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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 https://dx.doi.org/10.17504/protocols.io.inecdbe Copy   

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Authors: Kotaro Takahagi, Komaki Inoue, Minami Shimizu, Yukiko Uehara-Yamaguchi, Yoshihiko Onda, Keiichi Mochida
Group: GigaScience Press
Summary: This protocol provides an useful technique for detecting allele frequencies in the cDNA sample

Proper citation: Kotaro Takahagi, Komaki Inoue, Minami Shimizu, Yukiko Uehara-Yamaguchi, Yoshihiko Onda, Keiichi Mochida 2018. Detection of allele frequencies in the cDNA sample. protocols.io https://dx.doi.org/10.17504/protocols.io.nafdabn Copy   

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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 is a collection of protocols that accompany the Yuanyuan Fu, et. al 2017 GigaScience publication "Draft genome of the Tibetan medicinal herb, Rhodiola crenulata".

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. Protocols for "Draft genome of the Tibetan medicinal herb, Rhodiola crenulata". protocols.io https://dx.doi.org/10.17504/protocols.io.hrkb54w Copy   

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Authors: Huang Zhihai, Xu Jiang, Xiao Shuiming, Liao Baosheng, Gao Yuan, Zhai Chaochao, Qiu Xiaohui, Xu Wen, Chen Shilin
Group: GigaScience Press, High molecular weight DNA extraction from all kingdoms
Summary: 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.

Proper citation: 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 https://dx.doi.org/10.17504/protocols.io.gagbsbw Copy   

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Authors: 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
Group: GigaScience Press
Summary: 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...

Proper citation: 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 https://dx.doi.org/10.17504/protocols.io.gmbbu2n Copy   

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Authors: Ehtesham Mofiz
Group: GigaScience Press

Proper citation: Ehtesham Mofiz 2016. Draft genome assembly using parasitic mite population NGS DNA sample from mites extracted from host wound environment. protocols.io https://dx.doi.org/10.17504/protocols.io.exwbfpe Copy   

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Authors: Beijing Genomics Institute
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: Beijing Genomics Institute 2019. RNA Isolation from Plant Tissue Protocol 3: CTAB-PVP Method. protocols.io https://dx.doi.org/10.17504/protocols.io.4vygw7w Copy   

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Authors: Huang Zhihai, Xu Jiang, Xiao Shuiming, Liao Baosheng, Gao Yuan, Zhai Chaochao, Qiu Xiaohui, Xu Wen, Chen Shilin
Group: GigaScience Press
Summary: These methods accompany: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.

Proper citation: Huang Zhihai, Xu Jiang, Xiao Shuiming, Liao Baosheng, Gao Yuan, Zhai Chaochao, Qiu Xiaohui, Xu Wen, Chen Shilin 2016. Comparative optical genome analysis of two Pangolin species Manis pentadactyla and Manis javanica (protocols ). protocols.io https://dx.doi.org/10.17504/protocols.io.gaibsce Copy   

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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 https://dx.doi.org/10.17504/protocols.io.ew8bfhw Copy   

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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 https://dx.doi.org/10.17504/protocols.io.ez7bf9n Copy   

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Authors: 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
Group: GigaScience Press
Summary: 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...

Proper citation: 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 https://dx.doi.org/10.17504/protocols.io.gvvbw66 Copy   

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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 https://dx.doi.org/10.17504/protocols.io.bd3ti8nn Copy   

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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: Bionano genome map 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. Bionano genome mapping from animal tissue. protocols.io https://dx.doi.org/10.17504/protocols.io.bd7ei9je Copy   

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Authors: Qi Wang
Group: BGI, GIGA, GigaScience Press
Summary: The calculation of gut metabolic modules form gene profile

Proper citation: Qi Wang 2020. The calculation of gut metabolic modules form gene profile. protocols.io https://dx.doi.org/10.17504/protocols.io.be7ajhie Copy   

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Authors: Yasmin Bar El
Group: GigaScience Press
Summary: Calcium imaging - recording the calcium dynamics of cultures using fluorescent calcium dye, fluorescence microscopy and a camera.

Proper citation: Yasmin Bar El 2018. Calcium imaging. protocols.io https://dx.doi.org/10.17504/protocols.io.tqfemtn Copy   

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Authors: Yasmin Bar El
Group: GigaScience Press
Summary: Primary cortical neuronal-astrocyte cell culture preparation. Dissociation, preparation and plating of mice cortex neurons and glia cells on MEA.

Proper citation: Yasmin Bar El 2018. Neuron-astrocyte culture preparation. protocols.io https://dx.doi.org/10.17504/protocols.io.tqaemse Copy   

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Authors: Jim Leebens-Mack, Charlotte Carrigan
Group: GigaScience Press
Summary: Protocol implemented by: Jim Leebens-Mack and Charlotte Carrigan The first protocol used for isolation of total RNA was Qiagen’s RNeasy Plant Mini Kit (Qiagen, Valencia, CA). These kits are commercially available and widely used in RNA isolation. For detailed methods associated with this kit we refer readers to the “RNeasy Mini Handbook” available for download at www.qiagen.com. 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: Jim Leebens-Mack, Charlotte Carrigan 2019. RNA Isolation from Plant Tissue Protocol 1: Qiagen RNeasy Plant Mini Kit. protocols.io https://dx.doi.org/10.17504/protocols.io.4vxgw7n Copy   

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Authors: Xin Liu
Group: GigaScience Press, BGI
Summary: This protocol is used to clarity the process of total DNA extration for our Betta splendens genome.

Proper citation: Xin Liu 2018. DNA extration for the Betta splendens genome. protocols.io https://dx.doi.org/10.17504/protocols.io.qq6dvze Copy   

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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 5: pBIOZOL Method. protocols.io https://dx.doi.org/10.17504/protocols.io.4rdgv26 Copy   

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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 RNA 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. RNA extration for the R. crenulata genome. protocols.io https://dx.doi.org/10.17504/protocols.io.hrjb54n Copy   

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