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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 | 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 dx.doi.org/10.17504/protocols.io.38mgru6 | 2021-03-29 03:10:48 | |||
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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 | 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 dx.doi.org/10.17504/protocols.io.iamcac6 | 2021-03-29 03:10:52 | |
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RNA Isolation from Plant Tissue Protocol 9: CTAB/Acid Phenol/Silica Membrane Method Resource Report Resource Website |
Eric Carpenter | 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 dx.doi.org/10.17504/protocols.io.4yegxte | 2021-03-29 03:09:32 | ||||
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RNA Isolation from Plant Tissue Protocol 12: Hot Acid Phenol Method for Angiosperms Resource Report Resource Website |
Eric Carpenter | 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 dx.doi.org/10.17504/protocols.io.4rxgv7n | 2021-03-29 03:09:41 | ||||
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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 | 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 dx.doi.org/10.17504/protocols.io.bq6imzce | 2021-03-29 03:09:41 | |||
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Quality control for metagenomics data Resource Report Resource Website |
Qi Wang | 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 dx.doi.org/10.17504/protocols.io.be68jhhw | 2021-03-29 03:09:54 | |||
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Protocols for chromosome-level genome assembly of the spotted sea bass, Lateolabrax maculatus Resource Report Resource Website |
Changwei Shao, Chang Li, Na Wang, Yating Qin, Wenteng Xu, Qun Liu, Qian Zhou, Yong Zhao, Xihong Li, Shanshan Liu, Xiaowu Chen, Shahid Mahboob, Xin Liu, Songlin Chen | 10.17504/protocols.io.ssxeefn | GigaScience Press, BGI | Background: The spotted sea bass (Lateolabrax maculatus) is a valuable commercial fish that is widely cultured in China. While analyses using molecular markers and population genetics have been conducted, genomic resources are lacking.Finding: Here, we report a chromosome-scale assembly of the spotted sea bass genome by high-depth genome sequencing, assembly and annotation. The genome scale was 0.62 Gb with contig and scaffold N50 length to be 31 Kb and 1,040 Kb, respectively. Hi-C scaffolding of the genome resulted in 24 pseudochromosomes containing 77.68% of the total assembled sequences. A total of 132.38Mb repeat sequences were detected, accounting for 20.73% of the assemble genome. 22,015 protein-coding genes were predicted, of which 96.52% were homologous to proteins in various databases. In addition, we constructed a phylogenetic tree using 1,586 single-copy gene families and identified 125 unique gene families in the spotted sea bass genome.Conclusions: We assembled a spotted sea bass genome, which will be a valuable genomic resource to understand the biology of the spotted sea bass, and will also lead to the development of molecular breeding techniques to generate spotted sea bass with better economical traits. | Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China. Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China., BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China; BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China; BGI-Shenzhen, Shenzhen, 518083, China., Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China. Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China., BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China; BGI-Shenzhen, Shenzhen, 518083, China., Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China., BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China, Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China. Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China., BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China, Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China., BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China; BGI-Shenzhen, Shenzhen, 518083, China., Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China., Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia; Department of Zoology, GC University, Faisalabad, Pakistan., BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China; BGI-Shenzhen, Shenzhen, 518083, China., Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China. Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China. | 1 | 2018 | Changwei Shao, Chang Li, Na Wang, Yating Qin, Wenteng Xu, Qun Liu, Qian Zhou, Yong Zhao, Xihong Li, Shanshan Liu, Xiaowu Chen, Shahid Mahboob, Xin Liu, Songlin Chen 2018. Protocols for chromosome-level genome assembly of the spotted sea bass, Lateolabrax maculatus. protocols.io dx.doi.org/10.17504/protocols.io.ssxeefn | 2021-03-29 03:09:55 | |||
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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. | 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 dx.doi.org/10.17504/protocols.io.ew7bfhn | 2021-03-29 03:09:58 | |
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RNA Isolation from Plant Tissue Protocol 10: TRIzol LS Reagent Method Resource Report Resource Website |
Eric Carpenter | 10.17504/protocols.io.4rwgv7e | GigaScience Press | Implemented by: Michael Melkonian and Barbara Surek (algae) and Juan Carlos Villarreal (bryophytes)This protocol follows the procedures provided with the TRIzol LS Reagent (Invitrogen). TRIzol LS Reagent is a monophasic solution of phenol and guanidine isothiocyanate that can be used in isolation of total RNA from a wide variety of tissues and organisms, in addition to plants. This protocol was used in the isolation of total RNA from some algae samples (see Supplementary Table 1).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 10: TRIzol LS Reagent Method. protocols.io dx.doi.org/10.17504/protocols.io.4rwgv7e | 2021-03-29 03:10:09 | ||||
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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 | 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. | www.doi.org/10.5524/100486 | 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 dx.doi.org/10.17504/protocols.io.sjtecnn | 2021-03-29 03:10:10 | ||
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DNA extraction for the Betta splendens genome Resource Report Resource Website |
Kailong Ma | 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 dx.doi.org/10.17504/protocols.io.qvedw3e | 2021-03-29 03:10:17 | |||
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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 | 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 dx.doi.org/10.17504/protocols.io.im9cc96 | 2021-03-29 03:10:17 | |
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BGISEQ-500 10X library construction Resource Report Resource Website |
Ziqiang Chen | 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 dx.doi.org/10.17504/protocols.io.3jagkie | 2021-03-29 03:08:53 | |||
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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 | 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 dx.doi.org/10.17504/protocols.io.bkczksx6 | 2021-03-29 03:08:32 | |||
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An analytical pipeline of assembly and annotation of the Betta splendens genome. Resource Report Resource Website |
Xin Liu | 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 dx.doi.org/10.17504/protocols.io.qq9dvz6 | 2021-03-29 03:08:30 | |||
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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 | 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 dx.doi.org/10.17504/protocols.io.gahbsb6 | 2021-03-29 03:08:33 | |
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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 | 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 dx.doi.org/10.17504/protocols.io.pq7dmzn | 2021-03-29 03:08:38 | |
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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. | 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 dx.doi.org/10.17504/protocols.io.ew9bfh6 | 2021-03-29 03:08:41 | |
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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 | 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 dx.doi.org/10.17504/protocols.io.gxubxnw | 2021-03-29 03:09:03 | |||
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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 | 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 dx.doi.org/10.17504/protocols.io.bq9kmz4w | 2021-03-29 03:09:27 |
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