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 |
|---|---|---|---|---|---|---|---|
101,114 | DFP-induced mitophagy experiments | 0 | dx.doi.org/10.17504/protocols.io.e6nvw11m9lmk/v1 | https://www.protocols.io/view/dfp-induced-mitophagy-experiments-dey23fye | Elias Adriaenssens | TITLE: DFP-induced mitophagy experiments
AUTHORS: Elias Adriaenssens
[DESCRIPTION]
This protocol details the DFP-induced mitophagy experiments.
[STEPS]
SECTION: DFP-induced mitophagy
1. To induce mitophagy,
Treat the cells for 1440 min with 1 millimolar (mM) Deferiprone (DFP) (379409, Sigma Aldrich), an iron chelat... | ["[DFP-induced mitophagy] To induce mitophagy, \n\nTreat the cells for 1440 min with 1 millimolar (mM) Deferiprone (DFP) (379409, Sigma Aldrich), an iron chelator that mimics hypoxic conditions through stabilization of the transcription factor HIF1α and subsequent upregulation of NIX and BNIP3.", "[DFP-induced mitophag... |
80,707 | Flaviviruses (West Nile, Zika, Dengue) NS2B/NS3 Fluorescence Dose Response | 1 | null | https://www.protocols.io/view/flaviviruses-west-nile-zika-dengue-ns2b-ns3-fluore-cs3bwgin | Haim Barr, Noa Lahav | TITLE: Flaviviruses (West Nile, Zika, Dengue) NS2B/NS3 Fluorescence Dose Response
AUTHORS: Haim Barr, Noa Lahav
[DESCRIPTION]
This is a functional, biochemical assay used to identify treatments for viral infectious diseases related to viral Flaviviridae infection, (specifically West Nile, Zika, and Dengue) and targets... | ["[Determine which Flavivirus is needed and prepare solutions] Determine which Flavivirus is needed and prepare solutions based on the materials section.\n ReagentStockLoaded into GNFFinal in assay plateunitsDENV NS2B/NS3217000200100nMZIKV NS2B/NS3225000200100nMWNV NS2B/NS3222000200100nMSubstrate10000 105uMAssay bu... |
28,026 | Tn5 Library Prep for Deep Sequencing Loci of CRISPR/Cas9 Edited Cells. Single gene specific primer amplification (UDiTaS protocol with alterations) | null | dx.doi.org/10.17504/protocols.io.7k2hkye | https://www.protocols.io/view/tn5-library-prep-for-deep-sequencing-loci-of-crisp-7k2hkye | Eric Danner | TITLE: Tn5 Library Prep for Deep Sequencing Loci of CRISPR/Cas9 Edited Cells. Single gene specific primer amplification (UDiTaS protocol with alterations)
AUTHORS: Eric Danner
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This is the Tn5 gDNA prep published in the supplementary file of the U... | ["[Reagent Preparation]\nOrder the correct DNA oligos AB1WorkflowA.U.i5.N501UMITn5AATGATACGGCGACCACCGAGATCTACACTAGATCGCNNNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG2WorkflowA.U.i5.N(S)502UMITn5AATGATACGGCGACCACCGAGATCTACACCTCTCTATNNNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG3WorkflowA.U.i5_N(S)503UMITn5AATGATACGGCGACCACC... |
91,957 | LTEE Media Recipes | 1 | dx.doi.org/10.17504/protocols.io.81wgbyr31vpk/v3 | https://www.protocols.io/view/ltee-media-recipes-c52vy8e6 | Jesus E Chavarria-Palma, Zachary D Blount, Jeffrey E Barrick | TITLE: LTEE Media Recipes
AUTHORS: Jesus E Chavarria-Palma, Zachary D Blount, Jeffrey E Barrick
[DESCRIPTION]
This protocol describes recipes to prepare growth media and reagents used in the E. coli long-term evolution experiment (LTEE).
Section 1: DM-glucose, Davis-Mingioli liquid medium supplemented with glucose
... | ["[DM-glucose: Davis-Mingioli liquid medium supplemented with glucose] To prepare 1 L of DM, follow these steps.", "[DM-glucose: Davis-Mingioli liquid medium supplemented with glucose] Weigh dry components:\na. 5.34 g of or 7 gof \nb. 2 g of \nc. 1 g of \nd. 0.5 g of", "[DM-glucose: Davis-Mingioli liquid medi... |
19,107 | Optogenetic Stimulation of superior mesenteric ganglion in a model of septic shock | 1 | dx.doi.org/10.17504/protocols.io.wwbffan | https://www.protocols.io/view/optogenetic-stimulation-of-superior-mesenteric-gan-wwbffan | Kaitlin Murray, Jessica Sladek, Colin Reardon | TITLE: Optogenetic Stimulation of superior mesenteric ganglion in a model of septic shock
AUTHORS: Kaitlin Murray, Jessica Sladek, Colin Reardon
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol details how to use optogenetics to activate neurons in the superior mesenteric ganglion of a mouse... | ["[Optogenetic Stimulation]\nPlace anesthetized mouse supine on heating pad under stereo dissecting scope", "[Optogenetic Stimulation]\nMake a 1-inch incision on the right side of the mouse, directly under the rib cage", "[Optogenetic Stimulation]\nLocate the SMG", "[Optogenetic Stimulation]\nBegin optogenetc stimulati... |
106,415 | UDA-5'RNA-protocol | 0 | dx.doi.org/10.17504/protocols.io.n2bvjne15gk5/v1 | https://www.protocols.io/view/uda-5-39-rna-protocol-dj6p4rdn | Yun Li | TITLE: UDA-5'RNA-protocol
AUTHORS: Yun Li
[DESCRIPTION]
Droplet microfluidics-based single-cell combinatorial indexing sequencing represents an attractive way to balance cost, scalability, robustness, and accessibility. However, current methods need a tailored protocol for specific modality respectively, which may... | ["[GEM Generation & Barcoding.] Prepare Master Mix & Load Chromium Next GEM Chip K", "[GEM Generation & Barcoding.] A certain number of cells or nuclei were added to Master Mix (18.8ul RT Reagent B (2000165); 7.3ul 1.1ul Template Switch Oligo (3000228); 1.9ul Reducing Agent B (2000087) and 8.3ul RT Enzyme C(200... |
null | null | null | dx.doi.org/10.17504/protocols.io.vnge5bw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Fixation of mouse tissues for either histology or fluorescence microscopy is an essential first step in tissue preparation. In this protocol, we outline a reliable method for fixation and perfusion of mice for tissue histology or microscopy. Tissues prepared by this method can b... | ["{\"blocks\":[{\"key\":\"6do1c\",\"text\":\"Prepare 1.6% PFA in PBS (at least per mouse, half to be used during perfusion, half to be used as storage buffer overnight) MAKE THIS FRESH, DO NOT USE ANYTHING OLDER THAN 24 HOURS. Also, make sure PFA has been stored away from light, this will degrade it.\",\"type\":\"uns... |
29,765 | Azolla filiculoides sporocarp cryo-preservation | null | dx.doi.org/10.17504/protocols.io.9bdh2i6 | null | Paul Brouwer, Henriette Schluepmann | TITLE: Azolla filiculoides sporocarp cryo-preservation
AUTHORS: Paul Brouwer, Henriette Schluepmann
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Method extracted from </span><a href="https://doi.org/10.1111/nph.12708" style = "text-decoration:underline;color:blue;cursor:pointer;"><span styl... | ["Preliminary knowledge: cryo-preservatives were not effective but drying was.The cryopreservation protocols were explored on batches of 20-50 megasporocarps. Each condition was evaluated in duplicate. For cryopreservation involving cryoprotectant pre-treatment, 1 ml of the cryoprotective solution was added to the mega... |
65,255 | Fluxactive Complete Reviews – Legitimate Health Supplement For Prostate? | 3 | dx.doi.org/10.17504/protocols.io.q26g747pqgwz/v1 | https://www.protocols.io/view/fluxactive-complete-reviews-legitimate-health-supp-cbyfsptn | Fluxactive Complete Reviews | TITLE: Fluxactive Complete Reviews – Legitimate Health Supplement For Prostate?
AUTHORS: Fluxactive Complete Reviews
[DESCRIPTION]
https://www.24x7supplement.com/Fluxactive-Complete-Reviews/
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ru2d6ye | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol seeks to provide all information needed to allow regular spawning of Aiptasia and safe handling of the spawn.</p>
<p> </p>
<p>It is based on the protocol described in Grawunder et al., 2015.</p>
[GUIDELINES]
<p>This protocol refers to three different sizes of p... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.nzjdf4n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol for human intestine cell dissociation. </p>
[BEFORE_START]
<div title="Page 1">
<p><strong>Checklist prior to beginning:</strong><br />-Centrifuges, large and small, set to 4 C<br />-Make enzyme stock; place 2 tubes of enzyme on dry ice.<br />-Make 0.01% BSA/PBS (50... | [] |
92,720 | Traditional Chinese Medicine as add-on treatment of triple/quadruple therapy for Helicobacter pylori infection: an overview of systematic reviews and meta-analyses (Protocol) | 1 | dx.doi.org/10.17504/protocols.io.kqdg3x1rqg25/v1 | https://www.protocols.io/view/traditional-chinese-medicine-as-add-on-treatment-o-c6sqzedw | Xiaobei Si, Yu Lan | TITLE: Traditional Chinese Medicine as add-on treatment of triple/quadruple therapy for Helicobacter pylori infection: an overview of systematic reviews and meta-analyses (Protocol)
AUTHORS: Xiaobei Si, Yu Lan
[DESCRIPTION]
Background: In recent years, many studies reported the anti-Hp effects of Traditional Chinese M... | [] |
24,215 | Combining long-lasting insecticidal nets and indoor residual spraying for malaria prevention in Ethiopia: study protocol for a cluster randomized controlled trial | 1 | dx.doi.org/10.17504/protocols.io.3vxgn7n | https://www.protocols.io/view/combining-long-lasting-insecticidal-nets-and-indoo-3vxgn7n | Bernt Lindtjorn | TITLE: Combining long-lasting insecticidal nets and indoor residual spraying for malaria prevention in Ethiopia: study protocol for a cluster randomized controlled trial
AUTHORS: Bernt Lindtjorn
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Background: Long-lasting insecticidal nets (LLINs) and in... | [] |
78,127 | In situ Bcl-6 detection in formalin-fixed, paraffin-embedded (FFPE) pig tissues | 4 | dx.doi.org/10.17504/protocols.io.14egn2yy6g5d/v1 | https://www.protocols.io/view/in-situ-bcl-6-detection-in-formalin-fixed-paraffin-cqipvudn | Jayne E Wiarda, Crystal Loving | TITLE: In situ Bcl-6 detection in formalin-fixed, paraffin-embedded (FFPE) pig tissues
AUTHORS: Jayne E Wiarda, Crystal Loving
[DESCRIPTION]
An immunohistochemistry (IHC) staining protocol for in situ identification of porcine Bcl-6
[BEFORE_START]
Starting specimens:
Starting samples = FFPE tissues cut to 4 micron th... | ["[Baking] Before starting the assay: \nPreheat a dry oven to 60℃ \nLoad slides for assay into vertical slide rack\n\nBaking\nBake slides 20 min 60℃\n\nWhile slides bake:\nPrepare 0.05% PBS-T (can store at RT up to 1 month)", "[Deparaffinizing & Rehydrating] Immediately before deparaffinizing:\nAdd ~200 mL xylenes ... |
61,319 | Double Whole Mount In Situ Hybridization in Zebrafish | 4 | dx.doi.org/10.17504/protocols.io.4r3l2onnxv1y/v1 | https://www.protocols.io/view/double-whole-mount-in-situ-hybridization-in-zebraf-b75frq3n | D R. Hammond-Weinberger | TITLE: Double Whole Mount In Situ Hybridization in Zebrafish
AUTHORS: D R. Hammond-Weinberger
[DESCRIPTION]
This protocol has been optimized for serial detection of two chromogenic substrates in embryonic zebrafish (Danio rerio). Several stain pairings are included as options. Protocol begins with tissue preparation a... | ["[Day 1] Wear gloves and treat surfaces for RNAses.", "[Day 1] Rehydrate the embryos", "[Day 1] Wash embryos in 0.5 mL 75% Methanol/25% PBTween, rocking, for 5 min at Room temperature in 1.5 mL centrifuge tubes.", "[Day 1] Wash embryos in 0.5 mL 50% MeOH / 50% PBTween, rocking, for 5 min at Room temperature", "[Day ... |
99,880 | Phosphate Buffered Saline (PBS) | 1 | dx.doi.org/10.17504/protocols.io.kqdg35boev25/v3 | https://www.protocols.io/view/phosphate-buffered-saline-pbs-ddsg26bw | Allen Institute for Brain Science | TITLE: Phosphate Buffered Saline (PBS)
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
This protocol is used to prepare Phosphate Buffered Saline (PBS). PBS (-) and PBS (+) which includes Tween are used as biologically neutral wash solutions in many processes including In Situ Hybridization (ISH), Immunohisto... | [] |
40,847 | Collection of Protocols and Guidelines for Phase 3 study of Vaccine Candidate for COVID-19 | 2 | dx.doi.org/10.17504/protocols.io.bj5pkq5n | https://www.protocols.io/view/collection-of-protocols-and-guidelines-for-phase-3-bj5pkq5n | Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores | TITLE: Collection of Protocols and Guidelines for Phase 3 study of Vaccine Candidate for COVID-19
AUTHORS: Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This is a collection of protocols for: "Phase 3 randomized, double-blinded, placebo-... | [] |
35,361 | Bulk EV staining with CFDA-SE (with NAP-5 purification) | 1 | dx.doi.org/10.17504/protocols.io.ber9jd96 | https://www.protocols.io/view/bulk-ev-staining-with-cfda-se-with-nap-5-purificat-ber9jd96 | Aizea Morales Kastresana, Bryce Killingsworth, Jennifer Jones | TITLE: Bulk EV staining with CFDA-SE (with NAP-5 purification)
AUTHORS: Aizea Morales Kastresana, Bryce Killingsworth, Jennifer Jones
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A protocol for bulk CFSE staining of EVs.</div></div>
[STEPS]
?. [Preparing CFDA-SE dye aliquots]
Let a new vial of s... | ["[Preparing CFDA-SE dye aliquots]\nLet a new vial of solid CFSE-DA dye warm to RT (should take less than 10 minutes.)", "[Preparing CFDA-SE dye aliquots]\nPer the Vybrant™ CFDA SE Cell Tracer Kit instructions, sissolve the solids in the vial in anhydrous DMSO (based on the quantity of dye in each vial this creates a ... |
null | null | null | dx.doi.org/10.17504/protocols.io.eq3bdyn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For use in <a href="https://www.protocols.io/view/Polyacrylamide-Gel-System-For-Electrophoresis-Of-P-ep7bdrn" target="_blank">Polyacrylamide Gel System For Electrophoresis Of Proteins</a>.
[STEPS]
?.
?.
?. | [] |
80,841 | SARS-CoV-2 S-gene Sanger Sequencing | 1 | dx.doi.org/10.17504/protocols.io.3byl4jnwzlo5/v1 | https://www.protocols.io/view/sars-cov-2-s-gene-sanger-sequencing-cs7hwhj6 | Anna S. Cherkashina | TITLE: SARS-CoV-2 S-gene Sanger Sequencing
AUTHORS: Anna S. Cherkashina
[DESCRIPTION]
The presented protocol describes the analysis of fragments of the SARS-CoV-2 S-gene by the Sanger sequencing. Although whole-genome sequencing is the best method for identifying variants, this tool is not available for all laboratori... | ["[RNA Extraction] This section is carried out in accordance with the manufacturer's instructions for the Riboprep Nucleic Acid Isolation Kit, Amplisens, Moscow, Russia.\n\n1. Introduce 300 µl of lysis solution into the pure tubes.\n2. Add 100 µl each of samples and positive controls.\n3. Mix gently and place in thermo... |
91,948 | Protocol for the preparation of Wings and Wing Interference Pattern Imaging from ethanol preserved specimens | 4 | dx.doi.org/10.17504/protocols.io.bp2l6xyy1lqe/v1 | https://www.protocols.io/view/protocol-for-the-preparation-of-wings-and-wing-int-c52ky8cw | Saskia B. Bartsch, Jonathan Vogel, Anne Ankermann, Christoph Mayer, Ralph S. Peters | TITLE: Protocol for the preparation of Wings and Wing Interference Pattern Imaging from ethanol preserved specimens
AUTHORS: Saskia B. Bartsch, Jonathan Vogel, Anne Ankermann, Christoph Mayer, Ralph S. Peters
[DESCRIPTION]
This protocol aims to provide standardisation for the necessary steps, specifically to a) produc... | ["[Slide preparation] Using the microscope, transfer the ethanol-preserved specimen into a small petri dish or staining block filled with ethanol. \nDissect the right fore- and hindwings of the specimen by grabbing the base of the forewing with the fine forceps and spinning the wing while pushing the specimen into the ... |
25,443 | 2. winter protocol | null | dx.doi.org/10.17504/protocols.io.44bgysn | null | Darja Darja | TITLE: 2. winter protocol
AUTHORS: Darja Darja
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol of Savna</div></div>
[STEPS]
?. apple ABCDEFGHI1orangeorangeorange 2 orange 3 ... | ["apple ABCDEFGHI1orangeorangeorange 2 orange 3 4 orange orangeorangeorangeorangeorangeorange5 orange ora... |
67,455 | Dietavita Erfahrungen | 1 | dx.doi.org/10.17504/protocols.io.q26g742b9gwz/v1 | https://www.protocols.io/view/dietavita-erfahrungen-cd47s8zn | polbatra | TITLE: Dietavita Erfahrungen
AUTHORS: polbatra
[DESCRIPTION]
https://healthcare24hrs.com/diaetovita/
[GUIDELINES]
Diaetovita Erfahrungen Eine brillante Gewichtsabnahme-Ergänzung | Deutschlands beste Gewichtsverlustpillen
Wenn Sie überschüssiges Körperfett verlieren und in nur wenigen Wochen eine fitte Körperform e... | [] |
17,364 | Purification of Mouse Pancreatic Islets using Histopaque Gradient Centrifugation | null | dx.doi.org/10.17504/protocols.io.u7ueznw | https://www.protocols.io/view/purification-of-mouse-pancreatic-islets-using-hist-u7ueznw | Nancy Smith, Haopeng Lin, Mourad Ferdaoussi, Patrick Macdonald | TITLE: Purification of Mouse Pancreatic Islets using Histopaque Gradient Centrifugation
AUTHORS: Nancy Smith, Haopeng Lin, Mourad Ferdaoussi, Patrick Macdonald
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details the purification of mouse pancreatic islets using histopaque gradient ... | ["[Solution Prep - 1X Hanks Balanced Salt Solution (HBSS) - Sigma H6136]", "[Solution Prep - 1X Hanks' Balanced Salt Solution (HBSS) + BSA - Sigma H6136 and Coating]\nMeasure out 900ml of room temperature H2O\n[MiliQ water]", "[Solution Prep - 1X Hanks' Balanced Salt Solution (HBSS) + BSA - Sigma H6136 and Coating]\nWh... |
null | null | null | dx.doi.org/10.17504/protocols.io.ht9b6r6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?. | [] |
79,607 | Isolation of HMW gDNA from a bioreactor biofilm for long read sequencing | 1 | dx.doi.org/10.17504/protocols.io.q26g7yj4qgwz/v1 | https://www.protocols.io/view/isolation-of-hmw-gdna-from-a-bioreactor-biofilm-fo-cryxv7xn | Viola A Manning, Kristin Trippe | TITLE: Isolation of HMW gDNA from a bioreactor biofilm for long read sequencing
AUTHORS: Viola A Manning, Kristin Trippe
[DESCRIPTION]
This protocol describes isolation of HMW DNA for long read sequencing from a bioreactor biofilm.
[STEPS]
SECTION: Storing bioreactor biofilm
1. Aliquot 750 uL of biofilm into 1.5 mL... | ["[Storing bioreactor biofilm] Aliquot 750 uL of biofilm into 1.5 mL eppendorf tubes.", "[Storing bioreactor biofilm] Spin in microcentrifuge (eppendorf 5424) at ~21,000 x g for 5 minutes.5 min", "[Storing bioreactor biofilm] Resuspend pellet in 1 mL by pipetting up and down multiple times.", "[Storing bioreactor bio... |
41,598 | BSCI:414 Lab 1--Benchling and PCR | 1 | null | https://www.protocols.io/view/bsci-414-lab-1-benchling-and-pcr-bku6kwze | Harley King | TITLE: BSCI:414 Lab 1--Benchling and PCR
AUTHORS: Harley King
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Lab 1 Overview</div><div class = "text-block"> Discuss and Begin Lab Notebooks in Benchling</div><div class = "text-block"> Import and Explore DNA in Benchling</div><div class = "text-block"... | ["[Benchling Lab Notebook Tutorial]\nIntroduce last semester's lab notebooks.", "[Benchling Lab Notebook Tutorial]\nDiscuss features of a good lab notebook e.g. dates, navigation.", "[Students Begin Lab Notebook]\nSign into Benchling, join and find project \"USG BSCI:414 Fall 2020 Lab\".", "[Students Begin Lab Notebook... |
40,073 | Collection and midgut dissection of mosquito larvae | 3 | dx.doi.org/10.17504/protocols.io.bjdhki36 | https://www.protocols.io/view/collection-and-midgut-dissection-of-mosquito-larva-bjdhki36 | avinash.kale | TITLE: Collection and midgut dissection of mosquito larvae
AUTHORS: avinash.kale
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Collection and midgut dissection of mosquito larvae</span></div></div>
[STEPS] | [] |
38,313 | Collection of SOPs for Covid-19 Shutdown Re-Entry, Srivastava Lab | 2 | dx.doi.org/10.17504/protocols.io.bhnhj5b6 | https://www.protocols.io/view/collection-of-sops-for-covid-19-shutdown-re-entry-bhnhj5b6 | Srivastava Lab | TITLE: Collection of SOPs for Covid-19 Shutdown Re-Entry, Srivastava Lab
AUTHORS: Srivastava Lab
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Disclaimer</span><span>: The SOPs presented have been designed by the Srivastava Lab at Harvard University and are being ... | [] |
77,677 | Exploring the components of feedback facilitation: A systematic review | 1 | null | https://www.protocols.io/view/exploring-the-components-of-feedback-facilitation-cp4mvqu6 | Michael Sykes, Sarah Alderson, Owen Thomas, Karen Caulfield, Lisa Robinson, Matthew Quigley, Lavanya Gupta, Zahava Rosenberg-Yunger | TITLE: Exploring the components of feedback facilitation: A systematic review
AUTHORS: Michael Sykes, Sarah Alderson, Owen Thomas, Karen Caulfield, Lisa Robinson, Matthew Quigley, Lavanya Gupta, Zahava Rosenberg-Yunger
[DESCRIPTION]
Audit and feedback is a much-used intervention that involves the delivery of feedback ... | [] |
86,579 | Immune profiling using 16-color panel for PD patient PBMCs | 1 | dx.doi.org/10.17504/protocols.io.q26g7pp13gwz/v1 | https://www.protocols.io/view/immune-profiling-using-16-color-panel-for-pd-patie-cystxwen | Weiyi Peng | TITLE: Immune profiling using 16-color panel for PD patient PBMCs
AUTHORS: Weiyi Peng
[DESCRIPTION]
This is the protocol for immune profiling using 16-color panel for PD patient PBMCs.
[STEPS]
SECTION: Master tubes summary:
1. 1. Ghost dye stain: Day 1
2. Fc blocker: Day 1
3. Surface marker: Day 1
4. Intracellular... | ["[Master tubes summary:] 1. Ghost dye stain: Day 1 \n2. Fc blocker: Day 1 \n3. Surface marker: Day 1 \n4. Intracellular markers: Day 1 \n5. Foxp3 fix/perm buffer: Day 2 \n6. FoxP3 wash buffer: Day 1", "[Day 1 (the day before staining) for 16 colors staining:] Compo-Beads staining:", "[Day 1 (the day before staining) f... |
23,244 | Preparation of a cell-free expression system from Escherichia coli | null | dx.doi.org/10.17504/protocols.io.2xkgfkw | null | Renuka Kudva | TITLE: Preparation of a cell-free expression system from Escherichia coli
AUTHORS: Renuka Kudva
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes the procedure make an S30 derived E.coli cell lysate that lacks membrane components. Modified from a protocol published in </s... | ["Day 1: Make medium and autoclave 1. Wash all flasks with milliQ water.2. Prepare medium as described, autoclave. 4 erlenmeyer flasks, and one flask with 50 ml medium for overnight culture. (This protocol uses S30 medium, see materials). 3. Autoclave milliQ water to make the buffers.4. Prepare stock solutions of all... |
22,615 | CD Media for High Density Cultivation of Synechocystis sp. PCC 6803 | null | dx.doi.org/10.17504/protocols.io.2bxgapn | null | Oliver Mantovani, Dennis Dienst | TITLE: CD Media for High Density Cultivation of Synechocystis sp. PCC 6803
AUTHORS: Oliver Mantovani, Dennis Dienst
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">CellDeg's High Density Cultivation system allows for efficient accumulation of biomass of photosynthetic organisms, such as cyanobacteri... | ["Prepare the following 8 stock solutions ABCD1StockComponentsConcentrationStock concentration (g/L)2Stock AK2HPO44 M696.83Stock BMgSO4 + 7xH2O2 M493.04Stock CCaCl2 + 2xH20500 mM73.55Stock DFe-ammonium-citrate\n(Ammonium iron(III) citrate)150 mM39.36Stock ENaNO35 M4257Stock FKHCO32.5 M250.48EDTANa2EDTA150 mM55.89Trace... |
55,542 | ddPCR titration of AAV vectors | 1 | dx.doi.org/10.17504/protocols.io.b2gwqbxe | https://www.protocols.io/view/ddpcr-titration-of-aav-vectors-b2gwqbxe | Addgene The Nonprofit Plasmid Repository | TITLE: ddPCR titration of AAV vectors
AUTHORS: Addgene The Nonprofit Plasmid Repository
[DESCRIPTION]
This protocol describes ddPCR titration of AAV vectors. To see the full abstract and additional resources, visit https://www.addgene.org/protocols/aav-ddpcr-titration/.
Sample Data:
When analyzing data there shoul... | ["[Preparation] Before handling any viruses get materials ready.", "[Preparation] Ensure that primers, probe, 10X PCR buffer, and master mix are thawed.", "[Preparation] Vortex primers, probe and master mix for 15 s then spin 10 s in a mini centrifuge and place on ice.", "[Preparation] Wipe down a DG8 cartridge holder ... |
108,813 | RNA isolation | 0 | dx.doi.org/10.17504/protocols.io.dm6gpznpplzp/v1 | https://www.protocols.io/view/rna-isolation-dnhm5b46 | Angkana Kidtiwong | TITLE: RNA isolation
AUTHORS: Angkana Kidtiwong
[DESCRIPTION]
RNA isolation for sample stored in TRIzol reagent
[STEPS]
SECTION: RNA isolation
1.
Prepare the centrifuge at 4°C and meanwhile thaw the frozen sample (in TRIzol, stored at -80°C) at room temperature for about 10-15 minutes.
SECTION: RNA isolatio... | ["[RNA isolation] Prepare the centrifuge at 4°C and meanwhile thaw the frozen sample (in TRIzol, stored at -80°C) at room temperature for about 10-15 minutes.", "[RNA isolation] Add chloroform at 20% of the sample volume to the sample tube (typically, 1 ml of TRIzol sample, so add 200 µl of chloroform in sample tube) a... |
37,285 | DAB Solutions | null | dx.doi.org/10.17504/protocols.io.bgndjva6 | https://www.protocols.io/view/dab-solutions-bgndjva6 | Allen Institute for Brain Science | TITLE: DAB Solutions
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">3, 3´ Diaminobenzidine (DAB) is a commonly used chromogen for histological staining. In the presence of peroxidase enzyme, DAB produces a brown precipitate that is insoluble in alcohol a... | [] |
94,622 | Bacterial Genomics24 | 5 | dx.doi.org/10.17504/protocols.io.x54v9pxpzg3e/v1 | https://www.protocols.io/view/bacterial-genomics24-c8m6zu9e | George Odette | TITLE: Bacterial Genomics24
AUTHORS: George Odette
[DESCRIPTION]
This is the protocol for going through the bacterial genomics course.
[STEPS]
SECTION: Installing software for the Bacterial Genomics24
1. We will install many of the software we will use using conda.
Conda
To install conda, run the following script
... | ["[Installing software for the Bacterial Genomics24] We will install many of the software we will use using conda.\nConda\nTo install conda, run the following script\n\n \nOnce the download is complete, run this script:\n\n \nThe first time you call conda you might get the error below:\nconda: command not found\n If th... |
90,703 | Synthetic COI spike-ins for use in metabarcoding-based insect biodiversity surveys | 1 | dx.doi.org/10.17504/protocols.io.14egn33ryl5d/v2 | https://www.protocols.io/view/synthetic-coi-spike-ins-for-use-in-metabarcoding-b-c4tpywmn | Ela Iwaszkiewicz-Eggebrecht, Monika Prus-Frankowska, Piotr Łukasik | TITLE: Synthetic COI spike-ins for use in metabarcoding-based insect biodiversity surveys
AUTHORS: Ela Iwaszkiewicz-Eggebrecht, Monika Prus-Frankowska, Piotr Łukasik
[DESCRIPTION]
In the context of insect monitoring, metabarcoding has emerged as a pivotal method, revolutionizing the precision and scope of surveillanc... | ["[Sequence synthesizing, plasmid production and transformation into E. coli] Download FASTA file with spike-in sequences from GitHub: https://github.com/ela-iwaszkiewicz/Synthetic_COI_spike-ins", "[Plasmid isolation from E. coli] The plasmids were isolated from E. coli using a GeneMATRIX PLASMID\nMINIPREP (EURx) kit f... |
74,278 | Nf1 loxP site verification | 1 | dx.doi.org/10.17504/protocols.io.261ge3ryyl47/v1 | https://www.protocols.io/view/nf1-loxp-site-verification-ckseuwbe | Greig Couasnay, Florent Elefteriou | TITLE: Nf1 loxP site verification
AUTHORS: Greig Couasnay, Florent Elefteriou
[DESCRIPTION]
We have found that our Nf1 flox mouse colonies contained mice that had lost one of the two loxP sites inserted into the Nf1 gene (Parada laboratory, PMID:11297510, JAX# 017639), leading to loss of DNA recombination upon Cre-rec... | ["[Nf1 loxP site verification] Primers for the Nf1 loxP1 site:\nP1: 5’-CTTCAGACTGATTGTTGTACCTGA-3’\nP4: 5’-TGATTCCCACTTTGTGGTTCTAAG-3’ \nP3: 5'-ACCTCTCTAGCCTCAGGAATGA-3'\n\nPrimers for the Nf1 loxP2 site:\nLoxP2For: 5’-GCTTTAGCTTCTGGAAATGTGAA-3’ \nLoxP2Rev: 5’-GCGGGCTAAAATGGCAATGTCG-3’", "[Nf1 loxP site verification] ... |
null | null | null | dx.doi.org/10.17504/protocols.io.e3dbgi6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>BioLegend’s Red Blood Cell (RBC) Lysis Buffer (Cat. No. 420301) has been designed,<br />formulated, and tested to ensure optimal lysis of RBCs in single cell suspensions<br />of hematopoietic tissues, such as spleen, as well as RBCs derived from peripheral<br />blood. RBC Lys... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.k7ucznw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>IMPORTANCE: </strong>This review provides a comprehensive comparison of treatment outcomes between robot-assisted laparoscopic surgery (RLS) and conventional laparoscopic surgery (CLS) based on randomly-controlled trials (RCTs).</p>
<p><strong>OBJECTIVES: </strong>We ... | [] |
90,561 | iPSC-derived neurons sample preparation for ELISA assays | 1 | dx.doi.org/10.17504/protocols.io.dm6gp35jdvzp/v1 | https://www.protocols.io/view/ipsc-derived-neurons-sample-preparation-for-elisa-c4n9yvh6 | Laura Mahoney-Sanchez | TITLE: iPSC-derived neurons sample preparation for ELISA assays
AUTHORS: Laura Mahoney-Sanchez
[DESCRIPTION]
Cell lysis sample preparation for ELISA assays
[STEPS]
SECTION: Cell lysis
1. Cells were washed with cold PBS then lysed with 300 µL cold RIPA buffer (Thermo Fisher Scientific) supplemented with 1x of a cockta... | ["[Cell lysis] Cells were washed with cold PBS then lysed with 300 µL cold RIPA buffer (Thermo Fisher Scientific) supplemented with 1x of a cocktail of phosphatase and protease inhibitors (Life Technologies).", "[Cell lysis] Cell lysates were transferred into 1.5ml eppendorf tubes and centrifuged for 5 min at 3500rpm t... |
28,704 | Th9 Polarization of Mouse CD4+ Cells | null | dx.doi.org/10.17504/protocols.io.798hr9w | null | Sam Li | TITLE: Th9 Polarization of Mouse CD4+ Cells
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Isolation of CD4+ Cells From Lymph Nodes]
Harvest lymph nodes (superficial cervical, mandibular, axillary, inguinal, and mesenteric) from mice.
?. [Isolation of CD4+ Cells From Lymph Nodes]
Tease ly... | ["[Isolation of CD4+ Cells From Lymph Nodes]\nHarvest lymph nodes (superficial cervical, mandibular, axillary, inguinal, and mesenteric) from mice.", "[Isolation of CD4+ Cells From Lymph Nodes]\nTease lymph nodes through a sterile 70-µm nylon cell strainer to obtain single-cell suspensions in complete IMDM containing 1... |
76,830 | Modified Frame-projected Independent Fiber Photometry (FIP) System_Hardware | 4 | null | https://www.protocols.click/view/modified-frame-projected-independent-fiber-photome-cn96vh9e | Kenta M. Hagihara | TITLE: Modified Frame-projected Independent Fiber Photometry (FIP) System_Hardware
AUTHORS: Kenta M. Hagihara
[DESCRIPTION]
This is a step-by-step protocol to build a modified FIP (Frame-projected Independent FP) system. FIP was first implemented and reported by Kim et al. (2016). Their protocol is available here.
... | ["Adding optical filters, collimators, and the objective lens", "[Assemblying optical parts] Assemblying the cubes\n\n(This step-by-step part will have corresponding CAD models later.)", "Assemblysing the fiber positioning module", "Assemblysing the CMOS modules", "Connecting excitation light sources with fibers", "[Sy... |
28,698 | Treg Polarization of Mouse CD4+ Cells | null | dx.doi.org/10.17504/protocols.io.792hr8e | null | Sam Li | TITLE: Treg Polarization of Mouse CD4+ Cells
AUTHORS: Sam Li
[STEPS]
?. [Isolation of CD4+ Cells From Lymph Nodes:]
Harvest lymph nodes (superficial cervical, mandibular, axillary, inguinal, and mesenteric) from mice.
?. [Isolation of CD4+ Cells From Lymph Nodes:]
Tease lymph nodes through a sterile 70-µm nylon cell s... | ["[Isolation of CD4+ Cells From Lymph Nodes:]\nHarvest lymph nodes (superficial cervical, mandibular, axillary, inguinal, and mesenteric) from mice.", "[Isolation of CD4+ Cells From Lymph Nodes:]\nTease lymph nodes through a sterile 70-µm nylon cell strainer to obtain single-cell suspensions in complete RPMI containing... |
55,728 | ATAC-STARR-seq | 1 | dx.doi.org/10.17504/protocols.io.b2nqqddw | https://www.protocols.io/view/atac-starr-seq-b2nqqddw | Tyler Hansen, Emily Hodges | TITLE: ATAC-STARR-seq
AUTHORS: Tyler Hansen, Emily Hodges
[DESCRIPTION]
Transcriptional enhancers control cell-type specific gene expression in humans and dysfunction can lead to debilitating diseases, including cancer. Identifying bona-fide enhancers is difficult due to a lack of spatial or sequence constraints. In ... | ["[Anneling Oligos] Dilute oligos to 100 µM in STE buffer.", "[Anneling Oligos] Make Adaptor Mixes in 200μL PCR tubes:\n\nMix (Adaptor A) [50µL]: \n 5µL Tn5MERV oligo (100µM)\n 5µL Tn5_1 Oligo (100µM)\n 40µL H2O\n\nMix (Adaptor B) [50µL]: \n 5µL Tn5MERV oligo (100µM)\n 5µL Tn5_2_ME_Comp Oligo (100µM)\n ... |
21,203 | Coding Manual for Criminal Justice Reform Policy Documents | null | dx.doi.org/10.17504/protocols.io.yxtfxnn | null | Drew Gitomer | TITLE: Coding Manual for Criminal Justice Reform Policy Documents
AUTHORS: Drew Gitomer
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is an adaptation - because we were interested adapting Yanovitzky and Weber's tool for criminal justice reform.</div><div class = "text-block">All of the poli... | [] |
51,444 | Functional Characterization of the Human Islet Microvasculature Using Living Pancreas Slices | 4 | dx.doi.org/10.17504/protocols.io.bwgupbww | https://www.protocols.io/view/functional-characterization-of-the-human-islet-mic-bwgupbww | Luciana Mateus Gonçalves, Joana Almaça | TITLE: Functional Characterization of the Human Islet Microvasculature Using Living Pancreas Slices
AUTHORS: Luciana Mateus Gonçalves, Joana Almaça
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Pancreatic islets are clusters of endocrine cells that secrete different hormones to regulate blood gluc... | ["[Methods]\nHuman Organ DonorsWe obtained human living pancreas slices from de-identified cadaveric donors (from the head of the pancreas, n = 6 non-diabetic individuals, male and female, ages from 20 – 59 years old; information on the donors used in this study is provided in Table S1) from the Network of Pancreatic O... |
75,841 | Protocol 1: Protein-ligand docking | 3 | dx.doi.org/10.17504/protocols.io.3byl4j362lo5/v1 | https://www.protocols.io/view/protocol-1-protein-ligand-docking-cna9vah6 | Phaniendra Alugoju, Vishwambhar Vishnu Bhandare, Vishal S Patil, Krishna Swamy V K D, Prem Kumar Borugadda, Tewin Tencomnao | TITLE: Protocol 1: Protein-ligand docking
AUTHORS: Phaniendra Alugoju, Vishwambhar Vishnu Bhandare, Vishal S Patil, Krishna Swamy V K D, Prem Kumar Borugadda, Tewin Tencomnao
[DESCRIPTION]
Autodock Vina version 1.1.2 (RRID:SCR_011958) for docking. The grid box's dimensions were fixed at XYZ=30Å × 30Å × 30Å which was f... | [] |
57,294 | CRISPR gRNAs cloning | 1 | dx.doi.org/10.17504/protocols.io.x54v9yj3pg3e/v1 | https://www.protocols.io/view/crispr-grnas-cloning-b37nqrme | Anita Adami | TITLE: CRISPR gRNAs cloning
AUTHORS: Anita Adami
[DESCRIPTION]
This protocol details the procedure of CRISPR gRNAs cloning.
[STEPS]
SECTION: gRNA oligonucleotides design
1. To design your gRNAs, use CRISPick portal
(https://portals.broadinstitute.org/gppx/crispick/public).
SECTION: gRNA oligonucleotides cloning
2.... | ["[gRNA oligonucleotides design] To design your gRNAs, use CRISPick portal\n\n (https://portals.broadinstitute.org/gppx/crispick/public).", "[gRNA oligonucleotides cloning] Preparation of the gRNA oligonucleotides.", "[gRNA oligonucleotides cloning] Spin oligonucleotide tubes briefly.", "[gRNA oligonucleotides cloning]... |
64,726 | HyDrop Bead Generation & PCR Barcoding v1.0 | 1 | null | https://www.protocols.io/view/hydrop-bead-generation-amp-pcr-barcoding-v1-0-cbfwsjpe | Florian De Rop, Suresh Poovathingal, Stein Aerts | TITLE: HyDrop Bead Generation & PCR Barcoding v1.0
AUTHORS: Florian De Rop, Suresh Poovathingal, Stein Aerts
[DESCRIPTION]
Protocol for producing dissolvable barcoded hydrogel beads used in HyDrop experiments.
[STEPS]
SECTION: Hydrogel bead generation
1.
Hydrogel bead generation
Here, we will create an emulsi... | ["[Hydrogel bead generation] Hydrogel bead generation\nHere, we will create an emulsion of acrylamide monomers in a carrier oil containing TEMED. The monomer droplets will polymerise and form hydrogel beads. Ideally, you have a bead stock of around 3 mL of beads before you barcode, but 2 mL can work as well. It is best... |
81,494 | SARS-CoV-2 Spike Gene N terminal Domain targeted Sequencing | 4 | dx.doi.org/10.17504/protocols.io.x54v9d63zg3e/v1 | https://www.protocols.io/view/sars-cov-2-spike-gene-n-terminal-domain-targeted-s-cttwwnpe | Noor Saber Jawad, Nuha Joseph Kandala [Department of Biotechnology | TITLE: SARS-CoV-2 Spike Gene N terminal Domain targeted Sequencing
AUTHORS: Noor Saber Jawad, Nuha Joseph Kandala [Department of Biotechnology
[DESCRIPTION]
We use a simple and effective method for generating 757bp of the N terminal domain of thetheSARS-CoV-2 Spike gene for variant surveillance,
[STEPS]
SECTIO... | ["[RNA Extraction] The Automated extraction was handled using the ExiPrep™ 96 Lite (A-5250, BIONEER) with the ExiPrep™ Viral DNA/RNA extraction kit (K-4614, BIONEER).", "[RT-PCR Amplification] TaqPath™ COVID‑19 CE‑IVD RT‑PCR Kit (Multiplex real-time RT-PCR test intended for qualitatively detecting nucleic acid from SAR... |
59,435 | Important note on the medium type and plating procedure | 3 | dx.doi.org/10.17504/protocols.io.n92ldz8z7v5b/v1 | https://www.protocols.io/view/important-note-on-the-medium-type-and-plating-proc-b6ajracn | Carolyn N Bayer, Ana Gabriela Veiga Sepulchro, Maja Rennig, Morten Norholm | TITLE: Important note on the medium type and plating procedure
AUTHORS: Carolyn N Bayer, Ana Gabriela Veiga Sepulchro, Maja Rennig, Morten Norholm
[DESCRIPTION]
Important Information for the two tetA dual selection protocols "Gene knockout strategy" and "Tuning the expression of native genes".
[STEPS] | [] |
43,850 | Growth Conditions for SMC Proteins | 4 | dx.doi.org/10.17504/protocols.io.bn3imgke | https://www.protocols.io/view/growth-conditions-for-smc-proteins-bn3imgke | Adele L. Marston, Daniel Robertson, Vasso Makrantoni | TITLE: Growth Conditions for SMC Proteins
AUTHORS: Adele L. Marston, Daniel Robertson, Vasso Makrantoni
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A plethora of biological processes like gene transcription, DNA replication, DNA recombination, and chromosome segregation are mediated through prot... | ["[Growth Conditions for SMC Proteins]\nFor depletion of Cdc20, use a construct where CDC20 is under control of the methionine-repressible promoter, pMET3 (pMET3-CDC20).\nS. cerevisiae strains for mitotic studies are grown in YPDA at . The most consistent results, at least for cohesin, are obtained when cells are arre... |
30,998 | Clinical significance of EGFR mutation subtypes in lung adenocarcinoma : A multi-center Korean study | null | dx.doi.org/10.17504/protocols.io.bahwib7e | null | Hee-Young Yoon, Jeong-Seon Ryu, Yun Su Sim, Dojin Kim, Sung Yong Lee, Juwhan Choi, Sojung Park, Yon Ju Ryu, Jin Hwa Lee, Jung Hyun Chang | TITLE: Clinical significance of EGFR mutation subtypes in lung adenocarcinoma : A multi-center Korean study
AUTHORS: Hee-Young Yoon, Jeong-Seon Ryu, Yun Su Sim, Dojin Kim, Sung Yong Lee, Juwhan Choi, Sojung Park, Yon Ju Ryu, Jin Hwa Lee, Jung Hyun Chang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block... | ["Patient enrolment 1,020 patients were included in our study", "Study designDemographics and clinical information of subjects at time of diagnosis were obtained through medical records. The following variables were collected: age, sex, low body mass index (BMI", "Tissue preparation and DNA extractionWhen tissue is obt... |
null | null | null | dx.doi.org/10.17504/protocols.io.sdqea5w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Network science is a cross-disciplinary domain that focuses on the representation, analysis and modeling of complex systems as networks or graphs. In computational biology, Cytoscape is a very popular open source software platform for network modeling and visualization. As an... | ["[Install R subnetsim package version 0.2.1] {\"blocks\":[{\"key\":\"3lt36\",\"text\":\" \",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]},{\"key\":\"864r6\",\"text\":\"The analysis must be done in a R. It can be done through a console using command lines or through an inte... |
85,927 | Multiple Myeloma Banking Collection and Processing Protocol (WUSTL) | 1 | dx.doi.org/10.17504/protocols.io.14egn3276l5d/v1 | https://www.protocols.io/view/multiple-myeloma-banking-collection-and-processing-cx6fxrbn | Reyka Jayasinghe | TITLE: Multiple Myeloma Banking Collection and Processing Protocol (WUSTL)
AUTHORS: Reyka Jayasinghe
[DESCRIPTION]
MM banking Collection and Processing Protocol
[STEPS]
SECTION: Supplies
1.
70% EtOH.
PBS 1x (without Ca or Mg) [Fisher MT21-040CM]
0.5M EDTA ph 8.0 [Fisher NC9942732]
Bovine Serum Albumin (BSA)... | ["[Supplies] \t70% EtOH.\n\tPBS 1x (without Ca or Mg) [Fisher MT21-040CM]\n\t0.5M EDTA ph 8.0 [Fisher NC9942732]\n\tBovine Serum Albumin (BSA) [Sigma A2153]\n\tFetal Bovine Serum (FBS) [Fisher SH3007103]\n\tDimethyl Sulfoxide (DMSO) [Sigma D4540-100ml]\n\tAcridine Orange/Propidium Iodide (AO/PI) [Fisher NC02852... |
48,403 | Calculating number of Co-Migrated DNA Fragments across Pulsed Field gel electrophoresis (PFGE) profiles: Image analysis algorithm | 5 | dx.doi.org/10.17504/protocols.io.bthtnj6n | https://www.protocols.io/view/calculating-number-of-co-migrated-dna-fragments-ac-bthtnj6n | Ibrahim El-khalil Adam | TITLE: Calculating number of Co-Migrated DNA Fragments across Pulsed Field gel electrophoresis (PFGE) profiles: Image analysis algorithm
AUTHORS: Ibrahim El-khalil Adam
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The author describes a new image analysis algorithm that enables identification of ... | ["[IMAGE PROCESSING]\nLaunch the program", "[IMAGE PROCESSING]\nOpen PFGE image of interest. You should navigate to containing folder first.", "[IMAGE PROCESSING]\nIt is critical to tell the program if DNA bands are white in a black background or otherwise.", "[IMAGE PROCESSING]\nDefine lanes and then bands.sometimes, ... |
43,723 | Processing of Circular Dichroism Data Collected at B23 | 1 | dx.doi.org/10.17504/protocols.io.bnxjmfkn | https://www.protocols.io/view/processing-of-circular-dichroism-data-collected-at-bnxjmfkn | Rohanah Hussain, Charlotte S. Hughes, Giuliano Siligardi | TITLE: Processing of Circular Dichroism Data Collected at B23
AUTHORS: Rohanah Hussain, Charlotte S. Hughes, Giuliano Siligardi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">CD spectroscopy is the essential tool to quickly ascertain in the far-UV region the global conformational changes, the sec... | ["[Loading CDApps for Processing of Circular Dichroism Data Collected at B23]\nBelow are the initial steps required to load CDApps software:Open the CDApps software by:(a) On-site—Computer > Software (W:) > cd_programs > CD Apps > CD Apps.exe. Double click the CD Apps icon.(b) Off-site—double-clicking the CD Apps icon.... |
86,205 | Mitochondrial isolation from HeLa cells | 1 | dx.doi.org/10.17504/protocols.io.8epv5xjo4g1b/v1 | https://www.protocols.io/view/mitochondrial-isolation-from-hela-cells-cye5xtg6 | Louise Uoselis | TITLE: Mitochondrial isolation from HeLa cells
AUTHORS: Louise Uoselis
[DESCRIPTION]
Mitochondrial isolation and quantification from HeLa cells.
[STEPS]
SECTION: Mitochondrial isolation
1. Thaw cell pellets that have been frozen at -80 °C for at least 15 min, on ice.
SECTION: Mitochondrial isolation
2. Aliquot ... | ["[Mitochondrial isolation] Thaw cell pellets that have been frozen at -80 °C for at least 15 min, on ice.", "[Mitochondrial isolation] Aliquot out an amount of Solution B (220 millimolar (mM) mannitol, 70 millimolar (mM) sucrose, 1 millimolar (mM) EDTA, 20 millimolar (mM) HEPES-KOH pH 7.6) assuming for5 mL of Solution... |
19,444 | Immunofluorescence Assay to detect respiratory syncytial virus | null | dx.doi.org/10.17504/protocols.io.w8ufhww | null | Maria Lucia Silva, Talita Gagliardi, Eurico Arruda | TITLE: Immunofluorescence Assay to detect respiratory syncytial virus
AUTHORS: Maria Lucia Silva, Talita Gagliardi, Eurico Arruda
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">IF Protocol used to detect RSV in nasopharyngeal samples.</div></div>
[STEPS]
?. Fix the cells immerge them into a pure c... | ["Fix the cells immerge them into a pure cold acetone for 5min.", "Wash 3X the sample in PBS for 3min each and at room temperature (r.t.).", "Permeabilize the cells incubate with 0.1% Triton-X100 for 15min at r.t.", "Wash 3X the sample in PBS for 3min each and at r.t.", "Incubate the cells with 1:100 dilution of “anti-... |
68,099 | Peña Lab Onboarding | 1 | null | https://www.protocols.io/view/pe-a-lab-onboarding-cerbtd2n | Cate J Peña | TITLE: Peña Lab Onboarding
AUTHORS: Cate J Peña
[DESCRIPTION]
Onboarding for the Peña Lab includes a number of on-line and in-person trainings related to lab safety and animal care and use. It takes many hours to complete the online trainings, and several days for all of the in-person components. Please plan ahead, a... | ["[Welcome!] Updated 2022\n\nPeña Lab Onboarding at Princeton\n\nCourses for mouse handling, lab safety, and biosafety", "[Working with Animals] Complete the required AALAS Learning Library (ALL) training.\n\nMost steps to working with animals are outlined here: https://lar.princeton.edu/new-researcher\nThe information... |
64,845 | Attention! Simpli Health ACV Keto Gummies Reviews: Is SimpliHealth ACV Keto Works- Cost, Side Effects, Ingredients, Benefits, Where To Buy? | 3 | dx.doi.org/10.17504/protocols.io.ewov1n17pgr2/v1 | https://www.protocols.io/view/attention-simpli-health-acv-keto-gummies-reviews-i-cbjmskk6 | johnkikal | TITLE: Attention! Simpli Health ACV Keto Gummies Reviews: Is SimpliHealth ACV Keto Works- Cost, Side Effects, Ingredients, Benefits, Where To Buy?
AUTHORS: johnkikal
[DESCRIPTION]
Attention! Simpli Health ACV Keto Gummies Reviews: Is SimpliHealth ACV Keto Works- Cost, Side Effects, Ingredients, Benefits, Where To Bu... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.hpzb5p6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>A method to load algal cells with dextran-conjugated fluorescent dyes. This is a good way of testing and optimising conditions for biolistic DNA delivery.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
81,377 | FFPE RNA Quality Evaluation (Qiagen) -- University of Minnesota TMCs | 1 | dx.doi.org/10.17504/protocols.io.8epv5j4x5l1b/v1 | https://www.protocols.io/view/ffpe-rna-quality-evaluation-qiagen-university-of-m-ctp9wmr6 | Qiagen, Laura J Niedernhofer, David A Bernlohr | TITLE: FFPE RNA Quality Evaluation (Qiagen) -- University of Minnesota TMCs
AUTHORS: Qiagen, Laura J Niedernhofer, David A Bernlohr
[DESCRIPTION]
Completed prior to going through -omics and spatial technologies to evaluate FFPE blocks for their RNA quality.
[BEFORE_START]
Evaluate if this is required for processing ... | ["[Preparation of Samples for Processing] Create or request curls from the FFPE blocks (typically done by histologist). \nFollow recommendations as noted below. \nKeep curls in a 1.5mL tube at -80ºC until RNA isolation process.", "Qiagen Protocol: \n \n\nQiagen product website: https://www.qiagen.com/us/products/disc... |
null | null | null | dx.doi.org/10.17504/protocols.io.c56y9d | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is a storage solution that stabilizes and protectsRNA while inactivating RNase
[GUIDELINES]
<strong>Note:</strong> If you read the patent application, they refer to an ammonium sulfate concentration of 700g per L. What they really mean is add 700g to 1L (including EDTA and... | [] |
21,690 | Removal of genomic DNA from RNA preparations (Thermo Scientific )- (M4455 Version) | null | dx.doi.org/10.17504/protocols.io.ze2f3ge | null | Maximilian Dietsch | TITLE: Removal of genomic DNA from RNA preparations (Thermo Scientific )- (M4455 Version)
AUTHORS: Maximilian Dietsch
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Removal of genomic DNA from RNA preparations</div></div>
[STEPS]
?. AB1Add to an RNase free tube: 2RNA1 µg310X reaction buf... | ["AB1Add to an RNase free tube: 2RNA1 µg310X reaction buffer with MgCl21 µl4DNase I, RNase-free1 µl (1U)5Waterto 10 µl\nAB1Add to an RNase free tube: 2RNA1 µg310X reaction buffer with MgCl21 µl4DNase I, RNase-free1 µl (1U)5Waterto 10 µl", "Incubate at 37 °C for 30 min", "Add EDTA... |
96,990 | FUNDIS Setting up PCR for rDNA ITS Barcoding of Fungi using ONT Nanopore | 0 | null | https://www.protocols.io/view/fundis-setting-up-pcr-for-rdna-its-barcoding-of-fu-dax62fre | Harte Singer | TITLE: FUNDIS Setting up PCR for rDNA ITS Barcoding of Fungi using ONT Nanopore
AUTHORS: Harte Singer
[DESCRIPTION]
This protocol involves using pre-made dual-indexed master mix 96 well plates to run PCR on fungal specimens that have already had their DNA extracted, diluted and in PCR 8 strip tubes. Quality check incl... | ["[Setting up PCR] Remove DNA extracts from the freezer and allow to thaw before beginning. Note the plate number in your notebook (i.e. FDS-CA TB05) Take a photo of the plate showing the labeling.", "[Setting up PCR] Once thawed, spin DNA extracts down for 2 s in a benchtop PCR tube centrifuge.", "[Setting up PCR] Rem... |
106,884 | Environmental DNA (eDNA) indexing PCR protocol at MSU | 1 | dx.doi.org/10.17504/protocols.io.yxmvme1z5g3p/v1 | https://www.protocols.io/view/environmental-dna-edna-indexing-pcr-protocol-at-ms-dkmc4u2w | Jacoby Baker, Kathleen Pitz | TITLE: Environmental DNA (eDNA) indexing PCR protocol at MSU
AUTHORS: Jacoby Baker, Kathleen Pitz
[DESCRIPTION]
This sequencing protocol is intended to directly follow and use the PCR products of a primary PCR amplification protocol (e.g., 12S rRNA, 18S rRNA V9, cytochrome c oxidase subunit I (COI) mitochondrial gene... | ["[MIOP: Minimum Information about an Omics Protocol] MIOP Term\nValue\n \nmethodology category\n\n \nproject\n\n \npurpose\n\n \nanalyses\n\n \ngeographic location\n\n \nbroad-scale environmental context\n\n \nlocal environmental context\n\n \nenvironmental medium\n\n \ntarget\n\n \ncreator\n\n \nmaterials required\... |
63,324 | Condor CBD Gummies Are 100% Real & Effective and Available In A Variety Of Flavors. | 3 | dx.doi.org/10.17504/protocols.io.bp2l61mjrvqe/v1 | https://www.protocols.io/view/condor-cbd-gummies-are-100-real-amp-effective-and-b934r8qw | Condor CBD Gummies Review | TITLE: Condor CBD Gummies Are 100% Real & Effective and Available In A Variety Of Flavors.
AUTHORS: Condor CBD Gummies Review
[DESCRIPTION]
Condor CBD Gummies: Provide rapid relief from health issues and enhance mental clarity. Effectively cures joint. It relaxes your nerve cells, which gives you the ... | [] |
48,902 | Yeast two-hybrid interaction assay | 3 | dx.doi.org/10.17504/protocols.io.btzenp3e | https://www.protocols.io/view/yeast-two-hybrid-interaction-assay-btzenp3e | Mélanie Bonhivers, Anne-Lise Sahin, Nicolas LANDREIN | TITLE: Yeast two-hybrid interaction assay
AUTHORS: Mélanie Bonhivers, Anne-Lise Sahin, Nicolas LANDREIN
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protein-protein interaction can be tested using yeast two-hybrid assays. The bait protein is fused to the Gal4 DNA-binding domain (BD) and the prey ... | [] |
47,243 | Creolimax fragrantissima_culture method | 1 | null | https://www.protocols.io/view/creolimax-fragrantissima-culture-method-bsdjna4n | Meritxell Antó | TITLE: Creolimax fragrantissima_culture method
AUTHORS: Meritxell Antó
[STEPS]
?. [Growing medium]
BD Difco Marine Broth 2216 • Marine Agar 2216 https://legacy.bd.com/europe/regulatory/Assets/IFU/Difco_BBL/212185.pdf
?. [Growth conditions]
Temperature 12ºC
?. [Cryopreservation and recovery (from liquid cultures)]
Cry... | ["[Growing medium]\nBD Difco Marine Broth 2216 • Marine Agar 2216 https://legacy.bd.com/europe/regulatory/Assets/IFU/Difco_BBL/212185.pdf", "[Growth conditions]\nTemperature 12ºC", "[Cryopreservation and recovery (from liquid cultures)]\nCryopreservation (10%DMSO in Growing medium)1. Pre-grow the culture in appropriat... |
22,858 | Polyclonal Allelic Expression Assay Protocol | null | dx.doi.org/10.17504/protocols.io.2jigcke | null | Margot K Brandt, Alper Gokden, Marcello Ziosi, Tuuli Lappalainen | TITLE: Polyclonal Allelic Expression Assay Protocol
AUTHORS: Margot K Brandt, Alper Gokden, Marcello Ziosi, Tuuli Lappalainen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Polyclonal allelic expression assay for detecting the regulatory effects of genetic variants within transcripts using CRISPR/C... | ["Resuspend 500 ng of IDT gBlock gene fragment in 100 uL to make ~100 uM solution.", "Resuspend 5 nmol of ssDNA IDT ultramer oligos in 50 uL to make 100 uM solution.", "Perform gBlock PCR in order to amplify sufficient gblock for transfection (2X50ul reactions per gblock):5 uL gBlock F primer (10 uM)5 uL gBlock R prime... |
109,285 | HPF-FS of Solarion arianae for transmission electron microscopy | 0 | dx.doi.org/10.17504/protocols.io.dm6gpzp15lzp/v1 | https://www.protocols.io/view/hpf-fs-of-solarion-arianae-for-transmission-electr-dnyd5fs6 | Marek Valt | TITLE: HPF-FS of Solarion arianae for transmission electron microscopy
AUTHORS: Marek Valt
[DESCRIPTION]
This is an optimized version of the protocol for standard High Pressure Freezing followed by Freeze Substitution (HPF-FS) for transmission electron microscopy that was used for the fixation of the culture of Solari... | ["[Cell harvest] Centrifuge a well-grown culture at 1500 g at 4 °C.", "[Cryo-immobilization by high-pressure freezing] After high-pressure freezing, the samples were transferred to precooled (-90 °C) fixative medium (2% OsO4 in 100% acetone) and processed by automatic freeze substitution (Leica EM AFS), as follows:", "... |
66,724 | Acompanhamento da coleta actigráfica | 1 | dx.doi.org/10.17504/protocols.io.bp2l61651vqe/v1 | https://www.protocols.io/view/acompanhamento-da-coleta-actigr-fica-cdecs3aw | Alicia Rafaelly Vilefort Sales, Daniel Vartanian, Maria Augusta Medeiros Andrade | TITLE: Acompanhamento da coleta actigráfica
AUTHORS: Alicia Rafaelly Vilefort Sales, Daniel Vartanian, Maria Augusta Medeiros Andrade
[DESCRIPTION]
Este protocolo foi desenhado para o processo de coleta de dados do projeto de pesquisa Sono e Gravidez. Consulte a aba Guidelines para visualizar o fluxograma do processo ... | ["[Coleta de dados secundários] Confirmada que a gestação se encerrou, vá para o protocolo \"Coleta de dados secundários e procedimentos pós-parto\", disponível em: <https://www.protocols.io/private/FA39D1A34B8311EF80360A58A9FEAC02>.", "[Acompanhamento] Instrua a gestante quanto ao início do trabalho de parto.", "[Prep... |
90,258 | An overview of growth factors as the potential link between psoriasis and metabolic syndrome. | 1 | dx.doi.org/10.17504/protocols.io.6qpvr3rwzvmk/v1 | https://www.protocols.io/view/an-overview-of-growth-factors-as-the-potential-lin-c4dsys6e | Mateusz Matwiejuk, Hanna Myśliwiec, Adrian Chabowski, Iwona Flisiak | TITLE: An overview of growth factors as the potential link between psoriasis and metabolic syndrome.
AUTHORS: Mateusz Matwiejuk, Hanna Myśliwiec, Adrian Chabowski, Iwona Flisiak
[DESCRIPTION]
Psoriasis
is a chronic, complex, immunologically mediated, systematic disease that can
not only affect the skin but also the... | ["Records\nidentified", "Identification of records. Databases (n = 1) Pubmed", "Screening of records\n\nRecords screened (n = 1579)", "Records excluded (n = 1372 )\nNo data available\nAbstracts", "Reports assesed for eligibility (n = 207 )", "Reports excluded \n\nReason 1 (n = 38 ) Duplications\n\nReason 2 (n = 77 ) Ou... |
null | null | null | dx.doi.org/10.17504/protocols.io.gmubu6w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><u>Marchantia protoplast preparation (adapted from </u><u>Bopp and Vicktor 1988)</u></p>
[BEFORE_START]
<p>Perform surface sterilization of Marchantia spores (see Step 1-7 in protocol “Agrobacterium mediated transformation of Marchantia spores” by Dr. Susana Sauret-Gueto). L... | [] |
84,153 | Plasmid Construction and Gibson cloning | 4 | dx.doi.org/10.17504/protocols.io.8epv5x11ng1b/v1 | https://www.protocols.io/view/plasmid-construction-and-gibson-cloning-cwezxbf6 | Elias Adriaenssens | TITLE: Plasmid Construction and Gibson cloning
AUTHORS: Elias Adriaenssens
[DESCRIPTION]
This protocol describes plasmid construction.
[STEPS]
SECTION: Plasmid Construction
1. Obtain the sequences of all cDNAs by amplifying existing plasmids, HAP1 cDNA, or through gene synthesis (Genscript).
SECTION: Plasmid Construc... | ["[Plasmid Construction] Obtain the sequences of all cDNAs by amplifying existing plasmids, HAP1 cDNA, or through gene synthesis (Genscript).", "[Plasmid Construction] For insect cell expressions, the sequences are codon optimized and the gene is synthesized (Genscript).", "[Plasmid Construction] With the exception of ... |
29,687 | Batrachochytrium dendrobatidis electroporation | 1 | dx.doi.org/10.17504/protocols.io.88xhzxn | https://www.protocols.io/view/batrachochytrium-dendrobatidis-electroporation-88xhzxn | Andrew J. M. Swafford, Shane P. Hussey, Lillian K. Fritz-Laylin | TITLE: Batrachochytrium dendrobatidis electroporation
AUTHORS: Andrew J. M. Swafford, Shane P. Hussey, Lillian K. Fritz-Laylin
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Batrachochytrium dendrobatidis (BD) is a parasitic symbiote with many frogs. BD infection is devastating to most frog species... | ["[Media & Material Prep]\nMake 50 mL SM buffer (SM buffer should not be more than 7 days old).", "[Media & Material Prep]\nSM Buffer:\n5 mL\n[ KCL (Autoclaved)]\n750 µl\n[Sodium Phosphate Buffer (Filter Sterilized)]\n7.5 mL\n[MgCL2 (filter sterilized)]\n[Sodium Succinate dibasic acid hexahydrate]\n[D-Mannitol]\n[Steri... |
76,435 | HiFi-Slide spatial RNA-Sequencing | 4 | dx.doi.org/10.17504/protocols.io.3byl4by18vo5/v2 | https://www.protocols.io/view/hifi-slide-spatial-rna-sequencing-cnvtve6n | Tianyang Xu, Pei Lin, czhang, Diming Zhu, Riccardo Calandrelli, Sheng Zhong | TITLE: HiFi-Slide spatial RNA-Sequencing
AUTHORS: Tianyang Xu, Pei Lin, czhang, Diming Zhu, Riccardo Calandrelli, Sheng Zhong
[DESCRIPTION]
HiFi-Slide sequencing is a super-resolution spatial transcriptomics sequencing technology. This technique captures and spatially resolves genome-wide RNA expression in a submicro... | ["[Slide Preparation] Flow Cell Generation and Collection\n\nA recycled Illumina flow cell was used to provide spatial coordinates for RNA molecules. \nFor MiniSeq flow cells, a pre-run modification is necessary to replace the NaOCl solution with the Tween-20 solution in the reagent cartridge. We replaced the NaOCl sol... |
null | null | null | dx.doi.org/10.17504/protocols.io.mgdc3s6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Fluorescent activated cell sorting (FACS) is a specialized type of flow cytometry used for sorting and analyzing a heterogeneous mixture of cells into different subpopulations based on the specific light scattering and fluorescent characteristics (from the specific labels) of... | [] |
91,672 | Nephele DADA2 Workflow | 5 | dx.doi.org/10.17504/protocols.io.bp2l6xybzlqe/v1 | https://www.protocols.io/view/nephele-dada2-workflow-c5ryy57w | Nandie Elhadidy | TITLE: Nephele DADA2 Workflow
AUTHORS: Nandie Elhadidy
[DESCRIPTION]
A protocol outlining the workflow of utilizing DADA2 on Nephele with a provided practice dataset. DADA2 is a pipeline that provides species assignments using Amplicon Sequence Variants or ASVs which compare variants to a predetermined sequence throu... | ["[Downloading the Dataset] To download the practice dataset provided by Nephele, visit: https://nephele.niaid.nih.gov/user_guide_data/", "[Running DADA2] Click the Home tab.", "Download the first set of sequences listed as well as the mapping file.", "[Running DADA2] Choose the Analyze option.", "[Analysis of the Outp... |
61,963 | Labelled Amino Acids | 6 | dx.doi.org/10.17504/protocols.io.n2bvj6pqwlk5/v1 | https://www.protocols.io/view/labelled-amino-acids-b8rjrv4n | BOC Sciences | TITLE: Labelled Amino Acids
AUTHORS: BOC Sciences
[DESCRIPTION]
Isotope-labeled amino acids refer to the replacement of single or multiple atoms of the amino acid with isotopes, which can be radioactive isotopes or stable isotopes. Basically, isotope-labeled amino acids have identical structures and properties as... | [] |
98,523 | Thymectomy procedure to remove native thymus of NSG mice | 4 | dx.doi.org/10.17504/protocols.io.j8nlk4ybdg5r/v2 | https://www.protocols.io/view/thymectomy-procedure-to-remove-native-thymus-of-ns-dcf32tqn | Mohsen Khosravi-Maharlooei, Markus Holzl, Austin Chen, Megan Sykes | TITLE: Thymectomy procedure to remove native thymus of NSG mice
AUTHORS: Mohsen Khosravi-Maharlooei, Markus Holzl, Austin Chen, Megan Sykes
[DESCRIPTION]
This protocol details our approach to removing the native thymus from an NSG mouse. The NSG mouse thymus is atrophied, but through experiments in our lab, we have fo... | ["The anterior neck is shaved and disinfected with betadine and 70% alcohol consisting of three alternate swabs followed by a final application of betadine solution. Limbs are gently restrained using rubber bands.", "Using a pair of forceps, the skin at the junction of the neck and chest is grasped and a vertical midli... |
69,928 | Standard Operating Procedures | 2 | dx.doi.org/10.17504/protocols.io.5jyl8jne8g2w/v1 | https://www.protocols.click/view/standard-operating-procedures-cgigtubw | g.spencer | TITLE: Standard Operating Procedures
AUTHORS: g.spencer
[DESCRIPTION]
List of all SOPs for MSc CEP
[STEPS] | [] |
100,313 | Metabarcoding Fecal Swabs or Stomach Contents for Fish and Crustaceans using 2-PCR protocol and Illumina MiSeq | 4 | dx.doi.org/10.17504/protocols.io.ewov1qxokgr2/v2 | https://www.protocols.io/view/metabarcoding-fecal-swabs-or-stomach-contents-for-dd7z29p6 | Eldridge Wisely | TITLE: Metabarcoding Fecal Swabs or Stomach Contents for Fish and Crustaceans using 2-PCR protocol and Illumina MiSeq
AUTHORS: Eldridge Wisely
[DESCRIPTION]
This protocol describes a method to metabarcode a 170bp region of the mitochondrial16S rRNA gene of crustaceans and a 163-185bp region of the mitochondrial 12S rR... | ["[Prepare Primers] Order metabarcoding primers with diversity spacers and Illumina overhang sequences (Illumina, 2013): (Miya et al., 2015): \nTCGTCGGCAGCGTCAGATGTGTATAAGAGACAGNNNNGTCGGTAAAACTCGTGCCAGC\n \n (Miya et al., 2015): GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGNNNNCATAGTGGGGTATCTAATCCCAGTTTG\n\n Berry et al., 201... |
94,975 | Agrobacterium-mediated transformation of the chytrid fungus Spizellomyces punctatus (Sp) | 2 | dx.doi.org/10.17504/protocols.io.x54v9dd1pg3e/v2 | https://www.protocols.io/view/agrobacterium-mediated-transformation-of-the-chytr-c8y7zxzn | Sarah M Prostak, Edgar M Medina, Erik Kalinka, Lillian Fritz-Laylin | TITLE: Agrobacterium-mediated transformation of the chytrid fungus Spizellomyces punctatus (Sp)
AUTHORS: Sarah M Prostak, Edgar M Medina, Erik Kalinka, Lillian Fritz-Laylin
[DESCRIPTION]
This is a collection of protocols for Agrobacterium-mediated transformation of the chytrid fungus
Spizellomyces punctatus.
[GUIDELI... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.gc9bsz6 | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
<p>Be sure to mix and autoclave <strong>solution I</strong> and <strong>solution II</strong> separately before combining and adding trace metal solutions and vitamin solutions. Store media in 4ºC. Note, Vitamin stock solutions amounts are per mL Trace Metal stock solution amoun... | [] |
40,487 | Universal sandwich ELISA for investigating the binding of avian and mammalian immunoglobulins to Streptococcal protein-G (SpG) using a peroxidase-labeled Protein LAG conjugate (SpLAG-HRP). | 6 | dx.doi.org/10.17504/protocols.io.bjsfknbn | https://www.protocols.io/view/universal-sandwich-elisa-for-investigating-the-bin-bjsfknbn | Angel Justiz-Vaillant | TITLE: Universal sandwich ELISA for investigating the binding of avian and mammalian immunoglobulins to Streptococcal protein-G (SpG) using a peroxidase-labeled Protein LAG conjugate (SpLAG-HRP).
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. This ELISA is used to study th... | ["This ELISA is used to study the interaction of streptococcal protein-G (SpG) with different avian and mammalian immunoglobulins.", "The 96 well microtitre plate is coated overnight at 4°C with 2 µg/µl per well of SpG in carbonate-bicarbonate buffer pH 9.6.", "Then plate is treated with bovine serum albumin solution a... |
null | null | null | dx.doi.org/10.17504/protocols.io.k5vcy66 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Congenital Zika Syndrome (CZS) is associated with microcephaly and other malformations of the central nervous system. We identified that some of areas damaged by CZS are also known to influence the neural circuitry controlling the lower urinary tract (1). And decided to inves... | [] |
41,769 | FLASH amp | 4 | dx.doi.org/10.17504/protocols.io.bk2hkyb6 | https://www.protocols.io/view/flash-amp-bk2hkyb6 | eesha.sharma.phd | TITLE: FLASH amp
AUTHORS: eesha.sharma.phd
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">FLASH amp is a method that allows for room temperature detection and amplification of a viral RNA sequence of interest submitted as part of the Xprize competition. The main components of the reaction are not ... | ["[Set-up]\nResuspend freeze dried master mix 1 with of water\n7.04 µl", "[Set-up]\nAdd\n0.3 µl", "[Set-up]\nAdd Undisclosed enzyme Z\n0.5 µl", "[Set-up]\nAdd Undisclosed Enzyme Y\n0.5 µl", "[Set-up]\nAdd Undisclosed Enzyme X\n0.13 µl", "[Set-up]\nResuspend freeze dried master mix 2 in water and add to above\n1 µl",... |
63,888 | Attention! Ocuprime Reviews :Does Ocuprime Vision Support Scam or Legit!! | 3 | dx.doi.org/10.17504/protocols.io.5qpvob2exl4o/v1 | https://www.protocols.io/view/attention-ocuprime-reviews-does-ocuprime-vision-su-camqsc5w | burakjoker | TITLE: Attention! Ocuprime Reviews :Does Ocuprime Vision Support Scam or Legit!!
AUTHORS: burakjoker
[DESCRIPTION]
If you want to buy Ocuprime and enjoy all its benefits, all you have to do is visit the official sales page of the supplement. There you will be able to order what you want and get the discount that is... | [] |
42,051 | Fallopian Tube Single Cell Dissociation Protocol | 1 | dx.doi.org/10.17504/protocols.io.bmbbk2in | https://www.protocols.io/view/fallopian-tube-single-cell-dissociation-protocol-bmbbk2in | Nicole Ulrich, Yu-Chi Shen, Sue Hammoud | TITLE: Fallopian Tube Single Cell Dissociation Protocol
AUTHORS: Nicole Ulrich, Yu-Chi Shen, Sue Hammoud
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the single cell dissociation of cells from fallopian tubes.</div><div class = "text-block"><span>The single cell dissociati... | ["[Fallopian tube single cell dissociation]\nEach anatomic segment arrives in a separate tube in HBSS, at .\n0 Room temperature", "[Fallopian tube single cell dissociation]\nWeigh and bivalve each fallopian tube segment, but do not “mince” (- per tube).\n100 mg\n[tissue]", "[Fallopian tube single cell dissociation]\nPl... |
12,899 | Cell dissociation from nasal and bronchial brushings with cold-active protease for single-cell RNA-seq | null | dx.doi.org/10.17504/protocols.io.qubdwsn | null | Laure-Emmanuelle Zaragosi, Pascal Barbry | TITLE: Cell dissociation from nasal and bronchial brushings with cold-active protease for single-cell RNA-seq
AUTHORS: Laure-Emmanuelle Zaragosi, Pascal Barbry
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol provides details on the cell dissociation that should be performed to obtain s... | ["Perform nasal brush biopsy in the nasal cavity in the inferior nasal conca zone (UBERON_0005922) (to be performed by a medical doctor)", "Cut the cytology brush and place it in a 5 mL eppendorf tube containing 1 mL of ice-cold dissociation buffer.\n1 ml\nPREPARATION OF DISSOCIATION MIX (Fresh at each experiment)Ingre... |
51,045 | DNA extraction protocol for animal blood samples using the E.Z.N.A blood mini kit | 4 | dx.doi.org/10.17504/protocols.io.ewov141xpvr2/v1 | https://www.protocols.io/view/dna-extraction-protocol-for-animal-blood-samples-u-bv4dn8s6 | Louis-Stéphane Le Clercq, Desiré Lee Dalton, Antoinette Kotzé, Paul Grobler | TITLE: DNA extraction protocol for animal blood samples using the E.Z.N.A blood mini kit
AUTHORS: Louis-Stéphane Le Clercq, Desiré Lee Dalton, Antoinette Kotzé, Paul Grobler
[DESCRIPTION]
The E.Z.N.A. Blood DNA Mini Kit provides an easy and rapid method for the isolation of genomic DNA for consistent PCR and Southern ... | ["[Lyse] Transfer the into a sterile microcentrifuge tube and bring the volume up to 250 µL with 10mMTris-HCl, PBS, or Elution Buffer (provided).", "[Adjust binding conditions] Add 260 µL . Vortex at maximum speed for 20 s seconds.", "[Bind] Insert a HiBind DNA Mini Column (provided) into a 2 mL Collection Tube."... |
25,445 | Quantification of 16S rRNA Gene Copies Using ddPCR (probe-based assay: 338F-516P-805R) | 1 | dx.doi.org/10.17504/protocols.io.ewov1y6novr2/v1 | https://www.protocols.io/view/quantification-of-16s-rrna-gene-copies-using-ddpcr-44dgys6 | Eva Petrova, Roey Angel | TITLE: Quantification of 16S rRNA Gene Copies Using ddPCR (probe-based assay: 338F-516P-805R)
AUTHORS: Eva Petrova, Roey Angel
[DESCRIPTION]
This protocol is dedicated to evaluation of 16S rRNA bacteria gene copy number using Droplet Digital PCR technology (ddPCR) from Bio-Rad company. This is the up-to-date modificat... | ["[ddPCR reaction mixture] Reagent Final conc. 1 tube (25μl) plate (25μl x 100) PCR H2O 1.6 160 ReadyMix (Sigma) 1x 12.5 1250 MgCl2 (25mM) 4mM 2.5* 250* BSA (50μg/μl) 0.8 μg/μl 0.4 40 BAC 338F (10μM) 0.5 μM 1.25 125 BAC 805R (10μM) 0.5 μM 1.25 125 BAC 516P (10μM)† 0.2 μM 0.5 50 Template 5 5 x 100 ... |
54,435 | Wholemount Edu Staining (Zebrafish Larvae) | 4 | dx.doi.org/10.17504/protocols.io.n92ld9429g5b/v1 | https://www.protocols.io/view/wholemount-edu-staining-zebrafish-larvae-bzebp3an | Henna Myllymaki, Abigail Elliot, Yi Feng | TITLE: Wholemount Edu Staining (Zebrafish Larvae)
AUTHORS: Henna Myllymaki, Abigail Elliot, Yi Feng
[DESCRIPTION]
Methods for evaluating cell proliferation are important for research in the field of developmental biology, cancer biology and cell biology. Recent years, Click-iT EdU Assays by Invitrogen is gaining popul... | ["[EdU staining] Inject 2nl bolus of 500uM EdU into the yolk of embryos", "[EdU staining] Incubate at 28.5°C in the dark for 2.5 hours (this can be between 2 -3 hours, but be consistent between experiments; we have done 2 hours)", "[EdU staining] Fix in 4% PFA (30min, Room temperature)25 °C \n30 min", "[EdU staining] W... |
36,416 | Quantification of 18S rRNA Gene Copies Using ddPCR (probe-based assay: FungiQuant F-FungiQuant Prb-FungiQuant R) | 1 | dx.doi.org/10.17504/protocols.io.5qpvo5wr9l4o/v1 | https://www.protocols.io/view/quantification-of-18s-rrna-gene-copies-using-ddpcr-bfs8jnhw | Eva Petrova, Roey Angel | TITLE: Quantification of 18S rRNA Gene Copies Using ddPCR (probe-based assay: FungiQuant F-FungiQuant Prb-FungiQuant R)
AUTHORS: Eva Petrova, Roey Angel
[DESCRIPTION]
The protocol is dedicated to evaluation of 18S rRNA fungal gene copy number using Droplet Digital PCR technology (ddPCR) from Bio-Rad company. This is t... | ["[ddPCR reaction mixture] All reagencies must be equilibrated to RT (do not keep them on ice). Mix each of them properly before use.", "[ddPCR reaction mixture] Seal the plate (180°C, 5 s) with pierceable aluminium foil. \n\n \n5 s", "[ddPCR reaction mixture] Prepare the master mix according to the number of samples a... |
58,787 | Photo-Oxidation of MiniSOG Related to Cultured Neurons | 4 | dx.doi.org/10.17504/protocols.io.n2bvj63rplk5/v1 | https://www.protocols.io/view/photo-oxidation-of-minisog-related-to-cultured-neu-b5nbq5an | Daniela Boassa, Thomas Steinkellner, Matthew Madany, Matthias G. Haberl, Vivien Zell, Carolina Li, Junru Hu, Mason Mackey, Ranjan Ramachandra, Stephen Adams, Mark H. Ellisman, Thomas S. Hnasko | TITLE: Photo-Oxidation of MiniSOG Related to Cultured Neurons
AUTHORS: Daniela Boassa, Thomas Steinkellner, Matthew Madany, Matthias G. Haberl, Vivien Zell, Carolina Li, Junru Hu, Mason Mackey, Ranjan Ramachandra, Stephen Adams, Mark H. Ellisman, Thomas S. Hnasko
[DESCRIPTION]
This is a general protocol is for photo-o... | ["Plate cells in MaTek dishes.", "Fix in 2.5% glutaraldehyde in 0.1 M cacodylate buffer at room temperature for 5 min. Then, for one hour on ice.\n IMPORTANT: Keep Everything cold!", "Wash 5x for 1 min in 0.1M cacodylate buffer.", "Block for 30 min on ice with blocking buffer.", "Remove solution from plate and repla... |
98,842 | Crystallization of SARS-CoV-2 nsp15 NendoU | 1 | dx.doi.org/10.17504/protocols.io.36wgqn4yogk5/v1 | https://www.protocols.io/view/crystallization-of-sars-cov-2-nsp15-nendou-dcr22v8e | Peter Marples, Daren Fearon, Lizbé Koekemoer, Andre Schutzer de Godoy | TITLE: Crystallization of SARS-CoV-2 nsp15 NendoU
AUTHORS: Peter Marples, Daren Fearon, Lizbé Koekemoer, Andre Schutzer de Godoy
[DESCRIPTION]
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). The NSP15 endoribonuclease enzyme, known as NendoU, ... | ["[Crystallization experiment] Protein and buffer requirements:\n86.4 µL3.4 mg/mL \n2.88 mL \n2.88 µL seeds, no dilution", "[Crystallization experiment] Dispense 30 µL into SwissCI 3 lens plate reservoir wells using a 100 µl multi-channel pipette.\nDispense 300 28613.4 mg/mL to each lens using the SPT mosquito.\n... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.