficient cancer treatments.
    MeSH term(s) Anti-Bacterial Agents ; Microbial Sensitivity Tests ; Neoplasms/drug therapy
    Chemical Substances Anti-Bacterial Agents
    Language English
    Publishing date 2022-08-03
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2193510-5
    ISSN 1744-4292 ; 1744-4292
    ISSN (online) 1744-4292
    ISSN 1744-4292
    DOI 10.15252/msb.202211168
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Hunting down rare drug-tolerant cycling cells with Watermelon.

    Oren, Yaara

    Nature reviews. Cancer

    2022  Volume 22, Issue 8, Page(s) 434–435

    MeSH term(s) Humans ; Citrullus ; Drug Tolerance
    Language English
    Publishing date 2022-03-23
    Publishing country England
    Document type Journal Article ; Comment
    ZDB-ID 2062767-1
    ISSN 1474-1768 ; 1474-175X
    ISSN (online) 1474-1768
    ISSN 1474-175X
    DOI 10.1038/s41568-022-00483-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: ATF3 characterizes aggressive drug-tolerant persister cells in HGSOC.

    Böpple, Kathrin / Oren, Yaara / Henry, Whitney S / Dong, Meng / Weller, Sandra / Thiel, Julia / Kleih, Markus / Gaißler, Andrea / Zipperer, Damaris / Kopp, Hans-Georg / Aylon, Yael / Oren, Moshe / Essmann, Frank / Liang, Chunguang / Aulitzky, Walter E

    Cell death & disease

    2024  Volume 15, Issue 4, Page(s) 290

    Abstract: High-grade serous ovarian cancer (HGSOC) represents the most common and lethal subtype of ovarian cancer. Despite initial response to platinum-based standard therapy, patients commonly suffer from relapse that likely originates from drug-tolerant ... ...

    Abstract High-grade serous ovarian cancer (HGSOC) represents the most common and lethal subtype of ovarian cancer. Despite initial response to platinum-based standard therapy, patients commonly suffer from relapse that likely originates from drug-tolerant persister (DTP) cells. We generated isogenic clones of treatment-naïve and cisplatin-tolerant persister HGSOC cells. In addition, single-cell RNA sequencing of barcoded cells was performed in a xenograft model with HGSOC cell lines after platinum-based therapy. Published single-cell RNA-sequencing data from neo-adjuvant and non-treated HGSOC patients and patient data from TCGA were analyzed. DTP-derived cells exhibited morphological alterations and upregulation of epithelial-mesenchymal transition (EMT) markers. An aggressive subpopulation of DTP-derived cells showed high expression of the stress marker ATF3. Knockdown of ATF3 enhanced the sensitivity of aggressive DTP-derived cells to cisplatin-induced cell death, implying a role for ATF3 stress response in promoting a drug tolerant persister cell state. Furthermore, single cell lineage tracing to detect transcriptional changes in a HGSOC cell line-derived xenograft relapse model showed that cells derived from relapsed solid tumors express increased levels of EMT and multiple endoplasmic reticulum (ER) stress markers, including ATF3. Single cell RNA sequencing of epithelial cells from four HGSOC patients also identified a small cell population resembling DTP cells in all samples. Moreover, analysis of TCGA data from 259 HGSOC patients revealed a significant progression-free survival advantage for patients with low expression of the ATF3-associated partial EMT genes. These findings suggest that increased ATF3 expression together with partial EMT promote the development of aggressive DTP, and thereby relapse in HGSOC patients.
    MeSH term(s) Humans ; Activating Transcription Factor 3/metabolism ; Activating Transcription Factor 3/genetics ; Female ; Cisplatin/pharmacology ; Cisplatin/therapeutic use ; Cell Line, Tumor ; Drug Resistance, Neoplasm/genetics ; Drug Resistance, Neoplasm/drug effects ; Epithelial-Mesenchymal Transition/drug effects ; Epithelial-Mesenchymal Transition/genetics ; Ovarian Neoplasms/drug therapy ; Ovarian Neoplasms/genetics ; Ovarian Neoplasms/pathology ; Ovarian Neoplasms/metabolism ; Animals ; Mice ; Xenograft Model Antitumor Assays ; Gene Expression Regulation, Neoplastic/drug effects
    Chemical Substances Activating Transcription Factor 3 ; Cisplatin (Q20Q21Q62J) ; ATF3 protein, human
    Language English
    Publishing date 2024-04-24
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2541626-1
    ISSN 2041-4889 ; 2041-4889
    ISSN (online) 2041-4889
    ISSN 2041-4889
    DOI 10.1038/s41419-024-06674-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Aging-Associated Alterations in Mammary Epithelia and Stroma Revealed by Single-Cell RNA Sequencing.

    Li, Carman Man-Chung / Shapiro, Hana / Tsiobikas, Christina / Selfors, Laura M / Chen, Huidong / Rosenbluth, Jennifer / Moore, Kaitlin / Gupta, Kushali P / Gray, G Kenneth / Oren, Yaara / Steinbaugh, Michael J / Guerriero, Jennifer L / Pinello, Luca / Regev, Aviv / Brugge, Joan S

    Cell reports

    2020  Volume 33, Issue 13, Page(s) 108566

    Abstract: Aging is closely associated with increased susceptibility to breast cancer, yet there have been limited systematic studies of aging-induced alterations in the mammary gland. Here, we leverage high-throughput single-cell RNA sequencing to generate a ... ...

    Abstract Aging is closely associated with increased susceptibility to breast cancer, yet there have been limited systematic studies of aging-induced alterations in the mammary gland. Here, we leverage high-throughput single-cell RNA sequencing to generate a detailed transcriptomic atlas of young and aged murine mammary tissues. By analyzing epithelial, stromal, and immune cells, we identify age-dependent alterations in cell proportions and gene expression, providing evidence that suggests alveolar maturation and physiological decline. The analysis also uncovers potential pro-tumorigenic mechanisms coupled to the age-associated loss of tumor suppressor function and change in microenvironment. In addition, we identify a rare, age-dependent luminal population co-expressing hormone-sensing and secretory-alveolar lineage markers, as well as two macrophage populations expressing distinct gene signatures, underscoring the complex heterogeneity of the mammary epithelia and stroma. Collectively, this rich single-cell atlas reveals the effects of aging on mammary physiology and can serve as a useful resource for understanding aging-associated cancer risk.
    MeSH term(s) Aging/psychology ; Animals ; Biomarkers/metabolism ; Cells, Cultured ; Cellular Senescence ; Dendritic Cells/metabolism ; Epithelial Cells/metabolism ; Female ; Gene Expression Regulation ; Genes, Tumor Suppressor ; High-Throughput Nucleotide Sequencing/methods ; Lymphocytes/metabolism ; Macrophages/metabolism ; Mammary Glands, Animal/metabolism ; Mice, Inbred C57BL ; Single-Cell Analysis/methods ; Stromal Cells/metabolism ; Transcriptome
    Chemical Substances Biomarkers
    Language English
    Publishing date 2020-12-30
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2649101-1
    ISSN 2211-1247 ; 2211-1247
    ISSN (online) 2211-1247
    ISSN 2211-1247
    DOI 10.1016/j.celrep.2020.108566
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Cycling cancer persister cells arise from lineages with distinct programs.

    Oren, Yaara / Tsabar, Michael / Cuoco, Michael S / Amir-Zilberstein, Liat / Cabanos, Heidie F / Hütter, Jan-Christian / Hu, Bomiao / Thakore, Pratiksha I / Tabaka, Marcin / Fulco, Charles P / Colgan, William / Cuevas, Brandon M / Hurvitz, Sara A / Slamon, Dennis J / Deik, Amy / Pierce, Kerry A / Clish, Clary / Hata, Aaron N / Zaganjor, Elma /
    Lahav, Galit / Politi, Katerina / Brugge, Joan S / Regev, Aviv

    Nature

    2021  Volume 596, Issue 7873, Page(s) 576–582

    Abstract: Non-genetic mechanisms have recently emerged as important drivers of cancer therapy ... ...

    Abstract Non-genetic mechanisms have recently emerged as important drivers of cancer therapy failure
    MeSH term(s) Antioxidants/metabolism ; Cell Cycle/drug effects ; Cell Line, Tumor ; Cell Lineage/drug effects ; Cell Proliferation/drug effects ; Cell Survival/drug effects ; Clone Cells/drug effects ; Clone Cells/metabolism ; Clone Cells/pathology ; DNA Barcoding, Taxonomic ; Fatty Acids/metabolism ; Gene Expression Regulation, Neoplastic ; Humans ; Lentivirus/genetics ; Neoplasm Recurrence, Local/drug therapy ; Neoplasm Recurrence, Local/genetics ; Neoplasm Recurrence, Local/pathology ; Neoplasms/drug therapy ; Neoplasms/genetics ; Neoplasms/metabolism ; Neoplasms/pathology ; Oncogene Proteins/antagonists & inhibitors ; Oxidation-Reduction ; Oxidative Stress ; Reactive Oxygen Species/metabolism ; Transcription, Genetic/drug effects
    Chemical Substances Antioxidants ; Fatty Acids ; Oncogene Proteins ; Reactive Oxygen Species
    Language English
    Publishing date 2021-08-11
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/s41586-021-03796-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Genomic Avenue to Avian Colisepticemia

    Huja, Sagi / Oren, Yaara / Trost, Eva / Brzuszkiewicz, Elzbieta / Biran, Dvora / Blom, Jochen / Goesmann, Alexander / Gottschalk, Gerhard / Hacker, Jörg / Ron, Eliora Z / Dobrindt, Ulrich

    mBio. 2015 Feb. 27, v. 6, no. 1

    2015  

    Abstract: ABSTRACT Here we present an extensive genomic and genetic analysis of Escherichia coli strains of serotype O78 that represent the major cause of avian colisepticemia, an invasive infection caused by avian pathogenic Escherichia coli (APEC) strains. It is ...

    Abstract ABSTRACT Here we present an extensive genomic and genetic analysis of Escherichia coli strains of serotype O78 that represent the major cause of avian colisepticemia, an invasive infection caused by avian pathogenic Escherichia coli (APEC) strains. It is associated with high mortality and morbidity, resulting in significant economic consequences for the poultry industry. To understand the genetic basis of the virulence of avian septicemic E. coli , we sequenced the entire genome of a clinical isolate of serotype O78—O78:H19 ST88 isolate 789 (O78-9)—and compared it with three publicly available APEC O78 sequences and one complete genome of APEC serotype O1 strain. Although there was a large variability in genome content between the APEC strains, several genes were conserved, which are potentially critical for colisepticemia. Some of these genes are present in multiple copies per genome or code for gene products with overlapping function, signifying their importance. A systematic deletion of each of these virulence-related genes identified three systems that are conserved in all septicemic strains examined and are critical for serum survival, a prerequisite for septicemia. These are the plasmid-encoded protein, the defective ETT2 ( E . coli type 3 secretion system 2) type 3 secretion system ETT2 (sepsis), and iron uptake systems. Strain O78-9 is the only APEC O78 strain that also carried the regulon coding for yersiniabactin, the iron binding system of the Yersinia high-pathogenicity island. Interestingly, this system is the only one that cannot be complemented by other iron uptake systems under iron limitation and in serum.
    Keywords Escherichia coli ; Yersinia ; antibiotic resistance ; antibiotics ; bacteria ; birds ; blood serum ; financial economics ; genetic techniques and protocols ; morbidity ; mortality ; poultry industry ; regulon ; septicemia ; serotypes ; type III secretion system ; virulence
    Language English
    Dates of publication 2015-0227
    Size p. e01681-14.
    Publishing place American Society for Microbiology
    Document type Article
    ZDB-ID 2557172-2
    ISSN 2150-7511 ; 2161-2129
    ISSN (online) 2150-7511
    ISSN 2161-2129
    DOI 10.1128/mBio.01681-14
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  7. Article ; Online: The operonic location of auto-transcriptional repressors is highly conserved in bacteria.

    Rubinstein, Nimrod D / Zeevi, David / Oren, Yaara / Segal, Gil / Pupko, Tal

    Molecular biology and evolution

    2011  Volume 28, Issue 12, Page(s) 3309–3318

    Abstract: Bacterial genes are commonly encoded in clusters, known as operons, which share transcriptional regulatory control and often encode functionally related proteins that take part in certain biological pathways. Operons that are coregulated are known to ... ...

    Abstract Bacterial genes are commonly encoded in clusters, known as operons, which share transcriptional regulatory control and often encode functionally related proteins that take part in certain biological pathways. Operons that are coregulated are known to colocalize in the genome, suggesting that their spatial organization is under selection for efficient expression regulation. However, the internal order of genes within operons is believed to be poorly conserved, and hence expression requirements are claimed to be too weak to oppose gene rearrangements. In light of these opposing views, we set out to investigate whether the internal location of the regulatory genes within operons is under selection. Our analysis shows that transcription factors (TFs) are preferentially encoded as either first or last in their operons, in the two diverged model bacteria Escherichia coli and Bacillus subtilis. In a higher resolution, we find that TFs that repress transcription of the operon in which they are encoded (autorepressors), contribute most of this signal by specific preference of the first operon position. We show that this trend is strikingly conserved throughout highly diverged bacterial phyla. Moreover, these autorepressors regulate operons that carry out highly diverse biological functions. We propose a model according to which autorepressors are selected to be located first in their operons in order to optimize transcription regulation. Specifically, the first operon position helps autorepressors to minimize leaky transcription of the operon structural genes, thus minimizing energy waste. Our analysis provides statistically robust evidence for a paradigm of bacterial autorepressor preferential operonic location. Corroborated with our suggested model, an additional layer of operon expression control that is common throughout the bacterial domain is revealed.
    MeSH term(s) Bacillus subtilis/genetics ; Bacterial Proteins/genetics ; DNA-Binding Proteins/genetics ; Escherichia coli/genetics ; Escherichia coli Proteins/genetics ; Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Operon ; Regulatory Elements, Transcriptional/genetics ; Repressor Proteins/genetics ; Selection, Genetic ; Signal Transduction ; Transcription Factors/genetics ; Transcription, Genetic
    Chemical Substances Bacterial Proteins ; DNA-Binding Proteins ; Escherichia coli Proteins ; MarA protein, E coli ; MarR protein, E coli ; Repressor Proteins ; Transcription Factors ; multiple antibiotic resistance protein B
    Language English
    Publishing date 2011-12
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 998579-7
    ISSN 1537-1719 ; 0737-4038
    ISSN (online) 1537-1719
    ISSN 0737-4038
    DOI 10.1093/molbev/msr163
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Fur Is the Master Regulator of the Extraintestinal Pathogenic Escherichia coli Response to Serum

    Huja, Sagi / Oren, Yaara / Biran, Dvora / Meyer, Susann / Dobrindt, Ulrich / Bernhard, Joerg / Becher, Doerte / Hecker, Michael / Sorek, Rotem / Ron, Eliora Z

    mBio. 2014 Aug. 29, v. 5, no. 4

    2014  

    Abstract: Drug-resistant extraintestinal pathogenic Escherichia coli (ExPEC) strains are the major cause of colisepticemia (colibacillosis), a condition that has become an increasing public health problem in recent years. ExPEC strains are characterized by high ... ...

    Abstract Drug-resistant extraintestinal pathogenic Escherichia coli (ExPEC) strains are the major cause of colisepticemia (colibacillosis), a condition that has become an increasing public health problem in recent years. ExPEC strains are characterized by high resistance to serum, which is otherwise highly toxic to most bacteria. To understand how these bacteria survive and grow in serum, we performed system-wide analyses of their response to serum, making a clear distinction between the responses to nutritional immunity and innate immunity. Thus, mild heat inactivation of serum destroys the immune complement and abolishes the bactericidal effect of serum (inactive serum), making it possible to examine nutritional immunity. We used a combination of deep RNA sequencing and proteomics in order to characterize ExPEC genes whose expression is affected by the nutritional stress of serum and by the immune complement. The major change in gene expression induced by serum—active and inactive—involved metabolic genes. In particular, the serum metabolic response is coordinated by three transcriptional regulators, Fur, BasR, and CysB. Fur alone was responsible for more than 80% of the serum-induced transcriptional response. Consistent with its role as a major serum response regulator, deletion of Fur renders the bacteria completely serum sensitive. These results highlight the role of metabolic adaptation in colisepticemia and virulence. IMPORTANCE Drug-resistant extraintestinal pathogenic Escherichia coli (ExPEC) strains have emerged as major pathogens, especially in community- and hospital-acquired infections. These bacteria cause a large spectrum of syndromes, the most serious of which is septicemia, a condition with a high mortality rate. These bacterial strains are characterized by high resistance to serum, otherwise highly toxic to most bacteria. To understand the basis of this resistance, we carried out system-wide analyses of the response of ExPEC strains to serum by using proteomics and deep RNA sequencing. The major changes in gene expression induced by exposure to serum involved metabolic genes, not necessarily implicated in relation to virulence. One metabolic regulator—Fur—involved in iron metabolism was responsible for more than 80% of the serum-induced response, and its deletion renders the bacteria completely serum sensitive. These results highlight the role of metabolic adaptation in virulence.
    Keywords Escherichia coli ; RNA ; antibacterial properties ; antiserum ; bacteria ; blood serum ; complement ; drug resistance ; gene expression regulation ; genes ; heat inactivation ; innate immunity ; malnutrition ; metabolism ; mortality ; pathogens ; proteomics ; septicemia ; toxicity ; transcription (genetics) ; transcription factors ; virulence
    Language English
    Dates of publication 2014-0829
    Size p. e01460-14.
    Publishing place American Society for Microbiology
    Document type Article
    ZDB-ID 2557172-2
    ISSN 2150-7511 ; 2161-2129
    ISSN (online) 2150-7511
    ISSN 2161-2129
    DOI 10.1128/mBio.01460-14
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  9. Article: Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics

    Ludwig, Leif S / Lareau, Caleb A / Ulirsch, Jacob C / Christian, Elena / Muus, Christoph / Li, Lauren H / Pelka, Karin / Ge, Will / Oren, Yaara / Brack, Alison / Law, Travis / Rodman, Christopher / Chen, Jonathan H / Boland, Genevieve M / Hacohen, Nir / Rozenblatt-Rosen, Orit / Aryee, Martin J / Buenrostro, Jason D / Regev, Aviv /
    Sankaran, Vijay G

    Cell. 2019 Mar. 07, v. 176, no. 6

    2019  

    Abstract: Lineage tracing provides key insights into the fate of individual cells in complex organisms. Although effective genetic labeling approaches are available in model systems, in humans, most approaches require detection of nuclear somatic mutations, which ... ...

    Abstract Lineage tracing provides key insights into the fate of individual cells in complex organisms. Although effective genetic labeling approaches are available in model systems, in humans, most approaches require detection of nuclear somatic mutations, which have high error rates, limited scale, and do not capture cell state information. Here, we show that somatic mutations in mtDNA can be tracked by single-cell RNA or assay for transposase accessible chromatin (ATAC) sequencing. We leverage somatic mtDNA mutations as natural genetic barcodes and demonstrate their utility as highly accurate clonal markers to infer cellular relationships. We track native human cells both in vitro and in vivo and relate clonal dynamics to gene expression and chromatin accessibility. Our approach should allow clonal tracking at a 1,000-fold greater scale than with nuclear genome sequencing, with simultaneous information on cell state, opening the way to chart cellular dynamics in human health and disease.
    Keywords RNA ; barcoding ; chromatin ; enzymes ; gene expression ; genomics ; human health ; humans ; mitochondria ; mitochondrial DNA ; models ; nuclear genome ; somatic mutation
    Language English
    Dates of publication 2019-0307
    Size p. 1325-1339.e22.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2019.01.022
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  10. Article ; Online: Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics.

    Ludwig, Leif S / Lareau, Caleb A / Ulirsch, Jacob C / Christian, Elena / Muus, Christoph / Li, Lauren H / Pelka, Karin / Ge, Will / Oren, Yaara / Brack, Alison / Law, Travis / Rodman, Christopher / Chen, Jonathan H / Boland, Genevieve M / Hacohen, Nir / Rozenblatt-Rosen, Orit / Aryee, Martin J / Buenrostro, Jason D / Regev, Aviv /
    Sankaran, Vijay G

    Cell

    2019  Volume 176, Issue 6, Page(s) 1325–1339.e22

    Abstract: Lineage tracing provides key insights into the fate of individual cells in complex organisms. Although effective genetic labeling approaches are available in model systems, in humans, most approaches require detection of nuclear somatic mutations, which ... ...

    Abstract Lineage tracing provides key insights into the fate of individual cells in complex organisms. Although effective genetic labeling approaches are available in model systems, in humans, most approaches require detection of nuclear somatic mutations, which have high error rates, limited scale, and do not capture cell state information. Here, we show that somatic mutations in mtDNA can be tracked by single-cell RNA or assay for transposase accessible chromatin (ATAC) sequencing. We leverage somatic mtDNA mutations as natural genetic barcodes and demonstrate their utility as highly accurate clonal markers to infer cellular relationships. We track native human cells both in vitro and in vivo and relate clonal dynamics to gene expression and chromatin accessibility. Our approach should allow clonal tracking at a 1,000-fold greater scale than with nuclear genome sequencing, with simultaneous information on cell state, opening the way to chart cellular dynamics in human health and disease.
    MeSH term(s) Base Sequence ; Cell Lineage ; Chromatin ; Colorectal Neoplasms/genetics ; Colorectal Neoplasms/pathology ; DNA, Mitochondrial/genetics ; Genomics/methods ; HEK293 Cells ; Hematopoietic Stem Cells/physiology ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Mitochondria/genetics ; Mutation ; Single-Cell Analysis ; Transposases
    Chemical Substances Chromatin ; DNA, Mitochondrial ; Transposases (EC 2.7.7.-)
    Language English
    Publishing date 2019-02-28
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2019.01.022
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