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RNA Isolation from Plant Tissue Protocol 13: Trizol/RNAqueous Midi-Kit Resource Report Resource Website |
Eric Carpenter | 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 dx.doi.org/10.17504/protocols.io.4tjgwkn | 2021-03-29 03:13:01 | ||||
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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 |
Mofiz E., Holt, D., Seemann, T., Currie B.J., Fischer K., Papenfuss A.T. | 10.17504/protocols.io.ez7bf9n | GigaScience Press | This protocol is from:Mofiz E. et al., Genomic resources and draft reference assemblies of the human and porcine scabies mites, Sarcoptes scabiei var. hominis and var. suis. GigaScience. 2016. DOI: 10.1186/s13742-016-0129-2 http://dx.doi.org/10.1186/s13742-016-0129-2. | , , , , , , , | http://dx.doi.org/10.1186/s13742-016-0129-2 | 2 | 2016 | Mofiz E., Holt, D., Seemann, T., Currie B.J., Fischer K., Papenfuss A.T. 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.ez7bf9n | 2021-03-29 03:13:02 | ||
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Schistocephalus solidus culturing Resource Report Resource Website |
Hebert F.O., Grambauer S., Barber I., Landry C.R., Aubin-Horth N. | 10.17504/protocols.io.ew8bfhw | GigaScience Press | This protocol describes how the parasitic flatworms (S. solidus) were cultured in the lab for: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 | , , , , | 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. Schistocephalus solidus culturing. protocols.io dx.doi.org/10.17504/protocols.io.ew8bfhw | 2021-03-29 03:13:06 | |
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Amplification Free Paired End Library Construction Protocol Resource Report Resource Website |
Graham J Etherington, Darren Heavens, David Baker, Ashleigh Lister, Rose McNelly, Gonzalo Garcia, Bernardo Clavijo, Iain Macaulay, Wilfried Haerty, Federica Di Palma | 10.17504/protocols.io.bd3ti8nn | GigaScience Press | Amplification Free Paired End Library Construction Protocol. | The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom, The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom, The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom, The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom, The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom, The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom, The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom, The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom, The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom, The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom | 1 | 2020 | Graham J Etherington, Darren Heavens, David Baker, Ashleigh Lister, Rose McNelly, Gonzalo Garcia, Bernardo Clavijo, Iain Macaulay, Wilfried Haerty, Federica Di Palma 2020. Amplification Free Paired End Library Construction Protocol. protocols.io dx.doi.org/10.17504/protocols.io.bd3ti8nn | 2021-03-29 03:13:15 | |||
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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 | 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 dx.doi.org/10.17504/protocols.io.hrmb546 | 2021-03-29 03:13:16 | |
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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 | 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 dx.doi.org/10.17504/protocols.io.hrpb55n | 2021-03-29 03:14:01 | |
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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 | 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 dx.doi.org/10.17504/protocols.io.gxtbxnn | 2021-03-29 03:14:14 | |||
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The pipeline of Hi-C assembly Resource Report Resource Website |
Xin Liu | 10.17504/protocols.io.qradv2e | GigaScience Press, BGI, GIGA | From here, You can know detail methods of Hi-C assembly of the Betta splendens genome. | BGI-Shenzhen | 1 | 2018 | Xin Liu 2018. The pipeline of Hi-C assembly. protocols.io dx.doi.org/10.17504/protocols.io.qradv2e | 2021-03-29 03:15:21 | |||
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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 | 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 dx.doi.org/10.17504/protocols.io.im7cc9n | 2021-03-29 03:12:22 | |
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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 | 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 dx.doi.org/10.17504/protocols.io.k9icz4e | 2021-03-29 03:12:31 | |||
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Extraction Method E (PRP) 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.inecdbe | GigaScience Press | Gen-IALFirst All-tissue DNA extraction kit -This protocol provides an efficient DNA extraction and purification of fresh sample (tissue material) | Salleh FM, Ramos-Madrigal J, Peñaloza F, Liu S, Mikkel-Holger SS, Riddhi PP, Martins R, Lenz D, Fickel J, Roos C, Shamsir MS, Azman MS, Burton KL, Stephen JR, Wilting A, Gilbert MTP, An expanded mammal mitogenome dataset from Southeast Asia. GigaScience 6(8). doi: 10.1093/gigascience/gix053 | Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark | https://doi.org/10.1093/gigascience/gix053 | 1 | 2017 | Faezah Mohd Salleh, Jazmin Ramos-Madrigal, Fernando Penaloza, Shanlin Liu, Mikkel-Holger S Sinding, Riddhi P Patel, Renata Martins, Dorina Lenz, Jorns Fickel, Christian Roos, Mohd Shahir Shamsir, Mohammad Shahfiz Azman, Burton K Lim, Stephen J Rossiter, Andreas Wilting, M Thomas P Gilbert 2017. Extraction Method E (PRP). protocols.io dx.doi.org/10.17504/protocols.io.inecdbe | 2021-03-29 03:12:29 | |
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Simulating reads for detection of transportable element insertions Resource Report Resource Website |
Qichao Yu, Wei Zhang, Xiaolong Zhang, Yongli Zeng, Yeming Wang, Yanhui Wang, Liqin Xu, Xiaoyun Huang, Nannan Li, Xinlan Zhou, Jie Lu, Xiaosen Guo, Guibo Li, Yong Hou, Shiping Liu, Bo Li | 10.17504/protocols.io.imrcc56 | GigaScience Press | We simulate paired-end reads for testing the accuracy and sensitivity of our computer program for detection of transportable element (TE) insertions (also called Mobile Element Insertions, MEIs). we named the software "Specific Insertions Detector (SID)". | Yu Q, Zhang W, Zhang X, Zeng Y, Wang Y, Wang Y, Xu L, Huang X, Li N, Zhou X, Lu J, Guo X, Li G, Hou Y, Liu S, Li B, Population-wide sampling of retrotransposon insertion polymorphisms using deep sequencing and efficient detection. GigaScience 6(9). doi: 10.1093/gigascience/gix066 | BGI Shenzhen, BGI Shenzhen, BGI Shenzhen, BGI Shenzhen, BGI Shenzhen, BGI Shenzhen, BGI Shenzhen, BGI Shenzhen, BGI Shenzhen, BGI Shenzhen, BGI Shenzhen, BGI Shenzhen, BGI Shenzhen, BGI Shenzhen, BGI Shenzhen, BGI Shenzhen | https://doi.org/10.1093/gigascience/gix066 | 1 | 2018 | Qichao Yu, Wei Zhang, Xiaolong Zhang, Yongli Zeng, Yeming Wang, Yanhui Wang, Liqin Xu, Xiaoyun Huang, Nannan Li, Xinlan Zhou, Jie Lu, Xiaosen Guo, Guibo Li, Yong Hou, Shiping Liu, Bo Li 2018. Simulating reads for detection of transportable element insertions. protocols.io dx.doi.org/10.17504/protocols.io.imrcc56 | 2021-03-29 03:12:10 | |
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RNA Isolation from Plant Tissue Protocol 18: innuPREP Plant RNA Kit Resource Report Resource Website |
Eric Carpenter | 10.17504/protocols.io.4uxgwxn | GigaScience Press | Implemented by: Michael Melkonian and Barbara SurekA small number of algae samples were extracted using the innuPREP Plant RNA Kit (Analytik Jena, Jena Germany) with either the PL and RL lysis buffer. The method followed the manufacturer’s protocols and so they are not repeated here.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 18: innuPREP Plant RNA Kit. protocols.io dx.doi.org/10.17504/protocols.io.4uxgwxn | 2021-03-29 03:12:12 | ||||
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DNA extraction for human microbe samples. Resource Report Resource Website |
Lilan Hao | 10.17504/protocols.io.bcmriu56 | BGI, GIGA, GigaScience Press | This protocol is used to clarity the process of total DNA extration for human microbe samples. | BGI-Shenzhen, Shenzhen 518083, China. | 1 | 2020 | Lilan Hao 2020. DNA extraction for human microbe samples.. protocols.io dx.doi.org/10.17504/protocols.io.bcmriu56 | 2021-03-29 03:09:56 | |||
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Oxford Nanopore sequencing and library construction Resource Report Resource Website |
Rui Zhang | 10.17504/protocols.io.btignkbw | BGI, GIGA, GigaScience Press | This is a protocol for Oxford Nanopore sequencing and library construction, which was used in the humpback puffer genome sequence. | BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China | 1 | 2021 | Rui Zhang 2021. Oxford Nanopore sequencing and library construction. protocols.io dx.doi.org/10.17504/protocols.io.btignkbw | 2021-03-29 03:10:02 | |||
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Protocols for activity changes in Neuron-Astrocyte Networks in Culture Under the Effect of Norepinephrine Resource Report Resource Website |
Yasmin Bar El | 10.17504/protocols.io.tp9emr6 | GigaScience Press | Protocols for Primary cortical neuronal-astrocyte cell culture, Isolated astrocyte cell culture, Immunocytochemistry, Electrophysiology and Ca2+ imaging. | School of Physics and Astronomy, Tel-Aviv University, Tel-Aviv, Israel | 1 | 2018 | Yasmin Bar El 2018. Protocols for activity changes in Neuron-Astrocyte Networks in Culture Under the Effect of Norepinephrine. protocols.io dx.doi.org/10.17504/protocols.io.tp9emr6 | 2021-03-29 03:10:17 | |||
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Protocols for "Sequencing smart: De novo sequencing and assembly approaches for a non-model mammal" 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.bd3ri8m6 | GigaScience Press | Whilst much sequencing effort has focused on key mammalian model organisms such as mouse and human, little is known about the correlation between genome sequencing techniques for non-model mammals and genome assembly quality. This is especially relevant to non-model mammals, where the samples to be sequenced are often degraded and low quality. A key aspect when planning a genome project is the choice of sequencing data to generate. This decision is driven by several factors, including the biological questions being asked, the quality of DNA available, and the availability of funds. Cutting-edge sequencing technologies now make it possible to achieve highly contiguous, chromosome-level genome assemblies, but relies on good quality high-molecular-weight DNA. Here we use a range of different genomic technologies generated from a roadkill European Polecat (Mustela putorius) to assess various assembly techniques on this low-quality sample. We evaluated different approaches for de novo assemblies and discuss their value in relation to biological analyses. The high degree of variability between each de novo assembly method (assessed from the seven key metrics) highlights the importance of carefully devising the sequencing strategy to be able to carry out the desired analysis. Adding more data to genome assemblies does not always results in better assemblies so it is important to understand the nuances of genomic data integration explained here, in order to obtain cost-effective value-for-money when sequencing genomes. | 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. Protocols for "Sequencing smart: De novo sequencing and assembly approaches for a non-model mammal". protocols.io dx.doi.org/10.17504/protocols.io.bd3ri8m6 | 2021-03-29 03:10:19 | |||
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RNA Isolation from Plant Tissue Protocol 4: CTAB-PVP-TRIzol Method Resource Report Resource Website |
Eric Carpenter | 10.17504/protocols.io.4q5gvy6 | 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) | 1 | 2019 | Eric Carpenter 2019. RNA Isolation from Plant Tissue Protocol 4: CTAB-PVP-TRIzol Method. protocols.io dx.doi.org/10.17504/protocols.io.4q5gvy6 | 2021-03-29 03:10:15 | ||||
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Extraction method B 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.iadcaa6 | GigaScience Press | This protocol provides an efficient DNA extraction and purification of ancient bones. | 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 B. protocols.io dx.doi.org/10.17504/protocols.io.iadcaa6 | 2021-03-29 03:10:33 | |
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Electrophysiology Resource Report Resource Website |
Yasmin Bar El | 10.17504/protocols.io.tqeemte | GigaScience Press | Electrophysiology by MEA. Electrical recording and stimulation of the cultures using MEA set-up (by Multichannel Systems). | School of Physics and Astronomy, Tel-Aviv University, Tel-Aviv, Israel | 1 | 2018 | Yasmin Bar El 2018. Electrophysiology. protocols.io dx.doi.org/10.17504/protocols.io.tqeemte | 2021-03-29 03:10:29 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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