Protocols   Select Another Resource Report Type

Authors: Jhennifer Gomes Cordeiro, Caio Maximino, Diógenes Henrique de Siqueira-Silva
Group: Fish behavior and physiology, Medicinal Plants Southeastern Pará Research Group
Summary: 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.

Proper citation: 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 Copy   

•   Source:

Authors: Samantha Coy, Alyssa Alsante, Steven Wilhelm
Group: The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs)
Summary: Contact Dr. Steven Wilhelm ([email protected]) or Samantha Coy ([email protected]) for additional information regarding this protocol.

Proper citation: 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 Copy   

•   Source:

Authors: Mihir Kekre

Proper citation: Mihir Kekre 2021. C-SOP-201: Genomic DNA Quantification using a Qubit Fluorometer. protocols.io https:// Copy   

•   Source:

Authors: Hengyun Guan, Chunrong Wang, Lanzheng Liu, Guoliang Yang
Summary: This assay amplified the partial VP1 gene (Region C) of the norovirus genome. The yield products could be sequenced.

Proper citation: Hengyun Guan, Chunrong Wang, Lanzheng Liu, Guoliang Yang 2018. RT-PCR for NoV. protocols.io https://dx.doi.org/10.17504/protocols.io.q3sdyne Copy   

•   Source:

Authors: Jaysheel Bhavsar, Shawn Polson, K. Eric Wommack
Group: VERVE Net, Hurwitz Lab
Summary: 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] 

Proper citation: Jaysheel Bhavsar, Shawn Polson, K. Eric Wommack 2016. VIROME Tutorials. protocols.io https://dx.doi.org/10.17504/protocols.io.d8a9sd Copy   

•   Source:

Authors: 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
Group: Human Cell Atlas Method Development Community

Proper citation: 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:// Copy   

•   Source:

Authors: Pat Martinez
Group: Zymoseptoria community protocols (STBnet)
Summary: 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.)

Proper citation: Pat Martinez 2018. Protoplast method for Chromosome prep with Zymoseptoria tritici. protocols.io https://dx.doi.org/10.17504/protocols.io.s25egg6 Copy   

•   Source:

Authors: Joseph Patterson, Allyson Cole-Strauss, John Beck, Caryl Sortwell, Jack Lipton
Group: Coronavirus Method Development Community
Summary: 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.

Proper citation: 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 Copy   

•   Source:

Authors: Kylie James
Summary: 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.

Proper citation: Kylie James 2018. Gut_All Cells_Human. protocols.io https://dx.doi.org/10.17504/protocols.io.q3xdypn Copy   

•   Source:

Authors: Igor Mariano, Ana Luiza Amaral, Guilherme Morais Puga
Summary: 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.

Proper citation: 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 Copy   

•   Source:

Authors: Lucas G. Huggins, Sheena M. Cruickshank, Richard Preziosi, Kathryn J. Else
Summary: 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. 

Proper citation: 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 Copy   

•   Source:

Authors: Wen Aw

Proper citation: Wen Aw 2018. Fertility. protocols.io https://dx.doi.org/10.17504/protocols.io.r6yd9fw Copy   

•   Source:

Authors: David Dunigan and Irina Agarkova
Group: VERVE Net

Proper citation: David Dunigan and Irina Agarkova 2016. Immunoblot Screening of Chlorella Virus Plaques. protocols.io https://dx.doi.org/10.17504/protocols.io.euebete Copy   

•   Source:

Authors: New England Biolabs
Group: New England Biolabs (NEB)
Summary: 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.

Proper citation: 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 Copy   

•   Source:

Authors: Aparna Kumar, Dana Al-Azzeh, Schuele Lab
Summary: Manual counting of cells using a Hemocytometer.

Proper citation: Aparna Kumar, Dana Al-Azzeh, Schuele Lab 2019. Manual Cell Counting . protocols.io https://dx.doi.org/10.17504/protocols.io.5zng75e Copy   

•   Source:

Authors: Farnaz Shamsi
Summary: 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.

Proper citation: 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 Copy   

•   Source:

Authors: Susana Sauret-Gueto, Anthony West
Group: OpenPlant Project
Summary: Loop L1 and L2 type IIS assembly protocol, automated and minituarised for assembly of 500nl final volume reactions using the Labcyte Echo 550.

Proper citation: Susana Sauret-Gueto, Anthony West 2019. Loop assembly using Labcyte Echo 550. protocols.io https://dx.doi.org/10.17504/protocols.io.8zvhx66 Copy   

•   Source:

Authors: Naoto Mori, Takaharu Mochizuki, Fumiyoshi Yamazaki, Shiro Takei, Hidetoshi Mano, Takeshi Matsugi, Mitsutoshi Setou
Summary: 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.

Proper citation: 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 Copy   

•   Source:

Authors: Faezah Mohd Salleh, Jazmin Ramos-Madrigal, Fernando Penaloza, Shanlin Liu, Mikkel-Holger S Sinding, Riddhi P Patel, Renata Martins, Dorina Lenz, Jorns Fickel, Christian Roos, Mohd Shahir Shamsir, Mohammad Shahfiz Azman, Burton K Lim, Stephen J Rossiter, Andreas Wilting, M Thomas P Gilbert
Group: GigaScience Press
Summary: Gen-IALFirst All-tissue DNA extraction kit -This protocol provides an efficient DNA extraction and purification of fresh 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 E (PRP). protocols.io https://dx.doi.org/10.17504/protocols.io.inecdbe Copy   

•   Source:

Authors: Stanton Burnton
Group: VERVE Net
Summary: Tris-glycine buffer solution

Proper citation: Stanton Burnton 2016. Tris-glycine buffer. protocols.io https://dx.doi.org/10.17504/protocols.io.equbdww Copy   

•   Source: