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Authors: Omar Valencia
Summary: Results of the additive and multiplicative diversity partitioning of gobiid fishes
Proper citation: Omar Valencia 2018. Gamma-diversity partitioning of gobiid fishes (Teleostei: Gobiidae) ensemble along of Eastern Tropical Pacific: biological inventory, latitudinal variation and species turnover. protocols.io dx.doi.org/10.17504/protocols.io.s3iegke Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: This protocol describes the preparation of a fixed mouse brain specimen bonded to an agarose block for blockface imaging and sectioning using the TissueCyte 1000 system.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.
Proper citation: Allen Institute for Brain Science 2020. TissueCyte Specimen Embedding Acrylamide Coembedding. protocols.io dx.doi.org/10.17504/protocols.io.bdpvi5n6 Copy
Authors: Kwame Adusei, Alex Owusu-Ofori
Summary: Transfusion-transmitted malaria, Donor prevalence and health worker knowledge and practices. Protocols for preparation of blood smears (Thick and thin films), reporting of malaria parasites, blood grouping and design of questionnaires.
Proper citation: Kwame Adusei, Alex Owusu-Ofori 2018. PROTOCCOLS FOR PREPARATION OF BLOOD FILMS, REPORTING OF MALARIA PARASITES, BLOOD GROUPING AND QUESTIONNAIRE DESIGN. protocols.io dx.doi.org/10.17504/protocols.io.pq6dmze Copy
Authors: Robert Dobos
Proper citation: Robert Dobos 2020. Coccidioides_soil_habitat_model. protocols.io dx.doi.org/10.17504/protocols.io.bh6gj9bw Copy
Authors: Snehadri Sinha
Group: Aalto-Helsinki 2016
Summary: Gibson assembly using NEBuilder HiFi DNA assembly kit. Specification of the original NEB protocol.
Proper citation: Snehadri Sinha 2017. Gibson Assembly (NEBuilder). protocols.io dx.doi.org/10.17504/protocols.io.gzebx3e Copy
Authors: Manuel Richter
Summary: RA STRAIN SUPPLEMENT
Proper citation: Manuel Richter 2019. RA STRAIN SUPPLEMENT. protocols.io dx.doi.org/10.17504/protocols.io.8wjhxcn Copy
Authors: Dorota Czyzewska1*, Andrzej Ustymowicz2, Radoslaw Kowalewski3¶, Anna Zurada4¶, Jaroslaw Krejza5
Summary: Exclusion criteria: lower limb varices, history of leg surgery, trauma, infection, or thromboembolic events.Ultrasound examinations are performed in B-mode technique, equipped with a linear broadband (7.5-14-MHz) transducer. The right femoral vein and the inguinal ligament are examined in a supine position. The inguinal ligament is identified along its longitudinal axis. The measurements levels are identified as follow:- proximal level: 20 mm caudally to the inguinal ligament identified along the femoral artery imaged with US- distal level: 20 mm caudally to the inguinal crease visually identified and along the femoral artery imaged with USThe cross-sectional area (CSA) of the right femoral vein is examined at both levels in transverse plane and is measured automatically after manual tracing of the vessel on a static image in three leg positions: abduction, abduction + external rotation, abduction + external rotation + 90º knee flexion/frog-leg. Attention must be taken to avoid any compression or displacement of the examined vein.
Proper citation: Dorota Czyzewska1*, Andrzej Ustymowicz2, Radoslaw Kowalewski3¶, Anna Zurada4¶, Jaroslaw Krejza5 2017. Ultrasonographic measurements of the right femoral vein cross-sectional area. protocols.io dx.doi.org/10.17504/protocols.io.iq5cdy6 Copy
Authors: Fernando Guzman Chavez
Summary: Work instruction for 2xYT and 2xYTG medium preparationFollowing this recipe, you will obtain 1L of 2XYT medium2X YTis a standard growth medium used to cultivateE. coli. In cell-free system, this medium is commonly used to growth the cells.
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NOTE :The protocol described here is an adaptation from these papers:Adam D. Silverman, Nancy Kelley-Loughnane, Julius B. Lucks, and Michael C. Jewett (2019).Deconstructing Cell-Free Extract Preparation for in Vitro Activation of Transcriptional Genetic Circuitry. ACS Synthetic Biology, 403-414. DOI: 10.1021/acssynbio.8b00430.Andriy Didovyk, Taishi Tonooka, Lev Tsimring, and Jeff Hasty. (2017).Rapid and Scalable Preparation of Bacterial Lysates for Cell-Free Gene Expression. ACS Synthetic Biology, 2198-2208. DOI: 10.1021/acssynbio.7b00253.
Proper citation: Fernando Guzman Chavez 2020. 2XYT Medium (Version 2-0) Haseloff Lab. protocols.io dx.doi.org/10.17504/protocols.io.bigekbte Copy
Authors: Carmen Farid, Aisha A. Mahmoud, Hanaa M. Donia, Hafsa M. Ghatesh
Summary: Serum soluble CD200 levels in psoriasis patients was measured by ELISA (Human CD200 PicoKine™ ELISA Kit, Boster Biological Technology, Pleasanton CA, USA, Catalog # EK0993)), and CD200R expression level on both peripheral blood monocytes and lymphocytes were measured by flowcytometry using human CD200 R1 conjugated antibody(Human CD200 R1 Fluorescein-conjugated Antibody, Bio-Techne,Minneapolis, Minnesota, USA, Catalog # FAB3414F)). Cells were analyzed on a FACSCalibur flow cytometer using CellQuest pro software (BD Biosciences, San Diego, CA, USA). Membrane fluorescence intensity was estimated and expressed as mean fluorescence intensity (MFI).
Proper citation: Carmen Farid, Aisha A. Mahmoud, Hanaa M. Donia, Hafsa M. Ghatesh 2019. CD200 and CD200R levels in psoriasis patients. protocols.io dx.doi.org/10.17504/protocols.io.6zihf4e Copy
Authors: Angel Justiz-Vaillant
Group: University of the West Indies, [email protected]
Proper citation: Angel Justiz-Vaillant 2020. Purification of avian egg yolk immunoglobulins using the water dilution method and precipitation with isopropanol. . protocols.io dx.doi.org/10.17504/protocols.io.bjvpkn5n Copy
Authors: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen
Group: VERVE Net
Summary: For use in "One-step growth experiments (cyanophages)"
Proper citation: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen 2016. Remove unadsorbed phages. protocols.io dx.doi.org/10.17504/protocols.io.drb52m Copy
Authors: Verity Goodwin, Emily Souster, Charlotte Beaver, Adam Jackson, Rizwan Ansari, Mathew Garnett, Fiona Behan
Group: Cellular Generation and Phenotyping
Summary: This protocol is for the whole-genome CRISPR screening of stably expressing Cas9 cancer cell lines in triplicate using the commercially available Kusuke Yusa v1.1 whole genome gRNA library. It can be adapted for other gRNA libraries, under the assumption that there is a BFP reporter in the gRNA library. The protocol can be followed assuming the following is known:- The number of cells to be transduced - The number of days required for screening- How many cells to maintain throughout the screen- The number of cells required per pellet- The required coverage of the libraryThis protocol takes 16 days.Process diagram:
Proper citation: Verity Goodwin, Emily Souster, Charlotte Beaver, Adam Jackson, Rizwan Ansari, Mathew Garnett, Fiona Behan 2020. Guide RNA Library Transduction of Cas9 Cancer Cell Lines. protocols.io dx.doi.org/10.17504/protocols.io.bg2njyde Copy
Authors: Wilfried Gyselaers, Kathleen Tomsin, Staelens Anneleen, Vonck Sharona
Summary: A maternal cardiovascular profile was assessed in every pregnant woman combining three non-invasive techniques to obtain information about arteries, veins, heart and body fluid content (Table 1). A standardized protocol was used as reported in previous studies, as enlisted below.
Proper citation: Wilfried Gyselaers, Kathleen Tomsin, Staelens Anneleen, Vonck Sharona 2018. Hasselt University protocol for maternal hemodynamic profiling. protocols.io dx.doi.org/10.17504/protocols.io.tffejjn Copy
Authors: Brian Hie, Bryan Bryson, Bonnie Berger
Group: Human Cell Atlas Method Development Community
Summary: Scanorama enables efficient integration of heterogeneous scRNA-seq data sets.
Proper citation: Brian Hie, Bryan Bryson, Bonnie Berger 2019. Scanorama. protocols.io dx.doi.org/10.17504/protocols.io.9gch3sw Copy
Authors: Oskar Johansson, Adrian Clarke
Group: Protist Research to Optimize Tools in Genetics (PROT-G)
Summary: Mapping of transformed DNA within mutated diatoms. A stepwise specific PCR reaction that allow for identification of genome location of transformed fragments such as antibiotic resistance genes or GFP constructs. Degenerate primer 1: 5' - GCCGGACTTAGCGAGCA TGTGTAGTACCTTGCCG ATCCTNASATANSATANT TC - 3'Degenerate primer 2: 5' - GCCGGACTTAGCGAGCA TGTGTAGTACCTTGCCG ATCCCNTSABGNACYTN CTG - 3'Degenerate primer 3: 5' - GCCGGACTTAGCGAGCA TGTGTAGTACCTTGCCG ATCCNGACGARWGANA WGAC - 3'Degenerate primer 4: 5' - GCCGGACTTAGCGAGCA TGTGTAGTACCTTGCCG ATCCTAHATGDAGKACN TAC - 3'Specific primer 1: 5' - GCCGGACTTAGCGAGCA TGTGTAG - 3'Specific primer 2: 5' - CATGTGTAGTACCTTGC CGATCC - 3'Internal primers must be designed with regard to each construct that are to be mapped. They should not overlap but instead cover consecutive stretches of known DNA sequence of the transformed construct.
Proper citation: Oskar Johansson, Adrian Clarke 2019. Genomic mapping of transformed DNA fragments. protocols.io dx.doi.org/10.17504/protocols.io.yq2fvye Copy
Authors: Chih-Hao Wang, Yu-Hua Tseng, Yu-Hua Tseng
Group: Tseng Lab, Joslin Diabetes Center
Proper citation: Chih-Hao Wang, Yu-Hua Tseng, Yu-Hua Tseng 2021. Measurement of heat production (thermogenesis) in cells using ERthermAC dye_microplate method. protocols.io dx.doi.org/10.17504/protocols.io.bqprmvm6 Copy
Authors: JL Wang, D Xu1, H Zhou, AN Bai, W Lu
Group: EV
Proper citation: JL Wang, D Xu1, H Zhou, AN Bai, W Lu 2018. High-performance fractional order terminal sliding mode control strategy for DC-DC Buck converter. protocols.io dx.doi.org/10.17504/protocols.io.jtjcnkn Copy
Authors: Björn Brembs
Group: Brembs Lab
Proper citation: Björn Brembs 2015. Measuring Wingstroke Amplitude with Strokelitude. protocols.io dx.doi.org/10.17504/protocols.io.c8mzu5 Copy
Authors: Eric Carpenter
Group: GigaScience Press
Summary: Implemented by: Michael Melkonian and Barbara Surek (algae) and Juan Carlos Villarreal (bryophytes)This protocol follows the procedures provided with the TRIzol LS Reagent (Invitrogen). TRIzol LS Reagent is a monophasic solution of phenol and guanidine isothiocyanate that can be used in isolation of total RNA from a wide variety of tissues and organisms, in addition to plants. This protocol was used in the isolation of total RNA from some algae samples (see Supplementary Table 1).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 10: TRIzol LS Reagent Method. protocols.io dx.doi.org/10.17504/protocols.io.4rwgv7e Copy
Authors: Hansheng Zhao
Proper citation: Hansheng Zhao 2018. Alternative Splicing Analysis. protocols.io dx.doi.org/10.17504/protocols.io.phndj5e Copy
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