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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 8 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 8. protocols.io dx.doi.org/10.17504/protocols.io.gxvbxn6 Copy
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, High molecular weight DNA extraction from all kingdoms
Summary: 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...
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. Genomic DNA extraction from sea cucumber body-wall tissue. protocols.io dx.doi.org/10.17504/protocols.io.gk8buzw Copy
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 dx.doi.org/10.17504/protocols.io.tqfemtn Copy
Authors: Chang Li
Group: GigaScience Press, BGI, GIGA
Summary: This protocol is used to clarity the process of Hi-C library preparation for L.maculatus genome.
Proper citation: Chang Li 2018. Hi-C library preparation for the Lateolabrax maculatus genome. protocols.io dx.doi.org/10.17504/protocols.io.ss4eegw Copy
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 dx.doi.org/10.17504/protocols.io.tqaemse Copy
Authors: Eric Carpenter
Group: GigaScience Press
Summary: 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).
Proper citation: Eric Carpenter 2019. RNA Isolation from Plant Tissue Protocol 16: CTAB-Hot Acid Phenol Method for Algae. protocols.io dx.doi.org/10.17504/protocols.io.4uygwxw Copy
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 dx.doi.org/10.17504/protocols.io.4vxgw7n 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 5: pBIOZOL Method. protocols.io dx.doi.org/10.17504/protocols.io.4rdgv26 Copy
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 dx.doi.org/10.17504/protocols.io.qq6dvze 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 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 dx.doi.org/10.17504/protocols.io.hrjb54n Copy
Authors: Eric Carpenter
Group: GigaScience Press
Summary: Implemented by: Michael DeyholosThis protocol combines elements of standard CTAB, acid phenol, and silica-membrane protocols. The protocol was developed to extract total RNA from a wide range of plant species and tissues, and to do so in the smallest volume possible to yield >20 μg of total RNA using as little as 50 mg of fresh tissue. Maintaining a small extraction volume also allows for many samples to be processed in parallel in microcentrifuge tubes; at least 12 samples can be processed in 3–4 hours. The protocol has been used successfully with dozens of species, including tissues rich in polysaccharides and/or secondary metabolites. There are four organic extractions in total (three chloroform and one phenol:chloroform). For many species/tissues, the full set of chloroform extractions in the order specified is required to maximize RNA purity and to prevent phase inversion during the acid phenol extraction.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 8: CTAB/Acid Phenol/Silica Membrane Method. protocols.io dx.doi.org/10.17504/protocols.io.4yfgxtn Copy
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 Illumina sequencing. 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. Illumina PCR-Free library preparation. protocols.io dx.doi.org/10.17504/protocols.io.gvtbw6n Copy
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