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Protocols from "De novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer" Resource Report Resource Website |
Benjamin Istace, Anne Friedrich, Léo d’Agata, Sébastien Faye, Emilie Payen, Odette Beluche, Claudia Caradec, Sabrina Davidas, Corinne Cruaud, Gianni Liti, Arnaud Lemainque, Stefan Engelen, Patrick Wincker, Joseph Schacherer, Jean-Marc Aury | 10.17504/protocols.io.gvxbw7n | GigaScience Press, High molecular weight DNA extraction from all kingdoms | These protocols accompany the following GigaScience publication:Benjamin Istace, et al. (2017) De novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer. GigaScience... | Genoscope, France, Genoscope, France, Genoscope, France, Genoscope, France, Genoscope, France, Genoscope, France, Genoscope, France, Genoscope, France, Genoscope, France, Genoscope, France, Genoscope, France, Genoscope, France, Genoscope, France, Genoscope, France, Genoscope, France | https://doi.org/10.1093/gigascience/giw018 | 1 | 2017 | Benjamin Istace, Anne Friedrich, Léo d’Agata, Sébastien Faye, Emilie Payen, Odette Beluche, Claudia Caradec, Sabrina Davidas, Corinne Cruaud, Gianni Liti, Arnaud Lemainque, Stefan Engelen, Patrick Wincker, Joseph Schacherer, Jean-Marc Aury 2017. Protocols from "De novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer". protocols.io dx.doi.org/10.17504/protocols.io.gvxbw7n | 2021-03-29 03:11:57 | ||
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Protocols for "The female urinary microbiota in relation to the reproductive tract microbiota." Resource Report Resource Website |
Chen Chen, Lilan Hao, Weixia Wei, Fei Li, Liju Song, Xiaowei Zhang, Juanjuan Dai, Zhuye Jie, Jiandong Li, Xiaolei Song, Zirong Wang, Zhe Zhang, Liping Zeng, Hui Du, Huiru Tang, Tao Zhang, Huanming Yang, Jian Wang, Susanne Brix, Karsten Kristiansen, Xun Xu, Ruifang Wu, Huijue Jia | 10.17504/protocols.io.bp3wmqpe | GigaScience Press, BGI | Human urine is traditionally considered to be sterile, and whether the urine harbours distinct microbial communities has been a matter of debate. Potential links between female urine and reproductive tract microbial communities is currently not clear. Here, we collected urine samples from 147 Chinese women of reproductive age and explored the nature of colonization by 16S rRNA gene amplicon sequencing, quantitative real-time PCR, and live bacteria culture. To demonstrate the utility of this approach, the intra-individual Spearman's correlation was used to explore the relationship between urine and multiple sites of the reproductive tract. PERMANOVA was also performed to explore potential correlations between the lifestyle and various clinical factors and urinary bacterial communities. Our data demonstrated distinct bacterial communities in urine, indicative of a non-sterile environment. Streptococcus-dominated, Lactobacillus-dominated, and diverse type were the three most common urinary bacterial community types in the cohort. Detailed comparison of the urinary microbiota with multiple sites of the female reproductive tract microbiota demonstrated that the urinary microbiota were more similar to the microbiota in the cervix and uterine cavity than to those of the vagina in the same women. Our data demonstrate the potential connectivity among microbiota in the female urogenital system and provide insight and resources for exploring diseases of the urethra and genital tract. | BGI-Shenzhen, Shenzhen 518083, China., BGI-Shenzhen, Shenzhen 518083, China., Peking University Shenzhen Hospital, Shenzhen 518036, China., BGI-Shenzhen, Shenzhen 518083, China., BGI-Shenzhen, Shenzhen 518083, China., BGI-Shenzhen, Shenzhen 518083, China., Peking University Shenzhen Hospital, Shenzhen 518036, China., BGI-Shenzhen, Shenzhen 518083, China., BGI-Shenzhen, Shenzhen 518083, China., BGI-Shenzhen, Shenzhen 518083, China., BGI-Shenzhen, Shenzhen 518083, China., BGI-Shenzhen, Shenzhen 518083, China., Peking University Shenzhen Hospital, Shenzhen 518036, China., Peking University Shenzhen Hospital, Shenzhen 518036, China., Peking University Shenzhen Hospital, Shenzhen 518036, China., BGI-Shenzhen, Shenzhen 518083, China., BGI-Shenzhen, Shenzhen 518083, China., BGI-Shenzhen, Shenzhen 518083, China., Department of Biotechnology and Biomedicine, Technical University of Denmark, Soltofts Plads, Building 221, 2800 Kgs. Lyngby, Denmark., BGI-Shenzhen, Shenzhen 518083, China., BGI-Shenzhen, Shenzhen 518083, China., Peking University Shenzhen Hospital, Shenzhen 518036, China., BGI-Shenzhen, Shenzhen 518083, China. | 4 | 2020 | Chen Chen, Lilan Hao, Weixia Wei, Fei Li, Liju Song, Xiaowei Zhang, Juanjuan Dai, Zhuye Jie, Jiandong Li, Xiaolei Song, Zirong Wang, Zhe Zhang, Liping Zeng, Hui Du, Huiru Tang, Tao Zhang, Huanming Yang, Jian Wang, Susanne Brix, Karsten Kristiansen, Xun Xu, Ruifang Wu, Huijue Jia 2020. Protocols for "The female urinary microbiota in relation to the reproductive tract microbiota.". protocols.io dx.doi.org/10.17504/protocols.io.bp3wmqpe | 2021-03-29 03:08:14 | |||
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Sequencing Protocols for the One Thousand Plant Transcriptomes Initiative Resource Report Resource Website |
Eric J. Carpenter, Naim Matasci, Shuangxiu Wu, Jing Sun, Jun Yu, Fabio Rocha Jimenez Vieira, Chris Bowler, Richard G. Dorrell, Matt Gitzendanner, Ling Li, Wensi Du, Kristian Ullrich, Michael S. Barker, James H. Leebens-Mack, Gane Ka-Shu Wong | 10.17504/protocols.io.38jgrun | GigaScience Press, BGI | The 1000 Plants (1KP) initiative explored the genetic diversity of green plants (Viridiplantae) by sequencing RNA from 1,342 samples representing 1,173 species. All of the analyses done for the 1KP capstone, and previous studies on subsets of these data, are based on a series of de novo transcriptome assemblies and related outputs that will be described in this publication. We expect that these data will also be useful to other researchers with interests in specific gene families, either across the green plant tree of life or in more focused lineages. These protocols provide additional details on the sample and sequence processing, hopefully providing insight for reproducibility and tools for other researchers working on plant transcriptomics and evolution. | Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada., CyVerse, University of Arizona, Arizona, U.S.A.; Current address: Lawrence J. Ellison Institute for Transformative Medicine, University of Southern California, Los Angeles, CA 90033, U.S.A., CAS Key Laboratory of Genome Sciences and Information, Beijing, Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China., CAS Key Laboratory of Genome Sciences and Information, Beijing, Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China., CAS Key Laboratory of Genome Sciences and Information, Beijing, Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China., École Normale Supérieure, Paris., École Normale Supérieure, Paris., École Normale Supérieure, Paris., Department of Biology, University of Florida, Gainesville, Florida 32611, USA., BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, People’s Republic of China., BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, People’s Republic of China., Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany., Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ 85721 USA., Department of Plant Biology, University of Georgia, Athens, GA 30602, USA., Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada.BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, People’s Republic of China.Department of Medicine, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada. | 1 | 2019 | Eric J. Carpenter, Naim Matasci, Shuangxiu Wu, Jing Sun, Jun Yu, Fabio Rocha Jimenez Vieira, Chris Bowler, Richard G. Dorrell, Matt Gitzendanner, Ling Li, Wensi Du, Kristian Ullrich, Michael S. Barker, James H. Leebens-Mack, Gane Ka-Shu Wong 2019. Sequencing Protocols for the One Thousand Plant Transcriptomes Initiative. protocols.io dx.doi.org/10.17504/protocols.io.38jgrun | 2021-03-29 03:08:13 | |||
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Long Mate Pair Library Construction Protocol Resource Report Resource Website |
Graham J Etherington, Darren Heavens, David Baker, Ashleigh Lister, Rose McNelly, Gonzalo Garcia, Bernardo Clavijo, Iain Macaulay, Wilfried Haerty, Federica Di Palma | 10.17504/protocols.io.bd3ui8nw | GigaScience Press | Long Mate Pair Library Construction Protocol | The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom, The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom, The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom, The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom, The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom, The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom, The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom, The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom, The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom, The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom | 1 | 2020 | Graham J Etherington, Darren Heavens, David Baker, Ashleigh Lister, Rose McNelly, Gonzalo Garcia, Bernardo Clavijo, Iain Macaulay, Wilfried Haerty, Federica Di Palma 2020. Long Mate Pair Library Construction Protocol. protocols.io dx.doi.org/10.17504/protocols.io.bd3ui8nw | 2021-03-29 03:08:18 | |||
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RNA Isolation from Plant Tissue Protocol 11: Tri Reagent Method Resource Report Resource Website |
Eric Carpenter | 10.17504/protocols.io.4ydgxs6 | GigaScience Press | Implemented by: Michael Melkonian and Barbara SurekThe protocol for RNA isolation using TRI Reagent (Molecular Research Center, Cincinnati OH) is analogous to the TRIzol LS Reagent protocol except that 1 ml of TRI Reagent is added to each 250 μl of homogenized material (= approx. 50–100 mg packed cell volume) (step 3, Protocol 10). For background, TRI Reagent combines phenol and guanidine thiocyanate in a monophasic solution to inhibit RNase activity during RNA isolation.This protocol is part of a collection of eighteen protocols used to isolate total RNA from plant tissue. (RNA Isolation from Plant Tissue Collection: https://www.protocols.io/view/rna-isolation-from-plant-tissue-439gyr6) | 1 | 2019 | Eric Carpenter 2019. RNA Isolation from Plant Tissue Protocol 11: Tri Reagent Method. protocols.io dx.doi.org/10.17504/protocols.io.4ydgxs6 | 2021-03-29 03:08:20 | ||||
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RNA Isolation from Plant Tissue Resource Report Resource Website |
Marc T. J. Johnson, Eric J. Carpenter, Zhijian Tian, Richard Bruskiewich, Jason N. Burris, Charlotte T. Carrigan, Mark W. Chase, Neil D. Clarke, Sarah Covshoff, Claude W. dePamphilis, Patrick P. Edger, Falicia Goh, Sean Graham, Stephan Greiner, Julian M. Hibberd, Ingrid Jordon-Thaden, Toni M. Kutchan, James Leebens-Mack, Michael Melkonian, Nicholas Miles, Henrietta Myburg, Jordan Patterson, J. Chris Pires, Paula Ralph, Megan Rolf, Rowan F. Sage, Douglas Soltis, Pamela Soltis, Dennis Stevenson, C. Neal Stewart Jr, Barbara Surek, Christina J. M. Thomsen, Juan Carlos Villarreal, Xiaolei Wu, Yong Zhang, Michael K. Deyholos, Gane Ka-Shu Wong | 10.17504/protocols.io.439gyr6 | GigaScience Press | Methods for RNA isolationThese methods were originally included in Appendix S1 of "Evaluating Methods for Isolating Total RNA and Predicting the Success of Sequencing Phylogenetically Diverse Plant Transcriptomes" Marc T. J. Johnson et al. PLOS ONE, November 21, 2012. https://doi.org/10.1371/journal.pone.0050226Many of the protocols share elements or combine components from several methods. For each method, we describe the reagents and procedures used, and identify the researchers or institute that implemented the protocol.Due to the potential for contamination and degradation by RNase enzymes, as well as health concerns in handling some substances and chemicals, best practices in aseptic wet lab techniques must be practiced at all times during RNA isolation. Chief among these are the critical need to avoid contamination of samples by using extreme care when moving liquids and opening and closing tubes to avoid aerosols. Because of the risk of degradation by RNase enzymes, it is essential to use sterile RNase-free equipment, disposable plastics and solutions.RNase degradation and contamination can be avoided by keeping samples constantly frozen at low temperature (1. Many additional helpful tips for successful RNA isolation are available in Sambrook and Russell1 and in Appendix A of Qiagen’s RNeasy Mini Handbook downloadable from www.qiagen.com.1 Sambrook, J. & Russell, D.W. Molecular Cloning: A Laboratory Manual, 3rd ed. (Cold Spring HarborLaboratory Press, Cold Spring Harbor, NY, 2001). | Department of Biology, University of Toronto at Mississauga, Mississauga, Ontario, Canada, Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada, BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China, International Rice Research Institute, Metro Manila, Philippines, Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee, United States of America, Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom, Genome Institute of Singapore, Singapore, Singapore, Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom, Department of Biology and Intercollege Graduate Program in Plant Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, United States of America, Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States of America, Genome Institute of Singapore, Singapore, Singapore, Department of Botany and UBC Botanical Garden, University of British Columbia, Vancouver, British Columbia, Canada, Max Planck Institute for Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, Potsdam-Golm, Germany, Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom, Department of Biology, University of Florida, Gainesville, Florida, United States of America, Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America, Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America, Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America, Department of Botany, Cologne Biocenter, University of Cologne, Cologne, Germany, Department of Biology, University of Florida, Gainesville, Florida, United States of America, Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America, Department of Plant Biology, North Carolina State University, Raleigh, North Carolina, United States of America, Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada, Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States of America, Department of Biology and Intercollege Graduate Program in Plant Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, United States of America, Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America, Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada, Department of Biology, University of Florida, Gainesville, Florida, United States of America, Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America, New York Botanical Garden, Bronx, New York, United States of America, Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee, United States of America, Department of Botany, Cologne Biocenter, University of Cologne, Cologne, Germany, Department of Biology, University of Toronto at Mississauga, Mississauga, Ontario, Canada, Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, United States of America, BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China, BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China, Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada, Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada, BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, China, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada | 1 | 2019 | Marc T. J. Johnson, Eric J. Carpenter, Zhijian Tian, Richard Bruskiewich, Jason N. Burris, Charlotte T. Carrigan, Mark W. Chase, Neil D. Clarke, Sarah Covshoff, Claude W. dePamphilis, Patrick P. Edger, Falicia Goh, Sean Graham, Stephan Greiner, Julian M. Hibberd, Ingrid Jordon-Thaden, Toni M. Kutchan, James Leebens-Mack, Michael Melkonian, Nicholas Miles, Henrietta Myburg, Jordan Patterson, J. Chris Pires, Paula Ralph, Megan Rolf, Rowan F. Sage, Douglas Soltis, Pamela Soltis, Dennis Stevenson, C. Neal Stewart Jr, Barbara Surek, Christina J. M. Thomsen, Juan Carlos Villarreal, Xiaolei Wu, Yong Zhang, Michael K. Deyholos, Gane Ka-Shu Wong 2019. RNA Isolation from Plant Tissue. protocols.io dx.doi.org/10.17504/protocols.io.439gyr6 | 2021-03-29 03:09:30 | |||
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Protocols for "The genome analysis of Tripterygium wilfordii reveals TwCYP712K1 and TwCYP712K2 responsible for oxidation of friedelin in celastrol biosynthesis pathway" Resource Report Resource Website |
Tianlin Pei, Mengxiao Yan, Yu Kong, Hang Fan, Jie Liu, Mengying Cui, Yumin Fang, Binjie Ge, Jun Yang, Qing Zhao | 10.17504/protocols.io.bspfndjn | BGI, GIGA, GigaScience Press | Tripterygium wilfordii is a vine from the Celastraceae family that is used in traditional Chinese medicine (TCM). The active ingredient celastrol is a friedelane-type pentacyclic triterpenoid with putative roles as antitumor, immunosuppressive, and antiobesity agent. Here, we report a reference genome assembly of T. wilfordii with high-quality annotation by using a hybrid sequencing strategy, obtaining a 340.12 Mb total genome size, a contig N50 reaching 3.09 Mb. We successfully anchored 91.02% of the sequences into 23 pseudochromosomes using Hi-C technology and the superscaffold N50 reached 13.03 Mb. In addition, we annotated 31,593 structural genes, and a repeat percentage of 44.31%. Comparative evolutionary analyses showed that T. wilfordii diverged from species of Malpighiales approximately 102.4 million years ago. Based on integration of the genome, transcriptome and metabolite analyses, as well as in vivo and in vitro enzyme assays of the two CYP450 genes TwCYP712K1 and TwCYP712K2 the second biosynthesis step of celastrol was investigated. Syntenic analysis revealed that TwCYP712K1 and TwCYP712K2 were derived from a common ancestor. These results provide insights for further investigating pathways related to celastrol andvaluable information to aid the conservation of resources. In addition, they helped us understand the evolution of Celastrales. | Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China;State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China, Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China, Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China, Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China;State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China, Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China, Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China, Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China, Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China, Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China;State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China, Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China;State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China | 1 | 2021 | Tianlin Pei, Mengxiao Yan, Yu Kong, Hang Fan, Jie Liu, Mengying Cui, Yumin Fang, Binjie Ge, Jun Yang, Qing Zhao 2021. Protocols for "The genome analysis of Tripterygium wilfordii reveals TwCYP712K1 and TwCYP712K2 responsible for oxidation of friedelin in celastrol biosynthesis pathway". protocols.io dx.doi.org/10.17504/protocols.io.bspfndjn | 2021-03-29 03:09:43 | |||
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Protocols from "Comparative performance of the BGISEQ-500 vs Illumina sequencing platforms for palaeogenomic sequencing" Resource Report Resource Website |
Sarah Siu Tze Mak, Shyam Gopalakrishnan, Christian Caroe, Chunyu Geng, Shanlin Liu, Mikkel-Holger S Sinding, Lukas F K Kuderna, Wenwei Zhang, Shujin Fu, Filipe G Vieira, Mietje Germonpré, Hervé Bocherens, Sergey Fedorov, Bent Petersen, Thomas Sicheritz-Ponten, Tomas Marques-Bonet, Guojie Zhang, Hui Jiang, M Thomas P Gilbert | 10.17504/protocols.io.h99b996 | GigaScience Press | Ancient DNA research has been revolutionized following the development of ‘Next Generation’ Sequencing platforms. Although a number of such platforms have been applied to ancient DNA samples, the Illumina series are the dominant choice today, mainly because of high production capacities and short read production. Recently a potentially attractive alternative platform for palaeogenomic data generation has been developed, the BGISEQ-500, whose sequence output are comparable with the Illumina series. In this study, we modified the standard BGISEQ-500 library preparation specifically for use on degraded DNA, then directly compared the sequencing performance and data quality of the BGISEQ-500 to the Illumina HiSeq2500 platform, on DNA extracted from eight historic and ancient dog and wolf samples. The data generated was largely comparable between sequencing platforms, with no statistically significant difference observed for parameters including level (p=0.371) and average sequence length (p=0718) of endogenous nuclear DNA, sequence GC content (p=0.311), double-stranded DNA damage rate (p=0.309), and sequence clonality (p=0.093). Small significant differences were found in single strand DNA damage rate (δS, slightly lower for the BGISEQ-500, p=0.011) and the background rate of difference from the reference genome (θ, slightly higher for BGISEQ-500, p=0.012). This may result from the differences in amplification cycles used to PCR amplify the libraries. A significant difference was also observed in the mitochondrial DNA percentages recovered (p=0.018), although we believe this is likely a stochastic effect relating to the extremely low levels of mitochondria that were sequenced from three of the samples with overall very low levels of endogenous DNA. Although we acknowledge our analyses were limited to animal material, our observations suggest that the BGISEQ-500 holds the potential to represent valid and potentially valuable alternative platform for palaeogenomic data generation, that is worthy of future exploration by those interested in the sequencing and analysis of degraded DNA. .justify:after { content: ""; display:inline-block; width: 100%; } | Mak SST, Gopalakrishnan S, Carøe C, Geng C, Liu S, Sinding MS, Kuderna LF, Zhang W, Fu S, Vieira FG, Germonpré M, Bocherens H, Fedorov S, Petersen B, Sicheritz-Pontén T, Marques-Bonet T, Zhang G, Jiang H, Gilbert MTP, Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing. GigaScience 6(8). doi: 10.1093/gigascience/gix049 | University of Copenhagen, University of Copenhagen, University of Copenhagen, University of Copenhagen, University of Copenhagen, University of Copenhagen, University of Copenhagen, University of Copenhagen, University of Copenhagen, University of Copenhagen, University of Copenhagen, University of Copenhagen, University of Copenhagen, University of Copenhagen, University of Copenhagen, University of Copenhagen, University of Copenhagen, University of Copenhagen, University of Copenhagen | https://doi.org/10.1093/gigascience/gix049 | 1 | 2017 | Sarah Siu Tze Mak, Shyam Gopalakrishnan, Christian Caroe, Chunyu Geng, Shanlin Liu, Mikkel-Holger S Sinding, Lukas F K Kuderna, Wenwei Zhang, Shujin Fu, Filipe G Vieira, Mietje Germonpré, Hervé Bocherens, Sergey Fedorov, Bent Petersen, Thomas Sicheritz-Ponten, Tomas Marques-Bonet, Guojie Zhang, Hui Jiang, M Thomas P Gilbert 2017. Protocols from "Comparative performance of the BGISEQ-500 vs Illumina sequencing platforms for palaeogenomic sequencing". protocols.io dx.doi.org/10.17504/protocols.io.h99b996 | 2021-03-29 03:09:50 | |
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Oxford Nanopore sequencing and library construction Resource Report Resource Website |
Rui Zhang | 10.17504/protocols.io.btcwnixe | BGI, GIGA, GigaScience Press | The humpback puffer,Tetraodon palembangensis, is a species of poisonous freshwater pufferfish mainly distributed in Southeast Asia (Thailand, Laos, Malaysia and Indonesia). The humpback puffer has many interesting biological features, such as inactivity, tetrodotoxin production and body expansion. Here, we reported the first chromosome-level genome assembly of the humpback puffer. The genome size is 362 Mb with ~1.78 Mb contig N50 and ~15.8 Mb scaffold N50. Based on the genome, ~61.5Mb (18.11%) repeat sequences were identified, 19,925 genes were annotated, and 90.01% of these genes could be predicted with function. Finally, a phylogenetic tree of ten teleost fish species was constructed, which suggests that humpback puffer and T. nigroviridis shared a common ancestor at 18.1 MYA and diverged from T. rubripes at 45.8 MYA. The humpback puffer genome will be a valuable genomic resource to illustrate possible mechanisms of tetrodotoxin synthesis and tolerance. | BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China | 1 | 2021 | Rui Zhang 2021. Oxford Nanopore sequencing and library construction. protocols.io dx.doi.org/10.17504/protocols.io.btcwnixe | 2021-03-29 03:08:34 | |||
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Isolated astrocyte culture preparation - protocol 1 Resource Report Resource Website |
Yasmin Bar El | 10.17504/protocols.io.tqbemsn | GigaScience Press | Isolated astrocyte cell culture preparation. Dissociation, preparation and plating of mice cortex neurons and glia cells on MEA. Isolatioin process of the culture from neurons, to obtain an isolated astrocyte culture. | School of Physics and Astronomy, Tel-Aviv University, Tel-Aviv, Israel | 1 | 2018 | Yasmin Bar El 2018. Isolated astrocyte culture preparation - protocol 1. protocols.io dx.doi.org/10.17504/protocols.io.tqbemsn | 2021-03-29 03:08:37 | |||
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10x Genomics Library Construction Resource Report Resource Website |
Graham J Etherington, Darren Heavens, David Baker, Ashleigh Lister, Rose McNelly, Gonzalo Garcia, Bernardo Clavijo, Iain Macaulay, Wilfried Haerty, Federica Di Palma | 10.17504/protocols.io.bd3vi8n6 | GigaScience Press | 10x Genomics Library Construction | The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom, The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom, The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom, The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom, The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom, The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom, The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom, The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom, The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom, The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom | 1 | 2020 | Graham J Etherington, Darren Heavens, David Baker, Ashleigh Lister, Rose McNelly, Gonzalo Garcia, Bernardo Clavijo, Iain Macaulay, Wilfried Haerty, Federica Di Palma 2020. 10x Genomics Library Construction. protocols.io dx.doi.org/10.17504/protocols.io.bd3vi8n6 | 2021-03-29 03:07:49 | |||
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Extraction method C (FMS) Resource Report Resource Website |
Faezah Mohd Salleh, Jazmin Ramos-Madrigal, Fernando Penaloza, Shanlin Liu, Mikkel-Holger S Sinding, Riddhi P Patel, Renata Martins, Dorina Lenz, Jorns Fickel, Christian Roos, Mohd Shahir Shamsir, Mohammad Shahfiz Azman, Burton K Lim, Stephen J Rossiter, Andreas Wilting, M Thomas P Gilbert | 10.17504/protocols.io.inbcdan | GigaScience Press | This protocol provides an efficient DNA extraction and purification of historical museum hides, which potentially have been chemically tanned. | Salleh FM, Ramos-Madrigal J, Peñaloza F, Liu S, Mikkel-Holger SS, Riddhi PP, Martins R, Lenz D, Fickel J, Roos C, Shamsir MS, Azman MS, Burton KL, Stephen JR, Wilting A, Gilbert MTP, An expanded mammal mitogenome dataset from Southeast Asia. GigaScience 6(8). doi: 10.1093/gigascience/gix053 | Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark | https://doi.org/10.1093/gigascience/gix053 | 1 | 2017 | Faezah Mohd Salleh, Jazmin Ramos-Madrigal, Fernando Penaloza, Shanlin Liu, Mikkel-Holger S Sinding, Riddhi P Patel, Renata Martins, Dorina Lenz, Jorns Fickel, Christian Roos, Mohd Shahir Shamsir, Mohammad Shahfiz Azman, Burton K Lim, Stephen J Rossiter, Andreas Wilting, M Thomas P Gilbert 2017. Extraction method C (FMS). protocols.io dx.doi.org/10.17504/protocols.io.inbcdan | 2021-03-29 03:07:52 | |
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Fish genome assembly and annotation pipeline Resource Report Resource Website |
Chang Li | 10.17504/protocols.io.ss3eegn | GigaScience Press, BGI | From this protocol, we can know detail methods of assembly and annotation of the L. maculatus genome. | BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China. | 1 | 2018 | Chang Li 2018. Fish genome assembly and annotation pipeline. protocols.io dx.doi.org/10.17504/protocols.io.ss3eegn | 2021-03-29 03:11:18 | |||
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Total DNA extraction from plant tissue using CTAB method Resource Report Resource Website |
Robert Auber | 10.17504/protocols.io.bamnic5e | Wisecaver Lab, BGI, GIGA, GigaScience Press | Purdue University | 1 | 2019 | Robert Auber 2019. Total DNA extraction from plant tissue using CTAB method. protocols.io dx.doi.org/10.17504/protocols.io.bamnic5e | 2021-03-29 03:11:24 | ||||
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Short insert size WGS libraries preparation for assembly of the Lateolabrax maculatus genome Resource Report Resource Website |
Chang Li | 10.17504/protocols.io.sszeef6 | GigaScience Press, BGI | This protocol is used to clarity the process of the short insert size WGS libraries preparation for the L. maculatus. | BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China. | 1 | 2018 | Chang Li 2018. Short insert size WGS libraries preparation for assembly of the Lateolabrax maculatus genome. protocols.io dx.doi.org/10.17504/protocols.io.sszeef6 | 2021-03-29 03:11:42 | |||
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The pipeline of Hi-C assembly of the Scapharca broughtonii genome Resource Report Resource Website |
Chang-Ming Bai | 10.17504/protocols.io.z8cf9sw | BGI, GIGA, GigaScience Press | This protocol include the detailed methods of Hi-C assembly of the Scapharca broughtonii genome | Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences | 1 | 2019 | Chang-Ming Bai 2019. The pipeline of Hi-C assembly of the Scapharca broughtonii genome. protocols.io dx.doi.org/10.17504/protocols.io.z8cf9sw | 2021-03-29 03:11:48 | |||
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High-quality reference genome of the Siamese fighting fish Betta splendens, a model species for the study of aggression Resource Report Resource Website |
Guangyi Fan, Judy Chan, Kailong Ma, Simon Ming-Yuen Lee, Binrui Yang, He Zhang, Xianwei Yang, Chengcheng Shi, Henry Law, Zhitao Ren, Qiwu Xu, Qun Liu, Jiahao Wang, Wenbin Chen, Libin Shao, David Gonçalves, Andreia Ramos, Sara D. Cardoso, Min Guo, Jing Cai, Xun Xu, Jian Wang, Huanming Yang, Xin Liu, Yitao Wang | 10.17504/protocols.io.qvddw26 | GigaScience Press, BGI | Siamese fighting fish Betta splendens are notorious for their aggressiveness and accordingly have been widely used to study aggression. However, the lack of a reference genome has so far limited the understanding of the genetic basis of aggression in this species. Here we present the first reference genome assembly of the Siamese fighting fish.We first sequenced and de novo assembled a 465.24 Mb genome for the B. splendens variety Giant, with a weighted average (N50) scaffold size of 949.03 Kb and an N50 contig size of 19.01 Kb, covering 99.93% of the estimated genome size. To obtain a chromosome-level genome assembly, we constructed one Hi-C library and sequenced 75.24 Gb reads using the BGISEQ-500 platform. We anchored approximately 93% of the scaffold sequences into 21 chromosomes and evaluated the quality of our assembly using the high contact frequency heatmap and BUSCO. We also performed comparative chromosome analyses between Oryzias latipes and B. splendens, revealing a chromosome conservation evolution in B. splendens. We predicted a total of 23,981 genes assisted by RNA-seq data generated from brain, liver, muscle and heart tissues of Giant, and annotated 15% repetitive sequences in the genome. Additionally, we resequenced other five B. splendens varieties and detected ~3.4M single-nucleotide variations (SNVs) and 27,305 indels.We provide the first chromosome-level genome for the Siamese fighting fish. The genome will lay a valuable foundation for future research on aggression in B. splendens. | State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China, State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China, BGI-Shenzhen, Shenzhen 518083, China, State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China, State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China, BGI-Qingdao, Qingdao 266500, China, BGI-Qingdao, Qingdao 266500, China, BGI-Qingdao, Qingdao 266500, China, State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China, State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China, BGI-Qingdao, Qingdao 266500, China, BGI-Qingdao, Qingdao 266500, China, BGI-Qingdao, Qingdao 266500, China, BGI-Shenzhen, Shenzhen 518083, China, BGI-Qingdao, Qingdao 266500, China, Institute of Science and Environment, University of Saint Joseph, Macao SAR, China, Institute of Science and Environment, University of Saint Joseph, Macao SAR, China, Instituto Gulbenkian de Ciência, Oeiras, Portugal, State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China, State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China, BGI-Qingdao, Qingdao 266500, China, BGI-Shenzhen, Shenzhen 518083, China, BGI-Shenzhen, Shenzhen 518083, China, BGI-Qingdao, Qingdao 266500, China, State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China | 1 | 2018 | Guangyi Fan, Judy Chan, Kailong Ma, Simon Ming-Yuen Lee, Binrui Yang, He Zhang, Xianwei Yang, Chengcheng Shi, Henry Law, Zhitao Ren, Qiwu Xu, Qun Liu, Jiahao Wang, Wenbin Chen, Libin Shao, David Gonçalves, Andreia Ramos, Sara D. Cardoso, Min Guo, Jing Cai, Xun Xu, Jian Wang, Huanming Yang, Xin Liu, Yitao Wang 2018. High-quality reference genome of the Siamese fighting fish Betta splendens, a model species for the study of aggression. protocols.io dx.doi.org/10.17504/protocols.io.qvddw26 | 2021-03-29 03:08:45 | |||
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The calculation of gut metabolic modules from gene profile Resource Report Resource Website |
Qi Wang | 10.17504/protocols.io.bq6gmzbw | BGI, GIGA, GigaScience Press | The calculation of gut metabolic modules from gene profile | BGI | 1 | 2021 | Qi Wang 2021. The calculation of gut metabolic modules from gene profile. protocols.io dx.doi.org/10.17504/protocols.io.bq6gmzbw | 2021-03-29 03:08:54 | |||
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RNA Isolation from Plant Tissue Protocol 14: Ambion Trizol RNA Extraction in Microcentrifuge Tubes with Turbo DNAfree Digestion Resource Report Resource Website |
Eric Carpenter | 10.17504/protocols.io.4u6gwze | GigaScience Press | Implemented by: Ingrid Jordon-Thaden and Nicholas Miles (Soltis Labs)This procedure eliminates the mortar and pestle homogenization of tissues and instead grinds tissue in 2 ml microcentrifuge tubes. The method closely follows Ambion’s protocols and could be used in a 96-well format. This method worked great for species that proved to be difficult to extract with other methods (i.e. woody and aquatic plants).This protocol is part of a collection of eighteen protocols used to isolate total RNA from plant tissue. (RNA Isolation from Plant Tissue Collection: https://www.protocols.io/view/rna-isolation-from-plant-tissue-439gyr6) | 1 | 2019 | Eric Carpenter 2019. RNA Isolation from Plant Tissue Protocol 14: Ambion Trizol RNA Extraction in Microcentrifuge Tubes with Turbo DNAfree Digestion. protocols.io dx.doi.org/10.17504/protocols.io.4u6gwze | 2021-03-29 03:09:07 | ||||
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Protocols for The Healthy Brain Network Serial Scanning Initiative (Sessions 1-14) Resource Report Resource Website |
David O'Connor, Natan Vega Potler, Meagan Kovacs, Ting Xu, Lei Ai, John Pellman, Tamara Vanderwal, Lucas Parra, Samantha Cohen, Satrajit Ghosh, Jasmine Escalera, Natalie Grant-Villegas, Yael Osman, Anastasia Bui, R Cameron Craddock, Michael P Milham | 10.17504/protocols.io.gxcbxiw | GigaScience Press | These protocols accompany the following publication:David O'Connor, et. al. (2017) The Healthy Brain Network Serial Scanning Initiative. GigaScience... | , , , , , , , , , , , , , , , | 1 | 2017 | David O'Connor, Natan Vega Potler, Meagan Kovacs, Ting Xu, Lei Ai, John Pellman, Tamara Vanderwal, Lucas Parra, Samantha Cohen, Satrajit Ghosh, Jasmine Escalera, Natalie Grant-Villegas, Yael Osman, Anastasia Bui, R Cameron Craddock, Michael P Milham 2017. Protocols for The Healthy Brain Network Serial Scanning Initiative (Sessions 1-14). protocols.io dx.doi.org/10.17504/protocols.io.gxcbxiw | 2021-03-29 03:09:21 |
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