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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 | DOI: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 https://dx.doi.org/10.17504/protocols.io.bd3vi8n6 | 2021-04-15 09:15:22 | |||
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Oxford Nanopore sequencing and library construction Resource Report Resource Website |
Rui Zhang | DOI:10.17504/protocols.io.btifnkbn | 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 https://dx.doi.org/10.17504/protocols.io.btifnkbn | 2021-04-15 09:15:48 | |||
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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 | DOI: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 https://dx.doi.org/10.17504/protocols.io.38jgrun | 2021-04-15 09:15:31 | |||
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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 | DOI: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 https://dx.doi.org/10.17504/protocols.io.bd3ui8nw | 2021-04-15 09:15:52 | |||
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RNA Isolation from Plant Tissue Protocol 11: Tri Reagent Method Resource Report Resource Website |
Eric Carpenter | DOI: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 https://dx.doi.org/10.17504/protocols.io.4ydgxs6 | 2021-04-15 09:15:37 | ||||
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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 | DOI:10.17504/protocols.io.qsvdwe6 | 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 https://dx.doi.org/10.17504/protocols.io.qsvdwe6 | 2021-04-15 09:15:42 | |||
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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.bkczksx6 | GigaScience Press | The humpback puffer,Tetraodon palembangensis, also known as Pao palembangensis, is a species of poisonous freshwater pufferfish mainly distributed in Southeast Asia (Thailand, Laos, Malaysia and Indonesia). Despite interesting biological features, such as its very inactive nature, tetrodotoxin production and body expansion mechanisms, molecular research on the humpback puffer is still rare because of the lack of a high-quality reference genome. Here, we reported a first chromosome-level genome assembly of an adult humpback puffer, of which the genome size is 362 Mb with ~1.78 Mb contig N50 and ~15.8 Mb scaffold N50s. Based on the genome, ~61.5Mb (18.11%) repeat sequences were also identified, and totally 19,925 genes were annotated, 99.20% of which could be predicted with function using protein-coding function databases. Finally, a phylogenetic tree was constructed with single-copy gene families from ten teleost fishes. The humpback puffer genome will be a valuable genomic resource to illustrate possible mechanisms of tetrodotoxin synthesis and tolerance, providing clues for future detailed studies of biological toxins. | BGI-Qingdao, BGI-Shenzhen, Qingdao 26655¬¬5, China., BGI-Qingdao, BGI-Shenzhen, Qingdao 26655¬¬5, China., BGI-Qingdao, BGI-Shenzhen, Qingdao 26655¬¬5, China., BGI-Qingdao, BGI-Shenzhen, Qingdao 26655¬¬5, China., BGI-Qingdao, BGI-Shenzhen, Qingdao 26655¬¬5, China., BGI-Qingdao, BGI-Shenzhen, Qingdao 26655¬¬5, China., BGI-Qingdao, BGI-Shenzhen, Qingdao 26655¬¬5, China., BGI-Qingdao, BGI-Shenzhen, Qingdao 26655¬¬5, China., BGI-Qingdao, BGI-Shenzhen, Qingdao 26655¬¬5, China., BGI-Qingdao, BGI-Shenzhen, Qingdao 26655¬¬5, China., BGI-Qingdao, BGI-Shenzhen, Qingdao 26655¬¬5, China., BGI-Qingdao, BGI-Shenzhen, Qingdao 26655¬¬5, China. | 1 | 2020 | Rui Zhang, Chang Li, Mengjun Yu, Xiaoyun Huang, Mengqi Zhang, Shanshan Liu, Shanshan Pan, Weizhen Xue, Congyan Wang, Chunyan Mao, He Zhang, Guangyi Fan 2020. Protocols for "Chromosome-level genome assembly of the humpback puffer, Tetraodon palembangensis". protocols.io https://dx.doi.org/10.17504/protocols.io.bkczksx6 | 2021-04-15 09:15:55 | |||
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Irys NLRS DNA labeling and Data collection Resource Report Resource Website |
Huang Zhihai, Xu Jiang, Xiao Shuiming, Liao Baosheng, Gao Yuan, Zhai Chaochao, Qiu Xiaohui, Xu Wen, Chen Shilin | DOI:10.17504/protocols.io.gahbsb6 | GigaScience Press, BGI, GIGA, GigaScience Press | This protocol is provided by BioNano Genomics and was used in:Huang Zhihai, Xu Jiang, Xiao Shuiming, Liao Baosheng, Gao Yuan, Zhai Chaochao, Qiu Xiaohui, Xu Wen, Chen Shilin (2016): Supporting data for 'Comparative optical genome analysis of two Pangolin species Manis pentadactyla and Manis javanica'. GigaScience Database. | Huang Zhihai, Xu Jiang, Xiao Shuiming, Liao Baosheng, Gao Yuan, Zhai Chaochao, Qiu Xiaohui, Xu Wen, Chen Shilin; Comparative optical genome analysis of two pangolin species: Manis pentadactyla and Manis javanica. Gigascience 2016 1-5. doi: 10.1093/gigascience/giw001 | GigaScience, GigaScience, GigaScience, GigaScience, GigaScience, GigaScience, GigaScience, GigaScience, GigaScience | https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giw001/2756882/Comparative-optical-genome-analysis-of-two | 1 | 2016 | Huang Zhihai, Xu Jiang, Xiao Shuiming, Liao Baosheng, Gao Yuan, Zhai Chaochao, Qiu Xiaohui, Xu Wen, Chen Shilin 2016. Irys NLRS DNA labeling and Data collection. protocols.io https://dx.doi.org/10.17504/protocols.io.gahbsb6 | 2021-04-15 09:15:46 | |
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Isolated astrocyte culture preparation - protocol 1 Resource Report Resource Website |
Yasmin Bar El | DOI: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 https://dx.doi.org/10.17504/protocols.io.tqbemsn | 2021-04-15 09:15:57 | |||
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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 | DOI: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 https://dx.doi.org/10.17504/protocols.io.qvddw26 | 2021-04-15 09:15:59 | |||
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The calculation of gut metabolic modules from gene profile Resource Report Resource Website |
Qi Wang | DOI: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 https://dx.doi.org/10.17504/protocols.io.bq6gmzbw | 2021-04-15 09:16:02 | |||
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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 | DOI: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 https://dx.doi.org/10.17504/protocols.io.4u6gwze | 2021-04-15 09:16:09 | ||||
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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 | DOI: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 https://dx.doi.org/10.17504/protocols.io.gxcbxiw | 2021-04-15 09:16:11 | |||
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Mate-pair large libraries preparation for assembly of the Lateolabrax maculatus genome Resource Report Resource Website |
Chang Li | DOI:10.17504/protocols.io.ss2eege | GigaScience Press, BGI | This protocol is used to clarity the process of the mate-pair large libraries preparation for the L. maculatus. | 1 | 2018 | Chang Li 2018. Mate-pair large libraries preparation for assembly of the Lateolabrax maculatus genome. protocols.io https://dx.doi.org/10.17504/protocols.io.ss2eege | 2021-04-15 09:16:15 | ||||
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Illumina library construction for Extraction Method A, B, C (For FMS samples) and D, E (PRP and RM) 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.ingcdbw | GigaScience Press | Library building protocol for archival samples with single 8-nt adapters for Illumina platforms. | 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. Illumina library construction for Extraction Method A, B, C (For FMS samples) and D, E (PRP and RM). protocols.io https://dx.doi.org/10.17504/protocols.io.ingcdbw | 2021-04-15 09:16:12 | |
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RNA Isolation from Plant Tissue Protocol 9: CTAB/Acid Phenol/Silica Membrane Method Resource Report Resource Website |
Eric Carpenter | DOI:10.17504/protocols.io.4yegxte | GigaScience Press | Implemented by: Henrietta Myburg and Marc JohnsonThis protocol is a modification of protocol 8. It was developed after protocol 8 and several commercially available plant RNA isolation kits failed to produce a sufficient yield and quality of RNA from Oenothera spp. (Onagraceae) for next-generation sequencing. Oenothera are rich in polysaccharides, oils, flavonoids and complex ellagitannins that likely interfere with isolation.We suspect that this protocol will be most useful for species and tissues with complex secondarychemistry and rich in oils (e.g. some Rosaceae and Pinaceae). The most important modifications to this protocol versus Protocol 8 is the use of less plant tissue, more extraction buffer, and repeating solvent extractions until the interphase is clean of debris. The protocol is regrettably longer and more involved than Protocol 8. We attempted to remove or reduce the replication of the solvent extractions steps without success (i.e. yield and quality are always decreased in Oenothera when any steps are removed).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 9: CTAB/Acid Phenol/Silica Membrane Method. protocols.io https://dx.doi.org/10.17504/protocols.io.4yegxte | 2021-04-15 09:16:14 | ||||
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Protocols for "Linking gut microbiome to bone mineral density: a shotgun metagenomic study of 361 eldly women" 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.bq6imzce | 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 | 2021 | Qi Wang, Qiang Sun, Xiaoping Li, Zhefeng Wang, Haotian Zheng, Yanmei Ju, Ruijin Guo, Songlin Peng, Huijue Jia 2021. Protocols for "Linking gut microbiome to bone mineral density: a shotgun metagenomic study of 361 eldly women". protocols.io https://dx.doi.org/10.17504/protocols.io.bq6imzce | 2021-04-15 09:16:25 | |||
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RNA Isolation from Plant Tissue Protocol 12: Hot Acid Phenol Method for Angiosperms Resource Report Resource Website |
Eric Carpenter | DOI:10.17504/protocols.io.4rxgv7n | GigaScience Press | Implemented by: Sarah Covshoff, Rowan Sage and Julian HibberdThis RNA isolation method is a multi-component method involving an initial extraction by hotacid phenol and then a purification and DNase treatment using the RNeasy Mini Kit by Qiagen.The method described below is a modification of a method described by van Tunen et al.3.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) 3 van Tunen, A.J. et al. Cloning of the two chalcone flavanone isomerase genes from Petunia hybrida: coordinate, light‐ regulated and differential expression of flavonoid genes. The EMBO Journal 7, 1257‐1263 (1988). | 1 | 2019 | Eric Carpenter 2019. RNA Isolation from Plant Tissue Protocol 12: Hot Acid Phenol Method for Angiosperms. protocols.io https://dx.doi.org/10.17504/protocols.io.4rxgv7n | 2021-04-15 09:16:16 | ||||
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Quality control for metagenomics data Resource Report Resource Website |
Qi Wang | DOI:10.17504/protocols.io.be68jhhw | BGI, GIGA, GigaScience Press | Quality control for metagenomics data,including: remove low quality reads and host contamination reads. | BGI | 1 | 2020 | Qi Wang 2020. Quality control for metagenomics data. protocols.io https://dx.doi.org/10.17504/protocols.io.be68jhhw | 2021-04-15 09:16:18 | |||
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DNA extraction for human microbe samples. Resource Report Resource Website |
Lilan Hao | DOI:10.17504/protocols.io.bcmriu56 | BGI, GIGA, GigaScience Press | This protocol is used to clarity the process of total DNA extration for human microbe samples. | BGI-Shenzhen, Shenzhen 518083, China. | 1 | 2020 | Lilan Hao 2020. DNA extraction for human microbe samples.. protocols.io https://dx.doi.org/10.17504/protocols.io.bcmriu56 | 2021-04-15 09:16:18 |
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