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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 | DOI: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 https://dx.doi.org/10.17504/protocols.io.bspfndjn | 2021-04-15 09:16:16 | |||
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RNA extraction protocol (Trizol) Resource Report Resource Website |
Hebert F.O., Grambauer S., Barber I., Landry C.R., Aubin-Horth N. | DOI:10.17504/protocols.io.ew7bfhn | GigaScience Press | This protocol describes how to extract total RNA from flatworms. It is from:Hebert, F, O; Grambauer, S; Barber, I; Landry, C, R; Aubin-Horth, N (2016): Reference transcriptome sequence resource for the study of the Cestode Schistocephalus solidus, a threespine stickleback parasite. GigaScience Database. http://dx.doi.org/10.5524/100197 | Hébert FO, Grambauer S, Barber I, Landry CR, Aubin-Horth N, Transcriptome sequences spanning key developmental states as a resource for the study of the cestode , a threespine stickleback parasite. GigaScience doi: 10.1186/s13742-016-0128-3 | GigaScience, GigaScience, GigaScience, GigaScience, GigaScience | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4891850/ | 1 | 2016 | Hebert F.O., Grambauer S., Barber I., Landry C.R., Aubin-Horth N. 2016. RNA extraction protocol (Trizol). protocols.io https://dx.doi.org/10.17504/protocols.io.ew7bfhn | 2021-04-15 09:16:32 | |
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Extraction method B (FMS and CR) 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 | DOI:10.17504/protocols.io.im9cc96 | GigaScience Press | This protocol allows for adequate DNA extraction from fresh blood samples. | 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 B (FMS and CR). protocols.io https://dx.doi.org/10.17504/protocols.io.im9cc96 | 2021-04-15 09:16:41 | |
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DNA extraction for the Betta splendens genome Resource Report Resource Website |
Kailong Ma | DOI:10.17504/protocols.io.qvedw3e | GigaScience Press, BGI | This protocol is used to clarity the process of total DNA extraction for our Betta splendens genome. | BGI-Shenzhen | 1 | 2018 | Kailong Ma 2018. DNA extraction for the Betta splendens genome. protocols.io https://dx.doi.org/10.17504/protocols.io.qvedw3e | 2021-04-15 09:16:23 | |||
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Plumage pigments identification by High-performance liquid chromatography Resource Report Resource Website |
Guangqi Gao, Meng Xu, Yongchun Zuo, Yulan Yang, Chunling Bai, Junyang Xu, Zhuying Wei, Jiumeng Min, Guanghua Su, Xianqiang Zhou, Jun Guo, Yu Hao, Guiping Zhang, Xukui Yang, Xiaomin Xu, Randall B Widelitz, Cheng-Ming Chuong, Chi Zhang, Jun Yin, Guangpeng Li | DOI:10.17504/protocols.io.sjtecnn | GigaScience Press | As one of the most recognizable characteristics in birds, plumage colour has a high impact on understanding the evolution and mechanisms of colouration. Feather and skin are ideal tissues to explore the genomics and complexity of colour patterns in vertebrates. Two species of the genus Chrysolophus, golden pheasant (Chrysolophus pictus) and Lady Amherst’s pheasant (Chrysolophus amherstiae), exhibit brilliant colours in their plumage, but with extreme phenotypic differences, making these two species great models to investigate plumage colouration mechanisms in birds. Here we provide details of the protocols used for plumage pigments identification by High-performance liquid chromatography. The fat-soluble pigments (carotenoids) and oxidation products of melanins (TTCA and PTCA) can be qualitatively and quantificationally analyzed by HPLC with the corresponding standards, respectively. | The State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010070, China., BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China, The State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010070, China., BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China, The State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010070, China., BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China, The State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010070, China., BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China, The State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010070, China., BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China, College of Life Science, Inner Mongolia Agricultural University, Hohhot, 010018, China., College of Life Science, Inner Mongolia Agricultural University, Hohhot, 010018, China., BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China, BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China, BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China, Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA., Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA., BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China, College of Life Science, Inner Mongolia Agricultural University, Hohhot, 010018, China., The State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010070, China. | 1 | 2018 | Guangqi Gao, Meng Xu, Yongchun Zuo, Yulan Yang, Chunling Bai, Junyang Xu, Zhuying Wei, Jiumeng Min, Guanghua Su, Xianqiang Zhou, Jun Guo, Yu Hao, Guiping Zhang, Xukui Yang, Xiaomin Xu, Randall B Widelitz, Cheng-Ming Chuong, Chi Zhang, Jun Yin, Guangpeng Li 2018. Plumage pigments identification by High-performance liquid chromatography. protocols.io https://dx.doi.org/10.17504/protocols.io.sjtecnn | 2021-04-15 09:16:37 | |||
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RNA Isolation from Plant Tissue Protocol 4: CTAB-PVP-TRIzol Method Resource Report Resource Website |
Eric Carpenter | DOI:10.17504/protocols.io.4q5gvy6 | GigaScience Press, BGI | Implemented by: Beijing Genomics InstituteThis 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 4: CTAB-PVP-TRIzol Method. protocols.io https://dx.doi.org/10.17504/protocols.io.4q5gvy6 | 2021-04-15 09:16:40 | ||||
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Electrophysiology Resource Report Resource Website |
Yasmin Bar El | DOI:10.17504/protocols.io.tqeemte | GigaScience Press | Electrophysiology by MEA. Electrical recording and stimulation of the cultures using MEA set-up (by Multichannel Systems). | School of Physics and Astronomy, Tel-Aviv University, Tel-Aviv, Israel | 1 | 2018 | Yasmin Bar El 2018. Electrophysiology. protocols.io https://dx.doi.org/10.17504/protocols.io.tqeemte | 2021-04-15 09:16:46 | |||
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Illumina GAII Library Construction and Sequencing for RNA Seq 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 | DOI:10.17504/protocols.io.38mgru6 | GigaScience Press, BGI | Illumina GAII Library Construction and Sequencing for RNA Seq | 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. Illumina GAII Library Construction and Sequencing for RNA Seq. protocols.io https://dx.doi.org/10.17504/protocols.io.38mgru6 | 2021-04-15 09:16:29 | |||
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BGISeq-500 library construction Protocol 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 | DOI:10.17504/protocols.io.iamcac6 | GigaScience Press | This single-tube library construction protocol is for degraded DNA using BGISeq-500 sequencing platform. | Mak SST, Gopalakrishnan S, Carøe C, Geng C, Liu S, Sinding MS, Kuderna LFK, 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. BGISeq-500 library construction Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.iamcac6 | 2021-04-15 09:16:30 | |
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Protocols for "Shotgun Metagenomics of 361 elderly women reveals gut microbiome change in bone mass loss" Resource Report Resource Website |
Qi Wang, Qiang Sun, Xiaoping Li, Zhefeng Wang, Haotian Zheng, Yanmei Ju, Ruijin Guo, Songlin Peng, Huijue Jia | DOI:10.17504/protocols.io.bqwwmxfe | BGI, GIGA, GigaScience Press | Bone mass loss contributes to the risk of bone fracture in the elderly. Many factors including age, obesity, estrogen and diet, are associated with bone mass loss. Mice studies suggested that the gut microbiome might affect the bone mass by regulating the immune system, however there has been little evidence from human studies. Bone loss increases after menopause. Therefore, we have recruited 361 Chinese post-menopausal women to collect their fecal samples and metadata to conduct metagenome-wide association study (MWAS) to investigate the influence of the gut microbiome on bone health. Gut microbiome sequencing data were produced using BGISEQ500 sequencing, Bone mineral density (BMD) was calculated using Hologic dual energy X-ray machine, body mass index (BMI) and age were also recorded.This collected data allows exploration of the gut microbial diversity and their links to bone mass loss, as well as microbial markers for bone mineral density. In addition, these data are potentially useful in studying the role the gut microbiota might play in bone mass loss and in exploring the bone mass loss process. | BGI-Shenzhen, Shenzhen 518083, China;School of Future Technology, University of Chinese Academy of Sciences, Beijing, 101408, China., BGI-Shenzhen, Shenzhen 518083, China;Department of Statistical Sciences, University of Toronto, Toronto, Canada, BGI-Shenzhen, Shenzhen 518083, China, Department of Spine Surgery, Shenzhen People's Hospital, Ji Nan University Second College of Medicine, 518020, Shenzhen, China., BGI-Shenzhen, Shenzhen 518083, China;School of Future Technology, University of Chinese Academy of Sciences, Beijing, 101408, China., BGI-Shenzhen, Shenzhen 518083, China;School of Future Technology, University of Chinese Academy of Sciences, Beijing, 101408, China., BGI-Shenzhen, Shenzhen 518083, China;Macau University of Science and Technology, Taipa, Macau 999078, China, Department of Spine Surgery, Shenzhen People's Hospital, Ji Nan University Second College of Medicine, 518020, Shenzhen, China., BGI-Shenzhen, Shenzhen 518083, China; Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China | 1 | 2020 | Qi Wang, Qiang Sun, Xiaoping Li, Zhefeng Wang, Haotian Zheng, Yanmei Ju, Ruijin Guo, Songlin Peng, Huijue Jia 2020. Protocols for "Shotgun Metagenomics of 361 elderly women reveals gut microbiome change in bone mass loss". protocols.io https://dx.doi.org/10.17504/protocols.io.bqwwmxfe | 2021-04-15 09:16:58 | |||
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Illumina library construction Protocol 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 | DOI:10.17504/protocols.io.iajcacn | GigaScience Press | This single-tube library construction protocol is for degraded DNA using adapters for the Illumina platform. | Mak SST, Gopalakrishnan S, Carøe C, Geng C, Liu S, Sinding MS, Kuderna LFK, 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. Illumina library construction Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.iajcacn | 2021-04-15 09:16:36 | |
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Fish genome assembly and annotation pipeline Resource Report Resource Website |
Chang Li | DOI: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 https://dx.doi.org/10.17504/protocols.io.ss3eegn | 2021-04-15 09:16:38 | |||
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Total DNA extraction from plant tissue using CTAB method Resource Report Resource Website |
Robert Auber | DOI: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 https://dx.doi.org/10.17504/protocols.io.bamnic5e | 2021-04-15 09:16:41 | ||||
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RNA Isolation from Plant Tissue Protocol 17: Invitrogen PureLink-Qiagen RNeasy Hybrid Resource Report Resource Website |
Eric Carpenter | DOI:10.17504/protocols.io.4uwgwxe | GigaScience Press | Implemented by: Patrick Edger and J. Chris PiresFor a small number of samples the Invitrogen PureLink™ RNA Mini Kit (Cat #12183-018A) was used to isolate total RNA while the Qiagen RNeasy MinElute Cleanup Kit (Cat #74204) was used to purify and concentrate total RNA. The methods followed the manufacturer’s instructions and thus they are not repeated here.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 17: Invitrogen PureLink-Qiagen RNeasy Hybrid. protocols.io https://dx.doi.org/10.17504/protocols.io.4uwgwxe | 2021-04-15 09:17:00 | ||||
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The pipeline of Hi-C assembly of the Scapharca broughtonii genome Resource Report Resource Website |
Chang-Ming Bai | DOI: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 https://dx.doi.org/10.17504/protocols.io.z8cf9sw | 2021-04-15 09:17:01 | |||
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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 | DOI: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 https://dx.doi.org/10.17504/protocols.io.gvxbw7n | 2021-04-15 09:16:52 | ||
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Extraction method A 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 | DOI:10.17504/protocols.io.iabcaan | GigaScience Press | This protocol provides an efficient DNA extraction and purification of historical museum hides, which potentially have been chemically tanned. | Mak SST, Gopalakrishnan S, Carøe C, Geng C, Liu S, Sinding MS, Kuderna LFK, 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. Extraction method A. protocols.io https://dx.doi.org/10.17504/protocols.io.iabcaan | 2021-04-15 09:17:01 | |
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Simulating reads for detection of transportable element insertions Resource Report Resource Website |
Qichao Yu, Wei Zhang, Xiaolong Zhang, Yongli Zeng, Yeming Wang, Yanhui Wang, Liqin Xu, Xiaoyun Huang, Nannan Li, Xinlan Zhou, Jie Lu, Xiaosen Guo, Guibo Li, Yong Hou, Shiping Liu, Bo Li | DOI:10.17504/protocols.io.imrcc56 | GigaScience Press | We simulate paired-end reads for testing the accuracy and sensitivity of our computer program for detection of transportable element (TE) insertions (also called Mobile Element Insertions, MEIs). we named the software "Specific Insertions Detector (SID)". | Yu Q, Zhang W, Zhang X, Zeng Y, Wang Y, Wang Y, Xu L, Huang X, Li N, Zhou X, Lu J, Guo X, Li G, Hou Y, Liu S, Li B, Population-wide sampling of retrotransposon insertion polymorphisms using deep sequencing and efficient detection. GigaScience 6(9). doi: 10.1093/gigascience/gix066 | BGI Shenzhen, BGI Shenzhen, BGI Shenzhen, BGI Shenzhen, BGI Shenzhen, BGI Shenzhen, BGI Shenzhen, BGI Shenzhen, BGI Shenzhen, BGI Shenzhen, BGI Shenzhen, BGI Shenzhen, BGI Shenzhen, BGI Shenzhen, BGI Shenzhen, BGI Shenzhen | https://doi.org/10.1093/gigascience/gix066 | 1 | 2018 | Qichao Yu, Wei Zhang, Xiaolong Zhang, Yongli Zeng, Yeming Wang, Yanhui Wang, Liqin Xu, Xiaoyun Huang, Nannan Li, Xinlan Zhou, Jie Lu, Xiaosen Guo, Guibo Li, Yong Hou, Shiping Liu, Bo Li 2018. Simulating reads for detection of transportable element insertions. protocols.io https://dx.doi.org/10.17504/protocols.io.imrcc56 | 2021-04-15 09:17:07 | |
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RNA Isolation from Plant Tissue Protocol 18: innuPREP Plant RNA Kit Resource Report Resource Website |
Eric Carpenter | DOI:10.17504/protocols.io.4uxgwxn | GigaScience Press | Implemented by: Michael Melkonian and Barbara SurekA small number of algae samples were extracted using the innuPREP Plant RNA Kit (Analytik Jena, Jena Germany) with either the PL and RL lysis buffer. The method followed the manufacturer’s protocols and so they are not repeated here.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 18: innuPREP Plant RNA Kit. protocols.io https://dx.doi.org/10.17504/protocols.io.4uxgwxn | 2021-04-15 09:17:08 | ||||
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Protocols for "Chromosome-level genome assembly of the humpback puffer, Tetraodon palembangensis" Resource Report Resource Website |
Rui Zhang, Chang Li, Mengjun Yu, Xiaoyun Huang, Mengqi Zhang, Shanshan Liu, Shanshan Pan, Weizhen Xue, Congyan Wang, Chunyan Mao, He Zhang, Guangyi Fan | DOI:10.17504/protocols.io.bs8inhue | BGI, GIGA, GigaScience Press | In this study we assembled the first chromosome-level genome assembly of the humpback puffer (Tetraodon palembangensis), a species of poisonous freshwater pufferfish mainly distributed in Southeast Asia. This utilized Oxford Nanopore and BGISEQ-500 sequencing, stLFR libraries and Hi-C assembly, and the protocols for nucleic acid extraction, library construction and sequencing are all made available here. The resulting genome size was 362 Mb with a ~1.78 Mb contig N50 and ~15.8 Mb scaffold N50. Based on the assembled 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 successfully constructed using this and public data. These protocols are made available for others carrying vertebrate genome assembly, and the open data and published study for comparative genome studies. | BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.Department of Biology, Hong Kong Baptist University, Hong Kong, China, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China | 1 | 2021 | Rui Zhang, Chang Li, Mengjun Yu, Xiaoyun Huang, Mengqi Zhang, Shanshan Liu, Shanshan Pan, Weizhen Xue, Congyan Wang, Chunyan Mao, He Zhang, Guangyi Fan 2021. Protocols for "Chromosome-level genome assembly of the humpback puffer, Tetraodon palembangensis". protocols.io https://dx.doi.org/10.17504/protocols.io.bs8inhue | 2021-04-15 09:14:22 |
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