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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70,252 | Nucleoside analysis with high performance liquid chromatography (HPLC) | 1 | dx.doi.org/10.17504/protocols.io.5jyl8jn39g2w/v1 | https://www.protocols.io/view/nucleoside-analysis-with-high-performance-liquid-c-cguktwuw | Atanas Radkov | TITLE: Nucleoside analysis with high performance liquid chromatography (HPLC)
AUTHORS: Atanas Radkov
[DESCRIPTION]
This protocol details the detection of modified nucleosides using HPLC.
[STEPS]
SECTION: Run samples
5. Begin the gradient at 100% solution A, then ramp up to 25% solution B over 16 min, then ramp down... | ["[Run samples] Begin the gradient at 100% solution A, then ramp up to 25% solution B over 16 min, then ramp down to 0% solution B in 1 min, and finally stay at 0% solution B for 13 min (30 min total method time). Flow rate for the entire run should be 0.5 mL per min. Detect elution of compounds at 260 nm.", "[Run samp... |
83,158 | Adhesive Removal Test to assess sensorimotor deficits in parkinsonian mice | 1 | dx.doi.org/10.17504/protocols.io.6qpvr3x9bvmk/v1 | https://www.protocols.click/view/adhesive-removal-test-to-assess-sensorimotor-defic-cvfww3pe | natalia.lopezgonzalezdelrey, Zachary Gaertner, Elizabeth Phelan | TITLE: Adhesive Removal Test to assess sensorimotor deficits in parkinsonian mice
AUTHORS: natalia.lopezgonzalezdelrey, Zachary Gaertner, Elizabeth Phelan
[DESCRIPTION]
This behavior is used to asses fine motor movements in a mouse parkinsonian model. It checks for correct paw and mouth sensitivity (time-to-contact) a... | ["[Adhesive Removal Test] Total duration: 4 days", "[Protocol] Place the animal cage in the testing room to allow the animals to acclimate. 60 min", "[Protocol] Acclimating mice to testing box. 1 min", "Apply the two adhesive tape strips with equal pressure on each animal paw so that they cover the hairless part of the... |
44,316 | Western Blotting and RNA Isolation from Membrane | 4 | dx.doi.org/10.17504/protocols.io.bph4mj8w | https://www.protocols.io/view/western-blotting-and-rna-isolation-from-membrane-bph4mj8w | Eric L. Van Nostrand, Thai B. Nguyen, Chelsea Gelboin-Burkhart, Ruth Wang, Steven M. Blue, Gabriel A. Pratt, Ashley L. Louie, Gene W. Yeo | TITLE: Western Blotting and RNA Isolation from Membrane
AUTHORS: Eric L. Van Nostrand, Thai B. Nguyen, Chelsea Gelboin-Burkhart, Ruth Wang, Steven M. Blue, Gabriel A. Pratt, Ashley L. Louie, Gene W. Yeo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Profiling of RNA binding protein targets in vivo ... | ["[Wash Beads (Prechill Buffers to 4°C)]\nAdd , magnetically separate, remove the supernatant.\n[Wash buffer]", "[Wash Beads (Prechill Buffers to 4°C)]\nAdd , mix, add , mix, remove the supernatant.\n[Wash buffer]\n[High salt wash buffer]", "[Wash Beads (Prechill Buffers to 4°C)]\nWash 1× with , remove the supernatant.... |
97,988 | APEX2-based proximity biotinylation of NLRP3 and P4C (SidC) during inflammasome activation | 4 | dx.doi.org/10.17504/protocols.io.5qpvok55zl4o/v1 | https://www.protocols.io/view/apex2-based-proximity-biotinylation-of-nlrp3-and-p-dbxc2piw | Tao_Fu, Harper JW, Louis R R Hollingsworth, sharan_swarup | TITLE: APEX2-based proximity biotinylation of NLRP3 and P4C (SidC) during inflammasome activation
AUTHORS: Tao_Fu, Harper JW, Louis R R Hollingsworth, sharan_swarup
[DESCRIPTION]
APEX2-based proximity labeling for the discovery of proteins proximal to NLRP3. Aspects of this APEX2 protocol can be applied to other targe... | ["[Cell line construction and validation (brief overview)] The choice of cells, constructs, proximity biotinylation enzyme (e.g., TurboID vs. APEX2), treatments, etc. to employ for proximity biotinylation experiments depends on the experimental design. Here, mouse immortalized bone-marrow derived macrophages iBMDM cell... |
103,172 | mRNA extraction and cDNA preparation | 0 | dx.doi.org/10.17504/protocols.io.bp2l623n5gqe/v1 | https://www.protocols.io/view/mrna-extraction-and-cdna-preparation-dgzc3x2w | Shiyi Wang | TITLE: mRNA extraction and cDNA preparation
AUTHORS: Shiyi Wang
[DESCRIPTION]
mRNA extraction and cDNA preparation
[STEPS]
1. **Thaw and Resuspend Cells** - Thaw cells stored in TRIzol (15596026, Invitrogen). - Resuspend cells in 1 mL of TRIzol.
2. **Add Chloroform** - Add 200 μL of chloroform to the samples.
3. **Ce... | ["**Thaw and Resuspend Cells** - Thaw cells stored in TRIzol (15596026, Invitrogen). - Resuspend cells in 1 mL of TRIzol.", "**Add Chloroform** - Add 200 μL of chloroform to the samples.", "**Centrifuge Samples** - Centrifuge the samples at 12,000 g for 15 minutes at 4°C.", "**Collect Aqueous Phase** - Carefully collec... |
null | null | null | dx.doi.org/10.17504/protocols.io.nkgdctw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol presents a simple modification of the SMART-seq2 (Picelle et al, 2014) and SCRB-seq (Soumillon et al, 2014) protocols, with the goal of combining the sensitivity of SMART-Seq2 with the improved cost and throughput of 3' single cell protocols. Reverse transcripti... | [] |
76,549 | Fixation and staining of gemmule-hatched Ephydatia muelleri for fluorescence microscopy | 4 | dx.doi.org/10.17504/protocols.io.j8nlkwnx6l5r/v1 | https://www.protocols.io/view/fixation-and-staining-of-gemmule-hatched-ephydatia-cnzdvf26 | Scott Nichols | TITLE: Fixation and staining of gemmule-hatched Ephydatia muelleri for fluorescence microscopy
AUTHORS: Scott Nichols
[DESCRIPTION]
This protocol is intended for the preparation of gemmule-hatched freshwater sponges for imaging with an inverted scanning confocal microscope.
[STEPS]
SECTION: Fixation and washes
3. Re... | ["[Fixation and washes] Remove the culture medium from the outer well by pipetting or aspiration. Then, carefully remove the residual medium from the inner well using a p200 pipette to avoid damaging the tissue.", "[Permeabilization and Blocking] Add 3 mL of Block Solution to the outer edge of the dish, and incubate fo... |
58,408 | LB Broth Agar Plates with Antibiotics | 1 | dx.doi.org/10.17504/protocols.io.kxygxz974v8j/v1 | https://www.protocols.io/view/lb-broth-agar-plates-with-antibiotics-b5agq2bw | Bailey Clark | TITLE: LB Broth Agar Plates with Antibiotics
AUTHORS: Bailey Clark
[DESCRIPTION]
The abstract will be added later.
[STEPS]
SECTION: Preparation For Autoclave
1. Add 125 mL of deionized water to a 250 mL Erlenmeyer Flask.
SECTION: Preparation For Autoclave
2. Add 3.125 g of LB Broth powder (25 g per 1 L of water)... | ["[Preparation For Autoclave] Add 125 mL of deionized water to a 250 mL Erlenmeyer Flask.", "[Preparation For Autoclave] Add 3.125 g of LB Broth powder (25 g per 1 L of water) to the water in the Erlenmeyer Flask.", "[Preparation For Autoclave] Add 1.875 g of agar to the water ( 1.5% of 125 mL ) in the Erlenmeyer ... |
84,891 | Gastrointestinal transit | 4 | dx.doi.org/10.17504/protocols.io.4r3l22464l1y/v1 | https://www.protocols.click/view/gastrointestinal-transit-cw53xg8n | Connor Monahan | TITLE: Gastrointestinal transit
AUTHORS: Connor Monahan
[DESCRIPTION]
This protocol details measuring gastrointestinal transit time in mice
[STEPS]
SECTION: Procedure
1. Prepare a sterile solution of carmine red (300 µl; 6%; Sigma-Aldrich, Cat #C1022; St Louis, MO) suspended in 0.5% methylcellulose (Sigma-Aldrich, Ca... | ["[Procedure] Prepare a sterile solution of carmine red (300 µl; 6%; Sigma-Aldrich, Cat #C1022; St Louis, MO) suspended in 0.5% methylcellulose (Sigma-Aldrich, Cat #M0512; St Louis, MO).", "[Procedure] Administer 0.3 mL of carmine red solution by gavage through a 21-gauge round-tip feeding\nneedle.", "[Procedure] The t... |
64,405 | Tiger Woods Eagle Hemp CBD Gummies | 3 | dx.doi.org/10.17504/protocols.io.8epv59oqdg1b/v1 | https://www.protocols.io/view/tiger-woods-eagle-hemp-cbd-gummies-ca5vsg66 | DaidOlier | TITLE: Tiger Woods Eagle Hemp CBD Gummies
AUTHORS: DaidOlier
[DESCRIPTION]
->Tiger Woods Eagle Hemp CBD Gummies *Updated 2022* 'Reviews' Shocking Results Must Read!
[STEPS] | [] |
35,955 | Time-lapse killing assay (monolayer - IncuCyte) | 1 | dx.doi.org/10.17504/protocols.io.q26g7b6x8lwz/v1 | https://www.protocols.io/view/time-lapse-killing-assay-monolayer-incucyte-bfctjiwn | Philippa R Kennedy, Peter Hinderlie | TITLE: Time-lapse killing assay (monolayer - IncuCyte)
AUTHORS: Philippa R Kennedy, Peter Hinderlie
[DESCRIPTION]
Fluorescent target cells are plated in a monolayer in a 96 well plate. Effector cells are added to that plate and time-lapse imaging in combination with fluorescent indicators of cell death reveal the dyna... | ["Target cells are fluorescently labelled to differentiate them from effector cells.", "Enriched NK cells are added to the target cell monolayer at a 2:1 effector:target ratio, bringing the final volume to 200 μL.", "Labelled target cells are plated in a monolayer in a 96 well flat-bottom plate (Cat. No: 353072, Cornin... |
43,646 | Fungal Plate Photography | 3 | dx.doi.org/10.17504/protocols.io.bnu6meze | https://www.protocols.io/view/fungal-plate-photography-bnu6meze | Craig Bateman | TITLE: Fungal Plate Photography
AUTHORS: Craig Bateman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how to photograph fungal plates.</div><div class = "text-block"><span>This protocol is part of the Bark Beetle Mycobiome (BBM) Research Coordination Network. For more inform... | [] |
59,158 | Preparing Combined Indexed Primer Plates (IDT Ultramers) for the Illumina MiSeq - IDT UDIs | 4 | dx.doi.org/10.17504/protocols.io.6qpvr63wbvmk/v1 | https://www.protocols.io/view/preparing-combined-indexed-primer-plates-idt-ultra-b5zwq77e | André M Comeau, Alessi Kwawukume | TITLE: Preparing Combined Indexed Primer Plates (IDT Ultramers) for the Illumina MiSeq - IDT UDIs
AUTHORS: André M Comeau, Alessi Kwawukume
[DESCRIPTION]
The preparation of diluted combined (F+R) IDT working primer stocks of Illumina UDI primers for use in IMR PCR preps.
[STEPS]
SECTION: Order Primers
1. Use our Exce... | ["[Order Primers] Use our Excel template ( ) to copy existing 16S/18S/ITS primers or to design your own custom gene primers with the proper Illumina indices and Nextera adapter orientations. We order IDT “Ultramers” for such long primers (~80-90 nt) as their coupling efficiency is one of the highest available (critical... |
72,419 | RealTimePCR-Protocol-miRNA-SCALONMC | 6 | dx.doi.org/10.17504/protocols.io.4r3l277z3g1y/v1 | https://www.protocols.io/view/realtimepcr-protocol-mirna-scalonmc-ciybufsn | Marcela Scalon, Christine Souza Martins, Gabriel Ginani Ferreira, Franciele Schlemmer, Ricardo Titze de Almeida, Giane Regina Paludo | TITLE: RealTimePCR-Protocol-miRNA-SCALONMC
AUTHORS: Marcela Scalon, Christine Souza Martins, Gabriel Ginani Ferreira, Franciele Schlemmer, Ricardo Titze de Almeida, Giane Regina Paludo
[DESCRIPTION]
This protocol is intended as a guideline to perform the Real Time PCR (qPCR or rtPCR) procedure to detect and quantify m... | ["[Prepare the real-time PCR (qPCR or rtPCR) reaction mix] Determine the total number of PCR reactions to perform. On each reaction plate include:\n\n• A miRNA assay for each cDNA sample\n• Control assays\n• No template controls (NTCs) for each assay on the plate\n\nNotes:\n- It is possible to run multiple assays on on... |
13,138 | RT-PCR for NoV | null | dx.doi.org/10.17504/protocols.io.q3sdyne | null | Hengyun Guan, Chunrong Wang, Lanzheng Liu, Guoliang Yang | TITLE: RT-PCR for NoV
AUTHORS: Hengyun Guan, Chunrong Wang, Lanzheng Liu, Guoliang Yang
[DESCRIPTION]
<p>This assay amplified the partial VP1 gene (Region C) of the norovirus genome. The yield products could be sequenced.</p>
[STEPS]
?. [Reagents]
SuperScriptTM III One-Step RT-PCR with PlatinumTM TaqBy Life Technolog... | ["[Reagents]\nSuperScriptTM III One-Step RT-PCR with PlatinumTM TaqBy Life TechnologiesCatalog #:12574026", "[RNA extraction]\nExtract total RNA of specimens with the MagNA Pure LC Total Nucleic Acid Isolation Kit (Roche, Mannheim, Germany) according to the manufacturer's instructions.", "[Reaction system：]\nThe primer... |
null | null | null | dx.doi.org/10.17504/protocols.io.ikyccxw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Please contact Dr. Steven Wilhelm (wilhelm@utk.ed) for additional information regarding this protocol.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
85,319 | Cyanobacteria growth | 1 | dx.doi.org/10.17504/protocols.io.4r3l22o8xl1y/v1 | https://www.protocols.io/view/cyanobacteria-growth-cxjfxkjn | Ricardo M. Borges, Gabriela de Assis Ferreira, pauloihc | TITLE: Cyanobacteria growth
AUTHORS: Ricardo M. Borges, Gabriela de Assis Ferreira, pauloihc
[DESCRIPTION]
Este documento apresenta o protocolo para cultivar cianobactérias em água salgada, incluindo informações detalhadas sobre as soluções, cálculos e volumes necessários para o processo. É importante observar que as... | ["[Material] Preparo do meio de cultivo F/2:\n Para 1 litro de água destilada:\n41,5 gramas de sal marinho para aquario (Reef Salt)\n1 mL de solução de NaNO3\n1 mL de solução de NaH2PO4•H2O\n1 mL de solução de metais traço\nAutoclave: 15 minutos 1.5 ATM\nEspera esfriar\nAdiciona a solução de vitaminas antes do uso.", "... |
36,962 | Molecular dynamics simulation (Protein-Ligand) | 1 | dx.doi.org/10.17504/protocols.io.bgcajsse | https://www.protocols.io/view/molecular-dynamics-simulation-protein-ligand-bgcajsse | Hossein Tarrahimofrad, Amir Meimandipour, Sareh Arjmand, Mohammadtaghi Beigi Nassiri, Ehsan Jahangirian, Hossein Tavana, Javad Zamani, Somayyeh Rahimnahal, Saeed Aminzadeh | TITLE: Molecular dynamics simulation (Protein-Ligand)
AUTHORS: Hossein Tarrahimofrad, Amir Meimandipour, Sareh Arjmand, Mohammadtaghi Beigi Nassiri, Ehsan Jahangirian, Hossein Tavana, Javad Zamani, Somayyeh Rahimnahal, Saeed Aminzadeh
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The prepare... | [] |
50,015 | Fluo-4 Calcium Imaging | 1 | dx.doi.org/10.17504/protocols.io.bu37nyrn | https://www.protocols.io/view/fluo-4-calcium-imaging-bu37nyrn | Edinson Lucumi Moreno | TITLE: Fluo-4 Calcium Imaging
AUTHORS: Edinson Lucumi Moreno
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details the measurement of the firing activity of cultured iPSC derived neurons. This procedure is used to prepare cultured neurons for Calcium imaging.</div></div>
[STEPS]
?. ... | ["[Procedure for Calcium Fluo-4]\nPrepare Fluo-4 stock solution by adding of DMSO to vial.\n45 µl", "[Procedure for Calcium Fluo-4]\nPrepare aliquots of Fluo-4 stock in PCR Eppendorf tubes and store them at .\n5 µl\n-20 °C", "[Procedure for Calcium Fluo-4]\nTake one aliquot of Fluo-4 and transfer to of neurobasa... |
72,523 | Immunostaining infiltrating spheroids as preparation for quantitative light-sheet imaging | 1 | dx.doi.org/10.17504/protocols.io.eq2ly77krlx9/v1 | https://www.protocols.io/view/immunostaining-infiltrating-spheroids-as-preparati-ci3jugkn | Benedicte Bjørknes, Oliver Emil Neye, Petra Hamerlik, Liselotte Jauffred | TITLE: Immunostaining infiltrating spheroids as preparation for quantitative light-sheet imaging
AUTHORS: Benedicte Bjørknes, Oliver Emil Neye, Petra Hamerlik, Liselotte Jauffred
[DESCRIPTION]
Although various in vivo and in vitro models for studying glioblastoma cell invasion has progressed the field, there is still ... | [] |
83,062 | Preparation of mollusc larval shells for individual geochemical analysis | 1 | dx.doi.org/10.17504/protocols.io.bp2l61jwkvqe/v2 | https://www.protocols.click/view/preparation-of-mollusc-larval-shells-for-individua-cvcww2xe | Vincent Mouchi, Thomas Broquet, Thierry Comtet | TITLE: Preparation of mollusc larval shells for individual geochemical analysis
AUTHORS: Vincent Mouchi, Thomas Broquet, Thierry Comtet
[DESCRIPTION]
This protocol describes the digestion process of mollusc larvae and is modified from the procedure found in Becker et al. (2005). Here, we indicate the entire process to... | ["[Preparation of the digestion solution (for 20 mL final volume of approximately 15% H2O2)] In a glass beaker\nAdd 10 mL Suprapur® hydrogen peroxide (H2O2) 30%", "[Preparation of the digestion solution (for 20 mL final volume of approximately 15% H2O2)] Place the beaker with hydrogen peroxide on a magnetic stirrer an... |
null | null | null | dx.doi.org/10.17504/protocols.io.cjfujm | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This method describes frying protocols for tortilla chips. Chips or other foods are often fried in different oils and oil blends to assess the oxidative stability of the oil, thereby determining whether that particular oil or oil blend is suitable for frying. With this met... | [] |
55,543 | Mouse Perfusion Protocol | 1 | null | https://www.protocols.io/view/mouse-perfusion-protocol-b2gxqbxn | Angie Angie Santos, Olivier George, Lieselot Carrette | TITLE: Mouse Perfusion Protocol
AUTHORS: Angie Angie Santos, Olivier George, Lieselot Carrette
[DESCRIPTION]
This protocol lists materials, setup, and steps to perform a fast and successful mouse perfusion for brain harvesting.
[STEPS]
SECTION: Setting up
1.
Beakers and Solutions
Prepare the first beaker with col... | ["[Setting up] Beakers and Solutions\n\nPrepare the first beaker with cold PFA, on ice, cover with parafilm (leave small opening for the tube) \nPrepare the second beaker with cold PBS, on ice, cover with parafilm (leave small opening for the tube) \nPrepare a third beaker for waste collection (end of the line)\n\nPer... |
93,745 | Single-Molecule Antibody Slides For Fluorescence Microscopy | 1 | dx.doi.org/10.17504/protocols.io.ewov1qbbygr2/v1 | https://www.protocols.io/view/single-molecule-antibody-slides-for-fluorescence-m-c7srznd6 | Rebecca Andrews | TITLE: Single-Molecule Antibody Slides For Fluorescence Microscopy
AUTHORS: Rebecca Andrews
[DESCRIPTION]
This protocol describes how to create single-moelcule antibody slides for fluorescence microscopy.
[STEPS]
SECTION: Coverslip Cleaning
1. Coverslips (24 x 50 mm, #1, VWR,Catalogue Number 48404-453) were argon p... | ["[Coverslip Cleaning] Coverslips (24 x 50 mm, #1, VWR,Catalogue Number 48404-453) were argon plasma cleaned (Ar plasma cleaner, PDC-002, Harrick Plasma) for 30 min .", "[Surface preparation] A trimmed gasket was placed on top of the slide (CultureWell‱ Reusable Gasket, 6mm diameter, Grace Bio-Labs, SKU: 103280).", "[S... |
54,934 | Immunofluorescent Staining of Mouse Pancreas for Islet Cell Mass Analysis | 1 | dx.doi.org/10.17504/protocols.io.bzvwp67e | https://www.protocols.io/view/immunofluorescent-staining-of-mouse-pancreas-for-i-bzvwp67e | Islet and Pancreas Analysis Core | TITLE: Immunofluorescent Staining of Mouse Pancreas for Islet Cell Mass Analysis
AUTHORS: Islet and Pancreas Analysis Core
[DESCRIPTION]
This SOP defines the assay method used by the Vanderbilt Diabetes Center Islet and Pancreas Analysis (IPA) Core for quantitative determination of the islet cell composition and isle... | ["[Immunofluorescent staining] Gather reagents for immunostaining, noting that steps 9-11, 15, and 17-18 can be performed in Kartell staining chambers (each holds ~50 mL).", "[Imaging and analysis] Acquire images of stained pancreas sections using a high-resolution whole slide scanning system (Aperio ScanScope FL, Leic... |
70,266 | The effects of cognitive training in healthy community residing Thai elderly: a randomized controlled trial.092022 | 1 | dx.doi.org/10.17504/protocols.io.36wgqj92kvk5/v1 | https://www.protocols.io/view/the-effects-of-cognitive-training-in-healthy-commu-cgu2twye | Chaichana Nimnuan, Vitool Lohsoonthorn, Muthita Phanasathit | TITLE: The effects of cognitive training in healthy community residing Thai elderly: a randomized controlled trial.092022
AUTHORS: Chaichana Nimnuan, Vitool Lohsoonthorn, Muthita Phanasathit
[DESCRIPTION]
Aim: Cognitive training intervention (CTI) in the elderly is associated with a risk reduction of dementia; howeve... | ["[Study design] - 1:1 ratio 2-arm parallel single-blinded intervention randomized controlled trial study design (RCT) with a single-blinded assessor. \n- All cognitive function outcomes were assessed by trained blinded psychologists not involved in the recruitment process and experimental phase.\n- Study Endpoint Clas... |
58,664 | 2,4-dinitrophenylhydrazine alpha-ketoglutarate detection assay for Prolyl Hydroxylase Domain (PHD) proteins | 4 | dx.doi.org/10.17504/protocols.io.b5igq4bw | https://www.protocols.io/view/2-4-dinitrophenylhydrazine-alpha-ketoglutarate-det-b5igq4bw | sjwong | TITLE: 2,4-dinitrophenylhydrazine alpha-ketoglutarate detection assay for Prolyl Hydroxylase Domain (PHD) proteins
AUTHORS: sjwong
[DESCRIPTION]
The 2,4-dinitrophenylhydrazine (2,4-DNPH) alpha-ketoglutarate detection assay was developed to support the study of prolyl hydroxylase domain (PHD) proteins in a substrate-... | ["[Overview of assay schematic]", "[In vitro hydroxylation assay] Prepare 5 Eppendorf tubes containing 50 µl of 10% TCA.\nLabel tubes: 0 min, 1 min, 2 min, 5 min, 15 min.", "[In vitro hydroxylation assay] Prepare cofactor solution containing HEPES/MES, catalase, DTT, ascorbic acid, FeSO4, a-ketoglutarate, and peptide i... |
70,290 | RNA extraction, cDNA synthesis and Taqman qPCR | 1 | dx.doi.org/10.17504/protocols.io.36wgqj5rkvk5/v1 | https://www.protocols.io/view/rna-extraction-cdna-synthesis-and-taqman-qpcr-cgvstw6e | gurvir.virdi | TITLE: RNA extraction, cDNA synthesis and Taqman qPCR
AUTHORS: gurvir.virdi
[DESCRIPTION]
RNA extraction, cDNA synthesis and TaqMan qPCR on samples.
[STEPS]
SECTION: RNA extraction
1. Cell pellets are snap-frozen using dry ice.
SECTION: RNA extraction
2. RNA is extracted using the Maxwell® RSC simply RNACells kit (P... | ["[RNA extraction] Cell pellets are snap-frozen using dry ice.", "[RNA extraction] RNA is extracted using the Maxwell® RSC simply RNACells kit (Promega), and the Maxwell® RSC 48 instrument, following manufacturer instructions.", "[RNA extraction] After RNA extraction, RNA concentration and quality are measured and asse... |
null | null | null | dx.doi.org/10.17504/protocols.io.ek7bczn | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
<strong>What you need before you start:</strong><br />1. 20% nutrient Zobell plates <br />2. Top agar – 3.5 ml per plate<br /> a. 100% nutrient Zobell<br /> b. 6g agar/liter<br />3. Your host grown to exponential phase. You will need 0.4ml for each plate in the ass... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.c9zz75 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Here, we adapt the linker amplified shotgun library (LASL) approach to next generation sequencing by offering an alternate polymerase for challenging samples, developing a more efficient sizing step, integrating a “reconditioning PCR” step to increase yield and minim... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.dei3cd | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For use in '<a href="http://protocols.io/view/FASP-Kit-Protocol-ORNL-Developed-for-Bacteriophage-ddn25d" target="_blank">FASP Kit Protocol-ORNL Developed for Bacteriophage</a>'
[STEPS]
?. | [] |
93,463 | Protocolo de Manejo das Doses de Medicamentos para Tratamento de Mieloma Múltiplo em Função do Grau de Neuropatia Periférica Induzida por Quimioterapia (NPIQ) | 1 | dx.doi.org/10.17504/protocols.io.n2bvj3m3nlk5/v1 | https://www.protocols.io/view/protocolo-de-manejo-das-doses-de-medicamentos-para-c7hxzj7n | Leonardo Teodoro de Farias, Pryscila Rodrigues Moreira, Dra. Ana Carolina Figueiredo Modesto | TITLE: Protocolo de Manejo das Doses de Medicamentos para Tratamento de Mieloma Múltiplo em Função do Grau de Neuropatia Periférica Induzida por Quimioterapia (NPIQ)
AUTHORS: Leonardo Teodoro de Farias, Pryscila Rodrigues Moreira, Dra. Ana Carolina Figueiredo Modesto
[DESCRIPTION]
Objetivo
O objetivo deste protocolo é... | ["[IXAZOMIBE:] Mecanismo de Ação: Inibe reversivelmente os proteassomas, regulando a homeostase proteica intracelular.\n \nManejo de Dose para NPIQ:\nGrau 1 ou Grau 2 (com dor): Suspender o ixazomibe até que a neuropatia periférica se recupere para ≤ grau 1 sem dor ou até o valor basal. Após recuperação, retomar o ixaz... |
44,857 | Ef_electocomp_cells_OG1RF | 4 | null | https://www.protocols.io/view/ef-electocomp-cells-og1rf-bp2zmqf6 | Elizabeth Fozo | TITLE: Ef_electocomp_cells_OG1RF
AUTHORS: Elizabeth Fozo
[STEPS]
?. [E. faecalis Electrocompetent Cells (with Lysozyme)]
Inoculate 5-10 mL BHI or THB (I add fusidic acid at 25 ug/mL but not rifampicin) and incubate o/n at 37°C.
?. [E. faecalis Electrocompetent Cells (with Lysozyme)]
Dilute o/n culture 1:50 or 1:100 wi... | ["[E. faecalis Electrocompetent Cells (with Lysozyme)]\nInoculate 5-10 mL BHI or THB (I add fusidic acid at 25 ug/mL but not rifampicin) and incubate o/n at 37°C.", "[E. faecalis Electrocompetent Cells (with Lysozyme)]\nDilute o/n culture 1:50 or 1:100 with in 100 mL THB (with FA25) and incubate until culture OD at 600... |
92,892 | Dual-task training to improve gait parameters in people with Parkinson’s disease: a systematic review | 1 | dx.doi.org/10.17504/protocols.io.36wgq314olk5/v1 | https://www.protocols.io/view/dual-task-training-to-improve-gait-parameters-in-p-c6x4zfqw | Elisabetta Sarasso, Marco Parente, Federica Agosta, Massimo Filippi, Davide Corbetta | TITLE: Dual-task training to improve gait parameters in people with Parkinson’s disease: a systematic review
AUTHORS: Elisabetta Sarasso, Marco Parente, Federica Agosta, Massimo Filippi, Davide Corbetta
[DESCRIPTION]
People with Parkinson’s disease (PD) frequently exhibit changes in spatiotemporal gait parameters that... | ["[Search Strategy] Preparation of the search strategy and first running on April 2023", "[Records management, selection and data collection] Selection and collection starting in January 2024", "[Risk of bias assessment] Assessment planned after study selection", "[Data synthesis] Depending on data availability; if pos... |
54,156 | Jojo | 4 | dx.doi.org/10.17504/protocols.io.by5kpy4w | https://www.protocols.io/view/jojo-by5kpy4w | Chia-Hsien Shih | TITLE: Jojo
AUTHORS: Chia-Hsien Shih
[DESCRIPTION]
Nice
[STEPS]
1. Hhhh | ["Hhhh"] |
95,618 | Human-Derived Precision-Cut Lung Slices (hPCLS): Agarose Filling, Coring and Slicing Protocol | 0 | dx.doi.org/10.17504/protocols.io.36wgq3xr5lk5/v1 | https://www.protocols.io/view/human-derived-precision-cut-lung-slices-hpcls-agar-c9maz42e | Ricardo Pineda, John Sembrat, Carter Kessler, Nayra Cardenes, Melanie Königshoff | TITLE: Human-Derived Precision-Cut Lung Slices (hPCLS): Agarose Filling, Coring and Slicing Protocol
AUTHORS: Ricardo Pineda, John Sembrat, Carter Kessler, Nayra Cardenes, Melanie Königshoff
[DESCRIPTION]
Human Precision-Cut Lung Slices (hPCLS) are uniform tissue slices generated from human lungs. These slices contai... | ["[Core Slicing] Materials:\n• Agarose 2.0% in DMEM/F12 with antibiotics and fungizone warmed up and kept at 40-42°C\n• Double edge razor blades cut in half lengthwise and cleaned with ETOH to remove protective wax and oils.\n• Cyanoacrylate Glue (we like Loctite, super glue, gel control ).\n• Bucket with ice \n• DMEM/... |
62,940 | Nanopore (SQK-LSK109) without barcode | 4 | dx.doi.org/10.17504/protocols.io.5qpvob837l4o/v1 | https://www.protocols.io/view/nanopore-sqk-lsk109-without-barcode-b9p4r5qw | Wen-Ting Zeng | TITLE: Nanopore (SQK-LSK109) without barcode
AUTHORS: Wen-Ting Zeng
[DESCRIPTION]
Nanopore (SQK-LSK109) without barcode
[STEPS]
SECTION: Adapter ligation and clean-up
2. Spin down the Adapter Mix (AMX) and Quick T4 Ligase, and place on ice.
SECTION: DNA repair and end-prep
1.2. Using a thermal cycler, incubate a... | ["[Adapter ligation and clean-up] Spin down the Adapter Mix (AMX) and Quick T4 Ligase, and place on ice.", "[DNA repair and end-prep] Using a thermal cycler, incubate at 20 °C for 30 min and 65 °C for 30 min. Hold at 4 °C \n1.2", "[DNA repair and end-prep] Ensure the components are thoroughly mixed by pipetting, and sp... |
31,720 | Measuring relative reactivity of mouse TCRs against a mouse cancer cell line | null | dx.doi.org/10.17504/protocols.io.ba8gihtw | null | Bulent Arman Aksoy, Pinar Aksoy, Elinor Gottschalk, Jeff Hammerbacher | TITLE: Measuring relative reactivity of mouse TCRs against a mouse cancer cell line
AUTHORS: Bulent Arman Aksoy, Pinar Aksoy, Elinor Gottschalk, Jeff Hammerbacher
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol repurposes Promega's T Cell Activiation Bioassay workflow to be able to tes... | ["[Preparation of electroporation material]\nOrder, clone, and midi-prep all the TCR and mouse CD8 plasmids:and make sure they are of good quality for further applications.", "[Preparation of electroporation material]\nLinearize plasmids using the corresponding enzymes right at the end of their insertsPreferred enzyme ... |
92,211 | CODEX FFPE Staining and Fixation | 4 | dx.doi.org/10.17504/protocols.io.n92ldm6y9l5b/v1 | https://www.protocols.io/view/codex-ffpe-staining-and-fixation-c6atzaen | wbei | TITLE: CODEX FFPE Staining and Fixation
AUTHORS: wbei
[DESCRIPTION]
Detailed protocol for preparing, staining, and fixing FFPE slides for use with Akoya flowcells in the Akoya phenocycler (CODEX). Slides are ready to be used with the Akoya phenocycler and the Akoya protocol following this protocol.
[STEPS]
SECTION:... | ["[Staining] Bake slides at 70 °C in an oven/incubator", "[Staining] Deparaffinize and rehydrate the slides", "[Staining] Incubate slides for 21 min in xylene in a coplin jar", "[Staining] Place slides in ST4020 Linear Staining vial and start the staining protocol", "[Staining] Each step is 3 minutes\nXylene x3 -> 100%... |
100,021 | human alpha-synuclein and aggregated alpha-synuclein immunofluorescence staining | 0 | dx.doi.org/10.17504/protocols.io.ewov19om7lr2/v1 | https://www.protocols.io/view/human-alpha-synuclein-and-aggregated-alpha-synucl-ddwv27e6 | Pietro La Vitola | TITLE: human alpha-synuclein and aggregated alpha-synuclein immunofluorescence staining
AUTHORS: Pietro La Vitola
[DESCRIPTION]
This protocol is designed for human alpha-synuclein staining using the MJFR1-Alexa 488 (RRID:AB_2537217) antibody and either anti-SynO2 (RRID:AB_2632701) or MJFR-14-6-4-2 (RRID:AB_2714215... | ["[Day 1] Rinse brain slices (35µ) in TBS (0.05M Trizma base and 0.15M NaCl; pH: 7.6) 3X 10 min", "[Day 1] Quench brain slices in a solution containing 3%H2O2 and 10% Methanol in TBS 20 min", "[Day 1] Rinse brain slices in TBS (0.05M Trizma base and 0.15M NaCl; pH: 7.6) 3X 10 min", "[Day 1] Incubate in blocking buffer ... |
63,872 | Asset | 1 | dx.doi.org/10.17504/protocols.io.bp2l61pqdvqe/v1 | https://www.protocols.io/view/asset-cak8sczw | littlelife | TITLE: Asset
AUTHORS: littlelife
[DESCRIPTION]
Fixed asset management is the process of ensuring an organization's assets are accounted for, deployed, maintained, upgraded, and disposed of when the time comes. Put simply, it's making sure that the valuable items, tangible and intangible, in your organization are tra... | [] |
51,752 | Pseudoislets for diabetes research: Purifying and selective re-aggregating human islet cells | 4 | dx.doi.org/10.17504/protocols.io.bwsgpebw | https://www.protocols.io/view/pseudoislets-for-diabetes-research-purifying-and-s-bwsgpebw | Wei Liu, Craig Dorrell, Xiaojuan Chen | TITLE: Pseudoislets for diabetes research: Purifying and selective re-aggregating human islet cells
AUTHORS: Wei Liu, Craig Dorrell, Xiaojuan Chen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-style:italic;">In vitro </span><span>modeling of human islet cells for diabetes resea... | ["Human islet culture and single cell preparationIslets isolated from non-diabetic deceased human donors within 2-4 days post-isolation will be used in experiments. Islets and the dispersed cells are cultured at with 5% CO² in a CMRL-1066 supplemented CIT medium (Cellgro, Cat. #98-304-CV) with 10 IU/ml Heparin (Sagent... |
49,953 | Systematic Literature Review about Software for References Extraction | 1 | dx.doi.org/10.17504/protocols.io.buz9nx96 | https://www.protocols.io/view/systematic-literature-review-about-software-for-re-buz9nx96 | Alessia Cioffi | TITLE: Systematic Literature Review about Software for References Extraction
AUTHORS: Alessia Cioffi
[DESCRIPTION]
Converting unstructured data, i.e. data coded in a format which is not structured in a predefined way, such as PDF, into structured data, i.e. clearly defined types of data organised in a structure, has ... | ["[Create the materials for the research] The protocol reports the different and complementary steps required in order to make a systematic literature review. In this case, the topic of the research is focused on the retrieval of software for references extraction from PDF files. The structure of the review is split in... |
91,310 | Open field | 1 | dx.doi.org/10.17504/protocols.io.6qpvr32r2vmk/v1 | https://www.protocols.io/view/open-field-c5eny3de | Miquel Vila, Núria Peñuelas, Ariadna Laguna | TITLE: Open field
AUTHORS: Miquel Vila, Núria Peñuelas, Ariadna Laguna
[DESCRIPTION]
Open field
[STEPS]
1. Place the mice in a square open field arena of 80 x 80 cm of white methacrylate under brightly lit (300 lux).
2. Track the center and the periphery using a tracking software (SMART 3.0 Panlab-Harvard Apparatus).... | ["Place the mice in a square open field arena of 80 x 80 cm of white methacrylate under brightly lit (300 lux).", "Track the center and the periphery using a tracking software (SMART 3.0 Panlab-Harvard Apparatus).", "Clean the arena every time between animals."] |
13,615 | Human skin single cell dissociation | null | dx.doi.org/10.17504/protocols.io.ripd4dn | null | James Fletcher, Rachel Botting, Emily Stephenson, Peter Vegh, Muzlifah Haniffa | TITLE: Human skin single cell dissociation
AUTHORS: James Fletcher, Rachel Botting, Emily Stephenson, Peter Vegh, Muzlifah Haniffa
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Splitting dermis from epidermis, then dissociating single cells from human skin.</div></div>
[STEPS]
?. Cut skin into th... | ["Cut skin into thin strips, ~1.5cm wide", "Stretch the tissue using forceps, and using an 80μm guard on a dermatome cut the top layer of skin. Place this in ice cold PBS", "Cut a mesh of slits into the 200μm skin layer to aid enzymatic access", "Place the skin strips in a 50ml Falcon tube in RPMI + 2U/ml Dispase II", ... |
28,480 | Buffer preparation for OnePot PURE cell-free system | null | dx.doi.org/10.17504/protocols.io.728hqhw | null | Konstantinos Ragios | TITLE: Buffer preparation for OnePot PURE cell-free system
AUTHORS: Konstantinos Ragios
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">In this protocol we explain the procedure to create the Buffers used for Protein and Ribosome purification for the production of OnePot PURE cell-free system. </di... | ["Add the materials needed the buffer you want to produce in a beaker. The final concentration of the components for the different buffers is presented in Table 1 and Table 2", "Table 1: Buffers for Protein Purification ABCDE1CompoundBuffer ABuffer BBuffer HTStock buffer B2mMmMmMmM3HEPES505050504Ammonium chloride1000... |
60,205 | Expression of molecular markers in subpopulations of mouse stellate ganglion neurons | 4 | dx.doi.org/10.17504/protocols.io.8epv592bdg1b/v1 | https://www.protocols.io/view/expression-of-molecular-markers-in-subpopulations-b62mrgc6 | Daniele Neri, Lori Zeltser | TITLE: Expression of molecular markers in subpopulations of mouse stellate ganglion neurons
AUTHORS: Daniele Neri, Lori Zeltser
[DESCRIPTION]
This protocol is a direct application of the original RNAScope Fluroescent Multiplex Reagent Kit (ACDBio, Document Number 320293-USM, https://acdbio.com/sites/default/files/32... | [] |
79,935 | Retrieving SSH Journals Citation Information from three datasets (COCI, META and ERIH-PLUS) - Workflow | 5 | dx.doi.org/10.17504/protocols.io.n92ldpeenl5b/v1 | https://www.protocols.io/view/retrieving-ssh-journals-citation-information-from-csa7wahn | Marta Soricetti, Sara Vellone, Olga Pagnotta, ellepuntopi. | TITLE: Retrieving SSH Journals Citation Information from three datasets (COCI, META and ERIH-PLUS) - Workflow
AUTHORS: Marta Soricetti, Sara Vellone, Olga Pagnotta, ellepuntopi.
[DESCRIPTION]
Purpose: we want to find out
by looking at citations data contained in COCI, the number of citations included in Meta which ref... | ["[Reading Input Data] We started to analyse the datasets using pandas:\nMeta: csv dataset of Open Citations Meta \nCOCI: COCI dump\nERIH-PLUS: list of approved journals", "[Processing of Input Data] We tried to define a mapping of the datasets and this is the result:", "[Processing of Input Data] We processed the data... |
44,299 | PBMC Stimulation with Peptide Pools and Fluorospot Assay | 4 | dx.doi.org/10.17504/protocols.io.bphjmj4n | https://www.protocols.io/view/pbmc-stimulation-with-peptide-pools-and-fluorospot-bphjmj4n | cecilia , Alessandro Sette | TITLE: PBMC Stimulation with Peptide Pools and Fluorospot Assay
AUTHORS: cecilia , Alessandro Sette
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The purpose of this protocol is to stimulate PBMCs with peptide pools for 14 days followed by Fluorospot assay.</div></div>
[STEPS]
?. [Thawing of Cryo... | ["[Thawing of Cryopreserved PBMC]\nAdd (complete RPMI with 5% human serum) and per vial of cells to a 50 ml tube.\n[media]\n[Benzonase]", "[Thawing of Cryopreserved PBMC]\nPlace PBMC vials in water bath for approximately 60-90s.\n37 °C", "[Thawing of Cryopreserved PBMC]\nBefore cells are completely thawed, add them ... |
null | null | null | dx.doi.org/10.17504/protocols.io.eydbfs6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?. | [] |
88,656 | Preparation of cells for live-cell imaging of phosphoinositide reporters by total internal reflection fluorescence (TIRF) microscopy | 4 | dx.doi.org/10.17504/protocols.io.kxygx37jkg8j/v1 | https://www.protocols.io/view/preparation-of-cells-for-live-cell-imaging-of-phos-c2tqyemw | Ralitsa R Madsen | TITLE: Preparation of cells for live-cell imaging of phosphoinositide reporters by total internal reflection fluorescence (TIRF) microscopy
AUTHORS: Ralitsa R Madsen
[DESCRIPTION]
This protocol provides detailed instructions for transient expression of PIP3/PI(3,4)P2-selective PH domain-based reporters for subsequent ... | ["[Dish assembly and coating] Take the required number of Ibidi dishes that will be needed for the experiment, along with the equivalent number of inserts. (NB: you can reuse inserts once provided that they have been sterilised in 70% ethanol and dried since the last use; we do this by passing them through PBS once, th... |
null | null | null | dx.doi.org/10.17504/protocols.io.dpy5pv | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is a protocol from: <br /><br />Suttle, C. A. and J. A. Fuhrman. 2010. Chapter 15: Enumeration of virus particles in aquatic or sediment samples by epifluorescence microscopy. Manual of Aquatic Viral Ecology. Waco, TX:American Society of Limnology and Oceanography... | [] |
77,067 | Acute striatal or midbrain fiber photometry in head-fixed mice | 1 | dx.doi.org/10.17504/protocols.io.4r3l27yj4g1y/v1 | https://www.protocols.io/view/acute-striatal-or-midbrain-fiber-photometry-in-hea-cphjvj4n | Maite Azcorra | TITLE: Acute striatal or midbrain fiber photometry in head-fixed mice
AUTHORS: Maite Azcorra
[DESCRIPTION]
This protocol describes how to:
- Implant head plates on mice for head-fixation during behavior
- Train mice for head-fixed running on a cylindrical treadmill, and to receive rewards and air puffs while head-fixe... | ["[Head plate implant] Surgery preparation", "[Training and behavior] Rotational velocity of the treadmill during locomotion is sampled at 1,000 Hz by a rotary encoder (E2-5000, US Digital) attached to the axel of the treadmill and a custom LabView program.", "[Training and behavior] Habituate mice to run on the treadm... |
null | null | null | dx.doi.org/10.17504/protocols.io.c76zrd | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
We use this protocol to test if flies have preferance for darkness or light (phototactic or non-phototactic response).
[GUIDELINES]
We are using 3 day-old-flies (half of the experimental flies have their wings clipped, and half don’t).<br /><br />
[STEPS]
?.
?.
?.
?. ... | [] |
91,532 | Determining IIDP Minimal Donor Criteria | 1 | dx.doi.org/10.17504/protocols.io.4r3l28p4ql1y/v4 | https://www.protocols.io/view/determining-iidp-minimal-donor-criteria-c5mky44w | Integrated Islet Distribution Program | TITLE: Determining IIDP Minimal Donor Criteria
AUTHORS: Integrated Islet Distribution Program
[DESCRIPTION]
This SOP defines the pancreas donor profile acceptable for use in the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) sponsored research in the Integrated Islet Distribution Program (II... | ["[I.\tIIDP Donor Inclusion Criteria] The following are IIDP Inclusion Criteria for Pancreas Donors for Human Islet Isolation:", "[I.\tIIDP Donor Inclusion Criteria] A multi-organ donor or pancreas-only donor if the donor meets all the criteria for multi-organ donation", "[I.\tIIDP Donor Inclusion Criteria] Adequate in... |
100,972 | An end-to-end workflow to study newly synthesized mRNA following rapid protein depletion in Saccharomyces cerevisiae | 4 | dx.doi.org/10.17504/protocols.io.n2bvj3dj5lk5/v4 | https://www.protocols.io/view/an-end-to-end-workflow-to-study-newly-synthesized-deuk3euw | John B. Ridenour, Rafal Donczew | TITLE: An end-to-end workflow to study newly synthesized mRNA following rapid protein depletion in Saccharomyces cerevisiae
AUTHORS: John B. Ridenour, Rafal Donczew
[DESCRIPTION]
In this protocol, we describe an end-to-end workflow for rapidly degrading a target protein using the AID system and quantifying newly synth... | ["[Saccharomyces cerevisiae growth, IAA treatment, 4tU labeling, and rapid fixation] Add 5 ml of 100% methanol to a 50 ml conical tube for each sample to be collected. Keep tubes on dry ice. Three tubes are needed for each 40 ml culture.", "[Saccharomyces cerevisiae growth, IAA treatment, 4tU labeling, and rapid fixati... |
53,164 | Sanger sequencing of SARS-CoV-2 Spike protein | 4 | dx.doi.org/10.17504/protocols.io.bx6kprcw | https://www.protocols.io/view/sanger-sequencing-of-sars-cov-2-spike-protein-bx6kprcw | Tiago S. Salles*, Andrea Cony Cavalcanti*, Fabio Burack da Costa, Renata Campos Azevedo | TITLE: Sanger sequencing of SARS-CoV-2 Spike protein
AUTHORS: Tiago S. Salles*, Andrea Cony Cavalcanti*, Fabio Burack da Costa, Renata Campos Azevedo
[DESCRIPTION]
The SARS-CoV-2 responsible for the ongoing COVID pandemic reveals particular evolutionary dynamics and an extensive polymorphism, mainly in Spike protei... | ["RT-PCR\n\nProgram the thermal cycler before setting up the reaction. The thermal cycler should be preheated to 45–60°C.\nKeep all components, reaction mixes, and samples on ice. After preparation of the samples, transfer them to the preheated thermal cycler and immediately start the RT–PCR program.\nReaction mix shou... |
71,089 | MagAttract + Metapolyzyme metagenomic gDNA extraction from urine | 4 | dx.doi.org/10.17504/protocols.io.n2bvj8o5bgk5/v2 | https://www.protocols.io/view/magattract-metapolyzyme-metagenomic-gdna-extractio-chnrt5d6 | Natalie Ring | TITLE: MagAttract + Metapolyzyme metagenomic gDNA extraction from urine
AUTHORS: Natalie Ring
[DESCRIPTION]
A protocol for the metagenomic extraction of bacterial DNA from urine samples (optimised using dog urine), for use in a rapid diagnostics pipeline. At the end of the protocol, the DNA is cleaned up and ready for... | ["[Extended pre-lysis spin down] Pellet 2x 1.5 ml aliquots of urine in 1.5 ml tubes by centrifuging at maximum speed (~13,000 RPM/16,000 xg) for 20 minutes, then discard supernatant\n\n3 mL \n\n\n16,000 x g, 20 min, RT Room temperature", "[Metapolyzyme & Proteinase K Lysis] Resuspend cell pellets (which might be in... |
67,460 | Voronoi tesselation | 4 | dx.doi.org/10.17504/protocols.io.yxmvmnrx6g3p/v1 | https://www.protocols.io/view/voronoi-tesselation-cd5cs82w | adalberto.merighi, Laura Lossi | TITLE: Voronoi tesselation
AUTHORS: adalberto.merighi, Laura Lossi
[DESCRIPTION]
This protocol describes how to perform Voronoi tesselation analysis of cerebellar images. It can be used for any biological images to study cellular sociology and is based on a model of parametrization and quantitation of
cellular popula... | ["[Image processing with the Voronoi generator] Open the interactive Voronoi diagram (Thiessen polygon) generator (https://cfbrasz.github.io/Voronoi.html).", "[Image processing with the Voronoi generator] Upload the image to be analyzed as indicated in the figure above. To do so your image (size must be 900x900 pixels ... |
61,507 | Single cell analysis of iPSC-derived midbrain organoids | 4 | dx.doi.org/10.17504/protocols.io.q26g74xjkgwz/v1 | https://www.protocols.io/view/single-cell-analysis-of-ipsc-derived-midbrain-orga-b8bbrsin | María José Pérez J., michela.deleidi | TITLE: Single cell analysis of iPSC-derived midbrain organoids
AUTHORS: María José Pérez J., michela.deleidi
[DESCRIPTION]
The following script was used for analysis of gene corrected (GC) versus GBA1 mutant (MUT) midbrain organoids. The purpose was to combine, filter, integrate, and identify clusters and differential... | ["[Part 1. Data preparation]", "[Part 2. Quality control]", "[Part 3. Data preparation and normalization]", "[Part 4. Data integration and visualization (directly after Part 3)]", "[Part 5. Obtain information from the datasets]", "[Part 6. Merge and analyse subclusters]", "[Part 7. Create a subset of cells from a selec... |
null | null | null | dx.doi.org/10.17504/protocols.io.immcc46 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Method to chemically bleach Aiptasia<em> </em>in small volume dishes.</p>
<p> </p>
[GUIDELINES]
<p>You should see a response by the 2nd day at the latest, with noticably whiter anemones and visible pellets of expelled algae in the water. If not, sometimes the stock menthol ... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.dcc2sv | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<strong>per L:<br /></strong><br />20 g Sea Salts*<br />250 ml Basal Media <br />50 ml FeEDTA Stock <br />700 ml DIH<sub>2</sub>0 <br />0.1% vitamin supplement (optional)*<br /><br />*FeEDTA, carbon substrate and vitamins are added post-autoclaving once media has cooled to ~50&de... | [] |
99,202 | RoCK and ROI: bead modification, library generation and sequencing protocol | 0 | dx.doi.org/10.17504/protocols.io.rm7vzjyb5lx1/v1 | https://www.protocols.io/view/rock-and-roi-bead-modification-library-generation-dc5a2y2e | Giulia Moro, Konrad Basler, Erich Brunner | TITLE: RoCK and ROI: bead modification, library generation and sequencing protocol
AUTHORS: Giulia Moro, Konrad Basler, Erich Brunner
[DESCRIPTION]
Various tools have been developed to reliably identify, trace and analyze single cells in complex tissues. In recent years, these technologies have been combined with tran... | ["[Step 1 modification of full vial of RoCKseq beads: preparation of reagents] Thaw lambda exonuclease buffer, T4 polymerase buffer, 100 µM splint(s), polyA oligo and 10 mM dNTPs at room temperature and place on ice", "[Step 1 modification of full vial of RoCKseq beads: preparation of reagents] Preheat two thermomixers... |
106,923 | Pan-microbial metagenomics protocol | 0 | dx.doi.org/10.17504/protocols.io.eq2lyw5qpvx9/v1 | https://www.protocols.io/view/pan-microbial-metagenomics-protocol-dknj4vcn | Adela Alcolea-Medina, Luke Blagdon Snell, Chris Alder, Rahul Batra | TITLE: Pan-microbial metagenomics protocol
AUTHORS: Adela Alcolea-Medina, Luke Blagdon Snell, Chris Alder, Rahul Batra
[DESCRIPTION]
Please remember to cite the original manuscript: Alcolea-Medina et al. Unified metagenomic method for rapid detection of microorganisms in clinical samples. Commun Med (Lond). 2024 Jul 7... | ["[Preparation of quality controls:] Mix 300μL of control 1 and 300μL of control 2 in an Eppendorf. Label with date and LOT number.", "[Preparation of quality controls:] Vortex for 1 minute and Centrifuge at 1,200xg for 5min immediately prior to each use.", "[Preparation of quality controls:] Aliquot the volume specifi... |
21,347 | Yale - Triglycerides | null | dx.doi.org/10.17504/protocols.io.y4bfysn | null | John Stack, Gary Cline | TITLE: Yale - Triglycerides
AUTHORS: John Stack, Gary Cline
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Procedure used to determine the concentration of triglycerides in blood, serum, and plasma. Triglycerides are ... | ["Calibrate Cobas for Triglyceride analysis by running a multi-analyte calibrator and two control serum.", "Sample handling as performed by Cobas Mira Plus. a) Pipette 4 µL of sample into cuvette. b) Add 275 µL of Triglyceride liquid reagent. c) Incubate at 37ºC for 10 minutes. d) Absorbance is measured at... |
null | null | null | dx.doi.org/10.17504/protocols.io.i3pcgmn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Gene specific primers are retrieved from Primer Premier 6.0 and National Center for Biotechnology Information Software；Fluorescent dye are SYBR® Premix Ex Taq<sup>™ </sup>II (Tli RNaseH Plus)(TaKaRa,China).</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?. | [] |
27,197 | Evaluating a Community-Driven Cervical Cancer Prevention program in Western Kenya | null | dx.doi.org/10.17504/protocols.io.6s5heg6 | null | Megan Huchko, Elizabeth Bukusi, Craig R. Cohen | TITLE: Evaluating a Community-Driven Cervical Cancer Prevention program in Western Kenya
AUTHORS: Megan Huchko, Elizabeth Bukusi, Craig R. Cohen
[STEPS]
?. | [] |
26,342 | Make potassium orthophosphate solution | null | dx.doi.org/10.17504/protocols.io.5yeg7te | null | Gurdon Institute media kitchen | TITLE: Make potassium orthophosphate solution
AUTHORS: Gurdon Institute media kitchen
[STEPS]
?.
?. ABCDEF1SolutionPotassium
Orthophosphates 2Strength0.17M & 0.72pH: Batch size1.2L3Date
of preparation 45IngredientsQuantityAdded (tick)Manufacturer/Batch No.6KH2PO4 ( potassium
... | ["ABCDEF1SolutionPotassium\n Orthophosphates 2Strength0.17M & 0.72pH: Batch size1.2L3Date\n of preparation 45IngredientsQuantityAdded (tick)Manufacturer/Batch No.6KH2PO4 ( potassium\n dihydrogen orthophosphate)27.7g 7K2HPO4 (dipotassium hydrogen orthophosphat... |
41,331 | SDS page | 1 | dx.doi.org/10.17504/protocols.io.bkktkuwn | https://www.protocols.io/view/sds-page-bkktkuwn | Andreea S | TITLE: SDS page
AUTHORS: Andreea S
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">SDS-PAGE is an analytical technique used to separate proteins based on their molecular weight using electrophoresis. Peptides migrate faster due to less resistance from the gel matrix. The peptide used in this exper... | ["[SDS PAGE of a very small protein]\nCasting the gel: 1] Glass plates and spacers will be assembled in gel casting apparatus–see BioRad instruction manual. 2] The components will be mixed for the resolving gel as described in the subscript. 3] The resolving gel mixture will be poured into the gel plates to a level be... |
91,567 | Brain image simulation protocol | 5 | dx.doi.org/10.17504/protocols.io.4r3l22bxql1y/v1 | https://www.protocols.io/view/brain-image-simulation-protocol-c5npy5dn | Bin Fu | TITLE: Brain image simulation protocol
AUTHORS: Bin Fu
[DESCRIPTION]
This protocol details the method for simulating a brain image with small and large features
[STEPS]
1. 1. Prepare negative control images where no fluorescent puncta were labelled. These images are considered as background images.
2. 2. Select one o... | ["1. Prepare negative control images where no fluorescent puncta were labelled. These images are considered as background images.", "2. Select one or several cropped images containing large aggregates in the library and apply a sigmoid function to the selected cropped image where x in the sigmoid function is determined... |
42,321 | Toxicity assay for mosquito larvicidal activity-Part2 | 3 | dx.doi.org/10.17504/protocols.io.bmjrk4m6 | https://www.protocols.io/view/toxicity-assay-for-mosquito-larvicidal-activity-pa-bmjrk4m6 | avinash.kale | TITLE: Toxicity assay for mosquito larvicidal activity-Part2
AUTHORS: avinash.kale
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.j6qcrdw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?. | [] |
22,274 | S-Complete Medium | 1 | null | https://www.protocols.io/view/s-complete-medium-zzaf72e | Adrien Assie, Buck Samuel | TITLE: S-Complete Medium
AUTHORS: Adrien Assie, Buck Samuel
[DESCRIPTION]
Large quantities of C. elegans can be grown in a liquid medium. Liquid cultures of C. elegans are usually grown on S Medium using concentrated E. coliOP50 as a food source. This is the S-Complete medium recipe.
[STEPS]
1. 977 mLof S-Basal medi... | ["977 mLof S-Basal medium (Link below)", "1 mL of 5 mg/ mL cholesterol (dissolved in Et-OH)", "10 mL of 1 Molarity (M) Potassium Citrate Buffer, pH 6.0", "10 mLof Trace metals solution (sterile)", "3 mLof 1 Molarity (M)CaCl2 (sterile)", "3 mLof 1 Molarity (M) MgSO4 (sterile)"] |
null | null | null | dx.doi.org/10.17504/protocols.io.pq6dmze | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Transfusion-transmitted malaria, Donor prevalence and health worker knowledge and practices. Protocols for preparation of blood smears (Thick and thin films), reporting of malaria parasites, blood grouping and design of questionnaires.</p>
<p> </p>
<p> </p>
[STEPS]
?.
?.
?... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.jwtcpen | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Brief outline of the Campbell Lab's protocol for using ImageLab (Bio-Rad, freeware with registration) to calculate concentrations of protein in phytoplankton samples against a quantitative protein standard such as RbcL or PsbA. ImageLab can export an excel format, allowing fo... | [] |
33,159 | Markers of endothelial dysfunction and arterial stiffness in patients with early-stage autosomal dominant polycystic kidney disease: a meta-analysis | null | dx.doi.org/10.17504/protocols.io.bcmfiu3n | null | Ioannis Bellos | TITLE: Markers of endothelial dysfunction and arterial stiffness in patients with early-stage autosomal dominant polycystic kidney disease: a meta-analysis
AUTHORS: Ioannis Bellos
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Autosomal dominant polycystic kidney disease (ADPKD) represents the most... | ["Review title: Markers of endothelial dysfunction and arterial stiffness in patients with early-stage autosomal dominant polycystic kidney disease: a meta-analysis", "Review question: To assess whether autosomal dominant polycystic kidney disease (ADKPKD) is linked to endothelial dysfunction and arterial stiffness dur... |
97,983 | Basics of soldering | 0 | dx.doi.org/10.17504/protocols.io.n92ld8yynv5b/v1 | https://www.protocols.io/view/basics-of-soldering-dbw72phn | Eric S McLamore | TITLE: Basics of soldering
AUTHORS: Eric S McLamore
[DESCRIPTION]
This protocol describes the basic principles of soldering. An ANBES soldering station is used for this protocol, but most of the methods are interchangeable with other soldering irons. The process requires approximately 30 min, but timing can vary depen... | ["[Prepare equipment and materials] Wet sponge with DI water and place in soldering iron stand\nIf using a brass sponge it is not necessary to wet with DI water\nEnsure that soldering iron stand is properly positioned (Fig 1)\n\n \n\n \n\nInspect the soldering iron tip. The tip should be free of physical bends/scrapes,... |
93,091 | Microglia differentiation | 4 | dx.doi.org/10.17504/protocols.io.4r3l22zbjl1y/v1 | https://www.protocols.io/view/microglia-differentiation-c66bzhan | Riana Lo Bu, Frank Soldner | TITLE: Microglia differentiation
AUTHORS: Riana Lo Bu, Frank Soldner
[DESCRIPTION]
This protocol has been refined to differentiate microglia cells from hESC adapted to feeder free culture systems as described in the following protocol:
Protocol Overview
A. Flask Preparation
B. Poly-D-Lysine (PDL) plate coating
C. M... | ["[Flask preparation] Thaw matrigel on ice inside a 4 °C fridge. Chill all flasks, pipettes and materials to be used for flask preparation under the same conditions and keep everything as cold as possible throughout the procedure (do not use a freezer as it can cause the matrigel solution to freeze while platting).",... |
84,670 | A recipe for extremely reproducible enrichment analysis | 5 | dx.doi.org/10.17504/protocols.io.j8nlkwpdxl5r/v2 | https://www.protocols.click/view/a-recipe-for-extremely-reproducible-enrichment-ana-cww6xfhe | Mark Ziemann, Anusuiya Bora | TITLE: A recipe for extremely reproducible enrichment analysis
AUTHORS: Mark Ziemann, Anusuiya Bora
[DESCRIPTION]
Enrichment analysis is a popular computational biology technique for interpreting omics data, but typically these are conducted irreproducibly with web-based and graphical interface tools, which risks omit... | ["[Install Docker] Open a terminal. Docker is a tool for working with containers, including building and running them. It is essential for ensuring reprducibility. We will install it using the command line interface, also known as the \"terminal\". We're assuming this is the first time using Ubuntu, so you'll need know... |
18,069 | Recombinase polymerase amplification assay for detection of Mycobacterium ulcerans DNA | null | dx.doi.org/10.17504/protocols.io.vvve666 | null | Michael Frimpong, Hubert Senanu Ahor | TITLE: Recombinase polymerase amplification assay for detection of Mycobacterium ulcerans DNA
AUTHORS: Michael Frimpong, Hubert Senanu Ahor
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This document describes the standard operating procedure for the application of the real time Mu-RPA assay... | ["[1.\tPerforming the amplification: Rehydration of reaction pellets and ‘magnesium start’]\nFor each sample, prepare a mastermix as follows: 2.1 μl of Mu_RPA F1 (10μM), 2.1 μl of Mu_RPA R2 (10μM), 0.6 μl of Mu-RPA P (10μM), 29.5 μl of Rehydration Buffer and 8.2 μl of dH2O.", "[1.\tPerforming the amplification: Rehy... |
77,411 | Differentiation of human Dopamine Neurons (DaNs) from induced pluripotent stem cells (iPSCs) | 4 | dx.doi.org/10.17504/protocols.io.q26g7y1jqgwz/v1 | https://www.protocols.io/view/differentiation-of-human-dopamine-neurons-dans-fro-cpubvnsn | kaitlyn.cramb, Ana Belen Malpartida, Maria Claudia Caiazza, Richard Wade-Martins, Brent Ryan | TITLE: Differentiation of human Dopamine Neurons (DaNs) from induced pluripotent stem cells (iPSCs)
AUTHORS: kaitlyn.cramb, Ana Belen Malpartida, Maria Claudia Caiazza, Richard Wade-Martins, Brent Ryan
[DESCRIPTION]
This protocol employs a floor plate-based differentiation method to produce human midbrain dopaminergic... | ["[Differentiation of iPSCs into Neuronal Progenitor Cells (NPCs)] Day -2: Preparing plates for replating\nTwo days before intending on starting the differentiation (Day -2), add 1 mL/well in a 6-well plate of Geltrex one day prior to replating the iPSCs to begin the differentiation.", "[Differentiation of iPSCs into N... |
22,379 | Hydra Medium 4.0 | null | dx.doi.org/10.17504/protocols.io.z4jf8un | null | Rob Steele | TITLE: Hydra Medium 4.0
AUTHORS: Rob Steele
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This is the recipe for the medium that the Steele Lab currently uses for culturing all of its Hydra strains. A detailed description of the medium is in the following document: </span><a href="#" style =... | ["[Fill Tank]\nFill Nalgene tank with 100 liters of high purity water (Nanopure, MilliQ, or equivalent). The volume markings on the side of the tank are accurate enough for determining how much water you have added.", "[Add ingredients]\nAdd sodium bicarbonate Mix well with plastic paddle\n4.2 g", "[Add ingredients]\nA... |
37,671 | Fixing cell pellets | 1 | dx.doi.org/10.17504/protocols.io.bg2fjybn | https://www.protocols.io/view/fixing-cell-pellets-bg2fjybn | Verity Goodwin, Emily Souster, Mathew Garnett, Fiona Behan, Charlotte Beaver, Rizwan Ansari, Adam Jackson | TITLE: Fixing cell pellets
AUTHORS: Verity Goodwin, Emily Souster, Mathew Garnett, Fiona Behan, Charlotte Beaver, Rizwan Ansari, Adam Jackson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is designed to outline the process of fixing cell pellets in 1.5ml tubes. It has been developed ... | ["[Fixing]\nIn a fume hood, prepare a solution of 3.7% formaldehyde in PBS\nChemical safety: Formaldehyde 37% and 3.7% must be prepared and used only in the chemical fume hood, using chemical resistant gloves. Waste must be kept in the fume hood and disposed of appropriately.", "[Fixing]\nIn the fume hood, tap the tube... |
56,642 | SRA and Genbank BioSample-Linked Submission with Mercury_Prep and Mercury_Batch | 1 | dx.doi.org/10.17504/protocols.io.b3jaqkie | https://www.protocols.io/view/sra-and-genbank-biosample-linked-submission-with-m-b3jaqkie | Francis J Ambrosio | TITLE: SRA and Genbank BioSample-Linked Submission with Mercury_Prep and Mercury_Batch
AUTHORS: Francis J Ambrosio
[DESCRIPTION]
Submitting sequencing data to public data repositories is a meaningful yet tedious procedure. Linking submissions between SRA and Genbank will enhance the value of both submissions the the p... | ["[Data Preparation] The Titan Genomic Characterization workflow must be run prior to submitting sequences to SRA and Genbank in order to prepare the data for submission. Please use the Titan workflow that is compatible with your sequencing data.", "[Data Preparation] Please check that all samples have been analyzed us... |
34,813 | 10X TBS Buffer | null | dx.doi.org/10.17504/protocols.io.bd85i9y6 | null | Bryon Drown | TITLE: 10X TBS Buffer
AUTHORS: Bryon Drown
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Tris buffered saline (TBS) is a commonly used buffer with a wide range of applications in biochemistry. It is often more convenient to prepare a 10X solution so that additional components can be added when pre... | ["Weigh out Tris base\n3.13 g", "Weigh out Tris HCl\n27.45 g", "Weigh out sodium chloride\n88 g", "Dissolve in MilliQ water\n900 ml", "Measure and adjust to with concentrated HCl and/or NaOH", "Add MilliQ water to a final volume of 1 L"] |
39,256 | Sensitivity test of toehold | 1 | null | https://www.protocols.io/view/sensitivity-test-of-toehold-bijykcpw | Hung Liang Pai, Cheng-Ruei Yang | TITLE: Sensitivity test of toehold
AUTHORS: Hung Liang Pai, Cheng-Ruei Yang
[STEPS]
?. [Preparation]
Thaw the reagents including 1. DNase/ RNase free water (store in -20°C) 2. solution A (store in -80°C) 3. solution B (store in -80°C) 4. RNase inhibitor (store in -20°C) 5.toehold switches with invertase DNA (store in ... | ["[Preparation]\nThaw the reagents including 1. DNase/ RNase free water (store in -20°C) 2. solution A (store in -80°C) 3. solution B (store in -80°C) 4. RNase inhibitor (store in -20°C) 5.toehold switches with invertase DNA (store in 4°C) 6.miRNA as the trigger (store in 4°C)\non ice", "[Preparation]\nSterilize the be... |
45,859 | C-SOP-201: Genomic DNA Quantification using a Qubit Fluorometer | 4 | null | https://www.protocols.io/view/c-sop-201-genomic-dna-quantification-using-a-qubit-bq2bmyan | Mihir Kekre | TITLE: C-SOP-201: Genomic DNA Quantification using a Qubit Fluorometer
AUTHORS: Mihir Kekre
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">In order to prepare high quality double-stranded DNA libraries for Illumina WGS, extracted genomic DNA needs to... | ["[Before starting]\nThe buffer and BR/HS reagent (dye) should be stored at while the standards must be stored at . The reagent is light and humidity sensitive, it should be stored in the dark and exposed minimally during assay and sample preparation. When stored as directed, the reagent has a shelf-life of about 6 mo... |
93,871 | Ultrasound measurement of thoracolumbar fascia deformation | 4 | dx.doi.org/10.17504/protocols.io.eq2lyjbmwlx9/v1 | https://www.protocols.io/view/ultrasound-measurement-of-thoracolumbar-fascia-def-c7wpzpdn | Andreas AB Brandl | TITLE: Ultrasound measurement of thoracolumbar fascia deformation
AUTHORS: Andreas AB Brandl
[DESCRIPTION]
The authors describe a measurement method for recording the deformation of the thoracolumbar fascia in a clinical setting.
Since physiological (e.g. lack of activity, overload or delayed onset muscle soreness) o... | ["[Trunk extension task] The study participants sit on the treatment table with their feet touching the floor.", "[Trunk extension task] Participants are instructed to place their hands lightly on their thighs and keep their elbows close to their body.", "[Trunk extension task] They perform a slow bend of the upper bod... |
43,677 | PREPARING 6X NEB LOADING BUFFER CONTAINING GELGREEN (GG) labeled ‘6XNEB+GG’ | 3 | null | https://www.protocols.io/view/preparing-6x-neb-loading-buffer-containing-gelgree-bnv5me86 | TITLE: PREPARING 6X NEB LOADING BUFFER CONTAINING GELGREEN (GG) labeled ‘6XNEB+GG’
AUTHORS:
[STEPS] | [] | |
95,661 | Protocol TE Display sequencing (TED-Seq) | 4 | dx.doi.org/10.17504/protocols.io.dm6gp378pvzp/v1 | https://www.protocols.io/view/protocol-te-display-sequencing-ted-seq-c9nmz5c6 | pol.vendrell, Basile Leduque, Leandro Quadrana | TITLE: Protocol TE Display sequencing (TED-Seq)
AUTHORS: pol.vendrell, Basile Leduque, Leandro Quadrana
[DESCRIPTION]
Background: Mobilization of transposable elements (TEs) can generate large effect mutations. However, because new TE insertions are challenging to detect and transposition is typically rare, the actual... | ["[Before Starting] Before starting, be sure to have:\n\nP7_adapter_up\nP7_adapter_bottom\nP7 primer (P7_Primer_index#)\nPrimer for the 1st PCR (outer Primers)\nPrimer for the nested PCR (P7_Primer_index#, P5_linker_TE primer)\n\nNEBNext® UltraTM II DNA Library Prep Kit for Illumina® (New England Biolabs E7645, E7103) ... |
106,590 | Collection and shipment of specimen for Visium Spatial Transcriptomics (vST/Visium ST) | 0 | dx.doi.org/10.17504/protocols.io.36wgqn193gk5/v1 | https://www.protocols.io/view/collection-and-shipment-of-specimen-for-visium-spa-dkb64sre | Laura Robinson, Susan Sheehan, Gaven Garland, Ron Korstanje | TITLE: Collection and shipment of specimen for Visium Spatial Transcriptomics (vST/Visium ST)
AUTHORS: Laura Robinson, Susan Sheehan, Gaven Garland, Ron Korstanje
[DESCRIPTION]
These samples are part of the JAX-Sen project in the SenNet Consortium. Here we provide details on specimen collection and shipment procedures... | ["[Reagents and Materials:] 10% NBF fixative\nTweezers\nAppropriate container for fixing", "[Quality Key Points:] The tissue specimen should be always kept at 4 degrees Celsius and RNase-free. \nIt is crucial to not store the tissue specimen at RT to avoid any cell death, and tissue and/or RNA degradation.", "[Procedur... |
null | null | null | dx.doi.org/10.17504/protocols.io.fkibkue | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is a collection of G-Biosciences protocols: SpinOUT™ for Desalting & Buffer Exchange of Peptide & Protein Samples.</p>
<p>(Cat. # 786-170 to 786-173, 786-703 to 786-708, 786-865 to 786-869)</p>
[STEPS]
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.d7h9j5 | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
Heat dry block at 65o C<br /><br />Fly Griding Buffer (Adjust pH to 9.2)<br />
<table style="height: 161px;" width="535">
<tbody>
<tr>
<td> </td>
<td>For 100 mL</td>
</tr>
<tr>
<td>0.1M NaCl</td>
<td>584 mg</td>
</tr>
<tr>
<td>0.2M Sucrose</td>
<td>6.85g</td>
</tr>
<tr>
<td>
<p... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.im9cc96 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol allows for adequate DNA extraction from fresh blood samples.</p>
[BEFORE_START]
<p>Separate PCR-free facility</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.u2yeyfw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Material science is the science of researching organizational structure, nature, production process, the use efficiency of materials, and the interrelationship between them and physics, chemistry and metallurgy. Material science is an application science which is inseparable fro... | [] |
59,708 | A fluorescence-based in vitro scrambling assay for yeast MCP1 and human XK | 4 | dx.doi.org/10.17504/protocols.io.kxygxzyqdv8j/v1 | https://www.protocols.io/view/a-fluorescence-based-in-vitro-scrambling-assay-for-b6i4rcgw | Zhouping Hong, Karin Reinisch | TITLE: A fluorescence-based in vitro scrambling assay for yeast MCP1 and human XK
AUTHORS: Zhouping Hong, Karin Reinisch
[DESCRIPTION]
VPS13 proteins are proposed to function at contact sites between organelles as bridges for lipids to move directionally and in bulk between organellar membranes. VPS13s are found to... | ["[Protein purification] Constructs encoding MCP1 (pCMV10-3xFLAG-Prs-MCP1) or XK (pCMV10-3xFLAG-Prs-XK) were transfected into Expi293 cells at the density of ~3 million/ml. The protein expression was enhanced with 3.5 millimolar (mM) valproic acid (VPA) 18 hours after transfection. The cells were harvested 48 hours af... |
28,065 | Breast tumours dissociation | null | dx.doi.org/10.17504/protocols.io.7m9hk96 | null | Samah El Ghamrasni | TITLE: Breast tumours dissociation
AUTHORS: Samah El Ghamrasni
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A protocol designed to dissociate fresh breast tissues (surgical specimens and biopsies) for single-cell RNAseq.
</div><div class = "text-block">The protocol has been demonstrated to work... | ["[Tissue Dissociation]\nTransfer the tissue onto a 10 cm petri dish", "[Tissue Dissociation]\nRinse 1x briefly with ice cold PBS and aspirate PBS off.", "[Tissue Dissociation]\nUse a blade to carefully cut the sample into small pieces, approximately 3-4 mm in diameter.", "[Tissue Dissociation]\nTransfer pieces into 50... |
null | null | null | dx.doi.org/10.17504/protocols.io.ddf23m | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Purpose: This protocol describes the use of ImageJ to measure dimensions of viruses in TEM micrographs, but can be applied to the measurement of anything in any image. <br /><br />The ImageJ program can be downloaded free (<a href="http://rsbweb.nih.gov/ij/" target="_blank">http... | [] |
47,595 | HTAN Multiplex IHC Image Cytometry V0.1 | 5 | dx.doi.org/10.17504/protocols.io.bsqjndun | https://www.protocols.io/view/htan-multiplex-ihc-image-cytometry-v0-1-bsqjndun | Shamilene Sivagnanam, Courtney Betts, Lisa Coussens | TITLE: HTAN Multiplex IHC Image Cytometry V0.1
AUTHORS: Shamilene Sivagnanam, Courtney Betts, Lisa Coussens
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Understanding immune complexity within the tumor microenvironment provides valuable insight to tumor-immune composition, spatial interactions, a... | ["[File prep and Folder Structure]\nFOLDER AND FILE NAMING CONVENTIONMake sure folder and file naming convention is consistent throughout the entire study. Filenaming convention should be used when saving images during acquisition.\nNAMING SLIDE FOLDERS AND IMAGE FILESEach slide folder in a cohort batch should maintain... |
62,107 | Panda Express Keto: 100% Effective and Natural Ingredients! | 1 | dx.doi.org/10.17504/protocols.io.q26g743kkgwz/v1 | https://www.protocols.io/view/panda-express-keto-100-effective-and-natural-ingre-b8v3rw8n | jhdfgkot | TITLE: Panda Express Keto: 100% Effective and Natural Ingredients!
AUTHORS: jhdfgkot
[DESCRIPTION]
➢Product Name — Panda Express Keto
➢ Category — Weight Loss
➢ Principal Ingredient — BHB Ketones
➢ Benefits — Weight Loss and Fat Burner
➢Utilization route — Oral
➢Dose — 2 Pills/Day
➢ Side Effects — No Destructive Imp... | [] |
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