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Authors: Chang-Ming Bai, Lu-Sheng Xin, Umberto Rosani, Biao Wu, Qing-Chen Wang, Xiao-Ke Duan, Zhi-Hong Liu, Chong-Ming Wang
Group: GigaScience Press
Summary: Background: The blood clam, Scapharca (Anadara) broughtonii, is an economically and ecologically important marine bivalve of the Family Arcidae. The efforts that have been made to study their population genetics, breeding, cultivation and stock enrichment were somewhat hindered by the lack of a reference genome. Here, we reported the complete genome sequence of S. broughtonii, a first reference genome of the Family Arcidae.Funding: A total of 75.79 Gb clean data was generated with the PacBio and Oxford Nanopore platforms, which represented approx. 86× coverage of the S. broughtonii genome. De novo assembly of these long reads resulted in an 884.5 Mb genome, with a contig N50 of 1.80 Mb and scaffold N50 of 45.00 Mb, respectively. Genome Hi-C scaffolding resulted in 19 chromosomes containing 99.35% of bases of the assembled genome. Genome annotation revealed that a considerable part of the genome (46.1%) is composed by repeated sequences, while 24,045 protein-coding genes were predicted and 84.7% of them were annotated.Conclusion: We report here the chromosomal-level assembly of the S. broughtonii genome based on long read sequencing and Hi-C scaffolding. The genomic data could be served as reference genome for the Arcidae Family and will provide a valuable resource for the scientific community and aquaculture sector.

Proper citation: Chang-Ming Bai, Lu-Sheng Xin, Umberto Rosani, Biao Wu, Qing-Chen Wang, Xiao-Ke Duan, Zhi-Hong Liu, Chong-Ming Wang 2019. Key protocols for chromosome-level genome assembly of the Scapharca (Anadara) broughtonii.. protocols.io dx.doi.org/10.17504/protocols.io.zimf4c6 Copy   


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 dx.doi.org/10.17504/protocols.io.btifnkbn 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: Describes the library preparation for Nanopore sequencing from low input DNA according to the SQK-MAP006 protocolIt 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 Low Input protocol for library preparation for Nanopore sequencing. protocols.io dx.doi.org/10.17504/protocols.io.gvwbw7e Copy   


  • DOI: 10.17504/protocols.io.infcdbn

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 historic 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 F (CR). protocols.io dx.doi.org/10.17504/protocols.io.infcdbn Copy   


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 "Shotgun Metagenomics of 361 elderly women reveals gut microbiome change in bone mass loss". protocols.io dx.doi.org/10.17504/protocols.io.bq6hmzb6 Copy   


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 dx.doi.org/10.17504/protocols.io.qsvdwe6 Copy   


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: Southeast (SE) Asia is one of the most biodiverse regions in the world and it holds approximately 20% of all mammal species. Despite this, the majority of SE Asia’s genetic diversity is still poorly characterized. The growing interest in using environmental DNA (eDNA) to assess and monitor SE Asian species, in particular, threatened mammals - has created the urgent need to expand the available reference database of mitochondrial barcode and complete mitogenome sequences. We have partially addressed this need by generating 72 new mitogenome sequences reconstructed from DNA isolated from a range of historical and modern 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. Supporting data for "An expanded mammal mitogenome dataset from Southeast Asia". protocols.io dx.doi.org/10.17504/protocols.io.im6cc9e Copy   


Authors: Chang Li
Group: GigaScience Press, BGI
Summary: This protocol is used to clarity the process of total DNA extration for L. maculatus genome.

Proper citation: Chang Li 2018. DNA extraction for vertebrate tissues using Phenol:Chloroform:Isoamylol. protocols.io dx.doi.org/10.17504/protocols.io.ssyeefw Copy   


Authors: Chen Chen, Lilan Hao, Weixia Wei, Fei Li, Liju Song, Xiaowei Zhang, Juanjuan Dai, Zhuye Jie, Jiandong Li, Xiaolei Song, Zirong Wang, Zhe Zhang, Liping Zeng, Hui Du, Huiru Tang, Tao Zhang, Huanming Yang, Jian Wang, Susanne Brix, Karsten Kristiansen, Xun Xu, Ruifang Wu, Huijue Jia
Group: GigaScience Press, BGI
Summary: Human urine is traditionally considered to be sterile, and whether the urine harbours distinct microbial communities has been a matter of debate. Potential links between female urine and reproductive tract microbial communities is currently not clear. Here, we collected urine samples from 147 Chinese women of reproductive age and explored the nature of colonization by 16S rRNA gene amplicon sequencing, quantitative real-time PCR, and live bacteria culture. To demonstrate the utility of this approach, the intra-individual Spearman's correlation was used to explore the relationship between urine and multiple sites of the reproductive tract. PERMANOVA was also performed to explore potential correlations between the lifestyle and various clinical factors and urinary bacterial communities. Our data demonstrated distinct bacterial communities in urine, indicative of a non-sterile environment. Streptococcus-dominated, Lactobacillus-dominated, and diverse type were the three most common urinary bacterial community types in the cohort. Detailed comparison of the urinary microbiota with multiple sites of the female reproductive tract microbiota demonstrated that the urinary microbiota were more similar to the microbiota in the cervix and uterine cavity than to those of the vagina in the same women. Our data demonstrate the potential connectivity among microbiota in the female urogenital system and provide insight and resources for exploring diseases of the urethra and genital tract.

Proper citation: Chen Chen, Lilan Hao, Weixia Wei, Fei Li, Liju Song, Xiaowei Zhang, Juanjuan Dai, Zhuye Jie, Jiandong Li, Xiaolei Song, Zirong Wang, Zhe Zhang, Liping Zeng, Hui Du, Huiru Tang, Tao Zhang, Huanming Yang, Jian Wang, Susanne Brix, Karsten Kristiansen, Xun Xu, Ruifang Wu, Huijue Jia 2020. Protocols for "The female urinary microbiota in relation to the reproductive tract microbiota.". protocols.io dx.doi.org/10.17504/protocols.io.bpyumpww Copy   


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 dx.doi.org/10.17504/protocols.io.4uwgwxe Copy   


  • DOI: 10.17504/protocols.io.iabcaan

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 dx.doi.org/10.17504/protocols.io.iabcaan 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 dx.doi.org/10.17504/protocols.io.qq7dvzn 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 dx.doi.org/10.17504/protocols.io.38pgrvn 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 dx.doi.org/10.17504/protocols.io.bn7jmhkn Copy   


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 dx.doi.org/10.17504/protocols.io.nafdabn 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 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 dx.doi.org/10.17504/protocols.io.hrkb54w 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 dx.doi.org/10.17504/protocols.io.gmabu2e Copy   


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 dx.doi.org/10.17504/protocols.io.gaibsce 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 dx.doi.org/10.17504/protocols.io.ps5dng6 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 dx.doi.org/10.17504/protocols.io.4u3gwyn Copy   



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