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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: 10x Genomics Library Construction

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. 10x Genomics Library Construction. protocols.io https://dx.doi.org/10.17504/protocols.io.bd3vi8n6 Copy   

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Authors: Rui Zhang
Group: BGI, GIGA, GigaScience Press
Summary: The humpback puffer,Tetraodon palembangensis, is a species of poisonous freshwater pufferfish mainly distributed in Southeast Asia (Thailand, Laos, Malaysia and Indonesia). The humpback puffer has many interesting biological features, such as inactivity, tetrodotoxin production and body expansion. Here, we reported the first chromosome-level genome assembly of the humpback puffer. The genome size is 362 Mb with ~1.78 Mb contig N50 and ~15.8 Mb scaffold N50. Based on the genome, ~61.5Mb (18.11%) repeat sequences were identified, 19,925 genes were annotated, and 90.01% of these genes could be predicted with function. Finally, a phylogenetic tree of ten teleost fish species was constructed, which suggests that humpback puffer and T. nigroviridis shared a common ancestor at 18.1 MYA and diverged from T. rubripes at 45.8 MYA. The humpback puffer genome will be a valuable genomic resource to illustrate possible mechanisms of tetrodotoxin synthesis and tolerance.

Proper citation: Rui Zhang 2021. Oxford Nanopore sequencing and library construction. protocols.io https://dx.doi.org/10.17504/protocols.io.btifnkbn Copy   

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Authors: 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
Group: GigaScience Press, BGI
Summary: The 1000 Plants (1KP) initiative explored the genetic diversity of green plants (Viridiplantae) by sequencing RNA from 1,342 samples representing 1,173 species. All of the analyses done for the 1KP capstone, and previous studies on subsets of these data, are based on a series of de novo transcriptome assemblies and related outputs that will be described in this publication. We expect that these data will also be useful to other researchers with interests in specific gene families, either across the green plant tree of life or in more focused lineages. These protocols provide additional details on the sample and sequence processing, hopefully providing insight for reproducibility and tools for other researchers working on plant transcriptomics and evolution.

Proper citation: 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. Sequencing Protocols for the One Thousand Plant Transcriptomes Initiative. protocols.io https://dx.doi.org/10.17504/protocols.io.38jgrun 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: Long Mate Pair 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. Long Mate Pair Library Construction Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bd3ui8nw Copy   

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Authors: Eric Carpenter
Group: GigaScience Press
Summary: Implemented by: Michael Melkonian and Barbara SurekThe protocol for RNA isolation using TRI Reagent (Molecular Research Center, Cincinnati OH) is analogous to the TRIzol LS Reagent protocol except that 1 ml of TRI Reagent is added to each 250 μl of homogenized material (= approx. 50–100 mg packed cell volume) (step 3, Protocol 10). For background, TRI Reagent combines phenol and guanidine thiocyanate in a monophasic solution to inhibit RNase activity during RNA isolation.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 11: Tri Reagent Method. protocols.io https://dx.doi.org/10.17504/protocols.io.4ydgxs6 Copy   

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Authors: Guangyi Fan, Judy Chan, Kailong Ma, Simon Ming-Yuen Lee, Binrui Yang, He Zhang, Xianwei Yang, Chengcheng Shi, Henry Law, Zhitao Ren, Qiwu Xu, Qun Liu, Jiahao Wang, Wenbin Chen, Libin Shao, David Gonçalves, Andreia Ramos, Sara D. Cardoso, Min Guo, Jing Cai, Xun Xu, Jian Wang, Huanming Yang, Xin Liu, Yitao Wang
Group: GigaScience Press, BGI
Summary: Siamese fighting fish Betta splendens are notorious for their aggressiveness and accordingly have been widely used to study aggression. However, the lack of a reference genome has so far limited the understanding of the genetic basis of aggression in this species. Here we present the first reference genome assembly of the Siamese fighting fish.We first sequenced and de novo assembled a 465.24 Mb genome for the B. splendens variety Giant, with a weighted average (N50) scaffold size of 949.03 Kb and an N50 contig size of 19.01 Kb, covering 99.93% of the estimated genome size. To obtain a chromosome-level genome assembly, we constructed one Hi-C library and sequenced 75.24 Gb reads using the BGISEQ-500 platform. We anchored approximately 93% of the scaffold sequences into 21 chromosomes and evaluated the quality of our assembly using the high contact frequency heatmap and BUSCO. We also performed comparative chromosome analyses between Oryzias latipes and B. splendens, revealing a chromosome conservation evolution in B. splendens. We predicted a total of 23,981 genes assisted by RNA-seq data generated from brain, liver, muscle and heart tissues of Giant, and annotated 15% repetitive sequences in the genome. Additionally, we resequenced other five B. splendens varieties and detected ~3.4M single-nucleotide variations (SNVs) and 27,305 indels.We provide the first chromosome-level genome for the Siamese fighting fish. The genome will lay a valuable foundation for future research on  aggression in B. splendens.

Proper citation: Guangyi Fan, Judy Chan, Kailong Ma, Simon Ming-Yuen Lee, Binrui Yang, He Zhang, Xianwei Yang, Chengcheng Shi, Henry Law, Zhitao Ren, Qiwu Xu, Qun Liu, Jiahao Wang, Wenbin Chen, Libin Shao, David Gonçalves, Andreia Ramos, Sara D. Cardoso, Min Guo, Jing Cai, Xun Xu, Jian Wang, Huanming Yang, Xin Liu, Yitao Wang 2018. High-quality reference genome of the Siamese fighting fish Betta splendens, a model species for the study of aggression. protocols.io https://dx.doi.org/10.17504/protocols.io.qsvdwe6 Copy   

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Authors: Rui Zhang, Chang Li, Mengjun Yu, Xiaoyun Huang, Mengqi Zhang, Shanshan Liu, Shanshan Pan, Weizhen Xue, Congyan Wang, Chunyan Mao, He Zhang, Guangyi Fan
Group: GigaScience Press
Summary: The humpback puffer,Tetraodon palembangensis, also known as Pao palembangensis, is a species of poisonous freshwater pufferfish mainly distributed in Southeast Asia (Thailand, Laos, Malaysia and Indonesia). Despite interesting biological features, such as its very inactive nature, tetrodotoxin production and body expansion mechanisms, molecular research on the humpback puffer is still rare because of the lack of a high-quality reference genome. Here, we reported a first chromosome-level genome assembly of an adult humpback puffer, of which the genome size is 362 Mb with ~1.78 Mb contig N50 and ~15.8 Mb scaffold N50s. Based on the genome, ~61.5Mb (18.11%) repeat sequences were also identified, and totally 19,925 genes were annotated, 99.20% of which could be predicted with function using protein-coding function databases. Finally, a phylogenetic tree was constructed with single-copy gene families from ten teleost fishes. The humpback puffer genome will be a valuable genomic resource to illustrate possible mechanisms of tetrodotoxin synthesis and tolerance, providing clues for future detailed studies of biological toxins.

Proper citation: Rui Zhang, Chang Li, Mengjun Yu, Xiaoyun Huang, Mengqi Zhang, Shanshan Liu, Shanshan Pan, Weizhen Xue, Congyan Wang, Chunyan Mao, He Zhang, Guangyi Fan 2020. Protocols for "Chromosome-level genome assembly of the humpback puffer, Tetraodon palembangensis". protocols.io https://dx.doi.org/10.17504/protocols.io.bkczksx6 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, BGI, GIGA, GigaScience Press
Summary: This protocol is provided by BioNano Genomics and was used in: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. Irys NLRS DNA labeling and Data collection. protocols.io https://dx.doi.org/10.17504/protocols.io.gahbsb6 Copy   

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Authors: Yasmin Bar El
Group: GigaScience Press
Summary: Isolated astrocyte cell culture preparation. Dissociation, preparation and plating of mice cortex neurons and glia cells on MEA. Isolatioin process of the culture from neurons, to obtain an isolated astrocyte culture.

Proper citation: Yasmin Bar El 2018. Isolated astrocyte culture preparation - protocol 1. protocols.io https://dx.doi.org/10.17504/protocols.io.tqbemsn Copy   

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Authors: Guangyi Fan, Judy Chan, Kailong Ma, Simon Ming-Yuen Lee, Binrui Yang, He Zhang, Xianwei Yang, Chengcheng Shi, Henry Law, Zhitao Ren, Qiwu Xu, Qun Liu, Jiahao Wang, Wenbin Chen, Libin Shao, David Gonçalves, Andreia Ramos, Sara D. Cardoso, Min Guo, Jing Cai, Xun Xu, Jian Wang, Huanming Yang, Xin Liu, Yitao Wang
Group: GigaScience Press, BGI
Summary: Siamese fighting fish Betta splendens are notorious for their aggressiveness and accordingly have been widely used to study aggression. However, the lack of a reference genome has so far limited the understanding of the genetic basis of aggression in this species. Here we present the first reference genome assembly of the Siamese fighting fish.We first sequenced and de novo assembled a 465.24 Mb genome for the B. splendens variety Giant, with a weighted average (N50) scaffold size of 949.03 Kb and an N50 contig size of 19.01 Kb, covering 99.93% of the estimated genome size. To obtain a chromosome-level genome assembly, we constructed one Hi-C library and sequenced 75.24 Gb reads using the BGISEQ-500 platform. We anchored approximately 93% of the scaffold sequences into 21 chromosomes and evaluated the quality of our assembly using the high contact frequency heatmap and BUSCO. We also performed comparative chromosome analyses between Oryzias latipes and B. splendens, revealing a chromosome conservation evolution in B. splendens. We predicted a total of 23,981 genes assisted by RNA-seq data generated from brain, liver, muscle and heart tissues of Giant, and annotated 15% repetitive sequences in the genome. Additionally, we resequenced other five B. splendens varieties and detected ~3.4M single-nucleotide variations (SNVs) and 27,305 indels.We provide the first chromosome-level genome for the Siamese fighting fish. The genome will lay a valuable foundation for future research on  aggression in B. splendens.

Proper citation: Guangyi Fan, Judy Chan, Kailong Ma, Simon Ming-Yuen Lee, Binrui Yang, He Zhang, Xianwei Yang, Chengcheng Shi, Henry Law, Zhitao Ren, Qiwu Xu, Qun Liu, Jiahao Wang, Wenbin Chen, Libin Shao, David Gonçalves, Andreia Ramos, Sara D. Cardoso, Min Guo, Jing Cai, Xun Xu, Jian Wang, Huanming Yang, Xin Liu, Yitao Wang 2018. High-quality reference genome of the Siamese fighting fish Betta splendens, a model species for the study of aggression. protocols.io https://dx.doi.org/10.17504/protocols.io.qvddw26 Copy   

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

Proper citation: Qi Wang 2021. The calculation of gut metabolic modules from gene profile. protocols.io https://dx.doi.org/10.17504/protocols.io.bq6gmzbw Copy   

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Authors: Eric Carpenter
Group: GigaScience Press
Summary: Implemented by: Ingrid Jordon-Thaden and Nicholas Miles (Soltis Labs)This procedure eliminates the mortar and pestle homogenization of tissues and instead grinds tissue in 2 ml microcentrifuge tubes. The method closely follows Ambion’s protocols and could be used in a 96-well format. This method worked great for species that proved to be difficult to extract with other methods (i.e. woody and aquatic plants).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 14: Ambion Trizol RNA Extraction in Microcentrifuge Tubes with Turbo DNAfree Digestion. protocols.io https://dx.doi.org/10.17504/protocols.io.4u6gwze Copy   

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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: These protocols accompany the following publication: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. Protocols for The Healthy Brain Network Serial Scanning Initiative (Sessions 1-14). protocols.io https://dx.doi.org/10.17504/protocols.io.gxcbxiw Copy   

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Authors: Chang Li
Group: GigaScience Press, BGI
Summary: This protocol is used to clarity the process of the mate-pair large libraries preparation for the L. maculatus.

Proper citation: Chang Li 2018. Mate-pair large libraries preparation for assembly of the Lateolabrax maculatus genome. protocols.io https://dx.doi.org/10.17504/protocols.io.ss2eege Copy   

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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: Library building protocol for archival samples with single 8-nt adapters for Illumina platforms.

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. Illumina library construction for Extraction Method A, B, C (For FMS samples) and D, E (PRP and RM). protocols.io https://dx.doi.org/10.17504/protocols.io.ingcdbw Copy   

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Authors: Eric Carpenter
Group: GigaScience Press
Summary: Implemented by: Henrietta Myburg and Marc JohnsonThis protocol is a modification of protocol 8. It was developed after protocol 8 and several commercially available plant RNA isolation kits failed to produce a sufficient yield and quality of RNA from Oenothera spp. (Onagraceae) for next-generation sequencing. Oenothera are rich in polysaccharides, oils, flavonoids and complex ellagitannins that likely interfere with isolation.We suspect that this protocol will be most useful for species and tissues with complex secondarychemistry and rich in oils (e.g. some Rosaceae and Pinaceae). The most important modifications to this protocol versus Protocol 8 is the use of less plant tissue, more extraction buffer, and repeating solvent extractions until the interphase is clean of debris. The protocol is regrettably longer and more involved than Protocol 8. We attempted to remove or reduce the replication of the solvent extractions steps without success (i.e. yield and quality are always decreased in Oenothera when any steps are removed).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 9: CTAB/Acid Phenol/Silica Membrane Method. protocols.io https://dx.doi.org/10.17504/protocols.io.4yegxte Copy   

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Authors: Qi Wang, Qiang Sun, Xiaoping Li, Zhefeng Wang, Haotian Zheng, Yanmei Ju, Ruijin Guo, Songlin Peng, Huijue Jia
Group: BGI, GIGA, GigaScience Press
Summary: Bone mass loss contributes to the risk of bone fracture in the elderly. Many factors including age, obesity, estrogen and diet, are associated with bone mass loss. Mice studies suggested that the gut microbiome might affect the bone mass by regulating the immune system, however there has been little evidence from human studies. Bone loss increases after menopause. Therefore, we have recruited 361 Chinese post-menopausal women to collect their fecal samples and metadata to conduct metagenome-wide association study (MWAS) to investigate the influence of the gut microbiome on bone health. Gut microbiome sequencing data were produced using BGISEQ500 sequencing, Bone mineral density (BMD) was calculated using Hologic dual energy X-ray machine, body mass index (BMI) and age were also recorded.This collected data allows exploration of the gut microbial diversity and their links to bone mass loss, as well as microbial markers for bone mineral density. In addition, these data are potentially useful in studying the role the gut microbiota might play in bone mass loss and in exploring the bone mass loss process.

Proper citation: Qi Wang, Qiang Sun, Xiaoping Li, Zhefeng Wang, Haotian Zheng, Yanmei Ju, Ruijin Guo, Songlin Peng, Huijue Jia 2021. Protocols for "Linking gut microbiome to bone mineral density: a shotgun metagenomic study of 361 eldly women". protocols.io https://dx.doi.org/10.17504/protocols.io.bq6imzce Copy   

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Authors: Eric Carpenter
Group: GigaScience Press
Summary: Implemented by: Sarah Covshoff, Rowan Sage and Julian HibberdThis RNA isolation method is a multi-component method involving an initial extraction by hotacid phenol and then a purification and DNase treatment using the RNeasy Mini Kit by Qiagen.The method described below is a modification of a method described by van Tunen et al.3.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) 3 van Tunen, A.J. et al. Cloning of the two chalcone flavanone isomerase genes from Petunia hybrida: coordinate, light‐ regulated and differential expression of flavonoid genes. The EMBO Journal 7, 1257‐1263 (1988).

Proper citation: Eric Carpenter 2019. RNA Isolation from Plant Tissue Protocol 12: Hot Acid Phenol Method for Angiosperms. protocols.io https://dx.doi.org/10.17504/protocols.io.4rxgv7n Copy   

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Authors: Qi Wang
Group: BGI, GIGA, GigaScience Press
Summary: Quality control for metagenomics data,including: remove low quality reads and host contamination reads.

Proper citation: Qi Wang 2020. Quality control for metagenomics data. protocols.io https://dx.doi.org/10.17504/protocols.io.be68jhhw Copy   

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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 https://dx.doi.org/10.17504/protocols.io.bcmriu56 Copy   

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