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The pipeline of Hi-C assembly Resource Report Resource Website |
Xin Liu | DOI:10.17504/protocols.io.qradv2e | GigaScience Press, BGI, GIGA | From here, You can know detail methods of Hi-C assembly of the Betta splendens genome. | BGI-Shenzhen | 1 | 2018 | Xin Liu 2018. The pipeline of Hi-C assembly. protocols.io https://dx.doi.org/10.17504/protocols.io.qradv2e | 2021-04-15 09:15:43 | |||
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RNA extraction for the Betta splendens genome Resource Report Resource Website |
Kailong Ma | DOI:10.17504/protocols.io.qvfdw3n | GigaScience Press, BGI | This protocol is used to clarity the process of RNA extraction for our Betta splendens genome. | BGI-Shenzhen | 1 | 2018 | Kailong Ma 2018. RNA extraction for the Betta splendens genome. protocols.io https://dx.doi.org/10.17504/protocols.io.qvfdw3n | 2021-04-15 09:15:18 | |||
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SQK-MAP005 protocol for library preparation for Nanopore sequencing Resource Report Resource Website |
Benjamin Istace, Anne Friedrich, Léo dAgata, 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.gvubw6w | GigaScience Press | This protocol describes the library preparation for Nanopore sequencing according to the SQK-MAP005 protocol. It accompanies the 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 dAgata, 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. SQK-MAP005 protocol for library preparation for Nanopore sequencing. protocols.io https://dx.doi.org/10.17504/protocols.io.gvubw6w | 2021-04-15 09:15:19 | ||
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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 | DOI: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 https://dx.doi.org/10.17504/protocols.io.inbcdan | 2021-04-15 09:15:48 | |
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Key protocols for chromosome-level genome assembly of the Scapharca (Anadara) broughtonii. Resource Report Resource Website |
Chang-Ming Bai, Lu-Sheng Xin, Umberto Rosani, Biao Wu, Qing-Chen Wang, Xiao-Ke Duan, Zhi-Hong Liu, Chong-Ming Wang | DOI:10.17504/protocols.io.zimf4c6 | GigaScience Press | Background: The blood clam, Scapharca (Anadara) broughtonii, is an economically and ecologically important marine bivalve of the Family Arcidae. The efforts that have been made to study their population genetics, breeding, cultivation and stock enrichment were somewhat hindered by the lack of a reference genome. Here, we reported the complete genome sequence of S. broughtonii, a first reference genome of the Family Arcidae.Funding: A total of 75.79 Gb clean data was generated with the PacBio and Oxford Nanopore platforms, which represented approx. 86× coverage of the S. broughtonii genome. De novo assembly of these long reads resulted in an 884.5 Mb genome, with a contig N50 of 1.80 Mb and scaffold N50 of 45.00 Mb, respectively. Genome Hi-C scaffolding resulted in 19 chromosomes containing 99.35% of bases of the assembled genome. Genome annotation revealed that a considerable part of the genome (46.1%) is composed by repeated sequences, while 24,045 protein-coding genes were predicted and 84.7% of them were annotated.Conclusion: We report here the chromosomal-level assembly of the S. broughtonii genome based on long read sequencing and Hi-C scaffolding. The genomic data could be served as reference genome for the Arcidae Family and will provide a valuable resource for the scientific community and aquaculture sector. | Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology; Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology; Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China, Department of Biology, University of Padua, Padua 35121, Italy and Alfred Wegener Institute – Helmholtz Centre for Polar and Marine Research, Waddensea Station Sylt, Germany, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology; Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology; Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China, Biomarker Technologies Corporation, Beijing 101200, China, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology; Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology; Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China | 1 | 2019 | Chang-Ming Bai, Lu-Sheng Xin, Umberto Rosani, Biao Wu, Qing-Chen Wang, Xiao-Ke Duan, Zhi-Hong Liu, Chong-Ming Wang 2019. Key protocols for chromosome-level genome assembly of the Scapharca (Anadara) broughtonii.. protocols.io https://dx.doi.org/10.17504/protocols.io.zimf4c6 | 2021-04-15 09:15:23 | |||
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Extraction method F (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.infcdbn | GigaScience Press | Gen-IALFirst All-tissue DNA extraction kit -This protocol provides an efficient DNA extraction and purification of historic sample (tissue material) | 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 F (CR). protocols.io https://dx.doi.org/10.17504/protocols.io.infcdbn | 2021-04-15 09:15:27 | |
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SQK-MAP006 Low Input protocol for library preparation for Nanopore sequencing Resource Report Resource Website |
Benjamin Istace, Anne Friedrich, Léo dAgata, 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.gvwbw7e | GigaScience Press | Describes the library preparation for Nanopore sequencing from low input DNA according to the SQK-MAP006 protocolIt accompanies the 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 dAgata, 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. SQK-MAP006 Low Input protocol for library preparation for Nanopore sequencing. protocols.io https://dx.doi.org/10.17504/protocols.io.gvwbw7e | 2021-04-15 09:15:27 | ||
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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.bq6hmzb6 | 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 "Shotgun Metagenomics of 361 elderly women reveals gut microbiome change in bone mass loss". protocols.io https://dx.doi.org/10.17504/protocols.io.bq6hmzb6 | 2021-04-15 09:15:28 | |||
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BGISEQ-500 Sequencing Resource Report Resource Website |
Jie Huang, Xinming Liang, Yuankai Xuan, Chunyu Geng, Yuxiang Li, Haorong Lu, Shoufang Qu, Xianglin Mei, Hongbo Chen, Ting Yu, Nan Sun, Junhua Rao, Jiahao Wang, Wenwei Zhang, Ying Chen, Sha Liao, Hui Jiang, Xin Liu, Zhaopeng Yang, Feng Mu, Shangxian Gao | BGI, GigaScience Press | National Institutes for Food and Drug Control (NIFDC), BGI-Shenzhen, State Food and Drug Administration, BGI-Shenzhen, BGI-Shenzhen, BGI-Shenzhen, National Institutes for Food and Drug Control (NIFDC), State Food and Drug Administration, National Institutes for Food and Drug Control (NIFDC), National Institutes for Food and Drug Control (NIFDC), National Institutes for Food and Drug Control (NIFDC), BGI-Shenzhen, BGI-Qingdao, BGI-Shenzhen, BGI-Shenzhen, BGI-Shenzhen, BGI-Shenzhen, BGI-Shenzhen, National Institutes for Food and Drug Control (NIFDC), BGI-Shenzhen, National Institutes for Food and Drug Control (NIFDC) | https://doi.org/10.1093/gigascience/giy144 | 2 | 2020 | Jie Huang, Xinming Liang, Yuankai Xuan, Chunyu Geng, Yuxiang Li, Haorong Lu, Shoufang Qu, Xianglin Mei, Hongbo Chen, Ting Yu, Nan Sun, Junhua Rao, Jiahao Wang, Wenwei Zhang, Ying Chen, Sha Liao, Hui Jiang, Xin Liu, Zhaopeng Yang, Feng Mu, Shangxian Gao 2020. BGISEQ-500 Sequencing. protocols.io https:// | 2021-04-15 09:15:30 | ||||
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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 | DOI: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 https://dx.doi.org/10.17504/protocols.io.bp3wmqpe | 2021-04-15 09:15:32 | |||
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An analytical pipeline of assembly and annotation of the Betta splendens genome. Resource Report Resource Website |
Xin Liu | DOI:10.17504/protocols.io.qq9dvz6 | GigaScience Press, BGI | From here, You can learn about the detail methods of genome assembly and gene annotation of the Betta splendens genome. | BGI-Shenzhen | 1 | 2018 | Xin Liu 2018. An analytical pipeline of assembly and annotation of the Betta splendens genome.. protocols.io https://dx.doi.org/10.17504/protocols.io.qq9dvz6 | 2021-04-15 09:15:42 | |||
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Oxford Nanopore sequencing and library construction Resource Report Resource Website |
Rui Zhang | DOI: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 https://dx.doi.org/10.17504/protocols.io.btcwnixe | 2021-04-15 09:15:47 | |||
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Reference transcriptome sequence resource for the study of the Cestode Schistocephalus solidus, a threespine stickleback parasite. Resource Report Resource Website |
Hebert F.O., Grambauer S., Barber I., Landry C.R., Aubin-Horth N. | DOI:10.17504/protocols.io.ew9bfh6 | GigaScience Press | These methods accompany the following publication: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: 128 | , , , , | 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. Reference transcriptome sequence resource for the study of the Cestode Schistocephalus solidus, a threespine stickleback parasite.. protocols.io https://dx.doi.org/10.17504/protocols.io.ew9bfh6 | 2021-04-15 09:15:54 | |
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BGISEQ-500 Sequencing Resource Report Resource Website |
Jie Huang, Xinming Liang, Yuankai Xuan, Chunyu Geng, Yuxiang Li, Haorong Lu, Shoufang Qu, Xianglin Mei, Hongbo Chen, Ting Yu, Nan Sun, Junhua Rao, Jiahao Wang, Wenwei Zhang, Ying Chen, Sha Liao, Hui Jiang, Xin Liu, Zhaopeng Yang, Feng Mu, Shangxian Gao | DOI:10.17504/protocols.io.pq7dmzn | GigaScience Press, BGI, GIGA, GigaScience Press | BGISEQ-500 is a new desktop sequencer developed by BGI. Using DNA nanoball and combinational probe anchor synthesis developed from Complete Genomics™ sequencing technologies, it generates short reads at a large scale. | Huang J, Liang X, Xuan Y, Geng C, Li Y, Lu H, Qu S, Mei X, Chen H, Yu T, Sun N, Rao J, Wang J, Zhang W, Chen Y, Liao S, Jiang H, Liu X, Yang Z, Mu F, Gao S, Erratum to: A reference human genome dataset of the BGISEQ-500 sequencer. GigaScience 7(12). doi: 10.1093/gigascience/giy144 | National Institutes for Food and Drug Control (NIFDC), BGI-Shenzhen, State Food and Drug Administration, BGI-Shenzhen, BGI-Shenzhen, BGI-Shenzhen, National Institutes for Food and Drug Control (NIFDC), State Food and Drug Administration, National Institutes for Food and Drug Control (NIFDC), National Institutes for Food and Drug Control (NIFDC), National Institutes for Food and Drug Control (NIFDC), BGI-Shenzhen, BGI-Qingdao, BGI-Shenzhen, BGI-Shenzhen, BGI-Shenzhen, BGI-Shenzhen, BGI-Shenzhen, National Institutes for Food and Drug Control (NIFDC), BGI-Shenzhen, National Institutes for Food and Drug Control (NIFDC) | https://doi.org/10.1093/gigascience/giy144 | 1 | 2018 | Jie Huang, Xinming Liang, Yuankai Xuan, Chunyu Geng, Yuxiang Li, Haorong Lu, Shoufang Qu, Xianglin Mei, Hongbo Chen, Ting Yu, Nan Sun, Junhua Rao, Jiahao Wang, Wenwei Zhang, Ying Chen, Sha Liao, Hui Jiang, Xin Liu, Zhaopeng Yang, Feng Mu, Shangxian Gao 2018. BGISEQ-500 Sequencing. protocols.io https://dx.doi.org/10.17504/protocols.io.pq7dmzn | 2021-04-15 09:15:51 | |
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BGISEQ-500 10X library construction Resource Report Resource Website |
Ziqiang Chen | DOI:10.17504/protocols.io.3jagkie | GigaScience Press, BGI | BGISEQ-500 is a desktop sequencer developed by BGI. This protocol adjusts the process in order to apply the 10X contruction to the BGISEQ-500 rather than illumina. | bgi | 1 | 2019 | Ziqiang Chen 2019. BGISEQ-500 10X library construction. protocols.io https://dx.doi.org/10.17504/protocols.io.3jagkie | 2021-04-15 09:16:01 | |||
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The Healthy Brain Network Serial Scanning Initiative, Sessions 2-7 and 9-14 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.gxubxnw | GigaScience Press | This protocol describes MRI, voice recoding, and some basic physiological measurements and questionnaires for Sessions 2-7 and 9-14 of the following work:David O'Connor, et. al. (2017) The Healthy Brain Network Serial Scanning Initiative. GigaScience... | , , , , , , , , , , , , , , , | 2 | 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. The Healthy Brain Network Serial Scanning Initiative, Sessions 2-7 and 9-14. protocols.io https://dx.doi.org/10.17504/protocols.io.gxubxnw | 2021-04-15 09:16:09 | |||
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Extraction Method D (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.indcda6 | GigaScience Press | This protocol allows for adequate DNA extraction from archival 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 D (PRP and RM). protocols.io https://dx.doi.org/10.17504/protocols.io.indcda6 | 2021-04-15 09:16:09 | |
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Protocols for "Linking gut microbiome to bone mineral density: a shotgun metagenomic dataset from 361 elderly 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.bq9kmz4w | 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 dataset from 361 elderly women". protocols.io https://dx.doi.org/10.17504/protocols.io.bq9kmz4w | 2021-04-15 09:16:12 | |||
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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 | DOI: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 https://dx.doi.org/10.17504/protocols.io.439gyr6 | 2021-04-15 09:16:19 | |||
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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 | DOI: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 https://dx.doi.org/10.17504/protocols.io.h99b996 | 2021-04-15 09:16:29 |
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