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RNA extraction, small filters Resource Report Resource Website |
Darach Miller | 10.17504/protocols.io.feqbjdw | 1 | 2016 | Darach Miller 2016. RNA extraction, small filters. protocols.io dx.doi.org/10.17504/protocols.io.feqbjdw | 2021-03-29 03:09:52 | ||||||
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Generating Stable Transfection in Bodo saltans Resource Report Resource Website |
Fatma Gomaa, Zuhong Li, Roberto Docampo, Peter Girguis, Virginia Edgcomb | 10.17504/protocols.io.sh3eb8n | Protist Research to Optimize Tools in Genetics (PROT-G) | B. saltans cells were electroporated using a square-wave electroporator (Nepa21, Bulldog Bio, Inc.) using one poring pulse of 200 volts with a pulse duration of 25 ms and five transfer pulses of 60 volts with a pulse duration of 99 ms, with plasmid targeting the 18S region (18S-GFP). A schematic representation of the plasmid, the target locus and the expected site of integration into the B. saltans genome is shown in Figure 1. Electroporated cells were selected with 1 µg/ml of G418, added 24 hours after electroporation. Cells were washed and subcultured into fresh selection medium every 3-4 days. G418 resistant cells started to emerge 7-9 days post-electroporation. Cells were processed for genotyping analysis to confirm plasmid integration 3 weeks post-electroporation. DNA was extracted from pools of transfected and wild cells using the Qiagen DNeasy Blood & Tissue kit. PCR analyses were used to characterize the 18S-GFP tagging using 6 sets of PCR primers, as shown in Figure 1 C. Gel electrophoresis image (Figure 2) showing the amplified PCR products at the expected sizes. Amplified PCR#1 with primer sets Ribo_tag_forward & GFP reverse (800 bp)Amplified PCR #2 with primer sets Neo_forward & Ribo_tag_reverse (1000 bp)Amplified PCR #3 with primer sets TubR & IG forward ( 3 bands)Amplified PCR #4 with primer sets Tub_forward & IG reverse (3 bands)Amplified PCR #5 with primer sets Ribo_tag_forward & Ribo_tag_reverse (Wild (C) cells band at 350 bp, transfected cells S1 and S2 two bands, 350 bp and 2800 bp)Electroporated cells were selected with 1 µg/ml of G418, added 24 hours after electroporation. Cells were washed and subcultured into fresh selection medium every 3-4 days. G418 resistant cells started to emerge 7-9 days post-electroporation. Cells were processed for genotyping analysis to confirm plasmid integration 3 weeks post-electroporation. DNA was extracted from pools of transfected and wild cells using the Qiagen DNeasy Blood & Tissue kit. PCR analyses were used to characterize the 18S-GFP tagging using 6 sets of PCR primers, as shown in Figure 1 C. Gel electrophoresis image (Figure 2) showing the amplified PCR products at the expected sizes. Amplified PCR#1 with primer sets Ribo_tag_forward & GFP reverse (800 bp)Amplified PCR #2 with primer sets Neo_forward & Ribo_tag_reverse (1000 bp)Amplified PCR #3 with primer sets TubR & IG forward ( 3 bands)Amplified PCR #4 with primer sets Tub_forward & IG reverse (3 bands)Amplified PCR #5 with primer sets Ribo_tag_forward & Ribo_tag_reverse (Wild (C) cells band at 350 bp, transfected cells S1 and S2 two bands, 350 bp and 2800 bp)Cells were processed for genotyping analysis to confirm plasmid integration 3 weeks post-electroporation. DNA was extracted from pools of transfected and wild cells using the Qiagen DNeasy Blood & Tissue kit. PCR analyses were used to characterize the 18S-GFP tagging using 6 sets of PCR primers, as shown in Figure 1 C. Gel electrophoresis image (Figure 2) showing the amplified PCR products at the expected sizes. Amplified PCR#1 with primer sets Ribo_tag_forward & GFP reverse (800 bp)Amplified PCR #2 with primer sets Neo_forward & Ribo_tag_reverse (1000 bp)Amplified PCR #3 with primer sets TubR & IG forward ( 3 bands)Amplified PCR #4 with primer sets Tub_forward & IG reverse (3 bands)Amplified PCR #5 with primer sets Ribo_tag_forward & Ribo_tag_reverse (Wild (C) cells band at 350 bp, transfected cells S1 and S2 two bands, 350 bp and 2800 bp)PCR analyses were used to characterize the 18S-GFP tagging using 6 sets of PCR primers, as shown in Figure 1 C. Gel electrophoresis image (Figure 2) showing the amplified PCR products at the expected sizes. Amplified PCR#1 with primer sets Ribo_tag_forward & GFP reverse (800 bp)Amplified PCR #2 with primer sets Neo_forward & Ribo_tag_reverse (1000 bp)Amplified PCR #3 with primer sets TubR & IG forward ( 3 bands)Amplified PCR #4 with primer sets Tub_forward & IG reverse (3 bands)Amplified PCR #5 with primer sets Ribo_tag_forward & Ribo_tag_reverse (Wild (C) cells band at 350 bp, transfected cells S1 and S2 two bands, 350 bp and 2800 bp)Gel electrophoresis image (Figure 2) showing the amplified PCR products at the expected sizes. Amplified PCR#1 with primer sets Ribo_tag_forward & GFP reverse (800 bp)Amplified PCR #2 with primer sets Neo_forward & Ribo_tag_reverse (1000 bp)Amplified PCR #3 with primer sets TubR & IG forward ( 3 bands)Amplified PCR #4 with primer sets Tub_forward & IG reverse (3 bands)Amplified PCR #5 with primer sets Ribo_tag_forward & Ribo_tag_reverse (Wild (C) cells band at 350 bp, transfected cells S1 and S2 two bands, 350 bp and 2800 bp)Amplified PCR#1 with primer sets Ribo_tag_forward & GFP reverse (800 bp)Amplified PCR #2 with primer sets Neo_forward & Ribo_tag_reverse (1000 bp)Amplified PCR #3 with primer sets TubR & IG forward ( 3 bands)Amplified PCR #4 with primer sets Tub_forward & IG reverse (3 bands)Amplified PCR #5 with primer sets Ribo_tag_forward & Ribo_tag_reverse (Wild (C) cells band at 350 bp, transfected cells S1 and S2 two bands, 350 bp and 2800 bp)Figure 1: Schematic representation of the (A); the 18S- GFP plasmid; (B) Ribosomal operon in B. saltans genome (C); and the expected site of plasmid integration in B. saltans genome through homologous regions 1 and 2 (HR1, HR2).Figure 2: Agarose gel electrophoresis image of the amplified PCR products for B. saltans cells transfected with 18S-GFP Cassette (S1 and S2) and the wild type cells (C). The primers sets and the expected product sizes are mentioned above in the text.Figure 3: B. saltans cells transfected with 18S-GFP tagging cassette. On the left: a light microscopy image showing the B. saltans cells (around 4 cells at different level). On the right: GFP fluorescent signal detected in the transfected cell. Scale bar 10 μm. | Harvard University, University of Georgia, University of Georgia, Harvard University, Woods Hole Oceanographic Institution | 1 | 2018 | Fatma Gomaa, Zuhong Li, Roberto Docampo, Peter Girguis, Virginia Edgcomb 2018. Generating Stable Transfection in Bodo saltans. protocols.io dx.doi.org/10.17504/protocols.io.sh3eb8n | 2021-03-29 03:09:55 | |||
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Protocols for chromosome-level genome assembly of the spotted sea bass, Lateolabrax maculatus Resource Report Resource Website |
Changwei Shao, Chang Li, Na Wang, Yating Qin, Wenteng Xu, Qun Liu, Qian Zhou, Yong Zhao, Xihong Li, Shanshan Liu, Xiaowu Chen, Shahid Mahboob, Xin Liu, Songlin Chen | 10.17504/protocols.io.ssxeefn | GigaScience Press, BGI | Background: The spotted sea bass (Lateolabrax maculatus) is a valuable commercial fish that is widely cultured in China. While analyses using molecular markers and population genetics have been conducted, genomic resources are lacking.Finding: Here, we report a chromosome-scale assembly of the spotted sea bass genome by high-depth genome sequencing, assembly and annotation. The genome scale was 0.62 Gb with contig and scaffold N50 length to be 31 Kb and 1,040 Kb, respectively. Hi-C scaffolding of the genome resulted in 24 pseudochromosomes containing 77.68% of the total assembled sequences. A total of 132.38Mb repeat sequences were detected, accounting for 20.73% of the assemble genome. 22,015 protein-coding genes were predicted, of which 96.52% were homologous to proteins in various databases. In addition, we constructed a phylogenetic tree using 1,586 single-copy gene families and identified 125 unique gene families in the spotted sea bass genome.Conclusions: We assembled a spotted sea bass genome, which will be a valuable genomic resource to understand the biology of the spotted sea bass, and will also lead to the development of molecular breeding techniques to generate spotted sea bass with better economical traits. | Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China. Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China., BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China; BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China; BGI-Shenzhen, Shenzhen, 518083, China., Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China. Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China., BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China; BGI-Shenzhen, Shenzhen, 518083, China., Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China., BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China, Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China. Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China., BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China, Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China., BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China; BGI-Shenzhen, Shenzhen, 518083, China., Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China., Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia; Department of Zoology, GC University, Faisalabad, Pakistan., BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China; BGI-Shenzhen, Shenzhen, 518083, China., Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China. Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China. | 1 | 2018 | Changwei Shao, Chang Li, Na Wang, Yating Qin, Wenteng Xu, Qun Liu, Qian Zhou, Yong Zhao, Xihong Li, Shanshan Liu, Xiaowu Chen, Shahid Mahboob, Xin Liu, Songlin Chen 2018. Protocols for chromosome-level genome assembly of the spotted sea bass, Lateolabrax maculatus. protocols.io dx.doi.org/10.17504/protocols.io.ssxeefn | 2021-03-29 03:09:55 | |||
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Restriction Digest Resource Report Resource Website |
New England Biolabs | 10.17504/protocols.io.isycefw | New England Biolabs (NEB) | The following is a "typical" restriction endonuclease reaction. Please see the "guidelines" tab below for the NEB tips on optimizing restriction digests. | NEB, Ipswich, MA | https://www.neb.com/protocols/2012/12/07/optimizing-restriction-endonuclease-reactions | 2 | 2018 | New England Biolabs 2018. Restriction Digest. protocols.io dx.doi.org/10.17504/protocols.io.isycefw | 2021-03-29 03:09:55 | ||
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Outreach: "Is This Alive" station (designed for and used at AbGradCon 2018) Resource Report Resource Website |
Nadia Szeinbaum, Yael Toporek | 10.17504/protocols.io.ra2d2ge | Georgia Institute of Technology, Georgia Institute of Technology | 1 | 2018 | Nadia Szeinbaum, Yael Toporek 2018. Outreach: "Is This Alive" station (designed for and used at AbGradCon 2018). protocols.io dx.doi.org/10.17504/protocols.io.ra2d2ge | 2021-03-29 03:09:59 | |||||
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Mouse Cardiac Perfusion Fixation and Brain Collection Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.bd8vi9w6 | BICCN, Allen Institute for Brain Science | This protocol describes the procedures for intracardiac perfusion fixation of postnatal mice, including anesthesia, exsanguination, fixation, brain removal and post-fixation storage. Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number U19MH114830. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. | Allen Institute | 1 | 2020 | Allen Institute for Brain Science 2020. Mouse Cardiac Perfusion Fixation and Brain Collection. protocols.io dx.doi.org/10.17504/protocols.io.bd8vi9w6 | 2021-03-29 03:09:59 | |||
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1M Tris Resource Report Resource Website |
Ms Alex Aitken | 10.17504/protocols.io.c5vy65 | VERVE Net, Sullivan Lab | This shows how to make 1M Tris. | http://www.nhm.ac.uk/resources-rx/files/te-buffer_aug12-118648.pdf | 1 | 2016 | Ms Alex Aitken 2016. 1M Tris. protocols.io dx.doi.org/10.17504/protocols.io.c5vy65 | 2021-03-29 03:09:59 | |||
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Cell migration assay or Transwell assay Resource Report Resource Website |
Marzia Ognibene | 10.17504/protocols.io.bgd9js96 | Ognibene M, Pezzolo A (2020) Ezrin interacts with the tumor suppressor CHL1 and promotes neuronal differentiation of human neuroblastoma. PLoS ONE 15(12): e0244069. doi: 10.1371/journal.pone.0244069 | Laboratorio Cellule Staminali Post Natali e Terapie Cellulari, IRCCS Istituto Gaslini, Genova, Italy | https://doi.org/10.1371/journal.pone.0244069 | 1 | 2020 | Marzia Ognibene 2020. Cell migration assay or Transwell assay. protocols.io dx.doi.org/10.17504/protocols.io.bgd9js96 | 2021-03-29 03:09:56 | |||
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Culture and purification of Plasmodium berghei ookinetes Resource Report Resource Website |
Benito Recio Totoro | 10.17504/protocols.io.bmpgk5jw | A collection of protocols we use routinely in the lab to produce and purify ookinetes of Plasmodium berghei. | Instituto de Biotecnología - Universidad Nacional Autónoma de México; Centro de Investigaciones Sobre Enfermedades Infecciosas - Instituto Nacional de Salud Pública | 1 | 2020 | Benito Recio Totoro 2020. Culture and purification of Plasmodium berghei ookinetes. protocols.io dx.doi.org/10.17504/protocols.io.bmpgk5jw | 2021-03-29 03:09:58 | ||||
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SP3 (Single-Pot, Solid-Phase, Sample-Preperation) Protein Extraction for Dental Calculus Resource Report Resource Website |
Shevan Wilkin, Richard Hagan, Sandra Hebestreit, Madeleine Bleasdale, Ayushi Nayak, Li Tang, Traci N Billings, Nicole Boivin, Kristine Richter | 10.17504/protocols.io.bfgrjjv6 | Dental calculus from archaeoloigcal samples is now commonly extracted for palaeoproteomic analysis. This protocol combines an EDTA based pretreatment and a SP3 (single-pot, solid-phase-enhanced) protein extraction to prepare samples for LC-MS/MS analysis. This protocol is for moderate to well preserved archaeological calculus samples with a starting weight of 5-15 mg of calculus. We recommend batch sizes of 2-10 calculus samples, 1 extraction control (we use a powdered bone sample from an achaeological sheep bone as this should not be modern material), and 1 extraction blank. For the first time doing the protocol in a lab, we recommend using flanking blanks to identify any contaminants as from handling or from solutions.This protocol is based upon the original SP3 protocol published in Hughes et al. (2014) and the developments for palaeoproteomics of bone (Cleland et al., 2018). When using please cite the following three publications the protocol is based upon as well as the DOI for this protocol.Hughes, C. S., Foehr, S., Garfield, D. A., Furlong, E. E., Steinmetz, L. M., & Krijgsveld, J. (2014). Ultrasensitive proteome analysis using paramagnetic bead technology. Molecular Systems Biology, 10, 757. https://doi.org/10.15252/msb.20145625Hughes, C. S., Moggridge, S., Müller, T., Sorensen, P. H., Morin, G. B., & Krijgsveld, J. (2019). Single-pot, solid-phase-enhanced sample preparation for proteomics experiments. Nature Protocols, 14(1), 68–85. https://doi.org/10.1038/s41596-018-0082-xCleland, T. P. (2018). Human Bone Paleoproteomics Utilizing the Single-Pot, Solid-Phase-Enhanced Sample Preparation Method to Maximize Detected Proteins and Reduce Humics. Journal of Proteome Research, 17(11), 3976–3983. https://doi.org/10.1021/acs.jproteome.8b00637 |
Bleasdale, M., Richter, K.K., Janzen, A. et al. Ancient proteins provide evidence of dairy consumption in eastern Africa. Nat Commun 12, 632 (2021). https://doi.org/10.1038/s41467-020-20682-3 |
Max Planck Institute for the Science of Human History, Department of Archaeology University of York, Max Planck Institute for the Science of Human History, Max Planck Institute for the Science of Human History, Max Planck Institute for the Science of Human History, Max Planck Institute for the Science of Human History, Max Planck Institute for the Science of Human History, Max Planck Institute for the Science of Human History, Max Planck Institute for the Science of Human History | https://www.nature.com/articles/s41467-020-20682-3#citeas | 1 | 2020 | Shevan Wilkin, Richard Hagan, Sandra Hebestreit, Madeleine Bleasdale, Ayushi Nayak, Li Tang, Traci N Billings, Nicole Boivin, Kristine Richter 2020. SP3 (Single-Pot, Solid-Phase, Sample-Preperation) Protein Extraction for Dental Calculus. protocols.io dx.doi.org/10.17504/protocols.io.bfgrjjv6 | 2021-03-29 03:09:58 | ||
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RNA extraction protocol (Trizol) Resource Report Resource Website |
Hebert F.O., Grambauer S., Barber I., Landry C.R., Aubin-Horth N. | 10.17504/protocols.io.ew7bfhn | GigaScience Press | 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 | Hébert FO, Grambauer S, Barber I, Landry CR, Aubin-Horth N, Transcriptome sequences spanning key developmental states as a resource for the study of the cestode , a threespine stickleback parasite. GigaScience doi: 10.1186/s13742-016-0128-3 | GigaScience, GigaScience, GigaScience, GigaScience, GigaScience | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4891850/ | 1 | 2016 | Hebert F.O., Grambauer S., Barber I., Landry C.R., Aubin-Horth N. 2016. RNA extraction protocol (Trizol). protocols.io dx.doi.org/10.17504/protocols.io.ew7bfhn | 2021-03-29 03:09:58 | |
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De-salting of tryptic digested peptides Resource Report Resource Website |
avinash.kale | 10.17504/protocols.io.bjdqki5w | UM-DAE Centre for Excellence in Basic Sciences | domnic colvin | 1 | 2020 | avinash.kale 2020. De-salting of tryptic digested peptides. protocols.io dx.doi.org/10.17504/protocols.io.bjdqki5w | 2021-03-29 03:09:58 | ||||
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Integrated analysis of DNA methylation profiling and gene expression profiling identifies novel markers in lung cancer in Xuanwei, China Resource Report Resource Website |
Juan Wang | 10.17504/protocols.io.rsxd6fn | Background: Aberrant DNA methylation occurs frequently in cancer. The aim of this study was to identify novel methylation markers in lung cancer in Xuanwei, China, through integrated genome-wide DNA methylation and gene expression studies.Methods: Differentially methylated regions (DMRs) and differentially expressed genes (DEGs) were detected on 10 paired lung cancer tissues and noncancerous lung tissues by methylated DNA immunoprecipitation combined with microarray (MeDIP-chip) and gene expression microarray analyses, respectively. Integrated analysis of DMRs and DEGs was performed to screen out candidate methylation-related genes. Both methylation and expression changes of the candidate genes were further validated and analyzed.Results: Compared with normal lung tissues, lung cancer tissues expressed a total of 6,899 DMRs, including 5,788 hypermethylated regions and 1,111 hypomethylated regions. Integrated analysis of DMRs and DEGs identified 45 tumor-specific candidate genes: 38 genes whose DMRs were hypermethylated and expression was downregulated, and 7 genes whose DMRs were hypomethylated and expression was upregulated. The methylation and expression validation results identified 4 candidate genes (STXBP6, BCL6B, FZD10, and HSPB6) that were significantly hypermethylated and downregulated in most of the tumor tissues compared with the noncancerous lung tissues.Conclusions: This integrated analysis of genome-wide DNA methylation and gene expression in lung cancer in Xuanwei revealed several genes regulated by promoter methylation that have not been described in lung cancer before. These results provide new insight into the carcinogenesis of lung cancer in Xuanwei and represent promising new diagnostic and therapeutic targets. | Wang J, Duan Y, Meng Q, Gong R, Guo C, Zhao Y, Zhang Y (2018) Integrated analysis of DNA methylation profiling and gene expression profiling identifies novel markers in lung cancer in Xuanwei, China. PLoS ONE 13(10): e0203155. doi: 10.1371/journal.pone.0203155 | Department of Clinical Laboratory, the First Affiliated Hospital of Kunming Medical University, Kunming, China | https://doi.org/10.1371/journal.pone.0203155 | 1 | 2018 | Juan Wang 2018. Integrated analysis of DNA methylation profiling and gene expression profiling identifies novel markers in lung cancer in Xuanwei, China. protocols.io dx.doi.org/10.17504/protocols.io.rsxd6fn | 2021-03-29 03:09:56 | ||
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Mass Spectrometry analysis and Molecular MS/MS network Resource Report Resource Website |
Rene Flores Clavo, Cristian Daniel Asmat Ortega, Nataly Ruiz Quinones | 10.17504/protocols.io.br2fm8bn | Metabolomics Protocols & Workflows, RENE FLORES | Universidade Estadual de Campinas, Centro de Investigación en Innovación en Ciencias Activas Multidisciplinarias-CIICAM, Universidade Estadual de Campinas | 1 | 2021 | Rene Flores Clavo, Cristian Daniel Asmat Ortega, Nataly Ruiz Quinones 2021. Mass Spectrometry analysis and Molecular MS/MS network. protocols.io dx.doi.org/10.17504/protocols.io.br2fm8bn | 2021-03-29 03:09:59 | ||||
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Standard Operating Procedure for Solid Phase Adsorption Toxin Testing (SPATT) Assemblage and Extraction of HAB Toxins Resource Report Resource Website |
Kendra Negrey, Meredith Howard, Jayme Smith, Raphael Kudela, David Caron | 10.17504/protocols.io.xkpfkvn | SPATT has been developed and tested for a variety of resins (see review by Kudela, 2017). These Standard Operating Procedures (SOP) outline the use of the resin DIAON HP20 since it has been demonstrated to quantify microcystins, anatoxin-a, saxitoxin, domoic acid, and okadaic acid in fresh, brackish, and marine waters, all from the same SPATT sampling device (Lane et al. 2010; Miller et al. 2010, Kudela 2011, Gibble and Kudela, 2014, Howard et al., 2017, Kudela, 2017, Peacock et al., 2018). Cylindrospermopsin and nodularin have also been detected using SPATT with DIAON HP20 resin in California, however, the use of DIAON HP20 for these toxins has not been well characterized in the laboratory. This methodology is ready for wider adoption by the research, monitoring, and management communities interested in detecting and tracking the dynamics of freshwater and marine toxins. The SOP described herein for the assemblage and construction of SPATT bags can be used for deployment in freshwater, brackish and marine environments and the extraction process described below is for the analysis of both marine toxins and cyanotoxins. | University of California, Santa Cruz, University of California, Santa Cruz, University of Southern California, University of Southern California, University of Southern California | 1 | 2019 | Kendra Negrey, Meredith Howard, Jayme Smith, Raphael Kudela, David Caron 2019. Standard Operating Procedure for Solid Phase Adsorption Toxin Testing (SPATT) Assemblage and Extraction of HAB Toxins. protocols.io dx.doi.org/10.17504/protocols.io.xkpfkvn | 2021-03-29 03:09:58 | ||||
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COVID-19 ARTIC v3 Illumina library construction and sequencing protocol - short amplicons (275bp) Resource Report Resource Website |
Emma Betteridge, Naomi Park, Keith James, Jillian Durham, Josh Quick | 10.17504/protocols.io.bh4zj8x6 | Coronavirus Method Development Community | This SOP describes the procedure for generating cDNA from SARS-CoV-2 viral nucleic acid extracts and subsequently producing 275nt amplicons. This is followed by library construction, equivolume pooling of samples and quantitation, prior to sequencing on the Illumina NovaSeq. A key benefit of the short amplicon method is that it can be utilised on any Illumina platform with a 300 cycle (or greater) kit.It is an adaptation of the 400nt COVID-19 ARTIC v3 amplicon protocol which can be found here:https://www.protocols.io/view/covid-19-artic-v3-illumina-library-construction-an-bgxjjxknBoth the above protocols were adapted from the nCov-2019 sequencing protocol: https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w | Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, Wellcome Sanger Institute, University of Birmingham | 1 | 2020 | Emma Betteridge, Naomi Park, Keith James, Jillian Durham, Josh Quick 2020. COVID-19 ARTIC v3 Illumina library construction and sequencing protocol - short amplicons (275bp). protocols.io dx.doi.org/10.17504/protocols.io.bh4zj8x6 | 2021-03-29 03:10:01 | |||
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SW-LB Media (1L) Resource Report Resource Website |
Brian Smith, [email protected] Micro.tucson | 10.17504/protocols.io.xf2fjqe | This protocol will make one liter of salt water LB. Adjust volumes as necessary. | University of Arizona, University of Arizona | 1 | 2019 | Brian Smith, [email protected] Micro.tucson 2019. SW-LB Media (1L). protocols.io dx.doi.org/10.17504/protocols.io.xf2fjqe | 2021-03-29 03:09:56 | ||||
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p53 immunohistochemistry protocol Resource Report Resource Website |
Ratha-Korn Vilaichone, Natsuda Aumpan | 10.17504/protocols.io.bigjkbun | Aumpan N, Vilaichone R, Nunanan P, Chonprasertsuk S, Siramolpiwat S, Bhanthumkomol P, Pornthisarn B, Uchida T, Vilaichone V, Wongcha-Um A, Yamaoka Y, Mahachai V (2020) Predictors for development of complete and incomplete intestinal metaplasia (IM) associated with H. pylori infection: A large-scale study from low prevalence area of gastric cancer (IM-HP trial). PLoS ONE 15(10): e0239434. doi: 10.1371/journal.pone.0239434 | Gastroenterology Unit, Department of Medicine, Faculty of Medicine, Thammasat University Hospital, Department of Medicine, Chulabhorn International College of Medicine (CICM) at Thammasat University, Pathumthani, Digestive Diseases Research Center (DRC), Thammasat University Hospital, Pathumthani, Thailand, Gastroenterology Unit, Department of Medicine, Faculty of Medicine, Thammasat University Hospital | https://doi.org/10.1371/journal.pone.0239434 | 1 | 2020 | Ratha-Korn Vilaichone, Natsuda Aumpan 2020. p53 immunohistochemistry protocol. protocols.io dx.doi.org/10.17504/protocols.io.bigjkbun | 2021-03-29 03:10:00 | |||
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HTAPP_Dissociation of human neuroblastoma tumors to a single-cell suspension for single-cell RNA-seq using Papain Resource Report Resource Website |
Anand Patel, Asa Karlstrom, Brittney Gordon, Elizabeth Stewart, Michael Dyer | 10.17504/protocols.io.98ah9se | NCIHTAN | This protocol was used for the dissociation of fresh pediatric neuroblastoma samples from patient tumors or orthotopic patient derived xenografts. Using this method, we were able to prepare highly viable (>90%) single-cell suspensions compatible with droplet-based single-cell RNA-Seq technology (Slyper et al).For the Human Tumor Atlas Pilot Project (HTAPP), this protocol has been successfully applied to neuroblastoma resections collected from abdominal and paraspinal sites.Description of this protocol and guidance for testing and selecting methods for processing other tumor and sample types can be found in Slyper et al. | St. Jude Children's Research Hospital, St. Jude Children's Research Hospital, St. Jude Children's Research Hospital, St. Jude Children's Research Hospital, St. Jude Children's Research Hospital | 1 | 2020 | Anand Patel, Asa Karlstrom, Brittney Gordon, Elizabeth Stewart, Michael Dyer 2020. HTAPP_Dissociation of human neuroblastoma tumors to a single-cell suspension for single-cell RNA-seq using Papain. protocols.io dx.doi.org/10.17504/protocols.io.98ah9se | 2021-03-29 03:10:00 | |||
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RbCl Uber-Competent Cells Resource Report Resource Website |
Sricharan Kadimi | 10.17504/protocols.io.3hygj7w | UConn iGEM | A protocol kindly provided to our team by the advisor to the 2018 MIT iGEM team (Dr. Brian Teague). It is modified slightly from that version (made by Stefan Maas in 1997) to fit our needs. Stefan Maas' protocol is similar to the Hanahan, D. protocol from 1983.It worked pretty well to make good competent cells in Summer 2018 and we just used it again in Summer 2019. | University of Connecticut | 1 | 2019 | Sricharan Kadimi 2019. RbCl Uber-Competent Cells. protocols.io dx.doi.org/10.17504/protocols.io.3hygj7w | 2021-03-29 03:10:00 |
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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:
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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
