Cancer Cell Lines Part 1

Cancer Cell Lines Part 1

Author: John Masters

Publisher: Springer Science & Business Media

Published: 2006-04-11

Total Pages: 295

ISBN-13: 0306468727

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Continuous cell lines derived from human cancers are the most widely used resource in laboratory-based cancer research. The first 3 volumes of this series on Human Cell Culture are devoted to these cancer cell lines. The chapters in these first 3 volumes have a common aim. Their purpose is to address 3 questions of fundamental importance to the relevance of human cancer cell lines as model systems of each type of cancer: 1. Do the cell lines available accurately represent the clinical presentation? 2. Do the cell lines accurately represent the histopathology of the original tumors? 3. Do the cell lines accurately represent the molecular genetics of this type of cancer? The cancer cell lines available are derived, in most cases, from the more aggressive and advanced cancers. There are few cell lines derived from low grade organ-confined cancers. This gap can be filled with conditionally immortalized human cancer cell lines. We do not know why the success rate for establishing cell lines is so low for some types of cancer and so high for others. The histopathology of the tumor of origin and the extent to which the derived cell line retains the differentiated features of that tumor are critical. The concept that a single cell line derived from a tumor at a particular site is representative of tumors at that site is naïve and misleading.


Book Synopsis Cancer Cell Lines Part 1 by : John Masters

Download or read book Cancer Cell Lines Part 1 written by John Masters and published by Springer Science & Business Media. This book was released on 2006-04-11 with total page 295 pages. Available in PDF, EPUB and Kindle. Book excerpt: Continuous cell lines derived from human cancers are the most widely used resource in laboratory-based cancer research. The first 3 volumes of this series on Human Cell Culture are devoted to these cancer cell lines. The chapters in these first 3 volumes have a common aim. Their purpose is to address 3 questions of fundamental importance to the relevance of human cancer cell lines as model systems of each type of cancer: 1. Do the cell lines available accurately represent the clinical presentation? 2. Do the cell lines accurately represent the histopathology of the original tumors? 3. Do the cell lines accurately represent the molecular genetics of this type of cancer? The cancer cell lines available are derived, in most cases, from the more aggressive and advanced cancers. There are few cell lines derived from low grade organ-confined cancers. This gap can be filled with conditionally immortalized human cancer cell lines. We do not know why the success rate for establishing cell lines is so low for some types of cancer and so high for others. The histopathology of the tumor of origin and the extent to which the derived cell line retains the differentiated features of that tumor are critical. The concept that a single cell line derived from a tumor at a particular site is representative of tumors at that site is naïve and misleading.


Cancer Cell Culture

Cancer Cell Culture

Author: Ian A. Cree

Publisher: Humana Press

Published: 2016-08-23

Total Pages: 502

ISBN-13: 9781493956579

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With many recent advances, cancer cell culture research is more important than ever before. This timely edition of Cancer Cell Culture: Methods and Protocols covers the basic concepts of cancer cell biology and culture while expanding upon the recent shift in cell culture methods from the generation of new cell lines to the use of primary cells. There are methods to characterize and authenticate cell lines, to isolate and develop specific types of cancer cells, and to develop new cell line models. Functional assays are provided for the evaluation of clonogenicity, cell proliferation, apoptosis, adhesion, migration, invasion, senescence, angiogenesis, and cell cycle parameters. Other methods permit the modification of cells for transfection, drug resistance, immortalization, and transfer in vivo, the co-culture of different cell types, and the detection and treatment of contamination. In this new edition, specific emphasis is placed on safe working practice for both cells and laboratory researchers. These chapters contain the information critical to success – only by good practice and quality control will the results of cancer cell culture improve. Written in the successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and accessible, Cancer Cell Culture: Methods and Protocols serves as a practical guide for scientists of all backgrounds and aims to convey the appropriate sense of fascination associated with this research field.


Book Synopsis Cancer Cell Culture by : Ian A. Cree

Download or read book Cancer Cell Culture written by Ian A. Cree and published by Humana Press. This book was released on 2016-08-23 with total page 502 pages. Available in PDF, EPUB and Kindle. Book excerpt: With many recent advances, cancer cell culture research is more important than ever before. This timely edition of Cancer Cell Culture: Methods and Protocols covers the basic concepts of cancer cell biology and culture while expanding upon the recent shift in cell culture methods from the generation of new cell lines to the use of primary cells. There are methods to characterize and authenticate cell lines, to isolate and develop specific types of cancer cells, and to develop new cell line models. Functional assays are provided for the evaluation of clonogenicity, cell proliferation, apoptosis, adhesion, migration, invasion, senescence, angiogenesis, and cell cycle parameters. Other methods permit the modification of cells for transfection, drug resistance, immortalization, and transfer in vivo, the co-culture of different cell types, and the detection and treatment of contamination. In this new edition, specific emphasis is placed on safe working practice for both cells and laboratory researchers. These chapters contain the information critical to success – only by good practice and quality control will the results of cancer cell culture improve. Written in the successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and accessible, Cancer Cell Culture: Methods and Protocols serves as a practical guide for scientists of all backgrounds and aims to convey the appropriate sense of fascination associated with this research field.


Cancer Cell Lines Part 2

Cancer Cell Lines Part 2

Author: John Masters

Publisher: Springer Science & Business Media

Published: 2006-04-11

Total Pages: 376

ISBN-13: 0306468611

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Continuous cell lines derived from human cancers are the mostwidely used resource in laboratory-based cancer research. The first 3 volumes of this series on Human Cell Culture are devoted to these cancer cell lines. The chapters in these first 3 volumes have a common aim. Their purpose is to address 3 questions offundamental importance to the relevanceof human cancer cell lines as model systems of each type of cancer: 1. Do the cell lines available accurately represent the clinical presentation? 2. Do the cell lines accurately represent the histopathology of the original tumors? 3. Do the cell lines accurately represent the molecular genetics of this type of cancer? The cancer cell lines available are derived, in most cases, from the more aggressive and advanced cancers. There are few cell lines derived from low grade organ-confined cancers. This gap can be filled with conditionally immortalized human cancer cell lines. We do not know why the success rate for establishing cell lines is so low for some types of cancer and so high for others. The histopathology of the tumor of origin and the extent to which the derived cell line retains the differentiated features of that tumor are critical. The concept that a single cell line derived from a tumor at a particular site is representative oftumors at that site is naïve and misleading.


Book Synopsis Cancer Cell Lines Part 2 by : John Masters

Download or read book Cancer Cell Lines Part 2 written by John Masters and published by Springer Science & Business Media. This book was released on 2006-04-11 with total page 376 pages. Available in PDF, EPUB and Kindle. Book excerpt: Continuous cell lines derived from human cancers are the mostwidely used resource in laboratory-based cancer research. The first 3 volumes of this series on Human Cell Culture are devoted to these cancer cell lines. The chapters in these first 3 volumes have a common aim. Their purpose is to address 3 questions offundamental importance to the relevanceof human cancer cell lines as model systems of each type of cancer: 1. Do the cell lines available accurately represent the clinical presentation? 2. Do the cell lines accurately represent the histopathology of the original tumors? 3. Do the cell lines accurately represent the molecular genetics of this type of cancer? The cancer cell lines available are derived, in most cases, from the more aggressive and advanced cancers. There are few cell lines derived from low grade organ-confined cancers. This gap can be filled with conditionally immortalized human cancer cell lines. We do not know why the success rate for establishing cell lines is so low for some types of cancer and so high for others. The histopathology of the tumor of origin and the extent to which the derived cell line retains the differentiated features of that tumor are critical. The concept that a single cell line derived from a tumor at a particular site is representative oftumors at that site is naïve and misleading.


Cancer Cell Lines

Cancer Cell Lines

Author: Bernhard Ø Palsson

Publisher: Springer

Published: 2000-11-30

Total Pages: 399

ISBN-13: 9780792362258

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This book describes all human leukemia-lymphoma cell lines that have been established and that grow continuously under standardised in vitro conditions. These lines are derived from cells belonging to all the major hematopoietic cell lineages, i.e. B- and T-lymphocytes, natural killer cells, granulocytic cells and megakaryocytic cells. The clinical data, the culture conditions and the major phenotypic features of the cell lines are described with citations. This book is the first book describing human leukemia-lymphoma cell lines and will be of interest to scientists involved in the areas of hematology, oncology, immunology, molecular biology and cytogenetics. Cancer Cell Lines, Volumes 1-3: These 3 volumes provide a comprehensive text on the culture of established cell lines from every type of human cancer. The volumes provide a basic manual and reference resource for every cancer research scientist using human cancer cells.


Book Synopsis Cancer Cell Lines by : Bernhard Ø Palsson

Download or read book Cancer Cell Lines written by Bernhard Ø Palsson and published by Springer. This book was released on 2000-11-30 with total page 399 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes all human leukemia-lymphoma cell lines that have been established and that grow continuously under standardised in vitro conditions. These lines are derived from cells belonging to all the major hematopoietic cell lineages, i.e. B- and T-lymphocytes, natural killer cells, granulocytic cells and megakaryocytic cells. The clinical data, the culture conditions and the major phenotypic features of the cell lines are described with citations. This book is the first book describing human leukemia-lymphoma cell lines and will be of interest to scientists involved in the areas of hematology, oncology, immunology, molecular biology and cytogenetics. Cancer Cell Lines, Volumes 1-3: These 3 volumes provide a comprehensive text on the culture of established cell lines from every type of human cancer. The volumes provide a basic manual and reference resource for every cancer research scientist using human cancer cells.


Cancer Cell Culture

Cancer Cell Culture

Author: Simon P. Langdon

Publisher: Springer Science & Business Media

Published: 2008-02-01

Total Pages: 346

ISBN-13: 1592594069

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The culture of cancer cells is routinely practiced in many academic research centers, biotechnology companies, and hospital laboratories. Cancer Cell Culture: Methods and Protocols describes easy-to-follow methods to guide both novice and more experienced researchers seeking to use new techniques in their laboratories. Our present understanding of the cell and molecular biology of cancer has been derived mainly from the use of cultured cancer cells and we cover a number of the most widely used assays to study function in current use. Part I introduces the basic concept of cancer cell culture and this is followed by a description of the general techniques used in many cell culture facilities. The importance of cell line characterization is now widely recognized and methods to characterize and authenticate cell lines are described in Part II. Part III covers the isolation and development of specific cancer cell types and provides valuable tips for those wishing to derive new cell line models. A wide range of procedures encompassing many of the key functional features of cancer cells are described in Part IV including assays to evaluate clonogenicity, cell proliferation, apoptosis, adhesion, migration, invasion, senescence, angiogenesis, and cell cycle parameters. Methods to modify cancer cells are described in Part V, including protocols for transfection, development of drug-resistance, immortalization, and transfer in vivo. In Part VI methods of coculture of different cell types and contamination of cell lines are covered.


Book Synopsis Cancer Cell Culture by : Simon P. Langdon

Download or read book Cancer Cell Culture written by Simon P. Langdon and published by Springer Science & Business Media. This book was released on 2008-02-01 with total page 346 pages. Available in PDF, EPUB and Kindle. Book excerpt: The culture of cancer cells is routinely practiced in many academic research centers, biotechnology companies, and hospital laboratories. Cancer Cell Culture: Methods and Protocols describes easy-to-follow methods to guide both novice and more experienced researchers seeking to use new techniques in their laboratories. Our present understanding of the cell and molecular biology of cancer has been derived mainly from the use of cultured cancer cells and we cover a number of the most widely used assays to study function in current use. Part I introduces the basic concept of cancer cell culture and this is followed by a description of the general techniques used in many cell culture facilities. The importance of cell line characterization is now widely recognized and methods to characterize and authenticate cell lines are described in Part II. Part III covers the isolation and development of specific cancer cell types and provides valuable tips for those wishing to derive new cell line models. A wide range of procedures encompassing many of the key functional features of cancer cells are described in Part IV including assays to evaluate clonogenicity, cell proliferation, apoptosis, adhesion, migration, invasion, senescence, angiogenesis, and cell cycle parameters. Methods to modify cancer cells are described in Part V, including protocols for transfection, development of drug-resistance, immortalization, and transfer in vivo. In Part VI methods of coculture of different cell types and contamination of cell lines are covered.


Cancer Cell Lines

Cancer Cell Lines

Author: Bernhard Ø Palsson

Publisher: Springer Science & Business Media

Published: 2006-04-11

Total Pages: 399

ISBN-13: 0306468778

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This book describes all human leukemia-lymphoma cell lines that have been established and that grow continuously under standardised in vitro conditions. These lines are derived from cells belonging to all the major hematopoietic cell lineages, i.e. B- and T-lymphocytes, natural killer cells, granulocytic cells and megakaryocytic cells. The clinical data, the culture conditions and the major phenotypic features of the cell lines are described with citations. This book is the first book describing human leukemia-lymphoma cell lines and will be of interest to scientists involved in the areas of hematology, oncology, immunology, molecular biology and cytogenetics. Cancer Cell Lines, Volumes 1-3: These 3 volumes provide a comprehensive text on the culture of established cell lines from every type of human cancer. The volumes provide a basic manual and reference resource for every cancer research scientist using human cancer cells.


Book Synopsis Cancer Cell Lines by : Bernhard Ø Palsson

Download or read book Cancer Cell Lines written by Bernhard Ø Palsson and published by Springer Science & Business Media. This book was released on 2006-04-11 with total page 399 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes all human leukemia-lymphoma cell lines that have been established and that grow continuously under standardised in vitro conditions. These lines are derived from cells belonging to all the major hematopoietic cell lineages, i.e. B- and T-lymphocytes, natural killer cells, granulocytic cells and megakaryocytic cells. The clinical data, the culture conditions and the major phenotypic features of the cell lines are described with citations. This book is the first book describing human leukemia-lymphoma cell lines and will be of interest to scientists involved in the areas of hematology, oncology, immunology, molecular biology and cytogenetics. Cancer Cell Lines, Volumes 1-3: These 3 volumes provide a comprehensive text on the culture of established cell lines from every type of human cancer. The volumes provide a basic manual and reference resource for every cancer research scientist using human cancer cells.


The Immortal Life of Henrietta Lacks

The Immortal Life of Henrietta Lacks

Author: Rebecca Skloot

Publisher: Crown

Published: 2010-02-02

Total Pages: 386

ISBN-13: 0307589382

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#1 NEW YORK TIMES BESTSELLER • “The story of modern medicine and bioethics—and, indeed, race relations—is refracted beautifully, and movingly.”—Entertainment Weekly NOW A MAJOR MOTION PICTURE FROM HBO® STARRING OPRAH WINFREY AND ROSE BYRNE • ONE OF THE “MOST INFLUENTIAL” (CNN), “DEFINING” (LITHUB), AND “BEST” (THE PHILADELPHIA INQUIRER) BOOKS OF THE DECADE • ONE OF ESSENCE’S 50 MOST IMPACTFUL BLACK BOOKS OF THE PAST 50 YEARS • WINNER OF THE CHICAGO TRIBUNE HEARTLAND PRIZE FOR NONFICTION NAMED ONE OF THE BEST BOOKS OF THE YEAR BY The New York Times Book Review • Entertainment Weekly • O: The Oprah Magazine • NPR • Financial Times • New York • Independent (U.K.) • Times (U.K.) • Publishers Weekly • Library Journal • Kirkus Reviews • Booklist • Globe and Mail Her name was Henrietta Lacks, but scientists know her as HeLa. She was a poor Southern tobacco farmer who worked the same land as her slave ancestors, yet her cells—taken without her knowledge—became one of the most important tools in medicine: The first “immortal” human cells grown in culture, which are still alive today, though she has been dead for more than sixty years. HeLa cells were vital for developing the polio vaccine; uncovered secrets of cancer, viruses, and the atom bomb’s effects; helped lead to important advances like in vitro fertilization, cloning, and gene mapping; and have been bought and sold by the billions. Yet Henrietta Lacks remains virtually unknown, buried in an unmarked grave. Henrietta’s family did not learn of her “immortality” until more than twenty years after her death, when scientists investigating HeLa began using her husband and children in research without informed consent. And though the cells had launched a multimillion-dollar industry that sells human biological materials, her family never saw any of the profits. As Rebecca Skloot so brilliantly shows, the story of the Lacks family—past and present—is inextricably connected to the dark history of experimentation on African Americans, the birth of bioethics, and the legal battles over whether we control the stuff we are made of. Over the decade it took to uncover this story, Rebecca became enmeshed in the lives of the Lacks family—especially Henrietta’s daughter Deborah. Deborah was consumed with questions: Had scientists cloned her mother? Had they killed her to harvest her cells? And if her mother was so important to medicine, why couldn’t her children afford health insurance? Intimate in feeling, astonishing in scope, and impossible to put down, The Immortal Life of Henrietta Lacks captures the beauty and drama of scientific discovery, as well as its human consequences.


Book Synopsis The Immortal Life of Henrietta Lacks by : Rebecca Skloot

Download or read book The Immortal Life of Henrietta Lacks written by Rebecca Skloot and published by Crown. This book was released on 2010-02-02 with total page 386 pages. Available in PDF, EPUB and Kindle. Book excerpt: #1 NEW YORK TIMES BESTSELLER • “The story of modern medicine and bioethics—and, indeed, race relations—is refracted beautifully, and movingly.”—Entertainment Weekly NOW A MAJOR MOTION PICTURE FROM HBO® STARRING OPRAH WINFREY AND ROSE BYRNE • ONE OF THE “MOST INFLUENTIAL” (CNN), “DEFINING” (LITHUB), AND “BEST” (THE PHILADELPHIA INQUIRER) BOOKS OF THE DECADE • ONE OF ESSENCE’S 50 MOST IMPACTFUL BLACK BOOKS OF THE PAST 50 YEARS • WINNER OF THE CHICAGO TRIBUNE HEARTLAND PRIZE FOR NONFICTION NAMED ONE OF THE BEST BOOKS OF THE YEAR BY The New York Times Book Review • Entertainment Weekly • O: The Oprah Magazine • NPR • Financial Times • New York • Independent (U.K.) • Times (U.K.) • Publishers Weekly • Library Journal • Kirkus Reviews • Booklist • Globe and Mail Her name was Henrietta Lacks, but scientists know her as HeLa. She was a poor Southern tobacco farmer who worked the same land as her slave ancestors, yet her cells—taken without her knowledge—became one of the most important tools in medicine: The first “immortal” human cells grown in culture, which are still alive today, though she has been dead for more than sixty years. HeLa cells were vital for developing the polio vaccine; uncovered secrets of cancer, viruses, and the atom bomb’s effects; helped lead to important advances like in vitro fertilization, cloning, and gene mapping; and have been bought and sold by the billions. Yet Henrietta Lacks remains virtually unknown, buried in an unmarked grave. Henrietta’s family did not learn of her “immortality” until more than twenty years after her death, when scientists investigating HeLa began using her husband and children in research without informed consent. And though the cells had launched a multimillion-dollar industry that sells human biological materials, her family never saw any of the profits. As Rebecca Skloot so brilliantly shows, the story of the Lacks family—past and present—is inextricably connected to the dark history of experimentation on African Americans, the birth of bioethics, and the legal battles over whether we control the stuff we are made of. Over the decade it took to uncover this story, Rebecca became enmeshed in the lives of the Lacks family—especially Henrietta’s daughter Deborah. Deborah was consumed with questions: Had scientists cloned her mother? Had they killed her to harvest her cells? And if her mother was so important to medicine, why couldn’t her children afford health insurance? Intimate in feeling, astonishing in scope, and impossible to put down, The Immortal Life of Henrietta Lacks captures the beauty and drama of scientific discovery, as well as its human consequences.


Human Tumor Cells in Vitro

Human Tumor Cells in Vitro

Author: Jorgen Fogh

Publisher: Springer

Published: 2012-11-25

Total Pages: 557

ISBN-13: 9781475716498

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The study of cultured human tumor cells is a most obvious approach in experimental human cancer research. For many techniques in virology, immunology, biochemistry, and biophysics, for example, large amounts of cells may be required and such quantities are usually provided only when the cultures develop into established cell lines; when this happens, thorough characterization also becomes possible. The development of cell lines, therefore, is of prime importance. Recent major advances in research with animal cell systems see m to be a prologue for present and future efforts directed toward work with human tumor cells in culture. Conceivably, the most significant results in cancer research may develop from work with such cells, and so the time seemed right to define the present state of our knowledge. This is the first book dedicated exclusively to the subject: human tumor cells in vitro. Although so me of the fundamental aspects in the cultivation of human tumor ceIls, and the extent to which they represent human cancer in vivo are still unclear, I asked a number of the leading investigators in this area of research to collect and evaluate previous and present contributions, and to offer their thoughts on the questions to which answers are not yet available. Many of the chapters are concerned with techniques of cultivation. Cultures from some types of tumors have grown weIl; in many cases they have given rise to established cell lines.


Book Synopsis Human Tumor Cells in Vitro by : Jorgen Fogh

Download or read book Human Tumor Cells in Vitro written by Jorgen Fogh and published by Springer. This book was released on 2012-11-25 with total page 557 pages. Available in PDF, EPUB and Kindle. Book excerpt: The study of cultured human tumor cells is a most obvious approach in experimental human cancer research. For many techniques in virology, immunology, biochemistry, and biophysics, for example, large amounts of cells may be required and such quantities are usually provided only when the cultures develop into established cell lines; when this happens, thorough characterization also becomes possible. The development of cell lines, therefore, is of prime importance. Recent major advances in research with animal cell systems see m to be a prologue for present and future efforts directed toward work with human tumor cells in culture. Conceivably, the most significant results in cancer research may develop from work with such cells, and so the time seemed right to define the present state of our knowledge. This is the first book dedicated exclusively to the subject: human tumor cells in vitro. Although so me of the fundamental aspects in the cultivation of human tumor ceIls, and the extent to which they represent human cancer in vivo are still unclear, I asked a number of the leading investigators in this area of research to collect and evaluate previous and present contributions, and to offer their thoughts on the questions to which answers are not yet available. Many of the chapters are concerned with techniques of cultivation. Cultures from some types of tumors have grown weIl; in many cases they have given rise to established cell lines.


The Heterogeneity of Cancer Metabolism

The Heterogeneity of Cancer Metabolism

Author: Anne Le

Publisher: Springer

Published: 2018-06-26

Total Pages: 186

ISBN-13: 331977736X

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Genetic alterations in cancer, in addition to being the fundamental drivers of tumorigenesis, can give rise to a variety of metabolic adaptations that allow cancer cells to survive and proliferate in diverse tumor microenvironments. This metabolic flexibility is different from normal cellular metabolic processes and leads to heterogeneity in cancer metabolism within the same cancer type or even within the same tumor. In this book, we delve into the complexity and diversity of cancer metabolism, and highlight how understanding the heterogeneity of cancer metabolism is fundamental to the development of effective metabolism-based therapeutic strategies. Deciphering how cancer cells utilize various nutrient resources will enable clinicians and researchers to pair specific chemotherapeutic agents with patients who are most likely to respond with positive outcomes, allowing for more cost-effective and personalized cancer therapeutic strategies.


Book Synopsis The Heterogeneity of Cancer Metabolism by : Anne Le

Download or read book The Heterogeneity of Cancer Metabolism written by Anne Le and published by Springer. This book was released on 2018-06-26 with total page 186 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genetic alterations in cancer, in addition to being the fundamental drivers of tumorigenesis, can give rise to a variety of metabolic adaptations that allow cancer cells to survive and proliferate in diverse tumor microenvironments. This metabolic flexibility is different from normal cellular metabolic processes and leads to heterogeneity in cancer metabolism within the same cancer type or even within the same tumor. In this book, we delve into the complexity and diversity of cancer metabolism, and highlight how understanding the heterogeneity of cancer metabolism is fundamental to the development of effective metabolism-based therapeutic strategies. Deciphering how cancer cells utilize various nutrient resources will enable clinicians and researchers to pair specific chemotherapeutic agents with patients who are most likely to respond with positive outcomes, allowing for more cost-effective and personalized cancer therapeutic strategies.


RSEM: Accurate Transcript Quantification from RNA-Seq Data with Or Without a Reference Genome

RSEM: Accurate Transcript Quantification from RNA-Seq Data with Or Without a Reference Genome

Author: Applied Research Applied Research Press

Publisher:

Published: 2015-09-16

Total Pages: 44

ISBN-13: 9781517392185

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RNA-Seq is revolutionizing the way transcript abundances are measured. A key challenge in transcript quantification from RNA-Seq data is the handling of reads that map to multiple genes or isoforms. This issue is particularly important for quantification with de novo transcriptome assemblies in the absence of sequenced genomes, as it is difficult to determine which transcripts are isoforms of the same gene. A second significant issue is the design of RNA-Seq experiments, in terms of the number of reads, read length, and whether reads come from one or both ends of cDNA fragments. RSEM is an accurate and user-friendly software tool for quantifying transcript abundances from RNA-Seq data. As it does not rely on the existence of a reference genome, it is particularly useful for quantification with de novo transcriptome assemblies. In addition, RSEM has enabled valuable guidance for cost-efficient design of quantification experiments with RNA-Seq, which is currently relatively expensive.


Book Synopsis RSEM: Accurate Transcript Quantification from RNA-Seq Data with Or Without a Reference Genome by : Applied Research Applied Research Press

Download or read book RSEM: Accurate Transcript Quantification from RNA-Seq Data with Or Without a Reference Genome written by Applied Research Applied Research Press and published by . This book was released on 2015-09-16 with total page 44 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA-Seq is revolutionizing the way transcript abundances are measured. A key challenge in transcript quantification from RNA-Seq data is the handling of reads that map to multiple genes or isoforms. This issue is particularly important for quantification with de novo transcriptome assemblies in the absence of sequenced genomes, as it is difficult to determine which transcripts are isoforms of the same gene. A second significant issue is the design of RNA-Seq experiments, in terms of the number of reads, read length, and whether reads come from one or both ends of cDNA fragments. RSEM is an accurate and user-friendly software tool for quantifying transcript abundances from RNA-Seq data. As it does not rely on the existence of a reference genome, it is particularly useful for quantification with de novo transcriptome assemblies. In addition, RSEM has enabled valuable guidance for cost-efficient design of quantification experiments with RNA-Seq, which is currently relatively expensive.