id float64 1.55k 110k ⌀ | title stringlengths 1 256 ⌀ | template_id float64 0 6 ⌀ | doi stringlengths 39 49 ⌀ | url stringlengths 40 92 ⌀ | authors stringlengths 1 933 ⌀ | protocol_text stringlengths 34 1.08M | steps_list stringlengths 2 269k |
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68,560 | Preparation of 4% paraformaldehyde solution for transcardial perfusions and histology | 1 | dx.doi.org/10.17504/protocols.io.yxmvmndobg3p/v1 | https://www.protocols.io/view/preparation-of-4-paraformaldehyde-solution-for-tra-ce7qthmw | Alejandra Rangel, Rain Kwan, Asheeta Prasad | TITLE: Preparation of 4% paraformaldehyde solution for transcardial perfusions and histology
AUTHORS: Alejandra Rangel, Rain Kwan, Asheeta Prasad
[DESCRIPTION]
This protocol describes the safe preparation of 4% paraformaldehyde solution for use in tissue fixation in preparation for histology and immunohistochemistry. ... | ["[Spills] The following general procedures can be used for spills involving small volumes (mL size) of dilute solutions of formaldehyde (e.g.100 mL fixative solution of 4% formaldehyde) contained within a fume hood:", "[Spills] Wear appropriate personal protective equipment(PPE).", "[Spills] Remove any ignition source... |
55,435 | Ancient DNA extraction (chunk samples/high volume) | 1 | dx.doi.org/10.17504/protocols.io.n92ldzbpxv5b/v1 | https://www.protocols.io/view/ancient-dna-extraction-chunk-samples-high-volume-b2djqa4n | Marcel Keller, Christiana L Scheib | TITLE: Ancient DNA extraction (chunk samples/high volume)
AUTHORS: Marcel Keller, Christiana L Scheib
[DESCRIPTION]
Extraction protocol for ultra-short ancient DNA molecules from skeletal chunk samples modified from Dabney et al. (2013) PNAS (doi: 10.1073/pnas.1314445110).
[BEFORE_START]
Previous steps:
This protoco... | ["[Extraction] Clean table bench surface with DNA Exitus and wipe dry. Turn the hood on full power and open the glass.", "[Extraction] Move dry samples from the hood to the table bench and put down a new sheet of aluminum foil.", "[Extraction] Clean hood surface with DNA Exitus and put down a new sheet of aluminum foil... |
40,526 | 615.1 URMC HTC Non-Inflated Fresh-Frozen Embedded Lung and Associated Tissue | 4 | dx.doi.org/10.17504/protocols.io.bjtnknme | https://www.protocols.io/view/615-1-urmc-htc-non-inflated-fresh-frozen-embedded-bjtnknme | Gloria Pryhuber, Heidie Huyck, Lisa Rogers, Cory Poole | TITLE: 615.1 URMC HTC Non-Inflated Fresh-Frozen Embedded Lung and Associated Tissue
AUTHORS: Gloria Pryhuber, Heidie Huyck, Lisa Rogers, Cory Poole
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Purpose and Scope of the Procedure</div><div class = "text-block">- Rapid blocking, embedding and f... | ["[Fresh Tissue Frozen in Cryomolds]\nSlicing and blocking procedure should be accomplished in a grossing station or fume hood with the operator taking appropriate blood and body fluid precautions", "[Fresh Tissue Frozen in Cryomolds]\nKeep the surface of the lobes moist and cool at all times", "[Fresh Tissue Frozen in... |
100,688 | Refractive index adjusted imaging medium: Iodixanol (RI ~ 1.41 and 1.42) - Yeast | 0 | dx.doi.org/10.17504/protocols.io.5qpvok369l4o/v1 | https://www.protocols.io/view/refractive-index-adjusted-imaging-medium-iodixanol-dejq3cmw | Mathias Hammer, Ammeret Rossouw, Azra Lari, Ben Montpetit, David Grunwald | TITLE: Refractive index adjusted imaging medium: Iodixanol (RI ~ 1.41 and 1.42) - Yeast
AUTHORS: Mathias Hammer, Ammeret Rossouw, Azra Lari, Ben Montpetit, David Grunwald
[DESCRIPTION]
This protocol describes the steps to prepare imaging medium for Saccharomyces cerevisiae with adjusted refractive index. This medium i... | ["[Preparation of 30ml refractive index adjusted imaging medium with Iodixanol] Compound medium for autoclave", "[Preparation of 30ml refractive index adjusted imaging medium] Fill a 50 ml flask with 25 mLOptiPrep.\nAdd a magnetic stirring bar and place the flask on a stirring hot plate.", "[Preparation of 30ml refract... |
32,420 | Sample preparation protocol for cross-sectional microscopy of hair fibers | 1 | dx.doi.org/10.17504/protocols.io.bbwcipaw | https://www.protocols.io/view/sample-preparation-protocol-for-cross-sectional-mi-bbwcipaw | Tina Lasisi | TITLE: Sample preparation protocol for cross-sectional microscopy of hair fibers
AUTHORS: Tina Lasisi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how to prepare hair fibers for cross-sectional microscopy. </div><div class = "text-block"><span class = "embed-element"><ifra... | ["[Embedding Hairs ]\nThe following steps are for embedding hair fibers into the plastic chips.\nFor embedding you will need:hair samples2 prepared plastic chips per sample2 tweezers/forcepsa hot plate heated to isopropanol for cleaning\nPrepare hair sample for embedding. Take 3-5 hairs per sample and cut samples dow... |
101,253 | Collagen extraction from pretreated bone/tooth samples | 0 | dx.doi.org/10.17504/protocols.io.8epv5rrp4g1b/v1 | https://www.protocols.io/view/collagen-extraction-from-pretreated-bone-tooth-sam-de5d3g26 | Maciej T. Krajcarz, Dorothée G. Drucker, Magdalena Krajcarz, Hervé Bocherens | TITLE: Collagen extraction from pretreated bone/tooth samples
AUTHORS: Maciej T. Krajcarz, Dorothée G. Drucker, Magdalena Krajcarz, Hervé Bocherens
[DESCRIPTION]
This protocol presents the procedure of extracting collagen from a sample of bone or tooth, prior to stable isotope analysis, radiocarbon dating, and/or prot... | ["[Day 1 – Demineralization (the first A step of the ABA method)] Prepare twenty 50-mL (or similar size) glass beakers, one per sample and one per each internal standard. Label them with respective sample IDs (or internal standard IDs with a date of the extraction starting day) symbols using a water-proof marker.", "[D... |
95,587 | Reconstitution of human PINK1 and outer mitochondria TOM complex in yeast | 1 | dx.doi.org/10.17504/protocols.io.n2bvj37kwlk5/v1 | https://www.protocols.io/view/reconstitution-of-human-pink1-and-outer-mitochondr-c9kbz4sn | Olawale G. Raimi, Miratul Muqit | TITLE: Reconstitution of human PINK1 and outer mitochondria TOM complex in yeast
AUTHORS: Olawale G. Raimi, Miratul Muqit
[DESCRIPTION]
PTEN induced kinase 1(PINK1) is a mitochondria kinase that phosphorylates ubiquitin and Ubl domain of parkin coincidentally at structurally obscured S65 in both proteins and initiate ... | ["[Miniprep] Before cloning, codon optimise the human genes for yeast expression. To scale up the plasmids, carry out miniprep using the Qiagen miniprep kit following the manufacturer’s instructions.", "[Transformation of yeast cells] To start with the first plasmid, make culture of MATa cells in 5 mL of YP medium su... |
63,106 | Testing and validation of a Patient-Reported Outcome Measure for Older People with frailty and Acute Care needs (PROM-OPAC). | 1 | dx.doi.org/10.17504/protocols.io.5jyl856prl2w/v2 | https://www.protocols.io/view/testing-and-validation-of-a-patient-reported-outco-b9var62e | James D van Oppen | TITLE: Testing and validation of a Patient-Reported Outcome Measure for Older People with frailty and Acute Care needs (PROM-OPAC).
AUTHORS: James D van Oppen
[DESCRIPTION]
Aim: To refine, validate, and evaluate the early impact of a novel PROM instrument, the Patient-Reported Outcome Measure for Older People with fra... | ["[Preparatory work] Semi-structured interviews with 15-30 older people living with frailty with recent experience of UK emergency and acute care.\nQualitative analysis using blended approach of framework and comparative methods.\nOutcome: a framework to define outcome goals for acute healthcare among older people livi... |
24,354 | Serum, Blood and Body Weight Measurements in Pigs | null | dx.doi.org/10.17504/protocols.io.32agqae | null | Tim Nichols, Dave Clemmons | TITLE: Serum, Blood and Body Weight Measurements in Pigs
AUTHORS: Tim Nichols, Dave Clemmons
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span><span style = "font-weight:bold;"> </span></div><div class = "text-block">These assays are performed on all th... | ["Total cholesterol\nCholesterol is measured by a commercial, automated method (ANTECH® Inc. Cary, NC).", "Serum assays\nAll serum assays are measured by a commercial, automated method (ANTECH® Inc. Cary, NC).", "Red blood cell count, White blood cell count, Hemoglobin, Hematocrit, Platelet count\nWhite blood cell coun... |
34,742 | s3-ATAC | 1 | dx.doi.org/10.17504/protocols.io.bd6wi9fe | https://www.protocols.io/view/s3-atac-bd6wi9fe | Andrew Adey, Ryan Mulqueen | TITLE: s3-ATAC
AUTHORS: Andrew Adey, Ryan Mulqueen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for the s3 ATAC dhe. s3ATAC is a simplified sci-ATAC protocol using in vitro tagmentation to capture regions of open chromatin genome-wide in single cells. </div><div class = "text-bloc... | ["[Prepare Buffers]\nConstruct 50mL Nuclei Isolation Buffer (NIB-HEPES): ABC1Final ConcentrationStock ConcentrationVolume of Stock210 mM HEPES-KOH, pH 7.21M HEPES-KOH, pH 7.2500 uL310 mM NaCl5M NaCl100 uL43mM MgCl21M MgCl2150 uL50.1 % Igepal10% Igepal500 uL60.1 % Tween10% Tween500 uL7ddH20to 50mL (add 48.25mL)Store NI... |
98,089 | Hornwort (Anthoceros agrestis) biolistics-mediated transformation protocol | 0 | dx.doi.org/10.17504/protocols.io.3byl49792go5/v1 | https://www.protocols.io/view/hornwort-anthoceros-agrestis-biolistics-mediated-t-db2h2qb6 | Declan Lafferty, Fay-Wei Li | TITLE: Hornwort (Anthoceros agrestis) biolistics-mediated transformation protocol
AUTHORS: Declan Lafferty, Fay-Wei Li
[DESCRIPTION]
Here we report an efficient biolistics method for generating transient-expression and stable transgenic lines in the model hornwort, Anthoceros agrestis. An average of 569 (± 268) cells ... | ["For selection of transformed tissue, use AG medium with 0.2% sucrose and 10 mg/L hygromycin (for hygromycin selection) or other selection agent(s).", "[Growth media] For growing and maintaining gametophyte tissue, use AG medium (modified Hatcher’s medium containing additional 0.2% sucrose, 0.4 g ammonium nitrate, 100... |
38,304 | Quality of COVID-19 research in preprints: a meta-epidemiological study protocol | 1 | dx.doi.org/10.17504/protocols.io.bhm8j49w | https://www.protocols.io/view/quality-of-covid-19-research-in-preprints-a-meta-e-bhm8j49w | Yuki Kataoka, Shiho Oide, Takashi Ariie, Yasushi Tsujimoto, Toshi A. Furukawa | TITLE: Quality of COVID-19 research in preprints: a meta-epidemiological study protocol
AUTHORS: Yuki Kataoka, Shiho Oide, Takashi Ariie, Yasushi Tsujimoto, Toshi A. Furukawa
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Background:</div><div class = "text-block">No studies have comprehensively as... | [] |
91,327 | EpiPopSynth | 5 | dx.doi.org/10.17504/protocols.io.14egn3jn6l5d/v1 | https://www.protocols.io/view/epipopsynth-c5e7y3hn | km.zhu, Kang Liu, Junli Liu, Yepeng Shi, Xuan Li, Hongyang Zou, Huibin Du, Ling Yin | TITLE: EpiPopSynth
AUTHORS: km.zhu, Kang Liu, Junli Liu, Yepeng Shi, Xuan Li, Hongyang Zou, Huibin Du, Ling Yin
[DESCRIPTION]
Agent-based models have gained traction in exploring the intricate processes governing the spread of infectious diseases, particularly due to their proficiency in capturing nonlinear interactio... | ["[Population Generation] Process micro household survey data, re-group individuals into age groups, and remove irrelevant fields and non-family households.", "[Combinatorial Optimization] Use the number of households/people of different household sizes, age groups, and genders in regional demographic data as the least... |
45,067 | Measuring neutral lipids in fixed diatom cells using BODIPY 505/515 | 4 | dx.doi.org/10.17504/protocols.io.4r3l2427jg1y/v1 | https://www.protocols.io/view/measuring-neutral-lipids-in-fixed-diatom-cells-usi-bp9jmr4n | Phoebe Argyle, Jana Hinners, Nathan G. Walworth , Sinéad Collins, Naomi M. Levine, Martina A. Doblin | TITLE: Measuring neutral lipids in fixed diatom cells using BODIPY 505/515
AUTHORS: Phoebe Argyle, Jana Hinners, Nathan G. Walworth , Sinéad Collins, Naomi M. Levine, Martina A. Doblin
[DESCRIPTION]
This protocol is for the measuring neutral lipids in fixed diatom cells using BODIPY 505/515, as developed on the centri... | ["[Diatom sample preparation] Sample the diatom culture of interest. For 'tube mode' flow cytometry take minimum 500 µL into an eppendorf tube or other flow cytometry tube. For plate mode take 200 µL into a round-bottom flow cytometry plate.", "[Diatom sample preparation] If using live cells, go to step 6\n\nIf using ... |
47,405 | BIOSPECIMENS SOPs | 2 | dx.doi.org/10.17504/protocols.io.8epv5zerjv1b/v1 | https://www.protocols.io/view/biospecimens-sops-bsimncc6 | Clemens Scherzer, Bradley Hyman, Charles Jennings | TITLE: BIOSPECIMENS SOPs
AUTHORS: Clemens Scherzer, Bradley Hyman, Charles Jennings
[DESCRIPTION]
This collection explains Standard Operating Protocols for the Harvard Biomarkers Study.
[STEPS] | [] |
34,252 | Zeiss AxioImager Multi Channel 20X Image Capture | null | dx.doi.org/10.17504/protocols.io.bdpki5kw | null | Allen Institute for Brain Science | TITLE: Zeiss AxioImager Multi Channel 20X Image Capture
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the capture of 20X multi-channel images using human and mouse tissue.</div><div class = "text-block"><span style = "font-weight:b... | [] |
93,930 | Immunoblotting of α-synuclein species | 4 | dx.doi.org/10.17504/protocols.io.261gedb67v47/v1 | https://www.protocols.io/view/immunoblotting-of-synuclein-species-c7yizpue | arpine.sokratian, Nicole Bryant | TITLE: Immunoblotting of α-synuclein species
AUTHORS: arpine.sokratian, Nicole Bryant
[DESCRIPTION]
Immunoblotting (Western blotting) protocol is specifically designed to provide an information of protein separation, gel electrophoresis, transfer procedures optimized for a-synuclein protein.
[STEPS]
SECTION: SDS-PAGE... | ["[SDS-PAGE] Prepare stain-free gels in advance", "[SDS-PAGE] Before starting\na. Prepare samples, loading order, and antibodies/concentrations [save to excel sheet]", "[SDS-PAGE] Prepare buffers:\n1x running buffer, \n1x TBST, \nTransfer buffer (let cool in 4C while gel runs!)—Need around 1L for 2 gels\... |
21,576 | Semi-quantitative measure of roots colonization by arbuscular mycorrhizal fungi using standard light microscopy | null | dx.doi.org/10.17504/protocols.io.zbgf2jw | null | Florence Blanchard, Alexis Carteron, Xavier Guilbeault-Mayers, Etienne Laliberté | TITLE: Semi-quantitative measure of roots colonization by arbuscular mycorrhizal fungi using standard light microscopy
AUTHORS: Florence Blanchard, Alexis Carteron, Xavier Guilbeault-Mayers, Etienne Laliberté
[STEPS]
?. [Preparation]
Preparing slides for observation
.justify:after {
content: "";
... | ["[Preparation]\nPreparing slides for observation\n\n\t\t\t\t\t\t\t .justify:after {\n\t\t\t\t\t\t\t content: \"\";\n\t\t\t\t\t\t\t display:inline-block;\n\t\t\t\t\t\t\t width: 100%;\n\t\t\t\t\t\t\t }\nNotes: Roots were collected from living Acer saccharum seedlings from a greenhouse experiment.\nFor subsamp... |
25,624 | Automated Multi-plex Immunofluorescence with TSA for CD4, CD8, FOXP3, CD21, PD1 and CD68 in Follicular Lymphoma | null | dx.doi.org/10.17504/protocols.io.49ygz7w | null | Anna Maria Tsakiroglou, Catharine West, Sue Astley, Kim Linton, Martin Fergie, Richard Byers | TITLE: Automated Multi-plex Immunofluorescence with TSA for CD4, CD8, FOXP3, CD21, PD1 and CD68 in Follicular Lymphoma
AUTHORS: Anna Maria Tsakiroglou, Catharine West, Sue Astley, Kim Linton, Martin Fergie, Richard Byers
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Observing immune cell infiltrat... | ["[Building a spectra library]\nA spectral library is initially built using positive controls of follicular lymphoma tissue to enable unmixing the 6 fluorophore spectra and DAPI in the multi-plex experiment. To build the library, the spectrum of each individual fluorophore is acquired from single-plex experiments.The s... |
74,085 | dU-Tn5 stranded RNA-seq experiment | 4 | dx.doi.org/10.17504/protocols.io.dm6gpj92pgzp/v1 | https://www.protocols.io/view/du-tn5-stranded-rna-seq-experiment-ckkduus6 | Xiaoyuan Tao | TITLE: dU-Tn5 stranded RNA-seq experiment
AUTHORS: Xiaoyuan Tao
[DESCRIPTION]
In this protocol, we describe a novel Tn5-based stranded RNA-seq procedure, in which deoxy-UTP-labeled Tn5 (dU-Tn5) is applied in library construction to preserve the strand-specificity of transcripts. The stranded library preparation secti... | ["[mRNA purification] mRNA was purified from 1 μg of total RNA using oligo(dT)-attached mRNA capture magnetic beads (Vazyme, cat#401) following the user manual. The final purified mRNA was dissolved in 10.5 μl ddH2O.", "Second-strand cDNA was synthesized by adding 10 μl 5 x second strand buffer, 1 μl dUTP-containing dN... |
21,978 | Cell dissociation of fresh human lung tissue for single-cell RNA-seq | null | dx.doi.org/10.17504/protocols.io.zp2f5qe | null | Ilias Angelidis, Maximilian Strunz, Herbert Schiller | TITLE: Cell dissociation of fresh human lung tissue for single-cell RNA-seq
AUTHORS: Ilias Angelidis, Maximilian Strunz, Herbert Schiller
[STEPS]
?. Mince the tissue into small pieces using a pair of scissors. Transfer tissue chunks in a 50mL Falcon tube containing of ice cold PBS. This step is intended to wash away ... | ["Mince the tissue into small pieces using a pair of scissors. Transfer tissue chunks in a 50mL Falcon tube containing of ice cold PBS. This step is intended to wash away any remaining blood off the tissue.\n30 ml", "Transfer lung tissue in a petri dish and cut the required amount for your experiment (2x2x1)cm.", "Rem... |
null | null | null | dx.doi.org/10.17504/protocols.io.g7xbzpn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?. | [] |
93,624 | α-Synuclein Protein Preparation (Large scale) | 1 | dx.doi.org/10.17504/protocols.io.bp2l6xwmklqe/v1 | https://www.protocols.io/view/synuclein-protein-preparation-large-scale-c7nyzmfw | Michael X. Henderon, Lindsay Meyerdirk | TITLE: α-Synuclein Protein Preparation (Large scale)
AUTHORS: Michael X. Henderon, Lindsay Meyerdirk
[DESCRIPTION]
This protocol details α-synuclein protein preparation in a large scale.
[GUIDELINES]
Adapted from: Xiao Tu, Kelvin Luk, Jonathan Branch, Patrick O’Brien, Dustin Covell, Katelyn Becker, Volpicelli-Daley, ... | ["[Day 1: Transformation] Thaw E. coli (BL21(DE3)RIL) and DNA on ice.", "[Day 1: Transformation] Mix 1 µL-2 µL DNA (α-synuclein in pRK172 plasmid) with 20 µL competent cells and incubate 5-10 minutes on ice.", "[Day 1: Transformation] Heat-shock cells for 45 s in 42 °C water and place back on ice for 2 min.", "[Day 1:... |
70,637 | Qualitative & Quantitative Assessment of Human Islets Using Dithizone (DTZ) | 4 | dx.doi.org/10.17504/protocols.io.bp2l6bnkkgqe/v3 | https://www.protocols.io/view/qualitative-amp-quantitative-assessment-of-human-i-cg8mtzu6 | Human Islet Phenotyping Program (HIPP) of the IIDP | TITLE: Qualitative & Quantitative Assessment of Human Islets Using Dithizone (DTZ)
AUTHORS: Human Islet Phenotyping Program (HIPP) of the IIDP
[DESCRIPTION]
This Standard Operating Procedure is adapted from the work of the 'National Institutes of Health-Sponsored Clinical Islet Transplantation Consortium Phase 3 T... | ["[Preparation of Working Dithizone] Assemble all items described in Materials section.", "[Preparation of Working Dithizone] Prepare DTZ stain as described below. Observe all safety precautions when working with DMSO.", "[Preparation of Working Dithizone] Wearing gloves, dissolve 50 mg dithizone in 10 mL DMSO.", "[Pre... |
40,133 | Sending samples to the NCI Frederick EM Core | 1 | null | https://www.protocols.io/view/sending-samples-to-the-nci-frederick-em-core-bjfdkji6 | Bryce Killingsworth | TITLE: Sending samples to the NCI Frederick EM Core
AUTHORS: Bryce Killingsworth
[DESCRIPTION]
Protocol on how to ship EV sample to the NCI Frederick core.
[STEPS]
SECTION: Sending samples
1. If you are beginning a new project, you must put in a service request, select a CAN to draw funds from, and get approal from a... | ["[Sending samples] If you are beginning a new project, you must put in a service request, select a CAN to draw funds from, and get approal from an AO, using the \"New Request\" button on the NCI Frederick EM Core's website: https://ncifrederick.cancer.gov/services/accessioning/services/labservices/area/5\n\nPg 1: info... |
49,915 | Expression and purification of Rab12 (1-244) stoichiometrically phosphorylated at Ser106 (the LRRK2 site) | 1 | dx.doi.org/10.17504/protocols.io.buy3nxyn | https://www.protocols.io/view/expression-and-purification-of-rab12-1-244-stoichi-buy3nxyn | Axel Knebel , Pawel Lis, Dario Alessi | TITLE: Expression and purification of Rab12 (1-244) stoichiometrically phosphorylated at Ser106 (the LRRK2 site)
AUTHORS: Axel Knebel , Pawel Lis, Dario Alessi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A subset of small GTPases of the Rab family including Rab12 (Uniprot: Q6IQ22) have been ide... | ["[Transformation of plasmid into competent bacteria]\nMix of pET15b-6HisSUMO-Rab12 plasmid (around ) with - of the competent BL21(DE3) cells and incubate for .\n10 µl\n50 µl\n100 µl\non ice", "[Transformation of plasmid into competent bacteria]\nTransfer\tthe vial to a heat block equilibrated at and leave for .\n42... |
53,474 | outlineR: Artefact Processing and Extraction Protocol | 5 | dx.doi.org/10.17504/protocols.io.bygaptse | https://www.protocols.io/view/outliner-artefact-processing-and-extraction-protoc-bygaptse | David Nicolas Matzig | TITLE: outlineR: Artefact Processing and Extraction Protocol
AUTHORS: David Nicolas Matzig
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Geometric morphometric methods (GMM) in archaeology are experiencing a sharp increase in application and popularity since the last decade or so and seem to... | ["[Workspace Set-up]\nFor this project, create a new folder on your computer. In the following protocol, this project folder will be referred to as \"/project_folder\".", "[Workspace Set-up]\nInside of \"/project_folder\" create the following subfolders: one for the raw images (\"/project_folder/raw\"), one for the pre... |
null | null | null | dx.doi.org/10.17504/protocols.io.ud8es9w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
https://wickie.hlrs.de/platforms/index.php/Cray_XC40
[STEPS]
SECTION: Getting access to Hazel Hen
?.
SECTION: Test access and set up a workspace
?.
SECTION: Set up ssh
?.
SECTION: Get code via ssh+git
?.
SECTION: Prepare and build
?.
SECTION: Running jobs
?. | ["[Getting access to Hazel Hen] {\"blocks\":[{\"key\":\"8tl93\",\"text\":\"Request access to hazel hen via the ID of your project \",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]},{\"key\":\"197ms\",\"text\":\"https:\\/\\/www.hlrs.de\\/solutions-services\\/academic-users\\/h... |
29,233 | 6L Live PlmCasX Expression & Purification | null | dx.doi.org/10.17504/protocols.io.8srhwd6 | null | Liz O'Brien, Connor Tsuchida | TITLE: 6L Live PlmCasX Expression & Purification
AUTHORS: Liz O'Brien, Connor Tsuchida
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes methods to express and purify PlmCasX plasmids.</div></div>
[STEPS]
?. [Day 1: Grow pre-culture]
Set up pre-culture by either transforming p... | ["[Day 1: Grow pre-culture]\nSet up pre-culture by either transforming plasmid into Rosetta cells or using a small amount from a glycerol stock (steps found below).\nPerform all steps aseptically, next to a Bunsen burner.", "[Day 1: Grow pre-culture]\nAdd to a 500 ml baffled Erlenmeyer flask.\n[LB broth]", "[Day 1: Gr... |
23,842 | Elisa | null | dx.doi.org/10.17504/protocols.io.3iagkae | null | Alex Andre | TITLE: Elisa
AUTHORS: Alex Andre
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Titration of antibodies in the serum of patients.</div></div>
[STEPS]
?. [coating]
add ab at
1 Micromolar (µM)
?. [coating]
wash and keep at
?. [Blocking]
add 100ul BSA
?. [Blocking]
incubate
?. [Adding of sample]
add ... | ["[coating]\nadd ab at\n1 Micromolar (µM)", "[coating]\nwash and keep at", "[Blocking]\nadd 100ul BSA", "[Blocking]\nincubate", "[Adding of sample]\nadd the serum in the plate", "[Adding of sample]\nincubate", "[Adding of sample]\nWash", "[Detection]\nAdd Ab at\n10 Micromolar (µM)", "[Detection]\nincubate"] |
99,866 | Artificial Cerebrospinal Fluid VII (ACSF.VII) | 1 | dx.doi.org/10.17504/protocols.io.rm7vz81dxvx1/v2 | https://www.protocols.io/view/artificial-cerebrospinal-fluid-vii-acsf-vii-ddr2258e | Allen Institute for Brain Science | TITLE: Artificial Cerebrospinal Fluid VII (ACSF.VII)
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
This protocol is used to prepare Artificial Cerebrospinal Fluid VII (ACSF.VII). ACSF.VII is used for applications including fresh human brain tissue transportation and as a bathing solution during fresh human ... | [] |
34,382 | SARS-CoV-2 virus plaque assays [Biosafety Level 3] | null | dx.doi.org/10.17504/protocols.io.bdtni6me | null | tenOever Lab | TITLE: SARS-CoV-2 virus plaque assays [Biosafety Level 3]
AUTHORS: tenOever Lab
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Method to plaque the SARS-CoV-2 virus </div><div class = "text-block">Image attribution:</div><div class = "text-block"><span>Y tambe / CC BY-SA (</span><a href="http://cre... | ["[SARS-CoV2 virus plaque assays (Biosafety level 3)]\nSeed Vero E6 cells in 6-well plates overnight at (106 cells/well)\n37 °C", "[SARS-CoV2 virus plaque assays (Biosafety level 3)]\nDilute the SARS-CoV-2 virus logarithmically in infection media", "[SARS-CoV2 virus plaque assays (Biosafety level 3)]\nReplace media wi... |
95,584 | Untargeted lipidomics of Tagless Lyso-IP | 1 | dx.doi.org/10.17504/protocols.io.yxmvm3r8bl3p/v1 | https://www.protocols.io/view/untargeted-lipidomics-of-tagless-lyso-ip-c9j8z4rw | Wentao Dong, Eshaan S Rawat, Daniel Saarela, Monther Abu-Remaileh | TITLE: Untargeted lipidomics of Tagless Lyso-IP
AUTHORS: Wentao Dong, Eshaan S Rawat, Daniel Saarela, Monther Abu-Remaileh
[DESCRIPTION]
Lysosomal biology is increasingly implicated in neurodegenerative diseases and health. It has traditionally been difficult to profile the metabolomic homeostasis of the lysosome in d... | ["[Untargeted lipidomics of Tagless Lyso-IP] This method is following successful isolation of lysosomes the Tagless Lyso-IP method as described\nin: dx.doi.org/10.17504/protocols.io.x54v9yp51g3e/v1 (Tagless Lyso-IP).", "[Processing of nonpolar metabolite samples (lipids)] Resuspend the lysosomes attached to the magneti... |
20,911 | UC Davis - Gut Microbiome Analysis (Illumina-20K reads, 2X300bp) | null | dx.doi.org/10.17504/protocols.io.ynpfvdn | null | Trina Knotts | TITLE: UC Davis - Gut Microbiome Analysis (Illumina-20K reads, 2X300bp)
AUTHORS: Trina Knotts
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block"><span>The work of Gordon and colleagues (i.e., Nature. 2006 Dec 21;444(7122)... | ["Mice are singly housed in clean cages with fresh food and water and low bedding.", "Weigh mouse and “food-in” (grams of rodent diet provided at start of experiment).", "Save several pellets of rodent diet for analysis (e.g., for energy or macronutrient content)-Store at 4C in airtight container.", "At 24h, weigh mou... |
100,223 | Non-Photochemical Quenching (NPQ) Relaxation Analysis by CF imager FluorCam FC800-331 and FluorCam 7 Software | 0 | dx.doi.org/10.17504/protocols.io.eq2lyw7mmvx9/v1 | https://www.protocols.io/view/non-photochemical-quenching-npq-relaxation-analysi-dd4728zn | Lynn Doran, Steven J Burgess | TITLE: Non-Photochemical Quenching (NPQ) Relaxation Analysis by CF imager FluorCam FC800-331 and FluorCam 7 Software
AUTHORS: Lynn Doran, Steven J Burgess
[DESCRIPTION]
For assessment of Non-Photochemical Quenching (NPQ) relaxation in leaf discs using chlorophyll fluorescence on FluorCam FC800-331 and FluorCam 7 Softw... | ["[Setting up the CF Imager] Turn on the black power supply box. The switch is on when the - symbol is depressed and the O symbol is lifted.", "[Setting up the CF Imager] Turn on the Fluorcam CF Imager using the power button in the top left. The button will illuminate red when it is on.", "[Setting up the CF Imager] ... |
null | null | null | dx.doi.org/10.17504/protocols.io.hjzb4p6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The protocol was creating adapting components from the manual from Bio-Rad for the analysis software ImageLab. Data analyzed using the protocol here described have appear in the following publications:</p>
<pre>Zeitler AF, Gerrer KH, Haas R, Jiménez-Soto LF. Optimized semi-qu... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.dra52d | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Described is the procedure used to perform a onestep growth curve for cyanophage BBC1-P1 via plaque assay on <em>Synechococcus</em> sp. BBC1 (Suttle and Chan 1993).
[GUIDELINES]
The procedure is similar to that for bacteriophages with one major difference. Where bacteriophage g... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.qq9dvz6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>From here, You can learn about the detail methods of genome assembly and gene annotation of the Betta splendens genome.</p>
[STEPS]
?.
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71,183 | CTAB DNA extraction protocol for fungi | 4 | null | https://www.protocols.io/view/ctab-dna-extraction-protocol-for-fungi-chrpt55n | Erin Carr | TITLE: CTAB DNA extraction protocol for fungi
AUTHORS: Erin Carr
[DESCRIPTION]
CTAB Fungal DNA Extraction Protocol
Erin Carr- University of Nebraska-Lincoln
*Adapted from Cubero et al., 1999 and Lagonigro et al., 2004
February 2020; Updated August 15t... | ["[Preparing Yeast from liquid culture for DNA extraction] Grow fungi in preferred media type till fungi are in mid-exponential phase", "[Preparing Yeast from liquid culture for DNA extraction] Centrifuge fungal samples at 10,000x g for 1 minute and wash with water 3 times, centrifuging in between, then obtain as tight... |
104,905 | Fluorescent gelatin degradation protocol in 96-well plates | 0 | null | https://www.protocols.io/view/fluorescent-gelatin-degradation-protocol-in-96-wel-diph4dj6 | Bianca Cruz Pachane | TITLE: Fluorescent gelatin degradation protocol in 96-well plates
AUTHORS: Bianca Cruz Pachane
[DESCRIPTION]
Protocolo do ensaio de degradação de gelatina fluorescente, método de estudo da invasão celular que permite a avaliação da atividade gelatinase in vitro por análise de microscopia epifluorescente. Adaptado de P... | ["[Preparação da Placa Recoberta com Gelatina Fluorescente] Descongelar estoque de Gelatina Fluorescente a 5 mg/mL ou solução de uso a 0.2 mg/mL por 30 min a 37 °C (estufa ou banho-maria).", "[Preparação da Placa Recoberta com Gelatina Fluorescente] Preparar a solução de uso com PBS morno e mante-la a 37 °C até o uso.... |
88,036 | Double-fixation prior to ChIPs | 4 | dx.doi.org/10.17504/protocols.io.yxmvm396nl3p/v1 | https://www.protocols.io/view/double-fixation-prior-to-chips-cz8cx9sw | Jacob G Kirkland, Mary Bergwell, JinYoung Park | TITLE: Double-fixation prior to ChIPs
AUTHORS: Jacob G Kirkland, Mary Bergwell, JinYoung Park
[DESCRIPTION]
This protocol is for the double-fixation of chromatin regulators for chromatin precipitation. The double-fixation method can improve signal-to-noise ratios of chromatin regulator ChIPs, especially for transientl... | ["[Fresh DSG] Place DSG at room temperature for approximately 30 minutes before weighing it out.", "[Fresh DSG] Measure DSG and dissolve in DMSO accordingly (using approximately 80 ul of solution per sample)\n \n Number of Samples DSG (mg) Vol. DMSO (ul) 2 13 160 4 25 32... |
27,582 | Generating chemically competent (E. coli) cells | null | dx.doi.org/10.17504/protocols.io.666hhhe | null | Su Yin Phua, Nay Chi Khin, Estee Tee, Diep R. Ganguly, Kai Xun Chan, Veronica Albrecht-Borth, Barry J Pogson | TITLE: Generating chemically competent (E. coli) cells
AUTHORS: Su Yin Phua, Nay Chi Khin, Estee Tee, Diep R. Ganguly, Kai Xun Chan, Veronica Albrecht-Borth, Barry J Pogson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for generating chemically compotent (ie. for heat shock transformation... | ["[Prepare solutions A and B]\nIn a beaker, prepare 250 ml of Solution A:- 100 mM MgCl2 (hexahydrate = 5.08 g; anhydrous = 2.38 g)- 10 mM MOPS (0.52g)- Up to ~250 mL H2OAdjust to pH 7 using 1 M NaOH (slowly; ~900 μL)Transfer to measuring cylinder and ensure final volume = 250 mL", "[Prepare solutions A and B]\nIn a bea... |
41,652 | V-CHEK Coronavirus (SARS-CoV-2) Antigen Detection Kit | 6 | dx.doi.org/10.17504/protocols.io.bkwukxew | https://www.protocols.io/view/v-chek-coronavirus-sars-cov-2-antigen-detection-ki-bkwukxew | bill , covidtesting | TITLE: V-CHEK Coronavirus (SARS-CoV-2) Antigen Detection Kit
AUTHORS: bill , covidtesting
[STEPS]
?. [V-CHEK Test Procedure]
All specimens must be at room temperature before testing.
Expiration date:
Check expiration date on each individual test package or outer box before using. Do not use any test past the expirati... | ["[V-CHEK Test Procedure]\nAll specimens must be at room temperature before testing.\nExpiration date:\nCheck expiration date on each individual test package or outer box before using. Do not use any test past the expiration date on the label.\nDisposable gloves and safety glasses are recommended when running this test... |
108,539 | RNA Isolation from QIAzol sample with miRNeasy Mini Kit | 0 | dx.doi.org/10.17504/protocols.io.n2bvjn42pgk5/v1 | https://www.protocols.io/view/rna-isolation-from-qiazol-sample-with-mirneasy-min-dm8349yn | Stephan Schreiber | TITLE: RNA Isolation from QIAzol sample with miRNeasy Mini Kit
AUTHORS: Stephan Schreiber
[DESCRIPTION]
__________________________________________________________________________
Purpose
This SOP describes the procedure of total RNAextraction from cell and tissue samples using the Qiagen miRNeasy Mini kit and Ambion... | ["[A.\tPrepare sample and material (starting from 1 mL QIAzol sample)] Place the tube containing the sample (cell pellets or homogenized tissue in QIAzol reagent) on the bench top at room temperature (15-25 °C) for 5 min.", "[A.\tPrepare sample and material (starting from 1 mL QIAzol sample)] At this time, centrifuge t... |
46,306 | EVALUATION OF TEST COMPOUNDS EFFICACY IN REDUCTION OF NEUROLOGICAL DEFICITS IN THE RAT CHRONIC CEREBROVASCULAR INSUFFICIENCY MODEL (CVI) | 4 | dx.doi.org/10.17504/protocols.io.brgam3se | https://www.protocols.io/view/evaluation-of-test-compounds-efficacy-in-reduction-brgam3se | Denis Kurkin, Dmitry Bakulin, Dmitry Verkholyak, Nikolay Kovalev, Evgeny Morkovin, Ivan Tyurenkov | TITLE: EVALUATION OF TEST COMPOUNDS EFFICACY IN REDUCTION OF NEUROLOGICAL DEFICITS IN THE RAT CHRONIC CEREBROVASCULAR INSUFFICIENCY MODEL (CVI)
AUTHORS: Denis Kurkin, Dmitry Bakulin, Dmitry Verkholyak, Nikolay Kovalev, Evgeny Morkovin, Ivan Tyurenkov
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">T... | [] |
46,882 | Human Brain Vascular Pericytes (HBVP) Fixation and Staining | 4 | null | https://www.protocols.io/view/human-brain-vascular-pericytes-hbvp-fixation-and-s-br2am8ae | Daniel Manrique-Castano | TITLE: Human Brain Vascular Pericytes (HBVP) Fixation and Staining
AUTHORS: Daniel Manrique-Castano
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is suitable for the fixation and staining of cultured Human Brain Vascular Pericytes (HBVP).</div></div>
[STEPS]
?. [Cell fixation]
When... | ["[Cell fixation]\nWhen cultured pericytes have reached the desired confluence on Poly-D-Lysine or Matrigel-coated glass coverslips, they can be fixed and prepared for staining. Before starting cell manipulation, warm 2% Paraformaldehyde (PFA) at for .\n37 °C\nThis procedure is unsuitable to perform RNA or protein ex... |
80,313 | Protocol for quantification of BdDV-1 mycovirus of Batrachochytrium dendrobatidis by qPCR | 4 | dx.doi.org/10.17504/protocols.io.dm6gpjkydgzp/v1 | https://www.protocols.io/view/protocol-for-quantification-of-bddv-1-mycovirus-of-csnzwdf6 | Rebecca A. Clemons, Timothy Y. James | TITLE: Protocol for quantification of BdDV-1 mycovirus of Batrachochytrium dendrobatidis by qPCR
AUTHORS: Rebecca A. Clemons, Timothy Y. James
[DESCRIPTION]
This protocol is used for quantifying the amount of the DNA mycovirus BdDV-1 in DNA extracts or cDNA libraries. This virus is associated with the fungus Batracho... | ["[Protocol:] Wipe down pipettes with 70% ethanol and place in the biosafety hood with tips and 96 well plate. UV for at least 15 min (longer is fine).", "[Protocol:] After setting up hood to UV, prepare standard dilutions on the bench using barrier tips. Fill 6 1.5uL microcentrifuge tubes with 90 µL of PCR water. Labe... |
82,690 | Brain Slice Preparation for electrophysiology recording | 4 | dx.doi.org/10.17504/protocols.io.36wgqj2eovk5/v1 | https://www.protocols.click/view/brain-slice-preparation-for-electrophysiology-reco-cuzawx2e | Hong-Yuan Chu, Hong-yuan Chu | TITLE: Brain Slice Preparation for electrophysiology recording
AUTHORS: Hong-Yuan Chu, Hong-yuan Chu
[DESCRIPTION]
This protocol describes brain slice preparation for electrophysiology recording.
[BEFORE_START]
Before beginning
Wear PPEs before entering patch clamp room when making brain slice. i.e. gloves, coat, an... | ["[Prepare Bubbling Solutions] On the prior day, prepare the working aCSF and sucrose aCSF solution in a 1:10 dilution from stock solutions (1 part stock, 1 part bicarbonate, 8 part Milli-Q water).", "[Prepare Bubbling Solutions] On day of cutting, place sucrose aCSF solution in -20 °C freezer for 30-40 minutes.", "[Pr... |
27,343 | Metadata extraction Zeiss CZI, before conversion to JPEG/TIFF (MacOS) | null | dx.doi.org/10.17504/protocols.io.6xphfmn | null | scott john | TITLE: Metadata extraction Zeiss CZI, before conversion to JPEG/TIFF (MacOS)
AUTHORS: scott john
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Extract metadata from Zeiss CZI files before conversion to TIFF/JPEG, using macOS.</div><div class = "text-block">Require "Fiji" and legacy Java 6 runtime ... | ["Cheat Sheet for those using Zeiss CZI files and need to extract metadata before saving/converting file to TIFF/JPEGOn a Mac- with that caveat: MAC: Download Fijifrom https://imagej.net/Fiji/Downloads (This also has windows version- care read caution file)MAC: You will also need Javaolder version; legacy Java 6 runt... |
82,622 | Preparation and cryopreservation of human whole blood samples for analysis by flow cytometry (fresh or after cryobanking) | 4 | dx.doi.org/10.17504/protocols.io.x54v9d91zg3e/v1 | https://www.protocols.io/view/preparation-and-cryopreservation-of-human-whole-bl-cuw6wxhe | Wiebke Werner, Linda Hammerich | TITLE: Preparation and cryopreservation of human whole blood samples for analysis by flow cytometry (fresh or after cryobanking)
AUTHORS: Wiebke Werner, Linda Hammerich
[DESCRIPTION]
This protocol focuses on the preparation of human whole blood samples for analysis by flow cytometry.
It provides two options for sampl... | ["Depending on whether you want to perform flow cytometry on fresh or cryo-preserved samples, you can select different protocol options at this step.", "[Preparations] Label your 5 ml FACS tubes. You might need several tubes per sample, depending on the number of panels and controls you are planning to run.", "Prepare ... |
89,212 | Human Liver Sample Collection Protocol -- University of Minnesota TMCs | 1 | dx.doi.org/10.17504/protocols.io.yxmvm3prnl3p/v1 | https://www.protocols.io/view/human-liver-sample-collection-protocol-university-c3c4yiyw | Laura J Niedernhofer, David A Bernlohr, Steve Johnson | TITLE: Human Liver Sample Collection Protocol -- University of Minnesota TMCs
AUTHORS: Laura J Niedernhofer, David A Bernlohr, Steve Johnson
[DESCRIPTION]
Collection protocol obtained from the attached BioNet Specimen Procurement Agreement provided by the UMN CTSI Biorepository and Laboratory Services (BLS).
[... | ["[Preparation] Patient Identification: As soon as a patient is scheduled, the research team will email bionet@umn.edu a completed Specimen Procurement Request Form.", "[Preparation] Patient Consent: Researcher consents. The original signed consent form will be placed in the patient chart and scanned into Epic. BioNet ... |
98,662 | Protocol for metagenomics sampling, storage, and sequencing of rodent stool | 0 | dx.doi.org/10.17504/protocols.io.e6nvw15dwlmk/v1 | https://www.protocols.io/view/protocol-for-metagenomics-sampling-storage-and-seq-dcke2ute | Federica Pinto, Nicola Segata | TITLE: Protocol for metagenomics sampling, storage, and sequencing of rodent stool
AUTHORS: Federica Pinto, Nicola Segata
[DESCRIPTION]
This SOP provides guidelines for optimal rodent fecal sample collection and conservation practice with the scope of fecal microbiota characterisation by shotgun sequencing.
[STEPS]
... | ["[General guidelines for samples processing for shotgun sequencing] The protocols provided below are routinely applied by prof. Nicola Segata Lab and are based on results by the International Human Microbiome Standards (IHMS) consortium. \n\nBefore starting a metagenomic project/experiment, a list of considerations a... |
27,061 | Freezing and processing intestinal biopsies for the isolation of CD45+ leukocytes | null | dx.doi.org/10.17504/protocols.io.6nvhde6 | null | Oxford HCA, Nicholas Provine, Michael FitzPatrick, Melanie Dunstan | TITLE: Freezing and processing intestinal biopsies for the isolation of CD45+ leukocytes
AUTHORS: Oxford HCA, Nicholas Provine, Michael FitzPatrick, Melanie Dunstan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is designed for the freezing, thawing, and processing of human intestinal... | ["[Stage 1 - Collection in Endoscopy]\nCollect endoscopic biopsies into 50ml falcon tube with 5ml of cold MACS tissue storage solution.", "[Stage 1 - Collection in Endoscopy]\nEnsure all biopsies are immersed in the solution.", "[Stage 1 - Collection in Endoscopy]\nKeep on ice until ready to freeze.", "[Stage 1 - Colle... |
29,387 | Supplemental Table 1. Primer sequences used in mRNA expression analysis | null | dx.doi.org/10.17504/protocols.io.8xjhxkn | null | John Catravas | TITLE: Supplemental Table 1. Primer sequences used in mRNA expression analysis
AUTHORS: John Catravas
[STEPS]
?. | [] |
63,852 | Viaketo Capsules: suppléments de perte de poids sains et où acheter? | 1 | dx.doi.org/10.17504/protocols.io.5jyl89k76v2w/v1 | https://www.protocols.io/view/viaketo-capsules-suppl-ments-de-perte-de-poids-sai-cakkscuw | piklsalak | TITLE: Viaketo Capsules: suppléments de perte de poids sains et où acheter?
AUTHORS: piklsalak
[DESCRIPTION]
Capsules Viaketo : - Le monde d'aujourd'hui est tellement occupé que les gens n'ont pas le temps de profiter de leur propre vie. Les gens sont occupés à Viaketo Capsules gagner leur vie et oublient que le... | [] |
59,045 | TMR labeling of LRRK proteins | 6 | dx.doi.org/10.17504/protocols.io.ewov1nq5ogr2/v1 | https://www.protocols.io/view/tmr-labeling-of-lrrk-proteins-b5wdq7a6 | David Snead, Mariusz Matyszewski | TITLE: TMR labeling of LRRK proteins
AUTHORS: David Snead, Mariusz Matyszewski
[DESCRIPTION]
Protocol for non-specific TMR labeling of LRRK1 and LRRK2 RCKW proteins.
Protocol developed by David Snead and adapted by Mariusz Matyszewski for protocols.io.
Written as used in Snead, Matyszewski, Dickey et al. 2022.
[ST... | ["Typical reaction volume is 40 µL .\nAdd dye in 1:1 ratio to about 20 micromolar (µM) .", "Incubate at Room temperature for 60 min", "Remove excess dye by a buffer exchange through a Micro Bio-Spin P-6 desalting column (Bio-Rad). \nMake sure to equilibrate the column with the LRRK2 Storage buffer beforehand. Follow di... |
null | null | null | dx.doi.org/10.17504/protocols.io.h8wb9xe | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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77,892 | Sequencing SARS-CoV-2 from Animal Samples with NEBNext® ARTIC SARS-CoV-2 Companion Kit | 4 | dx.doi.org/10.17504/protocols.io.kqdg39w97g25/v1 | https://www.protocols.io/view/sequencing-sars-cov-2-from-animal-samples-with-neb-cqbcvsiw | Isabel Gautreau, Brianna Stenger | TITLE: Sequencing SARS-CoV-2 from Animal Samples with NEBNext® ARTIC SARS-CoV-2 Companion Kit
AUTHORS: Isabel Gautreau, Brianna Stenger
[DESCRIPTION]
This protocol is adapted for animal samples and is based on the methods for the NEBNext® ARTIC SARS-CoV-2 Companion Kit (Oxford Nanopore Technologies®), NEB #E7660S/L ... | ["[cDNA Synthesis] The presence of genomic DNA or carry-over products can interfere with sequencing accuracy, particularly for low copy targets. Therefore, it is important to carry out the appropriate no template control (NTC) reactions to demonstrate that positive reactions are meaningful.", "[cDNA Synthesis] Gently m... |
63,825 | Media Prep: 500mL of 1x PBST | 4 | null | https://www.protocols.io/view/media-prep-500ml-of-1x-pbst-cajrscm6 | Melanie Palma Avila, George Testo | TITLE: Media Prep: 500mL of 1x PBST
AUTHORS: Melanie Palma Avila, George Testo
[DESCRIPTION]
PBST is commonly used as a wash solution for Western blot membranes and microtiter plate wells in ELISA assays. The Phosphate Buffered Saline with Tween® 20 is an optimal formulation of pH stabilizers, salts and detergents de... | ["Perform a 1:10 dilution of 10x PBST using a sterile media bottle of 1L volume or greater (if necessary).", "Place cap directly on top of sterile media bottle (DO NOT tighten cap).", "Autoclave sterile media with 1x PBST: Liquid cycle: media (30 mins)", "Retrieve autoclaved 1x PBST & fully cap sterile media bottle for... |
58,411 | Unilateral intranigral AAV alpha synuclein mouse model | 4 | dx.doi.org/10.17504/protocols.io.n92ldzp5xv5b/v1 | https://www.protocols.io/view/unilateral-intranigral-aav-alpha-synuclein-mouse-m-b5ajq2cn | Pranay Srivastava, Waijiao Cai, Xiqun Chen | TITLE: Unilateral intranigral AAV alpha synuclein mouse model
AUTHORS: Pranay Srivastava, Waijiao Cai, Xiqun Chen
[DESCRIPTION]
This protocol details methods for the unilateral intranigral AAV alpha-synuclein injection
[STEPS]
1. Clean all equipment and surgical tools with 70% ethanol.
Turn on the heating pad and cov... | ["Clean all equipment and surgical tools with 70% ethanol.\nTurn on the heating pad and cover it with a paper towel.", "Clean and prepare injector needle.\nRinse 3x with 70% ethanol.\nRinse 3x with saline.", "Animals: adult mice.\nCoordinators: from lambda AP +0.09 cm, ML+0.12 cm, DV -0.44 cm\nInjection rate: 12 µl/hou... |
57,731 | Freezing of feeder-free hPSCs | 4 | dx.doi.org/10.17504/protocols.io.b4mbqu2n | https://www.protocols.io/view/freezing-of-feeder-free-hpscs-b4mbqu2n | Hanqin Li, Oriol Busquets, Steven Poser, Dirk Hockemeyer, Frank Soldner | TITLE: Freezing of feeder-free hPSCs
AUTHORS: Hanqin Li, Oriol Busquets, Steven Poser, Dirk Hockemeyer, Frank Soldner
[DESCRIPTION]
This protocol describes the process of freezing feeder-free human pluripotent stem cells (hPSCs) using Accutase or ReLeSR
Protocol overview:
A. Accutase
B. ReLeSR
General Notes:
For t... | ["[A. Accutase] hPSCs are ready to be frozen when the culture reaches 50-80% confluency.", "[A. Accutase] Before starting:\n a. Prepare Freezing Medium I and II and keep on ice.\n b. Pre-label appropriate number of cryovials (freeze approx. 2 vials/well of a 6-well plate)", "[A. Accutase] Wash hPSCs with DPBS.", ... |
60,298 | RasberryPi-computer based phenotyping for side view image process | 4 | dx.doi.org/10.17504/protocols.io.eq2lynp7pvx9/v2 | https://www.protocols.io/view/rasberrypi-computer-based-phenotyping-for-side-vie-b65irg4e | Li'ang Yu, Magdalena M Julkowska | TITLE: RasberryPi-computer based phenotyping for side view image process
AUTHORS: Li'ang Yu, Magdalena M Julkowska
[DESCRIPTION]
Imaging of plants can be done in an inexpensive way, using Raspberry Pi based setup. Here - we describe how we are processing the side-view images taken from 7 different sides - using the ... | ["[Data preparation] Download the data from RaspberryPi computer, where the images are being saved into one folder. If you have multiple stands for side-view image collection - download all the images into one folder entitled as your experiment. \n\nNOTE - please make sure that the RapberryPi's were recording the times... |
40,320 | Protocol of preparation of a Protein-LAG conjugated to horseradish peroxidase-labeled immunoglobulin Y (IgY-HRP). | 6 | dx.doi.org/10.17504/protocols.io.bjk8kkzw | https://www.protocols.io/view/protocol-of-preparation-of-a-protein-lag-conjugate-bjk8kkzw | Angel Justiz-Vaillant | TITLE: Protocol of preparation of a Protein-LAG conjugated to horseradish peroxidase-labeled immunoglobulin Y (IgY-HRP).
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Peroxidase-labeled anti-IgY conjugated to proteins L, A and G (SpLAG-anti-IgY-HRP) is a new develo... | ["Horseradish peroxidase-labeled IgY (Promega) (500 µl in 50 µl NaCO3 , pH 9.6) is mixed with freshly made sodium periodate solution (1.71 mg/ml). Then the mixture is incubated in the dark for 2 h.", "Mix 500 µg of staphylococcal protein-A (SpA) with an equal amount (500 micrograms) of a mix of horseradish peroxidase-s... |
35,362 | BD FACS Aria II Start-up and Calibration | null | dx.doi.org/10.17504/protocols.io.besajeae | null | Allen Institute for Brain Science | TITLE: BD FACS Aria II Start-up and Calibration
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol provides step by step instructions for performing single-cell sorting by using BD FACSAria II machine and BD FACSDiva software in preparation for s... | [] |
38,755 | SPARC_Duke_PelotGrill_OT2-OD025340_RatVagusNerve_Collection_Histology_Microscopy | 1 | dx.doi.org/10.17504/protocols.io.bh4bj8sn | https://www.protocols.io/view/sparc-duke-pelotgrill-ot2-od025340-ratvagusnerve-c-bh4bj8sn | J. Ashley Ezzell, Nicole A. Pelot, Kara A. Clissold, Warren M. Grill | TITLE: SPARC_Duke_PelotGrill_OT2-OD025340_RatVagusNerve_Collection_Histology_Microscopy
AUTHORS: J. Ashley Ezzell, Nicole A. Pelot, Kara A. Clissold, Warren M. Grill
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for collection, histological processing, and imaging of rat vagus nerves.</di... | ["[Collect rat vagus nerve samples.]\nWe collected vagus nerve samples from perfused Sprague-Dawley rats that were used in other experiments approved by the Duke University Institutional Animal Care and Use Committee.", "[Collect rat vagus nerve samples.]\nWe perfused the rats with ~300 mL phosphate buffered saline or ... |
97,355 | Data-Independent Acquisition (DIA) Data Processing using Spectronaut/directDIA (Biognosys): Secretome Analysis | 0 | dx.doi.org/10.17504/protocols.io.q26g71rz3gwz/v1 | https://www.protocols.io/view/data-independent-acquisition-dia-data-processing-u-dbbj2ikn | Joanna Bons, J P Rose, M A Watson, B Schilling | TITLE: Data-Independent Acquisition (DIA) Data Processing using Spectronaut/directDIA (Biognosys): Secretome Analysis
AUTHORS: Joanna Bons, J P Rose, M A Watson, B Schilling
[DESCRIPTION]
Proteolytic peptide measurement of secretome samples using Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) Acquisition by... | ["Search the DIA data with Spectronaut using the spectral library-free directDIA algorithm against a Human UniProt-SwissProt proteome database (https://www.uniprot.org/proteomes), applying the settings described in Table 1."] |
68,998 | TLC-CLIP | 4 | dx.doi.org/10.17504/protocols.io.rm7vzywr4lx1/v1 | https://www.protocols.io/view/tlc-clip-cfmetk3e | Christina Ernst, Julien Duc, Didier Trono | TITLE: TLC-CLIP
AUTHORS: Christina Ernst, Julien Duc, Didier Trono
[DESCRIPTION]
RNA-binding proteins are instrumental for post-transcriptional gene regulation, controlling all aspects throughout the lifecycle of RNA molecules. However, transcriptome-wide methods to profile RNA-protein interactions in vivo remain tec... | ["[UV crosslinking and generation of cell lysates] UV crosslinking and generation of cell lysates\n\nGrow desired cell line to ~80% confluency in appropriate culture conditions.", "[UV crosslinking and generation of cell lysates] Sonicate lysates for 10-20 seconds at 0.5sec ON and 0.5sec OFF at 10% amplitude to reduce ... |
null | null | null | dx.doi.org/10.17504/protocols.io.sebeban | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div title="Page 1">
<div>
<div>
<p>Endo F1 cleaves Asparagine-linked high mannose or hybrid oligosaccharides. It cleaves between the two N-acetylglucosamine residues in the diacetylchitobiose core of the oligosaccharide, generating a truncated sugar molecule with one N-acetylgl... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.es5beg6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol is a parody of an existing scientific journal article and is intended to showcase the features available on the protocols.io platform in order for VERVE Net members to develope future protocols. While the viral metagenomic analysis on Cabbage Patch Kids is impossib... | [] |
45,754 | COVID 19 testing using ATR spectrometer and AI. | 1 | dx.doi.org/10.17504/protocols.io.bqw2mxge | https://www.protocols.io/view/covid-19-testing-using-atr-spectrometer-and-ai-bqw2mxge | Driss LAHLOU KITANE, Salma LOUKMAN, Nabila Marchoudi, Nawfel Azami | TITLE: COVID 19 testing using ATR spectrometer and AI.
AUTHORS: Driss LAHLOU KITANE, Salma LOUKMAN, Nabila Marchoudi, Nawfel Azami
[STEPS]
?. Sample collection A sample of saliva swab or Naso-pharyngeal swab is collected using only swab with a synthetic tip. Swab is immediately inserted into sterile tubes containing 1... | ["Sample collection A sample of saliva swab or Naso-pharyngeal swab is collected using only swab with a synthetic tip. Swab is immediately inserted into sterile tubes containing 1ml of viral transport mediathe VTM used is the VTM-N of Citoswab\n[Saliva Swab or NP Swab]", "RNA extraction and Spectrometer preparationwe u... |
57,479 | Sandwich ELISA for the quantification of alpha-synuclein | 1 | dx.doi.org/10.17504/protocols.io.q26g748jqgwz/v1 | https://www.protocols.io/view/sandwich-elisa-for-the-quantification-of-alpha-syn-b4dfqs3n | Nathalie Lengacher, Brit Mollenhauer, Michael G. Schlossmacher | TITLE: Sandwich ELISA for the quantification of alpha-synuclein
AUTHORS: Nathalie Lengacher, Brit Mollenhauer, Michael G. Schlossmacher
[DESCRIPTION]
This protocol details the procedure to quantify total alpha-synuclein from tissue and biological fluids by ELISA.
[STEPS]
SECTION: Sandwich ELISA for alpha-synuclein
1.... | ["[Sandwich ELISA for alpha-synuclein]", "[Coating - Day 1] Coat 384-well plate with primary antibody.", "[Coating - Day 1] Make Coating buffer 200 millimolar (mM) NaHCO3 with 0.02% sodium azide (pH 9.6).", "[Coating - Day 1] 1 0 antibody most used is syn1 at 1:500 dilution (BD 610787).", "[Coating - Day 1] Add 25 µ... |
83,876 | Processing frozen cells for population-scale Oxford Nanopore long-read DNA sequencing SOP | 1 | dx.doi.org/10.17504/protocols.io.5jyl8pnk7g2w/v1 | https://www.protocols.click/view/processing-frozen-cells-for-population-scale-oxfor-cv6cw9aw | Pilar Alvarez Jerez, Kimberley J Billingsley, Cornelis Blauwendraat, on behalf of the CARD Long-read Team | TITLE: Processing frozen cells for population-scale Oxford Nanopore long-read DNA sequencing SOP
AUTHORS: Pilar Alvarez Jerez, Kimberley J Billingsley, Cornelis Blauwendraat, on behalf of the CARD Long-read Team
[DESCRIPTION]
Processing frozen cells for population-scale Oxford Nanopore long-read DNA sequencing SOP
At... | ["Part 1: Extracting Cell DNA (~2 hours per 8 samples)\n\nFrom: Circulomics HMW DNA Extraction Cultured Cells Protocol\n\nKit required: Nanobind CBB Big DNA Kit or Nanobind Tissue Big DNA Kit\nCell Input Requirements: 1x106 – 5x106 diploid human cells or equivalent \nCell counts should be accurately determined using a ... |
31,448 | CODEX - Poly-l-Lysine Cover-Slip Preparation | null | dx.doi.org/10.17504/protocols.io.baxyifpw | null | Leigh Propper, Franchesca Farris, Marda Jorgensen | TITLE: CODEX - Poly-l-Lysine Cover-Slip Preparation
AUTHORS: Leigh Propper, Franchesca Farris, Marda Jorgensen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Poly-Lysine Coverslip Preparation </div><div class = "text-block">This protocol describes the process of creating Poly-lysine-coated coversli... | ["Remove 12-15 cover-slips from box. Cover-Slip brand and type are REQUIRED, not suggested.", "Gently place the desired amount of cover-slips into the beaker, spreading them out and allowing both surfaces to have contact with the solution.", "Slowly swirl the beaker to spread the cover-slips around the base.", "Add 7 m... |
31,270 | Eudiometry (s. XVIII analysis of the percentage of O2 in the atmosphere) | null | dx.doi.org/10.17504/protocols.io.baseiebe | null | Josep Grau, Josep Bonet, Jordi Ferre | TITLE: Eudiometry (s. XVIII analysis of the percentage of O2 in the atmosphere)
AUTHORS: Josep Grau, Josep Bonet, Jordi Ferre
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Reproduction of a XVIII century procedure for the analysis of the volumetric percentage of Oxygen in the atmosphere. The proce... | ["[Preparation of the reactants]\nIn order to prepare 500 ml of polysulfide solution (sufficient for 4-5 measures), mix 391.5 g of distilled water with 74.5 g of S and 34 g of CaO. If larger volumes are required, take care to maintain the same percentages by weight (78.3 of water, 14.9 of S, and 6.8 of CaO)", "[Prepara... |
82,457 | Immunofluorescence of macrophages and microglia | 4 | dx.doi.org/10.17504/protocols.io.81wgbym7ovpk/v1 | https://www.protocols.click/view/immunofluorescence-of-macrophages-and-microglia-curzwv76 | Narayana Yadavalli, Shawn M. Ferguson | TITLE: Immunofluorescence of macrophages and microglia
AUTHORS: Narayana Yadavalli, Shawn M. Ferguson
[DESCRIPTION]
This protocol describes the fixation and staining of cultured cells in paraformaldehyde solution.
[STEPS]
SECTION: Immunofluorescence of macrophages and microglia
1. Plate 50,000 iPSC derived macrophage... | ["[Immunofluorescence of macrophages and microglia] Plate 50,000 iPSC derived macrophages or microglia or Neurons or BMDM’s cells on 22 x 22 mm glass coverslips in 24-well dishes in respective culture media.", "[Immunofluorescence of macrophages and microglia] Incubate at 37 °C in 5% CO2.", "[Immunofluorescence of ma... |
88,033 | mitochodnrial assays in human muscle biopsies | 4 | dx.doi.org/10.17504/protocols.io.81wgbxrb1lpk/v1 | https://www.protocols.io/view/mitochodnrial-assays-in-human-muscle-biopsies-cz79x9r6 | Bumsoo Ahn | TITLE: mitochodnrial assays in human muscle biopsies
AUTHORS: Bumsoo Ahn
[DESCRIPTION]
This protocol simultaneously measures mitochondrial respiration and hydrogen peroxide generation rates in human muscle biopsy tissues. The protocol also includes methods for measurement of mitochondrial sensitivity to ADP and respon... | [] |
49,006 | Introduction to Thai Ha clinic | 3 | dx.doi.org/10.17504/protocols.io.bt4nnqve | https://www.protocols.io/view/introduction-to-thai-ha-clinic-bt4nnqve | Thai Ha Clinic | TITLE: Introduction to Thai Ha clinic
AUTHORS: Thai Ha Clinic
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Thai Ha Clinic</div></div>
[STEPS] | [] |
87,736 | Preparation of biological monolayers for producing high-resolution scanning electron micrographs Code: PLOS2021 [PONE-D-21-26669] - [EMID:f8569bc7b537f6e4] | 3 | dx.doi.org/10.17504/protocols.io.n2bvjxmdnlk5/v2 | https://www.protocols.io/view/preparation-of-biological-monolayers-for-producin-czwyx7fw | Shireen Mentor, Franscious Cummings, David Fisher, shireen.mentor | TITLE: Preparation of biological monolayers for producing high-resolution scanning electron micrographs Code: PLOS2021 [PONE-D-21-26669] - [EMID:f8569bc7b537f6e4]
AUTHORS: Shireen Mentor, Franscious Cummings, David Fisher, shireen.mentor
[DESCRIPTION]
Scanning electron microscopy (SEM) provides a technical platform f... | [] |
98,841 | Crystallization of Enterovirus coxsackievirus A16 2A protease | 1 | dx.doi.org/10.17504/protocols.io.3byl49kdzgo5/v1 | https://www.protocols.io/view/crystallization-of-enterovirus-coxsackievirus-a16-dcrz2v76 | ryan Lithgo, Peter Marples, Lizbé Koekemoer, Daren Fearon | TITLE: Crystallization of Enterovirus coxsackievirus A16 2A protease
AUTHORS: ryan Lithgo, Peter Marples, Lizbé Koekemoer, Daren Fearon
[DESCRIPTION]
Picornaviridae coxsackievirus A16 is the causative agent of paediatric hand-foot-and-mouth disease, and a target for pandemic preparedness due to the risk of higher orde... | ["[Crystallization experiment] Protein and buffer requirements:\n43.2 µL20 mg/mL \n3.36 mL \n14.4 µL seeds, dilution 1:1000", "[Crystallization experiment] Dispense 35 µL into SwissCI 3 lens plate reservoir wells using a 100 µl multi-channel pipette.\nDispense 150 nL20 mg/mL to each lens using the SPT mosquito.\nDis... |
null | null | null | dx.doi.org/10.17504/protocols.io.dam2c5 | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<p><strong>Primers:<br /></strong>CPS1.1 primer A: GTA GWA TWT TYT AYA TTG AYG TWG G<br />CPS8.1 primer B: ART AYT TDC CDA YRW AWG GWT C<br /><br /><strong>Reaction Mix:<br /></strong></p>
<table style="width: 400px; height: 200px;">
<tbody>
<tr>
<td>Water</td>
<td>14.25μl</td... | [] |
108,464 | Study protocol for psychosocial impacts of COVID-19 pandemic on Australian based West Africans who survived the 2014-2016 Ebola epidemic | 0 | dx.doi.org/10.17504/protocols.io.5qpvokzk9l4o/v1 | https://www.protocols.io/view/study-protocol-for-psychosocial-impacts-of-covid-1-dm6q49dw | Sulaiman Lansana Mandoh, Phillip Taderera Bwititi, Ezekiel Uba Nwose | TITLE: Study protocol for psychosocial impacts of COVID-19 pandemic on Australian based West Africans who survived the 2014-2016 Ebola epidemic
AUTHORS: Sulaiman Lansana Mandoh, Phillip Taderera Bwititi, Ezekiel Uba Nwose
[DESCRIPTION]
During this COVID pandemic, people from West Africa had previously experienced the ... | ["[Introduction] Large-scale infectious disease outbreaks including epidemics and pandemics have affected the world, and West African countries such as Liberia and Sierra Leone, and to a lesser extent Guinea are no exception. The negative impact of disease outbreaks on these countries’ populations are known, especially... |
48,772 | Impact of reforms on the health system and access to care in Haiti and Bangladesh: a scoping review protocol | 1 | dx.doi.org/10.17504/protocols.io.btvcnn2w | https://www.protocols.io/view/impact-of-reforms-on-the-health-system-and-access-btvcnn2w | Treasure Udechukwu, Louise Carnapete, Shabab Haider , Valery Ridde | TITLE: Impact of reforms on the health system and access to care in Haiti and Bangladesh: a scoping review protocol
AUTHORS: Treasure Udechukwu, Louise Carnapete, Shabab Haider , Valery Ridde
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Objective: </span><span>Th... | ["[Title and author identification]\nImpact of reforms on the health system and access to care in Haiti and Bangladesh: a scoping review from 1991-2021Treasure Udechukwu1, Louise Carnapete1, Shabab Haider2, Valéry Ridde11. CEPED, Institute for Research on Sustainable Development, IRD-Université de Paris, Paris, France... |
61,218 | Preparation of 100mg/ml kanamycin solution | 4 | dx.doi.org/10.17504/protocols.io.36wgq7o3kvk5/v1 | https://www.protocols.io/view/preparation-of-100mg-ml-kanamycin-solution-b72arqae | Jenny Molloy, Nadine Mowoh | TITLE: Preparation of 100mg/ml kanamycin solution
AUTHORS: Jenny Molloy, Nadine Mowoh
[DESCRIPTION]
Kanamycin is an aminoglycoside antibiotic which binds the 30S ribosomal subunit; causes mis-translation. It is used for the selection of cells containing Kanamycin-resistant plasmids on plates and on liquid media at... | ["[Preparing 1000x kanamycin sulphate stock solution] Clean work surfaces and work space using freshly prepared 10 % (v/v) bleach, followed by 70 % (v/v) alcohol.", "[Preparing 1000x kanamycin sulphate stock solution] Using the electronic balance, carefully weigh out 0.4 g of kanamycin sulphate powder (CAS#: 70560-51-9... |
null | null | null | dx.doi.org/10.17504/protocols.io.nvyde7w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>To visual total protein in a given sample</p>
[STEPS]
?.
?.
?.
?. | [] |
58,776 | Algal Media Recipe from Cáceres Lab | 3 | null | https://www.protocols.io/view/algal-media-recipe-from-c-ceres-lab-b5myq47w | Carla Cáceres, Isabella Oleksy | TITLE: Algal Media Recipe from Cáceres Lab
AUTHORS: Carla Cáceres, Isabella Oleksy
[DESCRIPTION]
This is a protocol to make media to grow algae in. In the Duffy Lab, this media is used to grow Ankistrodesmus falcatus. This recipe comes from the Cáceres Lab.
[STEPS] | [] |
98,109 | Robust isolation protocol for mouse leukocytes from blood and liver resident cells for immunology research | 0 | dx.doi.org/10.17504/protocols.io.81wgbzpz3gpk/v1 | https://www.protocols.io/view/robust-isolation-protocol-for-mouse-leukocytes-fro-db252qg6 | Dorien De Pooter, Ben De Clerck, Koen Dockx, Domenica De Santis, Sarah Sauviller, Pascale Dehertogh, Matthias Beyens, Isabelle Bergiers, Isabel Nájera, Ellen Van Gulck, Nádia Conceição-Neto, Wim Pierson | TITLE: Robust isolation protocol for mouse leukocytes from blood and liver resident cells for immunology research
AUTHORS: Dorien De Pooter, Ben De Clerck, Koen Dockx, Domenica De Santis, Sarah Sauviller, Pascale Dehertogh, Matthias Beyens, Isabelle Bergiers, Isabel Nájera, Ellen Van Gulck, Nádia Conceição-Neto, Wim Pi... | [] |
38,312 | Cleaning Microscopes (Covid-19 Shutdown Re-Entry, Srivastava Lab) | 1 | dx.doi.org/10.17504/protocols.io.bhngj5bw | https://www.protocols.io/view/cleaning-microscopes-covid-19-shutdown-re-entry-sr-bhngj5bw | Srivastava Lab | TITLE: Cleaning Microscopes (Covid-19 Shutdown Re-Entry, Srivastava Lab)
AUTHORS: Srivastava Lab
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This is based on: </span><a href="https://www.gerbi-gmb.de/sites/default/files/2020-03/Recommendations_SARS-CoV-2_GerBI-GMB_2020-03-18.pdf" style = "... | ["When using the microscope and adjacent computer, always wear gloves", "Wipe hard surfaces (knobs, body of scope, screens) with 70% ethanol before use", "Place a new piece of plastic wrap over oculars before use\ncleaning oculars too frequently can cause the rubber to degrade", "When done, dispose of plastic wrap and ... |
37,786 | 50 mM Phosphate Buffer (with 0.02% sodium azide option) | 1 | dx.doi.org/10.17504/protocols.io.bg52jy8e | https://www.protocols.io/view/50-mm-phosphate-buffer-with-0-02-sodium-azide-opti-bg52jy8e | Allen Institute for Brain Science | TITLE: 50 mM Phosphate Buffer (with 0.02% sodium azide option)
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">50 mM Phosphate Buffer can be used as a general buffer solution for multiple applications. It is suitable for use as a buffer for specimen embedd... | [] |
95,480 | A low cost time-lapse imaging system for Hydra | 1 | dx.doi.org/10.17504/protocols.io.kxygx36xwg8j/v1 | https://www.protocols.io/view/a-low-cost-time-lapse-imaging-system-for-hydra-c9gyz3xw | Callen Hyland | TITLE: A low cost time-lapse imaging system for Hydra
AUTHORS: Callen Hyland
[DESCRIPTION]
Hydra is a genus of freshwater cnidarian polyp known for their ability to regenerate their entire body from tissue pieces. Despite their simple body plan and tissue organization, Hydra is capable of complex behaviors, including ... | ["[Assemble the imaging chamber] Cut the vinyl sheet to 84 mm X 100 mm and adhere to the LED light panel. You can use the lightpanel_film.svg file with a Cricut cutter.", "[Assemble the imaging chamber] Cut all cardboard panels for the outside of the imaging chamber. You can use the *.dxf files with a laser cutter or C... |
29,271 | Steps for Building an Open Source EI-MS Mass Spectral Library for GC-MS -based Metabolomics | null | dx.doi.org/10.17504/protocols.io.8txhwpn | null | Biswapriya Misra | TITLE: Steps for Building an Open Source EI-MS Mass Spectral Library for GC-MS -based Metabolomics
AUTHORS: Biswapriya Misra
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The objective of this protocol is to provide a set of instructions/ steps to guide ANY NEW USER to generate an open source EI-M... | ["MoNA- Mass bank of North America: https://mona.fiehnlab.ucdavis.edu/downloadsRTX5 Fiehnlib (1,118 spectra)GC-MS Spectra (15,114 spectra)ReSpect (6,374 spectra)HMDB (8,540 spectra)MetaboBASE (1,254 spectra)", "From individual open source libraries download all the \".msp\" or “.txt” files. Save them locally somewhere ... |
98,047 | High molecular weight DNA extraction from fungal spores for long read sequencing | 0 | dx.doi.org/10.17504/protocols.io.n92ld8ybnv5b/v2 | https://www.protocols.io/view/high-molecular-weight-dna-extraction-from-fungal-s-dby72pzn | Nonthakorn (Beatrice) Apirajkamol, Wee Tek Tay, Bishwo Mainali, Phillip Taylor, Thomas Kieran Walsh | TITLE: High molecular weight DNA extraction from fungal spores for long read sequencing
AUTHORS: Nonthakorn (Beatrice) Apirajkamol, Wee Tek Tay, Bishwo Mainali, Phillip Taylor, Thomas Kieran Walsh
[DESCRIPTION]
A modified extraction protocol is required to extract high quantity and quality DNA from fungal spores. We o... | ["[Cell disruption] Note: to obtain the best outcome, freshly made lysis buffer should be used.\nMake cell lysis buffer: 50mM Tris-HCL pH8.5, 50mM EDTA, 5% SDS, and 1% 2-mercaptoethanol", "[Cell disruption] Add 250 µl of 1.0 mm zirconia (ceramic) beads and 600 µl of cell lysis buffer in a 2ml microcentrifuge tube\n\nNo... |
77,739 | Protocol collection: Sampling and characterizing cheese rind microbial communities | 2 | dx.doi.org/10.17504/protocols.io.n2bvj8j5xgk5/v1 | https://www.protocols.io/view/protocol-collection-sampling-and-characterizing-ch-cp6jvrcn | Adair Borges, Emily C.P. Weiss | TITLE: Protocol collection: Sampling and characterizing cheese rind microbial communities
AUTHORS: Adair Borges, Emily C.P. Weiss
[DESCRIPTION]
Cheese rind microbiomes are a validated and stable experimental platform for microbial community research. These communities are relatively simple, reproducible, and easy to ... | [] |
43,891 | Preparo de Meio L15 | 4 | null | https://www.protocols.io/view/preparo-de-meio-l15-bn4tmgwn | Fabio Gomes | TITLE: Preparo de Meio L15
AUTHORS: Fabio Gomes
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocolo de Manutenção de Infecção (DENV e ZIKV) de Células C6/36 - PLO</div></div>
[STEPS]
?. [Preparo Meio L15]
Diluir 29g de triptose em 1L
?. [Preparo Meio L15]
Autoclavar e armazenar.
?. [Preparo M... | ["[Preparo Meio L15]\nDiluir 29g de triptose em 1L", "[Preparo Meio L15]\nAutoclavar e armazenar.", "[Preparo Meio L15]\nDiluir 0.75g de bicarbonato de sódio, 0.20g de L-glutaminaColocar em 800ml de água", "[Preparo Meio L15]\nAjustar o ph 7.4", "[Preparo Meio L15]\nAcrescentar ao meio 100ml da triptose autoclavada", "... |
60,085 | Testimony on a successful lab protocol to disrupt Chlorella vulgaris microalga cell wall | 1 | dx.doi.org/10.17504/protocols.io.b6wvrfe6 | https://www.protocols.io/view/testimony-on-a-successful-lab-protocol-to-disrupt-b6wvrfe6 | Diogo Coelho, Paula A. Lopes, José A. M. Prates | TITLE: Testimony on a successful lab protocol to disrupt Chlorella vulgaris microalga cell wall
AUTHORS: Diogo Coelho, Paula A. Lopes, José A. M. Prates
[DESCRIPTION]
Over the last decades, microalgae have gained popularity due to demand for novel environmental green solutions and development of innovative mass-produ... | ["[Construction of the CAZymes bank and production of microalgae Incubation of C. vulgaris suspension with individual CAZymes (glycoside hydrolases, glycosyl transferases, polysaccharide lyases and carbohydrate esterases)] Preparation of C. vulgaris suspension (20 mg/mL) resuspending the microalgae powder in PBS buffer... |
null | null | null | dx.doi.org/10.17504/protocols.io.ded3a5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This mixture is used with <a href="https://www.protocols.io/view/Cesium-Chloride-Dialysis-for-Viruses-c7jzkm" target="_blank">Cesium Chloride Dialysis for Viruses</a>
[GUIDELINES]
Needed:<br />- 3M NaCl<br />- 0.1M Tris-Cl, pH 7.5<br />- 0.1M MgCl2
[STEPS]
?.
?.
?.
?. | [] |
54,755 | 3’ mRNA-sequencing | 4 | dx.doi.org/10.17504/protocols.io.bzqbp5sn | https://www.protocols.io/view/3-mrna-sequencing-bzqbp5sn | Bryan Yoo, Jessica Griffiths, Sarkis Mazmanian | TITLE: 3’ mRNA-sequencing
AUTHORS: Bryan Yoo, Jessica Griffiths, Sarkis Mazmanian
[DESCRIPTION]
Protocol for RNAseq used in Yoo et al 2021
[STEPS]
SECTION: Tissue Collection and RNA extraction
1. Mice were cervically dislocated and the GI tract was removed.
SECTION: Tissue Collection and RNA extraction
2. 1cm of t... | ["[Tissue Collection and RNA extraction] Mice were cervically dislocated and the GI tract was removed.", "[Tissue Collection and RNA extraction] 1cm of tissue above and below the cecum were dissected and cleaned to represent tissue from the distal SI and proximal colon, respectively.", "[Tissue Collection and RNA extra... |
69,638 | Receptor-Ligand Visualization | 4 | dx.doi.org/10.17504/protocols.io.e6nvwjp32lmk/v1 | https://www.protocols.io/view/receptor-ligand-visualization-cf9etr3e | Long Dao | TITLE: Receptor-Ligand Visualization
AUTHORS: Long Dao
[DESCRIPTION]
Receptor-ligand binding has been analyzed at the protein level using isothermal titration calorimetry and surface plasmon resonance and at the cellular level using interaction-associated downstream gene induction/suppression. However, no currently av... | ["[Generation and labeling of cells] Extract and homogenize the spleens of FcγRIIB-KO (Taconic, model no. 580) and C57/BL6 mice (Jackson Labs, cat. no. 000664) with a 40-μm mesh filter.", "[Generation and labeling of cells] Isolate T Cells from the homogenized cells by using a MojoSort Mouse CD3 T cell Isolation Kit (B... |
70,088 | Coating coverslips for cell culture | 4 | dx.doi.org/10.17504/protocols.io.5qpvornd9v4o/v1 | https://www.protocols.io/view/coating-coverslips-for-cell-culture-cgpgtvjw | Chuyu Chen, Ciarra Smith | TITLE: Coating coverslips for cell culture
AUTHORS: Chuyu Chen, Ciarra Smith
[DESCRIPTION]
Coated cover-slips provide a nourishing adherent surface for cell culture. This protocol provides step by step instruction on how to coat coverslips for cell culture.
[STEPS]
SECTION: Poly L-Lysine/ Poly D-Lysine coating
1. Pr... | ["[Poly L-Lysine/ Poly D-Lysine coating] Precoat the coverslips with poly-L-lysine (P5899) or poly-D-lysine (P7280) at 100 μg/ml.", "[Poly L-Lysine/ Poly D-Lysine coating] This is incubated for 30 minutes or more at room temperature. The coverslips are washed with sterile water and allowed to dry.", "[Poly L-Lysine/ Po... |
70,560 | DNA extraction | 1 | dx.doi.org/10.17504/protocols.io.36wgqj98yvk5/v2 | https://www.protocols.io/view/dna-extraction-cg58ty9w | Emma Wang | TITLE: DNA extraction
AUTHORS: Emma Wang
[DESCRIPTION]
A protocol for DNA extraction
[STEPS]
1. Grind samples
2. add solution
3. spin for 5 min | ["Grind samples", "add solution", "spin for 5 min"] |
54,756 | Proteome Preparation and Analysis | 4 | dx.doi.org/10.17504/protocols.io.bzqcp5sw | https://www.protocols.io/view/proteome-preparation-and-analysis-bzqcp5sw | Bryan Yoo, Jessica Griffiths, Sarkis Mazmanian | TITLE: Proteome Preparation and Analysis
AUTHORS: Bryan Yoo, Jessica Griffiths, Sarkis Mazmanian
[DESCRIPTION]
Protocol for proteome preparation and analysis used in Yoo et al 2021
[STEPS]
SECTION: Protein Extraction
1. Mice were sacrificed 45 minutes after C21 administration and cecal contents were isolated and r... | ["[Protein Extraction] Mice were sacrificed 45 minutes after C21 administration and cecal contents were isolated and resuspended in 400μl of phosphate buffered solution, and centrifuged at x20,000g to spin down cells and lysate.", "[Protein Extraction] Protein was isolated from resulting supernatant using Wessel-Flüegg... |
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