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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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Histological staining of fish gonadal tissue Resource Report Resource Website |
Jhennifer Gomes Cordeiro, Caio Maximino, Diógenes Henrique de Siqueira-Silva | DOI:10.17504/protocols.io.ygvftw6 | Fish behavior and physiology, Medicinal Plants Southeastern Pará Research Group | This protocol describes the dissection, fixation, and histological processing of gonadal tissue of small and medium-sized fish. It has been used in our lab to describe the microanatomy of the gonads of Amazonian Characidae, as well as of ornamental fish such as zebrafish. | Universidade Federal do Sul e Sudeste do Pará, Universidade Federal do Sul e Sudeste do Pará, Universidade Federal do Sul e Sudeste do Pará | 1 | 2019 | Jhennifer Gomes Cordeiro, Caio Maximino, Diógenes Henrique de Siqueira-Silva 2019. Histological staining of fish gonadal tissue. protocols.io https://dx.doi.org/10.17504/protocols.io.ygvftw6 | 2021-04-15 09:14:24 | |||
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Long term Cryopreservation of Chloroviruses by Infection of Chlorella Resource Report Resource Website |
Samantha Coy, Alyssa Alsante, Steven Wilhelm | DOI:10.17504/protocols.io.tfuejnw | The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs) | Contact Dr. Steven Wilhelm ([email protected]) or Samantha Coy ([email protected]) for additional information regarding this protocol. | The University of Tennessee, Knoxville, The University of Tennessee, Knoxville, The University of Tennessee, Knoxville | 3 | 2018 | Samantha Coy, Alyssa Alsante, Steven Wilhelm 2018. Long term Cryopreservation of Chloroviruses by Infection of Chlorella. protocols.io https://dx.doi.org/10.17504/protocols.io.tfuejnw | 2021-04-15 09:14:28 | |||
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C-SOP-201: Genomic DNA Quantification using a Qubit Fluorometer Resource Report Resource Website |
Mihir Kekre | The Centre for Genomic Pathogen Surveillance, Oxford, United Kingdom | 1 | 2021 | Mihir Kekre 2021. C-SOP-201: Genomic DNA Quantification using a Qubit Fluorometer. protocols.io https:// | 2021-04-15 09:14:28 | ||||||
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RT-PCR for NoV Resource Report Resource Website |
Hengyun Guan, Chunrong Wang, Lanzheng Liu, Guoliang Yang | DOI:10.17504/protocols.io.q3sdyne | This assay amplified the partial VP1 gene (Region C) of the norovirus genome. The yield products could be sequenced. | Liu L, Guan H, Zhang Y, Wang C, Yang G, Ruan S, Zhao H, Han X (2018) The prevalence of non-GII.4 norovirus genotypes in acute gastroenteritis outbreaks in Jinan, China. PLoS ONE 13(12): e0209245. doi: 10.1371/journal.pone.0209245 | Jinan Center for Disease Control and Prevention, Jinan, China, Jinan Center for Disease Control and Prevention, Jinan, China, Jinan Center for Disease Control and Prevention, Jinan, China, Jinan Center for Disease Control and Prevention, Jinan, China | https://doi.org/10.1371/journal.pone.0209245 | 1 | 2018 | Hengyun Guan, Chunrong Wang, Lanzheng Liu, Guoliang Yang 2018. RT-PCR for NoV. protocols.io https://dx.doi.org/10.17504/protocols.io.q3sdyne | 2021-04-15 09:14:24 | ||
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VIROME Tutorials Resource Report Resource Website |
Jaysheel Bhavsar, Shawn Polson, K. Eric Wommack | DOI:10.17504/protocols.io.d8a9sd | VERVE Net, Hurwitz Lab | A collection of tutorials for the VIROME application. Wommack, K. E., J. Bhavsar, S. W. Polson, J. Chen, M. Dumas, S. Srinivasiah, M. Furman, S. Jamindar, and D. J. Nasko. 2012. VIROME: a standard operating procedure for analysis of viral metagenome sequences. Standards in Genomic Sciences 6:427-439 [PMC3558967] | , , | 1 | 2016 | Jaysheel Bhavsar, Shawn Polson, K. Eric Wommack 2016. VIROME Tutorials. protocols.io https://dx.doi.org/10.17504/protocols.io.d8a9sd | 2021-04-15 09:14:29 | |||
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5: User-friendly protocol: SABER RNA FISH in cells Resource Report Resource Website |
Jocelyn Y. Kishi, Sylvain W. Lapan, Brian J Beliveau, Emma R. West, Allen Zhu, Hiroshi M. Sasaki, Sinem Saka, Yu Wang, Constance L Cepko, Peng Yin | Human Cell Atlas Method Development Community | Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA; Department of Systems Biology, Harvard Medical School, Boston, MA, USA; These authors contributed equally, Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; These authors contributed equally, Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA; Department of Systems Biology, Harvard Medical School, Boston, MA, USA; Present address: Department of Genome Sciences, University of Washington, Seattle, WA, USA; These authors contributed equally; Correspondence: [email protected] (P.Y.), [email protected] (C.L.C.), [email protected] (B. J. B.), Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; These authors contributed equally, Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA; Department of Systems Biology, Harvard Medical School, Boston, MA, USA, Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA; Department of Systems Biology, Harvard Medical School, Boston, MA, USA, Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA; Department of Systems Biology, Harvard Medical School, Boston, MA, USA, Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA; Department of Systems Biology, Harvard Medical School, Boston, MA, USA, Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA; Correspondence: [email protected] (P.Y.), [email protected] (C.L.C.), [email protected] (B. J. B.), Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA; Department of Systems Biology, Harvard Medical School, Boston, MA, USA; Correspondence: [email protected] (P.Y.), [email protected] (C.L.C.), [email protected] (B. J. B.) | http://saber.fish/ | 1 | 2020 | Jocelyn Y. Kishi, Sylvain W. Lapan, Brian J Beliveau, Emma R. West, Allen Zhu, Hiroshi M. Sasaki, Sinem Saka, Yu Wang, Constance L Cepko, Peng Yin 2020. 5: User-friendly protocol: SABER RNA FISH in cells. protocols.io https:// | 2021-04-15 09:14:28 | ||||
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Protoplast method for Chromosome prep with Zymoseptoria tritici Resource Report Resource Website |
Pat Martinez | DOI:10.17504/protocols.io.s25egg6 | Zymoseptoria community protocols (STBnet) | Preparation of Zymoseptoria tritici isolates for extraction of chromosomes via pulsed-field electrophoresisPat Martinez 1990 (Bruce McDonald lab) (Simplified from Cooley, et al, Curr. Genet. 13:383-389.) | Bruce McDonald lab | 1 | 2018 | Pat Martinez 2018. Protoplast method for Chromosome prep with Zymoseptoria tritici. protocols.io https://dx.doi.org/10.17504/protocols.io.s25egg6 | 2021-04-15 09:14:28 | |||
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Modified Nasal Swab For Detection of Sars-Cov2 Resource Report Resource Website |
Joseph Patterson, Allyson Cole-Strauss, John Beck, Caryl Sortwell, Jack Lipton | DOI:10.17504/protocols.io.bfavjie6 | Coronavirus Method Development Community | The common methods of sample collection for the detection of SARS-Cov2 are either pharyngeal or nasopharyngeal. Both these methods require specific swabs that are in short supply, and both methods are not easily self-administered. A nasal swab can also be used to collect samples and is relatively easy to self-administer, yet obtaining nasal specific swabs can now also be a challenge. In order to address these issues, our group has optimized a protocol for self-administered nasal collection using buccal swabs that are not currently in high demand. With this method, we have been able to collect human samples with reliable results in RNA extraction based on RNaseP, and can detect SARS-Cov2 in known positive cases of COVID-19. | Michigan State University, Michigan State University, Michigan State University, Michigan State University, Michigan State University | 1 | 2020 | Joseph Patterson, Allyson Cole-Strauss, John Beck, Caryl Sortwell, Jack Lipton 2020. Modified Nasal Swab For Detection of Sars-Cov2. protocols.io https://dx.doi.org/10.17504/protocols.io.bfavjie6 | 2021-04-15 09:14:24 | |||
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Gut_All Cells_Human Resource Report Resource Website |
Kylie James | DOI:10.17504/protocols.io.q3xdypn | This protocol has been tested by me on human adult colon samples and given good results for scRNAseq. I suggest that you do an enrichment step afterwards, because the dissociation can be quite variable results in terms of the fraction of immune vs non-immune cells that are retreived. | Wellcome Sanger Institute | 1 | 2018 | Kylie James 2018. Gut_All Cells_Human. protocols.io https://dx.doi.org/10.17504/protocols.io.q3xdypn | 2021-04-15 09:14:24 | ||||
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Protocol of a systematic review with meta-analysis: Acute effects of physical exercise on blood pressure responsiveness to non-cardiopulmonary stress tests Resource Report Resource Website |
Igor Mariano, Ana Luiza Amaral, Guilherme Morais Puga | DOI:10.17504/protocols.io.bhw3j7gn | Laboratory stress tests can help compose the clinical profile of individuals and predict the development of future cardiovascular events and depression. These tests work by disturbing the individual's homeostasis to assess the body's responses to it. To assess responses to these stressors, several markers are used, of which we will highlight the blood pressure (BP).One of BP's control strategies is to perform physical exercises. It is known that even after a single exercise section, blood pressure levels can be below baseline levels at rest, but its influence on blood pressure levels under stress is still poorly understood. Thus, the objective of the scientific review proposed here is to answer the following question: what are the acute effects of physical exercise on BP responsiveness to non-cardiopulmonary stress tests in adults?For this, we will carry out a systematic review with meta-analysis on digital bases (PUBMED, LILACS, EMBASE and Psycinfo), of controlled studies that are carried out in adult humans and that indicate BP values under stress after a single session of physical exercises. | Laboratory of Cardiorespiratory and Metabolic Physiology. Federal University of Uberlândia., Laboratory of Cardiorespiratory and Metabolic Physiology. Federal University of Uberlândia., Laboratory of Cardiorespiratory and Metabolic Physiology. Federal University of Uberlândia. | 1 | 2020 | Igor Mariano, Ana Luiza Amaral, Guilherme Morais Puga 2020. Protocol of a systematic review with meta-analysis: Acute effects of physical exercise on blood pressure responsiveness to non-cardiopulmonary stress tests. protocols.io https://dx.doi.org/10.17504/protocols.io.bhw3j7gn | 2021-04-15 09:14:26 | ||||
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Copro-diagnostic molecular method for detection and identification of herpetofauna infecting nematodes Resource Report Resource Website |
Lucas G. Huggins, Sheena M. Cruickshank, Richard Preziosi, Kathryn J. Else | DOI:10.17504/protocols.io.i32cgqe | A non-invasive PCR-based methodology for sensitive detection and identification of parasitic nematode DNA released in the faeces of infected amphibians and reptiles as egg or tissue fragments (environmental DNA). A DNA extraction protocol optimised for liberation of DNA from resilient parasite eggs was developed alongside the design of a novel, nematode universal, degenerate primer pair that has broad-spectrum detection ability for shed nematode eDNA. | Huggins LG, Michaels CJ, Cruickshank SM, Preziosi RF, Else KJ (2017) A novel copro-diagnostic molecular method for qualitative detection and identification of parasitic nematodes in amphibians and reptiles. PLoS ONE 12(9): e0185151. doi: 10.1371/journal.pone.0185151 | University of Manchester, University of Manchester, Manchester Metropolitan University, University of Manchester | https://doi.org/10.1371/journal.pone.0185151 | 1 | 2017 | Lucas G. Huggins, Sheena M. Cruickshank, Richard Preziosi, Kathryn J. Else 2017. Copro-diagnostic molecular method for detection and identification of herpetofauna infecting nematodes. protocols.io https://dx.doi.org/10.17504/protocols.io.i32cgqe | 2021-04-15 09:14:23 | ||
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Fertility Resource Report Resource Website |
Wen Aw | DOI:10.17504/protocols.io.r6yd9fw | Aw WC, Towarnicki SG, Melvin RG, Youngson NA, Garvin MR, Hu Y, Nielsen S, Thomas T, Pickford R, Bustamante S, Vila-Sanjurjo A, Smyth GK, Ballard JWO (2018) Genotype to phenotype: Diet-by-mitochondrial DNA haplotype interactions drive metabolic flexibility and organismal fitness. PLoS Genet 14(11): e1007735. doi: 10.1371/journal.pgen.1007735 | [email protected] | https://doi.org/10.1371/journal.pgen.1007735 | 1 | 2018 | Wen Aw 2018. Fertility. protocols.io https://dx.doi.org/10.17504/protocols.io.r6yd9fw | 2021-04-15 09:14:29 | |||
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Immunoblot Screening of Chlorella Virus Plaques Resource Report Resource Website |
David Dunigan and Irina Agarkova | DOI:10.17504/protocols.io.euebete | VERVE Net | University of Nebraska-Lincoln | 1 | 2016 | David Dunigan and Irina Agarkova 2016. Immunoblot Screening of Chlorella Virus Plaques. protocols.io https://dx.doi.org/10.17504/protocols.io.euebete | 2021-04-15 09:14:25 | ||||
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Separating the Protein of Interest from MBP after TEV Protease Cleavage (NEB #E8201) Resource Report Resource Website |
New England Biolabs | DOI:10.17504/protocols.io.bfebjjan | New England Biolabs (NEB) | Both the MBP-tag and TEV Protease are polyhistidine-tagged for easy removal from the TEV Protease reaction. Loading the digest onto NEBExpress Ni Resin (NEB #S1428) sequesters both the MBP-tag and TEV Protease, thereby isolating the protein of interest in the column flow through. The binding capacity of NEBExpress Ni Resin is ≥ 10 mg/ml. The binding capacity will vary depending on the target protein, binding conditions and the accessibility of the His-tag. It is recommended to estimate the amount of the His-tagged MBP released by TEV Protease cleavage by first analyzing a sample by SDS-PAGE and comparing its band size and intensity to that of the provided MBP6 protein control. | New England Biolabs | https://www.neb.com/protocols/2020/02/06/separating-the-protein-of-interest-from-mbp-after-tev-protease-cleavage-neb-e8201 | 1 | 2020 | New England Biolabs 2020. Separating the Protein of Interest from MBP after TEV Protease Cleavage (NEB #E8201). protocols.io https://dx.doi.org/10.17504/protocols.io.bfebjjan | 2021-04-15 09:14:29 | ||
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Manual Cell Counting Resource Report Resource Website |
Aparna Kumar, Dana Al-Azzeh, Schuele Lab | DOI:10.17504/protocols.io.5zng75e | Manual counting of cells using a Hemocytometer. | Schuele Laboratory, Department of Pathology, Stanford University, Stanford, CA, Schuele Laboratory, Department of Pathology, Stanford University, Stanford, CA, Stanford University | 1 | 2019 | Aparna Kumar, Dana Al-Azzeh, Schuele Lab 2019. Manual Cell Counting . protocols.io https://dx.doi.org/10.17504/protocols.io.5zng75e | 2021-04-15 09:14:26 | ||||
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Isolation of Stromal Vascular Fraction (SVF) from mouse brown adipose tissue (BAT) for single cell RNA-seq Resource Report Resource Website |
Farnaz Shamsi | DOI:10.17504/protocols.io.bj64krgw | This protocol outlines the procedure for the isolation of the Stromal Vascular Fraction (SVF) from mouse brown adipose tissue (BAT) for single cell RNA-seq. This protocol uses a combination of Collagenase I and Dispase II to digest freshly isolated BAT. Compared to using Collagenase I alone, this combination results in a more efficient dissociation of the adipose vasculature. | Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA | 1 | 2020 | Farnaz Shamsi 2020. Isolation of Stromal Vascular Fraction (SVF) from mouse brown adipose tissue (BAT) for single cell RNA-seq. protocols.io https://dx.doi.org/10.17504/protocols.io.bj64krgw | 2021-04-15 09:14:23 | ||||
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Loop assembly using Labcyte Echo 550 Resource Report Resource Website |
Susana Sauret-Gueto, Anthony West | DOI:10.17504/protocols.io.8zvhx66 | OpenPlant Project | Loop L1 and L2 type IIS assembly protocol, automated and minituarised for assembly of 500nl final volume reactions using the Labcyte Echo 550. | Plant Sciences, University of Cambridge, OpenPlant, previously at Earlham Institute, Norwich | 1 | 2019 | Susana Sauret-Gueto, Anthony West 2019. Loop assembly using Labcyte Echo 550. protocols.io https://dx.doi.org/10.17504/protocols.io.8zvhx66 | 2021-04-15 09:14:25 | |||
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Drug distribution imaging of rabbit whole-eye section by MALDI mass spectrometry Resource Report Resource Website |
Naoto Mori, Takaharu Mochizuki, Fumiyoshi Yamazaki, Shiro Takei, Hidetoshi Mano, Takeshi Matsugi, Mitsutoshi Setou | DOI:10.17504/protocols.io.v7ae9ie | Matrix-assisted laser desorption/ionization–imaging mass spectrometry (MALDI-IMS) evaluates drug distribution in biological samples. However, there have been few investigations of drug distribution in ocular tissues, including whole-eye segments. In the present study, we explored the spatial distribution of atropine in a whole-eye segment using MALDI-IMS. Atropine is a reversible muscarinic receptor used to treat various diseases. However, its distribution in ocular tissues remains unknown. A 1% atropine solution was administered to a rabbit and after 30 min, its eye was enucleated, sectioned, and analyzed by MALDI-IMS. Atropine accumulated primarily in the tear menisci but was found at substantially lower concentrations in the tissue surrounding the conjunctival sacs. Relative differences in atropine levels between the anterior and posterior regions provided insights into the post-instillation behavior of atropine. Atropine signal intensities differed among corneal layers and between the superior and inferior eyeball regions. Differences in signal intensity among tissues indicated that the drug migrated to the posterior regions via a periocular scleral route. This information is useful for atropine delivery and indicates that MALDI-IMS is effective for revealing drug distribution in whole-eye sections. | Mori N, Mochizuki T, Yamazaki F, Takei S, Mano H, Matsugi T, Setou M (2019) MALDI imaging mass spectrometry revealed atropine distribution in the ocular tissues and its transit from anterior to posterior regions in the whole-eye of rabbit after topical administration. PLoS ONE 14(1): e0211376. doi: 10.1371/journal.pone.0211376 | Santen Pharmaceutical Co., Ltd., Santen Pharmaceutical Co., Ltd., Hamamatsu University School of Medicine, Chubu University, Santen Pharmaceutical Co., Ltd., Santen Pharmaceutical Co., Ltd., Hamamatsu University School of Medicine | https://doi.org/10.1371/journal.pone.0211376 | 2 | 2019 | Naoto Mori, Takaharu Mochizuki, Fumiyoshi Yamazaki, Shiro Takei, Hidetoshi Mano, Takeshi Matsugi, Mitsutoshi Setou 2019. Drug distribution imaging of rabbit whole-eye section by MALDI mass spectrometry. protocols.io https://dx.doi.org/10.17504/protocols.io.v7ae9ie | 2021-04-15 09:14:23 | ||
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Extraction Method E (PRP) Resource Report Resource Website |
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 | DOI:10.17504/protocols.io.inecdbe | GigaScience Press | Gen-IALFirst All-tissue DNA extraction kit -This protocol provides an efficient DNA extraction and purification of fresh sample (tissue material) | Salleh FM, Ramos-Madrigal J, Peñaloza F, Liu S, Mikkel-Holger SS, Riddhi PP, Martins R, Lenz D, Fickel J, Roos C, Shamsir MS, Azman MS, Burton KL, Stephen JR, Wilting A, Gilbert MTP, An expanded mammal mitogenome dataset from Southeast Asia. GigaScience 6(8). doi: 10.1093/gigascience/gix053 | Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark, Natural History Museum of Denmark, Copenhagen, Denmark | https://doi.org/10.1093/gigascience/gix053 | 1 | 2017 | 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 E (PRP). protocols.io https://dx.doi.org/10.17504/protocols.io.inecdbe | 2021-04-15 09:14:26 | |
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Tris-glycine buffer Resource Report Resource Website |
Stanton Burnton | DOI:10.17504/protocols.io.equbdww | VERVE Net | Tris-glycine buffer solution | 1 | 2016 | Stanton Burnton 2016. Tris-glycine buffer. protocols.io https://dx.doi.org/10.17504/protocols.io.equbdww | 2021-04-15 09:14:26 |
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