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Extraction method A (FMS and CR) Resource Report Resource Website |
Faezah Mohd Salleh, Jazmin Ramos-Madrigal, Fernando Penaloza, Shanlin Liu, Mikkel-Holger S Sinding, Riddhi P Patel, Renata Martins, Dorina Lenz, Jorns Fickel, Christian Roos, Mohd Shahir Shamsir, Mohammad Shahfiz Azman, Burton K Lim, Stephen J Rossiter, Andreas Wilting, M Thomas P Gilbert | DOI:10.17504/protocols.io.im7cc9n | GigaScience Press | This protocol allows for adequate DNA extraction from fresh tissue 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 A (FMS and CR). protocols.io https://dx.doi.org/10.17504/protocols.io.im7cc9n | 2021-04-15 09:14:21 | |
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HIFI-Barcode SOP – Assembling COI barcodes using high-throughput sequencing Resource Report Resource Website |
Shanlin Liu, Chentao Yang, Chengran Zhou, Xin Zhou | DOI:10.17504/protocols.io.k9icz4e | GigaScience Press, BGI | We developed an Illumina-based pipeline, HIFI-Barcode, to produce full-length COI barcodes from pooled PCR amplicons generated by individual specimens. Using indexed primer sets and high-throughput sequencing platform strategy, and optimized analysis pipeline, the analytical cost and chemistry cost will significantly be reduced. The new protocol includes DNA preparation, amplification, and data analysis pipeline. | Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Plant Protection, China Agricultural University, Beijing 100193, People’s Republic of China;BGI-Shenzhen, Shenzhen, 518083, China;Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark, BGI-Shenzhen, Shenzhen, 518083, China, BGI-Shenzhen, Shenzhen, 518083, China;Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610000, China., Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Plant Protection, China Agricultural University, Beijing 100193, People’s Republic of China | 3 | 2018 | Shanlin Liu, Chentao Yang, Chengran Zhou, Xin Zhou 2018. HIFI-Barcode SOP – Assembling COI barcodes using high-throughput sequencing. protocols.io https://dx.doi.org/10.17504/protocols.io.k9icz4e | 2021-04-15 09:14:27 | |||
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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 | DOI: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 https://dx.doi.org/10.17504/protocols.io.iaecabe | 2021-04-15 09:14:26 | |
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Whole genome de-novo assembly and annotation protocol for Apostichopus japonicus 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 | DOI:10.17504/protocols.io.gmabu2e | GigaScience Press | This protocol is for the whole genome de novo assembly and annotation for apostichopus japonicus genome, but can be useful in other marine invertebrate genomes. It 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. Whole genome de-novo assembly and annotation protocol for Apostichopus japonicus genome. protocols.io https://dx.doi.org/10.17504/protocols.io.gmabu2e | 2021-04-15 09:14:29 | ||
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RNA Isolation from Plant Tissue Protocol 15: Hot Acid Phenol Method for Algae Resource Report Resource Website |
Eric Carpenter | DOI:10.17504/protocols.io.4u3gwyn | GigaScience Press | Implemented by: Falicia Goh and Neil ClarkeThis RNA isolation method is modified from that described by Köhrer and Domdey5.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) 5 Kohrer, K. & Domdey, H. Preparation of high molecular weight RNA. Methods in Enzymology 194, 398‐405 (1991). | 1 | 2019 | Eric Carpenter 2019. RNA Isolation from Plant Tissue Protocol 15: Hot Acid Phenol Method for Algae. protocols.io https://dx.doi.org/10.17504/protocols.io.4u3gwyn | 2021-04-15 09:14:33 | ||||
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RNA Isolation from Plant Tissue Protocol 13: Trizol/RNAqueous Midi-Kit Resource Report Resource Website |
Eric Carpenter | DOI:10.17504/protocols.io.4tjgwkn | GigaScience Press | Implemented by: Megan Rolf and Toni M. KutchanThis protocol is based on a combination of two methods: The Trizol method described byChomczynski and Sacchi4 and the Ambion® RNAqueous®-Midi Kit (Life Technologies, Carlsbad,CA), with minor modifications.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) 4Chomczynski, P. & Sacchi, N. Single‐step method of RNA isolation by acid guanidinium thiocyanatephenol‐chloroform extraction. Analytical Biochemistry 163, 156‐159 (1987). | 1 | 2019 | Eric Carpenter 2019. RNA Isolation from Plant Tissue Protocol 13: Trizol/RNAqueous Midi-Kit. protocols.io https://dx.doi.org/10.17504/protocols.io.4tjgwkn | 2021-04-15 09:14:48 | ||||
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RNA Isolation from Plant Tissue Protocol 7: pBIOZOL-LiCl Method Resource Report Resource Website |
Eric Carpenter | DOI: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 https://dx.doi.org/10.17504/protocols.io.4rvgv66 | 2021-04-15 09:14:57 | ||||
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DNA extration for the R. crenulata genome Resource Report Resource Website |
Yuanyuan Fu, Liangwei Li, Shijie Hao, Rui Guan, Guangyi Fan, Chengcheng Shi, Haibo Wan, Wenbin Chen, He Zhang, Guocheng Liu, Jihua Wang, Lulin Ma, Jianling You, Xuemei Ni, Zhen Yue, Xun Xu, Xiao Sun, Xin Liu, Simon Ming-Yuen Lee | DOI:10.17504/protocols.io.hrmb546 | GigaScience Press | This protocol is used to clarify the process of total DNA extration for our R. crenulata genome. | Fu Y, Li L, Hao S, Guan R, Fan G, Shi C, Wan H, Chen W, Zhang H, Liu G, Wang J, Ma L, You J, Ni X, Yue Z, Xu X, Sun X, Liu X, Lee SM, Draft genome sequence of the Tibetan medicinal herb . GigaScience 6(6). doi: 10.1093/gigascience/gix033 | Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China | https://doi.org/10.1093/gigascience/gix033 | 1 | 2017 | Yuanyuan Fu, Liangwei Li, Shijie Hao, Rui Guan, Guangyi Fan, Chengcheng Shi, Haibo Wan, Wenbin Chen, He Zhang, Guocheng Liu, Jihua Wang, Lulin Ma, Jianling You, Xuemei Ni, Zhen Yue, Xun Xu, Xiao Sun, Xin Liu, Simon Ming-Yuen Lee 2017. DNA extration for the R. crenulata genome. protocols.io https://dx.doi.org/10.17504/protocols.io.hrmb546 | 2021-04-15 09:14:39 | |
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The Healthy Brain Network Serial Scanning Initiative, Session 8 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.gxvbxn6 | GigaScience Press | This protocol describes MRI and ADHD Quotient Test for Session 8 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, Session 8. protocols.io https://dx.doi.org/10.17504/protocols.io.gxvbxn6 | 2021-04-15 09:14:42 | |||
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Genomic DNA extraction from sea cucumber body-wall tissue 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 | DOI:10.17504/protocols.io.gk8buzw | GigaScience Press, High molecular weight DNA extraction from all kingdoms | This is a DNA extraction protocol from sea cucumber (Apostichopus japonicus) body-wall tissue. It 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. Genomic DNA extraction from sea cucumber body-wall tissue. protocols.io https://dx.doi.org/10.17504/protocols.io.gk8buzw | 2021-04-15 09:15:02 | ||
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Protocols for "Draft genome of the aquatic moss Fontinalis antipyretica (Fontinalaceae, Bryophyta)" Resource Report Resource Website |
Yang Liu, Huan Liu, Hongfeng Chen, Bernard Goffinet, Nikisha Patel, Ziqiang Chen, Shanshan Dong, Sibo Wang, Linzhou Li, Jin Yu | DOI:10.17504/protocols.io.bn7jmhkn | GigaScience Press, BGI | Background:Mosses compose one of the three lineages that form the sister group to extant vascular plants. Having emerged from an early split in the diversification of embryophytes, mosses may offer complementary insights into the evolution of traits following the transition to and colonization of land. Here, we report the draft nuclear genome of Fontinalis antipyretica (Fontinalaceae, Hypnales), a charismatic aquatic moss widespread in temperate regions of the Northern Hemisphere. Wesequenced and de novo assembled its genome using the 10 × genomics method. The genome comprises 385.2 Mbp, with a scaffold N50 of 45.8 Kbp. The assembly captured 87.2% of the 430 genes in the BUSCO viridiplantae odb10 dataset.The newly generated F. antipyreticagenome is the third genome of mosses, and the second genome for a seedless aquatic plant. | State Key Laboratory of Agricultural Genomics, China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China, State Key Laboratory of Agricultural Genomics, China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China, Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269-3043, USA, Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269-3043, USA, College of Chinese Medicine Materials, Jilin Agricultural University, Changchun 130012, China , Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen 518004, China, State Key Laboratory of Agricultural Genomics, China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China, State Key Laboratory of Agricultural Genomics, China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China, State Key Laboratory of Agricultural Genomics, China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China | 1 | 2020 | Yang Liu, Huan Liu, Hongfeng Chen, Bernard Goffinet, Nikisha Patel, Ziqiang Chen, Shanshan Dong, Sibo Wang, Linzhou Li, Jin Yu 2020. Protocols for "Draft genome of the aquatic moss Fontinalis antipyretica (Fontinalaceae, Bryophyta)". protocols.io https://dx.doi.org/10.17504/protocols.io.bn7jmhkn | 2021-04-15 09:15:17 | |||
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SOAP-denovo-trans assembly Resource Report Resource Website |
Eric J. Carpenter, Naim Matasci, Shuangxiu Wu, Jing Sun, Jun Yu, Fabio Rocha Jimenez Vieira, Chris Bowler, Richard G. Dorrell, Matt Gitzendanner, Ling Li, Wensi Du, Kristian Ullrich, Michael S. Barker, James H. Leebens-Mack, Gane Ka-Shu Wong | DOI:10.17504/protocols.io.38pgrvn | GigaScience Press, BGI | SOAP-denovo-trans assembly protocol used to assemble plant transcriptomes for the 1KP project. | 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. SOAP-denovo-trans assembly. protocols.io https://dx.doi.org/10.17504/protocols.io.38pgrvn | 2021-04-15 09:15:16 | |||
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RNA extration for the Betta splendens genome Resource Report Resource Website |
Xin Liu | DOI:10.17504/protocols.io.qq7dvzn | GigaScience Press, BGI | This protocol is used to clarity the process of RNA extration for our Betta splendens genome. | BGI-Shenzhen | 1 | 2018 | Xin Liu 2018. RNA extration for the Betta splendens genome. protocols.io https://dx.doi.org/10.17504/protocols.io.qq7dvzn | 2021-04-15 09:15:14 | |||
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The pipeline of assembly and annotation Resource Report Resource Website |
Yuanyuan Fu, Liangwei Li, Shijie Hao, Rui Guan, Guangyi Fan, Chengcheng Shi, Haibo Wan, Wenbin Chen, He Zhang, Guocheng Liu, Jihua Wang, Lulin Ma, Jianling You, Xuemei Ni, Zhen Yue, Xun Xu, Xiao Sun, Xin Liu, Simon Ming-Yuen Lee | DOI:10.17504/protocols.io.hrpb55n | GigaScience Press | This protocol provides the detailed methods of assembly and annotation of the R. crenulata genome. | Fu Y, Li L, Hao S, Guan R, Fan G, Shi C, Wan H, Chen W, Zhang H, Liu G, Wang J, Ma L, You J, Ni X, Yue Z, Xu X, Sun X, Liu X, Lee SM, Draft genome sequence of the Tibetan medicinal herb . GigaScience 6(6). doi: 10.1093/gigascience/gix033 | Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China | https://doi.org/10.1093/gigascience/gix033 | 1 | 2017 | Yuanyuan Fu, Liangwei Li, Shijie Hao, Rui Guan, Guangyi Fan, Chengcheng Shi, Haibo Wan, Wenbin Chen, He Zhang, Guocheng Liu, Jihua Wang, Lulin Ma, Jianling You, Xuemei Ni, Zhen Yue, Xun Xu, Xiao Sun, Xin Liu, Simon Ming-Yuen Lee 2017. The pipeline of assembly and annotation. protocols.io https://dx.doi.org/10.17504/protocols.io.hrpb55n | 2021-04-15 09:14:54 | |
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The Healthy Brain Network Serial Scanning Initiative, Session 1 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.gxtbxnn | GigaScience Press | This protocol describes MRI and ADHD Quotient Test for Session 1 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, Session 1. protocols.io https://dx.doi.org/10.17504/protocols.io.gxtbxnn | 2021-04-15 09:14:58 | |||
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BGISEQ-500 WGS library construction 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.ps5dng6 | GigaScience Press, BGI, GIGA, GigaScience Press | BGISEQ-500 is a 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. Library construction on the platform includes fragmentation, size selection, end repair and A-tailing, adaptor ligation, PCR amplification, and splint circularization. | Li F, Chen C, Wei W, Wang Z, Dai J, Hao L, Song L, Zhang X, Zeng L, Du H, Tang H, Liu N, Yang H, Wang J, Madsen L, Brix S, Kristiansen K, Xu X, Li J, Wu R, Jia H, The metagenome of the female upper reproductive tract. GigaScience 7(10). doi: 10.1093/gigascience/giy107 | National Institutes for food and drug Control (NIFDC), BGI-Shenzhen, State Food and Drug Administration Hubei Center for Medical Equipment Quality Supervision and Testing, BGI-Shenzhen, BGI-Shenzhen, BGI-Shenzhen, National Institutes for food and drug Control (NIFDC), State Food and Drug Administration Hubei Center for Medical Equipment Quality Supervision and Testing, 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/giy107 | 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 WGS library construction. protocols.io https://dx.doi.org/10.17504/protocols.io.ps5dng6 | 2021-04-15 09:15:31 | |
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Hi-C library preparation for the Lateolabrax maculatus genome Resource Report Resource Website |
Chang Li | DOI:10.17504/protocols.io.ss4eegw | GigaScience Press, BGI, GIGA | This protocol is used to clarity the process of Hi-C library preparation for L.maculatus genome. | BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China. | 1 | 2018 | Chang Li 2018. Hi-C library preparation for the Lateolabrax maculatus genome. protocols.io https://dx.doi.org/10.17504/protocols.io.ss4eegw | 2021-04-15 09:14:59 | |||
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RNA Isolation from Plant Tissue Protocol 16: CTAB-Hot Acid Phenol Method for Algae Resource Report Resource Website |
Eric Carpenter | DOI:10.17504/protocols.io.4uygwxw | GigaScience Press | Implemented by: Falicia Goh and Neil ClarkeThis RNA isolation method is a combination and modification of the hot acid phenol method (protocol 14) and that described by Asif et al6. This method was used for two taxa (P. cruentum and B. braunii). 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) 6 Asif, M.H., Dhawan, P. & Nath, P. A simple procedure for the isolation of high quality RNA from ripening banana fruit. Plant Molecular Biology Reporter 18, 109‐115 (2000). | 1 | 2019 | Eric Carpenter 2019. RNA Isolation from Plant Tissue Protocol 16: CTAB-Hot Acid Phenol Method for Algae. protocols.io https://dx.doi.org/10.17504/protocols.io.4uygwxw | 2021-04-15 09:15:07 | ||||
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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 | DOI: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 https://dx.doi.org/10.17504/protocols.io.gmebu3e | 2021-04-15 09:15:19 | ||
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DNA Extraction for plant samples by CTAB Resource Report Resource Website |
Ting Yang, Chenyu Wu | DOI: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 https://dx.doi.org/10.17504/protocols.io.pzqdp5w | 2021-04-15 09:15:21 |
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