Protocols   Select Another Resource Report Type

Authors: Tianlin Pei, Mengxiao Yan, Yu Kong, Hang Fan, Jie Liu, Mengying Cui, Yumin Fang, Binjie Ge, Jun Yang, Qing Zhao
Group: BGI, GIGA, GigaScience Press
Summary: Tripterygium wilfordii is a vine from the Celastraceae family that is used in traditional Chinese medicine (TCM). The active ingredient celastrol is a friedelane-type pentacyclic triterpenoid with putative roles as antitumor, immunosuppressive, and antiobesity agent. Here, we report a reference genome assembly of T. wilfordii with high-quality annotation by using a hybrid sequencing strategy, obtaining a 340.12 Mb total genome size, a contig N50 reaching 3.09 Mb. We successfully anchored 91.02% of the sequences into 23 pseudochromosomes using Hi-C technology and the superscaffold N50 reached 13.03 Mb. In addition, we annotated 31,593 structural genes, and a repeat percentage of 44.31%. Comparative evolutionary analyses showed that T. wilfordii diverged from species of Malpighiales approximately 102.4 million years ago. Based on integration of the genome, transcriptome and metabolite analyses, as well as in vivo and in vitro enzyme assays of the two CYP450 genes TwCYP712K1 and TwCYP712K2 the second biosynthesis step of celastrol was investigated. Syntenic analysis revealed that TwCYP712K1 and TwCYP712K2 were derived from a common ancestor. These results provide insights for further investigating pathways related to celastrol andvaluable information to aid the conservation of resources. In addition, they helped us understand the evolution of Celastrales.

Proper citation: Tianlin Pei, Mengxiao Yan, Yu Kong, Hang Fan, Jie Liu, Mengying Cui, Yumin Fang, Binjie Ge, Jun Yang, Qing Zhao 2021. Protocols for "The genome analysis of Tripterygium wilfordii reveals TwCYP712K1 and TwCYP712K2 responsible for oxidation of friedelin in celastrol biosynthesis pathway". protocols.io https://dx.doi.org/10.17504/protocols.io.bspfndjn Copy   

•   Source:

Authors: Hebert F.O., Grambauer S., Barber I., Landry C.R., Aubin-Horth N.
Group: GigaScience Press
Summary: This protocol describes how to extract total RNA from flatworms. It is from: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. RNA extraction protocol (Trizol). protocols.io https://dx.doi.org/10.17504/protocols.io.ew7bfhn Copy   

•   Source:

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 blood 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 B (FMS and CR). protocols.io https://dx.doi.org/10.17504/protocols.io.im9cc96 Copy   

•   Source:

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

Proper citation: Kailong Ma 2018. DNA extraction for the Betta splendens genome. protocols.io https://dx.doi.org/10.17504/protocols.io.qvedw3e Copy   

•   Source:

Authors: Guangqi Gao, Meng Xu, Yongchun Zuo, Yulan Yang, Chunling Bai, Junyang Xu, Zhuying Wei, Jiumeng Min, Guanghua Su, Xianqiang Zhou, Jun Guo, Yu Hao, Guiping Zhang, Xukui Yang, Xiaomin Xu, Randall B Widelitz, Cheng-Ming Chuong, Chi Zhang, Jun Yin, Guangpeng Li
Group: GigaScience Press
Summary: As one of the most recognizable characteristics in birds, plumage colour has a high impact on understanding the evolution and mechanisms of colouration. Feather and skin are ideal tissues to explore the genomics and complexity of colour patterns in vertebrates. Two species of the genus Chrysolophus, golden pheasant (Chrysolophus pictus) and Lady Amherst’s pheasant (Chrysolophus amherstiae), exhibit brilliant colours in their plumage, but with extreme phenotypic differences, making these two species great models to investigate plumage colouration mechanisms in birds. Here we provide details of the protocols used for plumage pigments identification by High-performance liquid chromatography. The fat-soluble pigments (carotenoids) and oxidation products of melanins (TTCA and PTCA) can be qualitatively and quantificationally analyzed by HPLC with the corresponding standards, respectively.

Proper citation: Guangqi Gao, Meng Xu, Yongchun Zuo, Yulan Yang, Chunling Bai, Junyang Xu, Zhuying Wei, Jiumeng Min, Guanghua Su, Xianqiang Zhou, Jun Guo, Yu Hao, Guiping Zhang, Xukui Yang, Xiaomin Xu, Randall B Widelitz, Cheng-Ming Chuong, Chi Zhang, Jun Yin, Guangpeng Li 2018. Plumage pigments identification by High-performance liquid chromatography. protocols.io https://dx.doi.org/10.17504/protocols.io.sjtecnn Copy   

•   Source:

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 https://dx.doi.org/10.17504/protocols.io.4q5gvy6 Copy   

•   Source:

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

•   Source:

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: Illumina GAII Library Construction and Sequencing for RNA Seq

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. Illumina GAII Library Construction and Sequencing for RNA Seq. protocols.io https://dx.doi.org/10.17504/protocols.io.38mgru6 Copy   

•   Source:

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 single-tube library construction protocol is for degraded DNA using BGISeq-500 sequencing platform.

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. BGISeq-500 library construction Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.iamcac6 Copy   

•   Source:

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 2020. Protocols for "Shotgun Metagenomics of 361 elderly women reveals gut microbiome change in bone mass loss". protocols.io https://dx.doi.org/10.17504/protocols.io.bqwwmxfe Copy   

•   Source:

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 single-tube library construction protocol is for degraded DNA using adapters for the Illumina platform.

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. Illumina library construction Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.iajcacn Copy   

•   Source:

Authors: Chang Li
Group: GigaScience Press, BGI
Summary: From this protocol, we can know detail methods of assembly and annotation of the L. maculatus genome.

Proper citation: Chang Li 2018. Fish genome assembly and annotation pipeline. protocols.io https://dx.doi.org/10.17504/protocols.io.ss3eegn Copy   

•   Source:

Authors: Robert Auber
Group: Wisecaver Lab, BGI, GIGA, GigaScience Press

Proper citation: Robert Auber 2019. Total DNA extraction from plant tissue using CTAB method. protocols.io https://dx.doi.org/10.17504/protocols.io.bamnic5e Copy   

•   Source:

Authors: Eric Carpenter
Group: GigaScience Press
Summary: Implemented by: Patrick Edger and J. Chris PiresFor a small number of samples the Invitrogen PureLink™ RNA Mini Kit (Cat #12183-018A) was used to isolate total RNA while the Qiagen RNeasy MinElute Cleanup Kit (Cat #74204) was used to purify and concentrate total RNA. The methods followed the manufacturer’s instructions and thus 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 17: Invitrogen PureLink-Qiagen RNeasy Hybrid. protocols.io https://dx.doi.org/10.17504/protocols.io.4uwgwxe Copy   

•   Source:

Authors: Chang-Ming Bai
Group: BGI, GIGA, GigaScience Press
Summary: This protocol include the detailed methods of Hi-C assembly of the Scapharca broughtonii genome

Proper citation: Chang-Ming Bai 2019. The pipeline of Hi-C assembly of the Scapharca broughtonii genome. protocols.io https://dx.doi.org/10.17504/protocols.io.z8cf9sw Copy   

•   Source:

Authors: Benjamin Istace, Anne Friedrich, Léo d’Agata, 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, High molecular weight DNA extraction from all kingdoms
Summary: These protocols accompany the following 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 d’Agata, 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. Protocols from "De novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer". protocols.io https://dx.doi.org/10.17504/protocols.io.gvxbw7n Copy   

•   Source:

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 historical museum hides, which potentially have been chemically tanned.

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 A. protocols.io https://dx.doi.org/10.17504/protocols.io.iabcaan Copy   

•   Source:

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 https://dx.doi.org/10.17504/protocols.io.imrcc56 Copy   

•   Source:

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 https://dx.doi.org/10.17504/protocols.io.4uxgwxn Copy   

•   Source:

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: BGI, GIGA, GigaScience Press
Summary: In this study we assembled the first chromosome-level genome assembly of the humpback puffer (Tetraodon palembangensis), a species of poisonous freshwater pufferfish mainly distributed in Southeast Asia. This utilized Oxford Nanopore and BGISEQ-500 sequencing, stLFR libraries and Hi-C assembly, and the protocols for nucleic acid extraction, library construction and sequencing are all made available here. The resulting genome size was 362 Mb with a ~1.78 Mb contig N50 and ~15.8 Mb scaffold N50. Based on the assembled 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 successfully constructed using this and public data. These protocols are made available for others carrying vertebrate genome assembly, and the open data and published study for comparative genome studies.

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 2021. Protocols for "Chromosome-level genome assembly of the humpback puffer, Tetraodon palembangensis". protocols.io https://dx.doi.org/10.17504/protocols.io.bs8inhue Copy   

•   Source: