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Authors: Eric Carpenter
Group: GigaScience Press
Summary: 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).
Proper citation: Eric Carpenter 2019. RNA Isolation from Plant Tissue Protocol 13: Trizol/RNAqueous Midi-Kit. protocols.io dx.doi.org/10.17504/protocols.io.4tjgwkn Copy
Authors: Mofiz E., Holt, D., Seemann, T., Currie B.J., Fischer K., Papenfuss A.T.
Group: GigaScience Press
Summary: 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.
Proper citation: 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 Copy
Authors: Hebert F.O., Grambauer S., Barber I., Landry C.R., Aubin-Horth N.
Group: GigaScience Press
Summary: 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
Proper citation: 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 Copy
Authors: Graham J Etherington, Darren Heavens, David Baker, Ashleigh Lister, Rose McNelly, Gonzalo Garcia, Bernardo Clavijo, Iain Macaulay, Wilfried Haerty, Federica Di Palma
Group: GigaScience Press
Summary: Amplification Free Paired End Library Construction Protocol.
Proper citation: 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 Copy
Authors: 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
Group: GigaScience Press
Summary: This protocol is used to clarify the process of total DNA extration for our R. crenulata genome.
Proper citation: 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 Copy
Authors: 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
Group: GigaScience Press
Summary: This protocol provides the detailed methods of assembly and annotation of the R. crenulata genome.
Proper citation: 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 Copy
Authors: 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
Group: GigaScience Press
Summary: 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...
Proper citation: 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 Copy
Authors: Xin Liu
Group: GigaScience Press, BGI, GIGA
Summary: From here, You can know detail methods of Hi-C assembly of the Betta splendens genome.
Proper citation: Xin Liu 2018. The pipeline of Hi-C assembly. protocols.io dx.doi.org/10.17504/protocols.io.qradv2e Copy
Authors: 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
Group: GigaScience Press
Summary: This protocol allows for adequate DNA extraction from fresh tissue samples.
Proper citation: 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 Copy
Authors: Shanlin Liu, Chentao Yang, Chengran Zhou, Xin Zhou
Group: GigaScience Press, BGI
Summary: 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.
Proper citation: 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 Copy
Authors: 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
Group: GigaScience Press
Summary: Gen-IALFirst All-tissue DNA extraction kit -This protocol provides an efficient DNA extraction and purification of fresh sample (tissue material)
Proper citation: 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 Copy
Authors: 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
Group: GigaScience Press
Summary: 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)".
Proper citation: 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 Copy
Authors: Eric Carpenter
Group: GigaScience Press
Summary: 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)
Proper citation: Eric Carpenter 2019. RNA Isolation from Plant Tissue Protocol 18: innuPREP Plant RNA Kit. protocols.io dx.doi.org/10.17504/protocols.io.4uxgwxn Copy
Authors: Lilan Hao
Group: BGI, GIGA, GigaScience Press
Summary: This protocol is used to clarity the process of total DNA extration for human microbe samples.
Proper citation: Lilan Hao 2020. DNA extraction for human microbe samples.. protocols.io dx.doi.org/10.17504/protocols.io.bcmriu56 Copy
Authors: Rui Zhang
Group: BGI, GIGA, GigaScience Press
Summary: This is a protocol for Oxford Nanopore sequencing and library construction, which was used in the humpback puffer genome sequence.
Proper citation: Rui Zhang 2021. Oxford Nanopore sequencing and library construction. protocols.io dx.doi.org/10.17504/protocols.io.btignkbw Copy
Authors: Yasmin Bar El
Group: GigaScience Press
Summary: Protocols for Primary cortical neuronal-astrocyte cell culture, Isolated astrocyte cell culture, Immunocytochemistry, Electrophysiology and Ca2+ imaging.
Proper citation: 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 Copy
Authors: Graham J Etherington, Darren Heavens, David Baker, Ashleigh Lister, Rose McNelly, Gonzalo Garcia, Bernardo Clavijo, Iain Macaulay, Wilfried Haerty, Federica Di Palma
Group: GigaScience Press
Summary: 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.
Proper citation: 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 Copy
Authors: Eric Carpenter
Group: GigaScience Press, BGI
Summary: 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)
Proper citation: Eric Carpenter 2019. RNA Isolation from Plant Tissue Protocol 4: CTAB-PVP-TRIzol Method. protocols.io dx.doi.org/10.17504/protocols.io.4q5gvy6 Copy
Authors: 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
Group: GigaScience Press
Summary: This protocol provides an efficient DNA extraction and purification of ancient bones.
Proper citation: 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 Copy
Authors: Yasmin Bar El
Group: GigaScience Press
Summary: Electrophysiology by MEA. Electrical recording and stimulation of the cultures using MEA set-up (by Multichannel Systems).
Proper citation: Yasmin Bar El 2018. Electrophysiology. protocols.io dx.doi.org/10.17504/protocols.io.tqeemte Copy
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