Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
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 https://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 https://dx.doi.org/10.17504/protocols.io.k9icz4e 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 sorft tissue.
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 C. protocols.io https://dx.doi.org/10.17504/protocols.io.iaecabe 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
Summary: This protocol is for the whole genome de novo assembly and annotation for apostichopus japonicus genome, but can be useful in other marine invertebrate genomes. 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. Whole genome de-novo assembly and annotation protocol for Apostichopus japonicus genome. protocols.io https://dx.doi.org/10.17504/protocols.io.gmabu2e Copy
Authors: Eric Carpenter
Group: GigaScience Press
Summary: Implemented by: Falicia Goh and Neil ClarkeThis RNA isolation method is modified from that described by Köhrer and Domdey5.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) 5 Kohrer, K. & Domdey, H. Preparation of high molecular weight RNA. Methods in Enzymology 194, 398‐405 (1991).
Proper citation: Eric Carpenter 2019. RNA Isolation from Plant Tissue Protocol 15: Hot Acid Phenol Method for Algae. protocols.io https://dx.doi.org/10.17504/protocols.io.4u3gwyn Copy
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 https://dx.doi.org/10.17504/protocols.io.4tjgwkn Copy
Authors: Eric Carpenter
Group: GigaScience Press, BGI
Summary: Implemented by: Beijing Genomics Institute 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 7: pBIOZOL-LiCl Method. protocols.io https://dx.doi.org/10.17504/protocols.io.4rvgv66 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 https://dx.doi.org/10.17504/protocols.io.hrmb546 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 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 https://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 https://dx.doi.org/10.17504/protocols.io.gk8buzw Copy
Authors: Yang Liu, Huan Liu, Hongfeng Chen, Bernard Goffinet, Nikisha Patel, Ziqiang Chen, Shanshan Dong, Sibo Wang, Linzhou Li, Jin Yu
Group: GigaScience Press, BGI
Summary: Background:Mosses compose one of the three lineages that form the sister group to extant vascular plants. Having emerged from an early split in the diversification of embryophytes, mosses may offer complementary insights into the evolution of traits following the transition to and colonization of land. Here, we report the draft nuclear genome of Fontinalis antipyretica (Fontinalaceae, Hypnales), a charismatic aquatic moss widespread in temperate regions of the Northern Hemisphere. Wesequenced and de novo assembled its genome using the 10 × genomics method. The genome comprises 385.2 Mbp, with a scaffold N50 of 45.8 Kbp. The assembly captured 87.2% of the 430 genes in the BUSCO viridiplantae odb10 dataset.The newly generated F. antipyreticagenome is the third genome of mosses, and the second genome for a seedless aquatic plant.
Proper citation: Yang Liu, Huan Liu, Hongfeng Chen, Bernard Goffinet, Nikisha Patel, Ziqiang Chen, Shanshan Dong, Sibo Wang, Linzhou Li, Jin Yu 2020. Protocols for "Draft genome of the aquatic moss Fontinalis antipyretica (Fontinalaceae, Bryophyta)". protocols.io https://dx.doi.org/10.17504/protocols.io.bn7jmhkn Copy
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: SOAP-denovo-trans assembly protocol used to assemble plant transcriptomes for the 1KP project.
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. SOAP-denovo-trans assembly. protocols.io https://dx.doi.org/10.17504/protocols.io.38pgrvn Copy
Authors: Xin Liu
Group: GigaScience Press, BGI
Summary: This protocol is used to clarity the process of RNA extration for our Betta splendens genome.
Proper citation: Xin Liu 2018. RNA extration for the Betta splendens genome. protocols.io https://dx.doi.org/10.17504/protocols.io.qq7dvzn 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 https://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 https://dx.doi.org/10.17504/protocols.io.gxtbxnn Copy
Authors: Jie Huang, Xinming Liang, Yuankai Xuan, Chunyu Geng, Yuxiang Li, Haorong Lu, Shoufang Qu, Xianglin Mei, Hongbo Chen, Ting Yu, Nan Sun, Junhua Rao, Jiahao Wang, Wenwei Zhang, Ying Chen, Sha Liao, Hui Jiang, Xin Liu, Zhaopeng Yang, Feng Mu, Shangxian Gao
Group: GigaScience Press, BGI, GIGA, GigaScience Press
Summary: BGISEQ-500 is a desktop sequencer developed by BGI. Using DNA nanoball and combinational probe anchor synthesis developed from Complete Genomics™ sequencing technologies, it generates short reads at a large scale. Library construction on the platform includes fragmentation, size selection, end repair and A-tailing, adaptor ligation, PCR amplification, and splint circularization.
Proper citation: Jie Huang, Xinming Liang, Yuankai Xuan, Chunyu Geng, Yuxiang Li, Haorong Lu, Shoufang Qu, Xianglin Mei, Hongbo Chen, Ting Yu, Nan Sun, Junhua Rao, Jiahao Wang, Wenwei Zhang, Ying Chen, Sha Liao, Hui Jiang, Xin Liu, Zhaopeng Yang, Feng Mu, Shangxian Gao 2018. BGISEQ-500 WGS library construction. protocols.io https://dx.doi.org/10.17504/protocols.io.ps5dng6 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 https://dx.doi.org/10.17504/protocols.io.ss4eegw 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 https://dx.doi.org/10.17504/protocols.io.4uygwxw 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
Summary: These protocols accompany 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. Protocols for "Draft genome of the sea cucumber Apostichopus japonicus and genetic polymorphism among color variants". protocols.io https://dx.doi.org/10.17504/protocols.io.gmebu3e Copy
Authors: Ting Yang, Chenyu Wu
Group: GigaScience Press, BGI
Summary: DNA extraction of −80◦C stored leaves by CTAB.
Proper citation: Ting Yang, Chenyu Wu 2018. DNA Extraction for plant samples by CTAB. protocols.io https://dx.doi.org/10.17504/protocols.io.pzqdp5w Copy
Can't find your Protocol?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. If you want to find a specific protocol and you know the DOI of the protocol already, it's easier to enter a DOI to search. You can refine the search results using Facets on the left side of the search results page. If you are on the table view, you can also search in a specific column by clicking the column title and enter the keywords.
If you still could not find your protocol in the search results, please help us by adding it into the system — it's easy. Create and publish your protocols at Protocols.io.
Welcome to the dkNET Resources search. From here you can search through a compilation of resources used by dkNET and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that dkNET has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on dkNET then you can log in from here to get additional features in dkNET such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
You can save any searches you perform for quick access to later from here.
We recognized your search term and included synonyms and inferred terms along side your term to help get the data you are looking for.
If you are logged into dkNET you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the sources that were queried against in your search that you can investigate further.
Here are the categories present within dkNET that you can filter your data on
Here are the subcategories present within this category that you can filter your data on
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
Email: info_at_ dknet.org
