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Mate-pair large libraries preparation for assembly of the Lateolabrax maculatus genome Resource Report Resource Website |
Chang Li | 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 dx.doi.org/10.17504/protocols.io.ss2eege | 2021-03-29 03:09:24 | ||||
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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 | 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 dx.doi.org/10.17504/protocols.io.ingcdbw | 2021-03-29 03:09:24 | |
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RNA extraction for the Betta splendens genome Resource Report Resource Website |
Kailong Ma | 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 dx.doi.org/10.17504/protocols.io.qvfdw3n | 2021-03-29 03:07:33 | |||
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DNA Extraction for plant samples by CTAB Resource Report Resource Website |
Ting Yang, Chenyu Wu | 10.17504/protocols.io.pzqdp5w | GigaScience Press, BGI | DNA extraction of −80◦C stored leaves by CTAB. | BGI-Shenzhen, BGI-Shenzhen | 1 | 2018 | Ting Yang, Chenyu Wu 2018. DNA Extraction for plant samples by CTAB. protocols.io dx.doi.org/10.17504/protocols.io.pzqdp5w | 2021-03-29 03:07:42 | |||
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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 | 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 dx.doi.org/10.17504/protocols.io.gvubw6w | 2021-03-29 03:07:37 | ||
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Protocols for "Draft genome of the sea cucumber Apostichopus japonicus and genetic polymorphism among color variants" Resource Report Resource Website |
Jihoon Jo, Jooseong Oh, Hyun Gwan Lee, Hyun Hee Hong, Sung Gwon Lee, Seongmin Cheon, Elizabeth MA Kern, Soyeong Jin, Sung Jin Cho, Joong Ki Park, Chungoo Park | 10.17504/protocols.io.gmebu3e | GigaScience Press | These protocols accompany the following GigaScience publication:Jihoon Jo, et al. (2016): Draft genome of the sea cucumber Apostichopus japonicus and genetic polymorphism among color variants. GigaScience... | School of Biological Sciences and Technology, Chonnam National University, School of Biological Sciences and Technology, Chonnam National University, School of Biological Sciences and Technology, Chonnam National University, School of Biological Sciences and Technology, Chonnam National University, School of Biological Sciences and Technology, Chonnam National University, School of Biological Sciences and Technology, Chonnam National University, School of Biological Sciences and Technology, Chonnam National University, School of Biological Sciences and Technology, Chonnam National University, School of Biological Sciences and Technology, Chonnam National University, School of Biological Sciences and Technology, Chonnam National University, School of Biological Sciences and Technology, Chonnam National University | https://doi.org/10.1093/gigascience/giw006 | 1 | 2016 | Jihoon Jo, Jooseong Oh, Hyun Gwan Lee, Hyun Hee Hong, Sung Gwon Lee, Seongmin Cheon, Elizabeth MA Kern, Soyeong Jin, Sung Jin Cho, Joong Ki Park, Chungoo Park 2016. Protocols for "Draft genome of the sea cucumber Apostichopus japonicus and genetic polymorphism among color variants". protocols.io dx.doi.org/10.17504/protocols.io.gmebu3e | 2021-03-29 03:07:38 | ||
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Hiseq 2000 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.38kgruw | GigaScience Press, BGI | Hiseq 2000 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. Hiseq 2000 Library Construction and Sequencing for RNA Seq. protocols.io dx.doi.org/10.17504/protocols.io.38kgruw | 2021-03-29 03:10:36 | |||
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Immunocytochemistry Resource Report Resource Website |
Yasmin Bar El | 10.17504/protocols.io.tqdems6 | GigaScience Press | Immunocytochemistry for morphology analysis. Staining of cell culture in order to obtain fluorescence images of the culture. | School of Physics and Astronomy, Tel-Aviv University, Tel-Aviv, Israel | 1 | 2018 | Yasmin Bar El 2018. Immunocytochemistry. protocols.io dx.doi.org/10.17504/protocols.io.tqdems6 | 2021-03-29 03:10:41 | |||
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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 | 10.17504/protocols.io.bqwwmxfe | BGI, GIGA, GigaScience Press | Bone mass loss contributes to the risk of bone fracture in the elderly. Many factors including age, obesity, estrogen and diet, are associated with bone mass loss. Mice studies suggested that the gut microbiome might affect the bone mass by regulating the immune system, however there has been little evidence from human studies. Bone loss increases after menopause. Therefore, we have recruited 361 Chinese post-menopausal women to collect their fecal samples and metadata to conduct metagenome-wide association study (MWAS) to investigate the influence of the gut microbiome on bone health. Gut microbiome sequencing data were produced using BGISEQ500 sequencing, Bone mineral density (BMD) was calculated using Hologic dual energy X-ray machine, body mass index (BMI) and age were also recorded.This collected data allows exploration of the gut microbial diversity and their links to bone mass loss, as well as microbial markers for bone mineral density. In addition, these data are potentially useful in studying the role the gut microbiota might play in bone mass loss and in exploring the bone mass loss process. | BGI-Shenzhen, Shenzhen 518083, China;School of Future Technology, University of Chinese Academy of Sciences, Beijing, 101408, China., BGI-Shenzhen, Shenzhen 518083, China;Department of Statistical Sciences, University of Toronto, Toronto, Canada, BGI-Shenzhen, Shenzhen 518083, China, Department of Spine Surgery, Shenzhen People's Hospital, Ji Nan University Second College of Medicine, 518020, Shenzhen, China., BGI-Shenzhen, Shenzhen 518083, China;School of Future Technology, University of Chinese Academy of Sciences, Beijing, 101408, China., BGI-Shenzhen, Shenzhen 518083, China;School of Future Technology, University of Chinese Academy of Sciences, Beijing, 101408, China., BGI-Shenzhen, Shenzhen 518083, China;Macau University of Science and Technology, Taipa, Macau 999078, China, Department of Spine Surgery, Shenzhen People's Hospital, Ji Nan University Second College of Medicine, 518020, Shenzhen, China., BGI-Shenzhen, Shenzhen 518083, China; Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China | 1 | 2020 | Qi Wang, Qiang Sun, Xiaoping Li, Zhefeng Wang, Haotian Zheng, Yanmei Ju, Ruijin Guo, Songlin Peng, Huijue Jia 2020. Protocols for "Shotgun Metagenomics of 361 elderly women reveals gut microbiome change in bone mass loss". protocols.io dx.doi.org/10.17504/protocols.io.bqwwmxfe | 2021-03-29 03:11:12 | |||
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Illumina library construction Protocol Resource Report Resource Website |
SARAH SIU TZE MAK, SHYAM GOPALAKRISHNAN, CHRISTIAN CAROE, CHUNYU GENG, SHANLIN LIU, MIKKEL-HOLGER S SINDING, LUKAS F K KUDERNA, WENWEI ZHANG, SHUJIN FU, FILIPE G VIEIRA, MIETJE GERMONPRÉ, HERVÉ BOCHERENS, SERGEY FEDOROV, BENT PETERSEN, THOMAS SICHERITZ-PONTEN, TOMAS MARQUES-BONET, GUOJIE ZHANG, HUI JIANG, M THOMAS P GILBERT | 10.17504/protocols.io.iajcacn | GigaScience Press | This single-tube library construction protocol is for degraded DNA using adapters for the Illumina platform. | Mak SST, Gopalakrishnan S, Carøe C, Geng C, Liu S, Sinding MS, Kuderna LFK, Zhang W, Fu S, Vieira FG, Germonpré M, Bocherens H, Fedorov S, Petersen B, Sicheritz-Pontén T, Marques-Bonet T, Zhang G, Jiang H, Gilbert MTP, Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing. GigaScience 6(8). doi: 10.1093/gigascience/gix049 | UNIVERSITY OF COPENHAGEN, UNIVERSITY OF COPENHAGEN, UNIVERSITY OF COPENHAGEN, UNIVERSITY OF COPENHAGEN, UNIVERSITY OF COPENHAGEN, UNIVERSITY OF COPENHAGEN, UNIVERSITY OF COPENHAGEN, UNIVERSITY OF COPENHAGEN, UNIVERSITY OF COPENHAGEN, UNIVERSITY OF COPENHAGEN, UNIVERSITY OF COPENHAGEN, UNIVERSITY OF COPENHAGEN, UNIVERSITY OF COPENHAGEN, UNIVERSITY OF COPENHAGEN, UNIVERSITY OF COPENHAGEN, UNIVERSITY OF COPENHAGEN, UNIVERSITY OF COPENHAGEN, UNIVERSITY OF COPENHAGEN, UNIVERSITY OF COPENHAGEN | https://doi.org/10.1093/gigascience/gix049 | 1 | 2017 | SARAH SIU TZE MAK, SHYAM GOPALAKRISHNAN, CHRISTIAN CAROE, CHUNYU GENG, SHANLIN LIU, MIKKEL-HOLGER S SINDING, LUKAS F K KUDERNA, WENWEI ZHANG, SHUJIN FU, FILIPE G VIEIRA, MIETJE GERMONPRÉ, HERVÉ BOCHERENS, SERGEY FEDOROV, BENT PETERSEN, THOMAS SICHERITZ-PONTEN, TOMAS MARQUES-BONET, GUOJIE ZHANG, HUI JIANG, M THOMAS P GILBERT 2017. Illumina library construction Protocol. protocols.io dx.doi.org/10.17504/protocols.io.iajcacn | 2021-03-29 03:11:12 | |
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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.bs8inhue | BGI, GIGA, GigaScience Press | In this study we assembled the first chromosome-level genome assembly of the humpback puffer (Tetraodon palembangensis), a species of poisonous freshwater pufferfish mainly distributed in Southeast Asia. This utilized Oxford Nanopore and BGISEQ-500 sequencing, stLFR libraries and Hi-C assembly, and the protocols for nucleic acid extraction, library construction and sequencing are all made available here. The resulting genome size was 362 Mb with a ~1.78 Mb contig N50 and ~15.8 Mb scaffold N50. Based on the assembled genome, ~61.5Mb (18.11%) repeat sequences were identified, 19,925 genes were annotated, and 90.01% of these genes could be predicted with function. Finally, a phylogenetic tree of ten teleost fish species was successfully constructed using this and public data. These protocols are made available for others carrying vertebrate genome assembly, and the open data and published study for comparative genome studies. | BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.Department of Biology, Hong Kong Baptist University, Hong Kong, China, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China | 1 | 2021 | Rui Zhang, Chang Li, Mengjun Yu, Xiaoyun Huang, Mengqi Zhang, Shanshan Liu, Shanshan Pan, Weizhen Xue, Congyan Wang, Chunyan Mao, He Zhang, Guangyi Fan 2021. Protocols for "Chromosome-level genome assembly of the humpback puffer, Tetraodon palembangensis". protocols.io dx.doi.org/10.17504/protocols.io.bs8inhue | 2021-03-29 03:12:25 | |||
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Megabase DNA Extraction from Animal Blood 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.gagbsbw | GigaScience Press, High molecular weight DNA extraction from all kingdoms | This protocol provides an efficient and reliable technique for obtaining HMW DNA(>1Mb) from animal blood. It accompanies: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. | 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. Megabase DNA Extraction from Animal Blood. protocols.io dx.doi.org/10.17504/protocols.io.gagbsbw | 2021-03-29 03:12:38 | ||
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Extraction method C 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.iaecabe | GigaScience Press | This protocol provides an efficient DNA extraction and purification of ancient sorft tissue. | Mak SST, Gopalakrishnan S, Carøe C, Geng C, Liu S, Sinding MS, Kuderna LFK, Zhang W, Fu S, Vieira FG, Germonpré M, Bocherens H, Fedorov S, Petersen B, Sicheritz-Pontén T, Marques-Bonet T, Zhang G, Jiang H, Gilbert MTP, Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing. GigaScience 6(8). doi: 10.1093/gigascience/gix049 | UNIVERSITY OF COPENHAGEN, UNIVERSITY OF COPENHAGEN, UNIVERSITY OF COPENHAGEN, UNIVERSITY OF COPENHAGEN, UNIVERSITY OF COPENHAGEN, UNIVERSITY OF COPENHAGEN, UNIVERSITY OF COPENHAGEN, UNIVERSITY OF COPENHAGEN, UNIVERSITY OF COPENHAGEN, UNIVERSITY OF COPENHAGEN, UNIVERSITY OF COPENHAGEN, UNIVERSITY OF COPENHAGEN, UNIVERSITY OF COPENHAGEN, UNIVERSITY OF COPENHAGEN, UNIVERSITY OF COPENHAGEN, UNIVERSITY OF COPENHAGEN, UNIVERSITY OF COPENHAGEN, UNIVERSITY OF COPENHAGEN, UNIVERSITY OF COPENHAGEN | https://doi.org/10.1093/gigascience/gix049 | 1 | 2017 | SARAH SIU TZE MAK, SHYAM GOPALAKRISHNAN, CHRISTIAN CAROE, CHUNYU GENG, SHANLIN LIU, MIKKEL-HOLGER S SINDING, LUKAS F K KUDERNA, WENWEI ZHANG, SHUJIN FU, FILIPE G VIEIRA, MIETJE GERMONPRÉ, HERVÉ BOCHERENS, SERGEY FEDOROV, BENT PETERSEN, THOMAS SICHERITZ-PONTEN, TOMAS MARQUES-BONET, GUOJIE ZHANG, HUI JIANG, M THOMAS P GILBERT 2017. Extraction method C. protocols.io dx.doi.org/10.17504/protocols.io.iaecabe | 2021-03-29 03:12:38 | |
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SNPs calling of Apostichopus japonicus color-variants genome Resource Report Resource Website |
Jihoon Jo, Jooseong Oh, Hyun Gwan Lee, Hyun Hee Hong, Sung Gwon Lee, Seongmin Cheon, Elizabeth MA Kern, Soyeong Jin, Sung Jin Cho, Joong Ki Park, Chungoo Park | 10.17504/protocols.io.gmbbu2n | GigaScience Press | SNPs calling protocol for analysis the genetic polymorphism among natural color variants. This protocol accompanies the following GigaScience publication:Jihoon Jo, et al. (2016): Draft genome of the sea cucumber Apostichopus japonicus and genetic polymorphism among color variants. GigaScience... | School of Biological Sciences and Technology, Chonnam National University, School of Biological Sciences and Technology, Chonnam National University, School of Biological Sciences and Technology, Chonnam National University, School of Biological Sciences and Technology, Chonnam National University, School of Biological Sciences and Technology, Chonnam National University, School of Biological Sciences and Technology, Chonnam National University, School of Biological Sciences and Technology, Chonnam National University, School of Biological Sciences and Technology, Chonnam National University, School of Biological Sciences and Technology, Chonnam National University, School of Biological Sciences and Technology, Chonnam National University, School of Biological Sciences and Technology, Chonnam National University | https://doi.org/10.1093/gigascience/giw006 | 1 | 2016 | Jihoon Jo, Jooseong Oh, Hyun Gwan Lee, Hyun Hee Hong, Sung Gwon Lee, Seongmin Cheon, Elizabeth MA Kern, Soyeong Jin, Sung Jin Cho, Joong Ki Park, Chungoo Park 2016. SNPs calling of Apostichopus japonicus color-variants genome. protocols.io dx.doi.org/10.17504/protocols.io.gmbbu2n | 2021-03-29 03:12:46 | ||
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Draft genome assembly using parasitic mite population NGS DNA sample from mites extracted from host wound environment Resource Report Resource Website |
Ehtesham Mofiz | 10.17504/protocols.io.exwbfpe | GigaScience Press | Mofiz E, Holt DC, Seemann T, Currie BJ, Fischer K, Papenfuss AT, Genomic resources and draft assemblies of the human and porcine varieties of scabies mites, var. and var. . GigaScience doi: 129 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4890329/ | 1 | 2016 | Ehtesham Mofiz 2016. Draft genome assembly using parasitic mite population NGS DNA sample from mites extracted from host wound environment. protocols.io dx.doi.org/10.17504/protocols.io.exwbfpe | 2021-03-29 03:12:55 | |||
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RNA Isolation from Plant Tissue Protocol 3: CTAB-PVP Method Resource Report Resource Website |
Beijing Genomics Institute | 10.17504/protocols.io.4vygw7w | GigaScience Press, BGI | Implemented by: Beijing Genomics InstituteThis protocol is part of a collection of eighteen protocols used to isolate total RNA from plant tissue. (RNA Isolation from Plant Tissue Collection: https://www.protocols.io/view/rna-isolation-from-plant-tissue-439gyr6) | Beijing Genomics Institute | 1 | 2019 | Beijing Genomics Institute 2019. RNA Isolation from Plant Tissue Protocol 3: CTAB-PVP Method. protocols.io dx.doi.org/10.17504/protocols.io.4vygw7w | 2021-03-29 03:12:58 | |||
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SQK-MAP006 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 | 10.17504/protocols.io.gvvbw66 | GigaScience Press | This protocol describes the library preparation for Nanopore sequencing according to the SQK-MAP006 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-MAP006 protocol for library preparation for Nanopore sequencing. protocols.io dx.doi.org/10.17504/protocols.io.gvvbw66 | 2021-03-29 03:13:14 | ||
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RNA Isolation from Plant Tissue Protocol 7: pBIOZOL-LiCl Method Resource Report Resource Website |
Eric Carpenter | 10.17504/protocols.io.4rvgv66 | GigaScience Press, BGI | Implemented by: Beijing Genomics Institute 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 7: pBIOZOL-LiCl Method. protocols.io dx.doi.org/10.17504/protocols.io.4rvgv66 | 2021-03-29 03:13:17 | ||||
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The calculation of gut metabolic modules form gene profile Resource Report Resource Website |
Qi Wang | 10.17504/protocols.io.be7ajhie | BGI, GIGA, GigaScience Press | The calculation of gut metabolic modules form gene profile | BGI | 1 | 2020 | Qi Wang 2020. The calculation of gut metabolic modules form gene profile. protocols.io dx.doi.org/10.17504/protocols.io.be7ajhie | 2021-03-29 03:13:23 | |||
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Bionano genome mapping from animal tissue Resource Report Resource Website |
Graham J Etherington, Darren Heavens, David Baker, Ashleigh Lister, Rose McNelly, Gonzalo Garcia, Bernardo Clavijo, Iain Macaulay, Wilfried Haerty, Federica Di Palma | 10.17504/protocols.io.bd7ei9je | GigaScience Press | Bionano genome map 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. Bionano genome mapping from animal tissue. protocols.io dx.doi.org/10.17504/protocols.io.bd7ei9je | 2021-03-29 03:13:27 |
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