NASA GeneLab RNA-seq consensus pipeline: Standardized processing of short-read RNA-seq data
Summary: With the development of transcriptomic technologies, we are able to quantify precise changes in gene expression profiles from astronauts and other organisms exposed to spaceflight. Members of NASA GeneLab and GeneLab-associated analysis working groups (AWGs) have developed a consensus pipel...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2021-04-01
|
| Series: | iScience |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2589004221003291 |
| id |
doaj-db05f4c13f9d4050b634492f121e3d68 |
|---|---|
| record_format |
Article |
| collection |
DOAJ |
| language |
English |
| format |
Article |
| sources |
DOAJ |
| author |
Eliah G. Overbey Amanda M. Saravia-Butler Zhe Zhang Komal S. Rathi Homer Fogle Willian A. da Silveira Richard J. Barker Joseph J. Bass Afshin Beheshti Daniel C. Berrios Elizabeth A. Blaber Egle Cekanaviciute Helio A. Costa Laurence B. Davin Kathleen M. Fisch Samrawit G. Gebre Matthew Geniza Rachel Gilbert Simon Gilroy Gary Hardiman Raúl Herranz Yared H. Kidane Colin P.S. Kruse Michael D. Lee Ted Liefeld Norman G. Lewis J. Tyson McDonald Robert Meller Tejaswini Mishra Imara Y. Perera Shayoni Ray Sigrid S. Reinsch Sara Brin Rosenthal Michael Strong Nathaniel J. Szewczyk Candice G.T. Tahimic Deanne M. Taylor Joshua P. Vandenbrink Alicia Villacampa Silvio Weging Chris Wolverton Sarah E. Wyatt Luis Zea Sylvain V. Costes Jonathan M. Galazka |
| spellingShingle |
Eliah G. Overbey Amanda M. Saravia-Butler Zhe Zhang Komal S. Rathi Homer Fogle Willian A. da Silveira Richard J. Barker Joseph J. Bass Afshin Beheshti Daniel C. Berrios Elizabeth A. Blaber Egle Cekanaviciute Helio A. Costa Laurence B. Davin Kathleen M. Fisch Samrawit G. Gebre Matthew Geniza Rachel Gilbert Simon Gilroy Gary Hardiman Raúl Herranz Yared H. Kidane Colin P.S. Kruse Michael D. Lee Ted Liefeld Norman G. Lewis J. Tyson McDonald Robert Meller Tejaswini Mishra Imara Y. Perera Shayoni Ray Sigrid S. Reinsch Sara Brin Rosenthal Michael Strong Nathaniel J. Szewczyk Candice G.T. Tahimic Deanne M. Taylor Joshua P. Vandenbrink Alicia Villacampa Silvio Weging Chris Wolverton Sarah E. Wyatt Luis Zea Sylvain V. Costes Jonathan M. Galazka NASA GeneLab RNA-seq consensus pipeline: Standardized processing of short-read RNA-seq data iScience Omics Space Sciences |
| author_facet |
Eliah G. Overbey Amanda M. Saravia-Butler Zhe Zhang Komal S. Rathi Homer Fogle Willian A. da Silveira Richard J. Barker Joseph J. Bass Afshin Beheshti Daniel C. Berrios Elizabeth A. Blaber Egle Cekanaviciute Helio A. Costa Laurence B. Davin Kathleen M. Fisch Samrawit G. Gebre Matthew Geniza Rachel Gilbert Simon Gilroy Gary Hardiman Raúl Herranz Yared H. Kidane Colin P.S. Kruse Michael D. Lee Ted Liefeld Norman G. Lewis J. Tyson McDonald Robert Meller Tejaswini Mishra Imara Y. Perera Shayoni Ray Sigrid S. Reinsch Sara Brin Rosenthal Michael Strong Nathaniel J. Szewczyk Candice G.T. Tahimic Deanne M. Taylor Joshua P. Vandenbrink Alicia Villacampa Silvio Weging Chris Wolverton Sarah E. Wyatt Luis Zea Sylvain V. Costes Jonathan M. Galazka |
| author_sort |
Eliah G. Overbey |
| title |
NASA GeneLab RNA-seq consensus pipeline: Standardized processing of short-read RNA-seq data |
| title_short |
NASA GeneLab RNA-seq consensus pipeline: Standardized processing of short-read RNA-seq data |
| title_full |
NASA GeneLab RNA-seq consensus pipeline: Standardized processing of short-read RNA-seq data |
| title_fullStr |
NASA GeneLab RNA-seq consensus pipeline: Standardized processing of short-read RNA-seq data |
| title_full_unstemmed |
NASA GeneLab RNA-seq consensus pipeline: Standardized processing of short-read RNA-seq data |
| title_sort |
nasa genelab rna-seq consensus pipeline: standardized processing of short-read rna-seq data |
| publisher |
Elsevier |
| series |
iScience |
| issn |
2589-0042 |
| publishDate |
2021-04-01 |
| description |
Summary: With the development of transcriptomic technologies, we are able to quantify precise changes in gene expression profiles from astronauts and other organisms exposed to spaceflight. Members of NASA GeneLab and GeneLab-associated analysis working groups (AWGs) have developed a consensus pipeline for analyzing short-read RNA-sequencing data from spaceflight-associated experiments. The pipeline includes quality control, read trimming, mapping, and gene quantification steps, culminating in the detection of differentially expressed genes. This data analysis pipeline and the results of its execution using data submitted to GeneLab are now all publicly available through the GeneLab database. We present here the full details and rationale for the construction of this pipeline in order to promote transparency, reproducibility, and reusability of pipeline data; to provide a template for data processing of future spaceflight-relevant datasets; and to encourage cross-analysis of data from other databases with the data available in GeneLab. |
| topic |
Omics Space Sciences |
| url |
http://www.sciencedirect.com/science/article/pii/S2589004221003291 |
| work_keys_str_mv |
AT eliahgoverbey nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT amandamsaraviabutler nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT zhezhang nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT komalsrathi nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT homerfogle nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT willianadasilveira nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT richardjbarker nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT josephjbass nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT afshinbeheshti nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT danielcberrios nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT elizabethablaber nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT eglecekanaviciute nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT helioacosta nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT laurencebdavin nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT kathleenmfisch nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT samrawitggebre nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT matthewgeniza nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT rachelgilbert nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT simongilroy nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT garyhardiman nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT raulherranz nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT yaredhkidane nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT colinpskruse nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT michaeldlee nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT tedliefeld nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT normanglewis nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT jtysonmcdonald nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT robertmeller nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT tejaswinimishra nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT imarayperera nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT shayoniray nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT sigridsreinsch nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT sarabrinrosenthal nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT michaelstrong nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT nathanieljszewczyk nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT candicegttahimic nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT deannemtaylor nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT joshuapvandenbrink nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT aliciavillacampa nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT silvioweging nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT chriswolverton nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT sarahewyatt nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT luiszea nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT sylvainvcostes nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata AT jonathanmgalazka nasagenelabrnaseqconsensuspipelinestandardizedprocessingofshortreadrnaseqdata |
| _version_ |
1721507868818014208 |
| spelling |
doaj-db05f4c13f9d4050b634492f121e3d682021-04-26T05:58:00ZengElsevieriScience2589-00422021-04-01244102361NASA GeneLab RNA-seq consensus pipeline: Standardized processing of short-read RNA-seq dataEliah G. Overbey0Amanda M. Saravia-Butler1Zhe Zhang2Komal S. Rathi3Homer Fogle4Willian A. da Silveira5Richard J. Barker6Joseph J. Bass7Afshin Beheshti8Daniel C. Berrios9Elizabeth A. Blaber10Egle Cekanaviciute11Helio A. Costa12Laurence B. Davin13Kathleen M. Fisch14Samrawit G. Gebre15Matthew Geniza16Rachel Gilbert17Simon Gilroy18Gary Hardiman19Raúl Herranz20Yared H. Kidane21Colin P.S. Kruse22Michael D. Lee23Ted Liefeld24Norman G. Lewis25J. Tyson McDonald26Robert Meller27Tejaswini Mishra28Imara Y. Perera29Shayoni Ray30Sigrid S. Reinsch31Sara Brin Rosenthal32Michael Strong33Nathaniel J. Szewczyk34Candice G.T. Tahimic35Deanne M. Taylor36Joshua P. Vandenbrink37Alicia Villacampa38Silvio Weging39Chris Wolverton40Sarah E. Wyatt41Luis Zea42Sylvain V. Costes43Jonathan M. Galazka44Department of Genome Sciences, University of Washington, Seattle, WA 98195, USALogyx, LLC, Mountain View, CA 94043, USA; Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USADepartment of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA 19104, USADepartment of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA 19104, USAThe Bionetics Corporation, NASA Ames Research Center, Moffett Field, CA 94035, USA; Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USAInstitute for Global Food Security (IGFS) & School of Biological Sciences, Queen's University Belfast, Belfast, UKDepartment of Botany, University of Wisconsin, Madison, WI 53706, USAMRC Versus Arthritis Centre for Musculoskeletal Ageing Research, Royal Derby Hospital, University of Nottingham & National Institute for Health Research Nottingham Biomedical Research Centre, Derby DE22 3DT, UKKBR, NASA Ames Research Center, Moffett Field, CA 94035, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USASpace Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USACenter for Biotechnology and Interdisciplinary Studies, Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USASpace Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USADepartments of Pathology, and of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USAInstitute of Biological Chemistry, Washington State University, Pullman, WA 99164, USACenter for Computational Biology & Bioinformatics, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USASpace Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA; KBR, NASA Ames Research Center, Moffett Field, CA 94035, USAPhylos Bioscience, Portland, OR 97214, USANASA Postdoctoral Program, Universities Space Research Association, NASA Ames Research Center, Moffett Field, CA 94035, USADepartment of Botany, University of Wisconsin, Madison, WI 53706, USAInstitute for Global Food Security (IGFS) & School of Biological Sciences, Queen's University Belfast, Belfast, UK; Medical University of South Carolina, Charleston, SC, USACentro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, SpainCenter for Pediatric Bone Biology and Translational Research, Texas Scottish Rite Hospital for Children, 2222 Welborn St., Dallas, TX 75219, USALos Alamos National Laboratory, Bioscience Division, Los Alamos, NM 87545, USAExobiology Branch, NASA Ames Research Center, Mountain View, CA 94035, USA; Blue Marble Space Institute of Science, Seattle, WA 98154, USADepartment of Medicine, University of California San Diego, San Diego, CA 92093, USAInstitute of Biological Chemistry, Washington State University, Pullman, WA 99164, USADepartment of Radiation Medicine, Georgetown University Medical Center, Washington, DC 20007, USADepartment of Neurobiology and Pharmacology, Morehouse School of Medicine, Atlanta, GA 30310, USADepartment of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USADepartment of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USANGM Biopharmaceuticals, South San Francisco, CA 94080, USASpace Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USACenter for Computational Biology & Bioinformatics, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USANational Jewish Health, Center for Genes, Environment, and Health, 1400 Jackson Street, Denver, CO 80206, USAOhio Musculoskeletal and Neurological Institute and Department of Biomedical Sciences, Ohio University, Athens, OH 43147, USADepartment of Biology, University of North Florida, Jacksonville, FL 32224, USADepartment of Biomedical and Health Informatics, Children's Hospital of Philadelphia and the Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USADepartment of Biology, Louisiana Tech University, Ruston, LA 71272, USACentro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, SpainInstitute of Computer Science, Martin-Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, Halle 06120, GermanyDepartment of Botany and Microbiology, Ohio Wesleyan University, Delaware, OH, USADepartment of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA; Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, OH 45701, USABioServe Space Technologies, Aerospace Engineering Sciences Department, University of Colorado Boulder, Boulder 80303 USASpace Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA; Corresponding authorSpace Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA; Corresponding authorSummary: With the development of transcriptomic technologies, we are able to quantify precise changes in gene expression profiles from astronauts and other organisms exposed to spaceflight. Members of NASA GeneLab and GeneLab-associated analysis working groups (AWGs) have developed a consensus pipeline for analyzing short-read RNA-sequencing data from spaceflight-associated experiments. The pipeline includes quality control, read trimming, mapping, and gene quantification steps, culminating in the detection of differentially expressed genes. This data analysis pipeline and the results of its execution using data submitted to GeneLab are now all publicly available through the GeneLab database. We present here the full details and rationale for the construction of this pipeline in order to promote transparency, reproducibility, and reusability of pipeline data; to provide a template for data processing of future spaceflight-relevant datasets; and to encourage cross-analysis of data from other databases with the data available in GeneLab.http://www.sciencedirect.com/science/article/pii/S2589004221003291OmicsSpace Sciences |