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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38,958 | SOLUTION- 05 - Wash solution (PBS/FBS) for PBMC | 3 | dx.doi.org/10.17504/protocols.io.biankade | https://www.protocols.io/view/solution-05-wash-solution-pbs-fbs-for-pbmc-biankade | Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino | TITLE: SOLUTION- 05 - Wash solution (PBS/FBS) for PBMC
AUTHORS: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino
[STEPS] | [] |
27,354 | Creating Diffusion Tensor Images (DTI) | null | dx.doi.org/10.17504/protocols.io.6x2hfqe | null | Laurel Dieckhaus | TITLE: Creating Diffusion Tensor Images (DTI)
AUTHORS: Laurel Dieckhaus
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This procedure describes the steps required to create diffusion tensor images (DTI) from data from the MRI scanner. </div><div class = "text-block"><span style = "font-weight:bold;... | ["[Set Up Directory with Required Files]\nOpen a new terminal.", "[Set Up Directory with Required Files]\nCreate a directory to place data. (If not already created.)", "[Set Up Directory with Required Files]\nGo to the directory that you plan to use.", "[Set Up Directory with Required Files]\nCopy directory where your ... |
49,474 | Peripheral PRV injection - Kidney & Liver Protocol | 3 | dx.doi.org/10.17504/protocols.io.bujanuie | https://www.protocols.io/view/peripheral-prv-injection-kidney-amp-liver-protocol-bujanuie | Clara Huesing, Heike Muenzberg, Andrea Zsombok, Andrei Derbenev | TITLE: Peripheral PRV injection - Kidney & Liver Protocol
AUTHORS: Clara Huesing, Heike Muenzberg, Andrea Zsombok, Andrei Derbenev
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Pseudorabies viral injections allow for retrograde tracing with fluorescent markers. This protocol demonstrates how to in... | [] |
28,461 | ChroPack - Protein A | null | dx.doi.org/10.17504/protocols.io.72mhqc6 | null | Alexandra Ehl, David Frommholz, Nadine Stefanczyk | TITLE: ChroPack - Protein A
AUTHORS: Alexandra Ehl, David Frommholz, Nadine Stefanczyk
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Purification Guide for the Isolation of Antibodies with ChroPack Columns by DALEX Biotech.</span></div><div class = "text-block">Wi... | ["[What do you want to do?]\nDo you want to purify antibodies or sanitize your column?Please choose below.", "[Equilibration]\nConnect the column to your FPLC system. Set the flow rate to 1 bed volume per minute. Wash the column with 5 volumes deionized water (bed volume is written on the column).\nA dry column can be ... |
45,619 | ALM Window Surgery | 1 | dx.doi.org/10.17504/protocols.io.bqstmwen | https://www.protocols.io/view/alm-window-surgery-bqstmwen | Kayvon Daie, Tim Wang, Amrita Singh, Arseny Finkelstein, JJ Kim, Marton Rozsa, Karel Svoboda | TITLE: ALM Window Surgery
AUTHORS: Kayvon Daie, Tim Wang, Amrita Singh, Arseny Finkelstein, JJ Kim, Marton Rozsa, Karel Svoboda
[DESCRIPTION]
Protocol for Head Post and Cranial Window Surgery developed at Janelia Research Campus in the Svoboda Lab
Developed by Karel Svoboda for Trachtenberg et al 2002
Improved by Ant... | ["[Animal Preparation] Weigh the mouse and transfer it to a new cage if needed (i.e. if it's group housed, or if its cage is dirty.)\nIf mice do not have ear tags - denote first mouse removed as the first animal number etc.and cross out number on the original cage.\nIf the mice have ear tags, use the animal number that... |
52,214 | Primate Hair Cortisol Processing l | 1 | dx.doi.org/10.17504/protocols.io.bw8wphxe | https://www.protocols.io/view/primate-hair-cortisol-processing-l-bw8wphxe | Kimberley Phillips, Matthew Lopez | TITLE: Primate Hair Cortisol Processing l
AUTHORS: Kimberley Phillips, Matthew Lopez
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a protocol to quantify cortisol concentration from hair. Cortisol is a glucocorticoid hormone which is prominent in primates and can be used as a retrospectiv... | ["[Preparation before obtaining shaved hair ]\nHair clippers should be cleaned with alcohol before and after each use.", "[Obtaining shaved hair ]\nShave the hair from the upper back of the animal using electric clippers.", "[Obtaining shaved hair ]\nThe hair should be shaved close without nicking the skin, as this can... |
null | null | null | dx.doi.org/10.17504/protocols.io.j5kcq4w | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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40,530 | 617.1 URMC HTC BSL2+ Non-Inflated Fresh-Frozen Embedded Lung and Associated Tissue | 4 | dx.doi.org/10.17504/protocols.io.bjtsknne | https://www.protocols.io/view/617-1-urmc-htc-bsl2-non-inflated-fresh-frozen-embe-bjtsknne | Gloria S Pryhuber, Heidie Huyck, Lisa Rogers, Cory Poole | TITLE: 617.1 URMC HTC BSL2+ Non-Inflated Fresh-Frozen Embedded Lung and Associated Tissue
AUTHORS: Gloria S Pryhuber, Heidie Huyck, Lisa Rogers, Cory Poole
[DESCRIPTION]
Purpose and Scope of the Procedure
- Safe work with unfixed potentially or known SARS CoV2 / COVID-19+ infected tissue
- Rapid blocking, embedding a... | ["[Fresh Tissue Frozen in Cryomolds] Slicing and blocking procedure should be accomplished in a grossing station or fume hood with the operator taking appropriate blood and body fluid precautions", "[Fresh Tissue Frozen in Cryomolds] Prepare dry ice-ethanol (or isobutane) bath by covering bottom of flat ice bucket or s... |
63,846 | EMP 16S rRNA PCR | 4 | null | https://www.protocols.io/view/emp-16s-rrna-pcr-cakescte | Allyson Hirsch, George Testo | TITLE: EMP 16S rRNA PCR
AUTHORS: Allyson Hirsch, George Testo
[DESCRIPTION]
The 16S protocol detailed here is designed to amplify prokaryotes (bacteria and archaea) using paired-end 16S community sequencing on the Illumina platform. Primers 515F–806R target the V4 region of the 16S SSU rRNA.
[BEFORE_START]
The prime... | ["[Preparing PCR Hood] Decontaminate a PCR hood with DNA Away and Ethanol.", "[Preparing PCR Hood] Place materials inside of the PCR Hood (refer to materials section).", "[Preparing PCR Hood] Turn on the UV setting for at least 30 min.", "[Preparing Master Mix] Pour PCR water into a 50mL conical and make the master mix... |
52,111 | Checklist for organizing and managing data | 1 | null | https://www.protocols.io/view/checklist-for-organizing-and-managing-data-bw5ppg5n | Chris Berndsen | TITLE: Checklist for organizing and managing data
AUTHORS: Chris Berndsen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">When planning an experiment, making a plan for data organization is a key step. Data are the currency of science and allow for confirmation of results. Moreover, your data may ai... | ["[Data organization]\nCreate a separate folder for each type of experiment. Data should be sorted to keep data from the same experiment together.", "[Data organization]\nCreate separate sub-folders for distinct trials or data collection times within each experiment folder.", "[Data organization]\nKeep analysis files s... |
105,876 | Striatal Mitochondria Isolation Protocol | 0 | dx.doi.org/10.17504/protocols.io.5jyl82qz6l2w/v1 | https://www.protocols.io/view/striatal-mitochondria-isolation-protocol-djmu4k6w | Livia Hecke Morais | TITLE: Striatal Mitochondria Isolation Protocol
AUTHORS: Livia Hecke Morais
[DESCRIPTION]
Striatal Mitochondria Isolation Protocol used in the Mazmanian lab for Seahorse experiments and others
[STEPS]
SECTION: Reagents
1. Reagents
500 mL of MSHE (pH 7.2) for isolation
● 210 mM mannitol (Sigma, Cat #M1902) (1... | ["[Reagents] Reagents\n\n \n500 mL of MSHE (pH 7.2) for isolation\n\n● 210 mM mannitol (Sigma, Cat #M1902) (19.13 g) \n \n● 70 mM sucrose (Sigma, Cat #S0389) (11.98 g)\n\n● 5 mM HEPES (Sigma, Cat #H3537) (2.5 mL of 1M stock)\n \n● 1 mM EGTA (Sigma, Cat #E3889) (2 mL of 250 mM stock)\n\n● 0.2% fat... |
70,918 | PCR cleanup and size selection with magnetic beads | 4 | dx.doi.org/10.17504/protocols.io.36wgqj45xvk5/v1 | https://www.protocols.io/view/pcr-cleanup-and-size-selection-with-magnetic-beads-chhet33e | Dominik Buchner | TITLE: PCR cleanup and size selection with magnetic beads
AUTHORS: Dominik Buchner
[DESCRIPTION]
This protocol describes how to clean up PCR products or DNA extracts and perform a size selection with carboxylated-magnetic beads and a PEG-NaCl buffer. It can also be used for volume reduction of a sample or for buffer e... | ["Shake the cleanup solution until the beads are homogeneously resuspended", "Add 30 µL and 32 µL to a 250 µL U-bottom assay plate", "Add 10 µL of sample.", "To bind the DNA to the beads shake at", "Place the plate on a magnet to pellet the beads for 2 min", "Discard the supernatant by pipetting", "With the plate stil... |
null | null | null | dx.doi.org/10.17504/protocols.io.fbbbiin | null | null | TITLE: No Title
AUTHORS:
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43,307 | Purification of the Recombinant RNA Chaperone CspA | 1 | dx.doi.org/10.17504/protocols.io.bnijmccn | https://www.protocols.io/view/purification-of-the-recombinant-rna-chaperone-cspa-bnijmccn | Pilar Menendez-Gil, Carlos J. Caballero, Cristina Solano, Alejandro Toledo-Arana | TITLE: Purification of the Recombinant RNA Chaperone CspA
AUTHORS: Pilar Menendez-Gil, Carlos J. Caballero, Cristina Solano, Alejandro Toledo-Arana
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is part 3.1 of the "Fluorescent Molecular Beacons Mimicking RNA Secondary Structures to Study RNA C... | ["[Growth of Bacteria Expressing the GST-CspA Fusion Protein]\nStreak the E. coli BL21 (DE3) pGEX-6P-2::cspA strain in an LB agar plate supplemented with .\n[ampicillin]", "[Growth of Bacteria Expressing the GST-CspA Fusion Protein]\nInoculate a colony of the previous culture into a sterile test tube containing LB medi... |
58,098 | Serotyping | 4 | dx.doi.org/10.17504/protocols.io.b4ysqxwe | https://www.protocols.io/view/serotyping-b4ysqxwe | lydiariver | TITLE: Serotyping
AUTHORS: lydiariver
[DESCRIPTION]
Serotyping of Streptococcus agalactiae isolates was carried out by ImmuLex® Strep-B Latex (Statens Serum Institut, Copenhagen, Denmark), classifying them in serotypes 1a,1b, II, III, IV, V, VII, VIII, or IX.
[STEPS]
1. Use one colony from a 5-10% blood agar pla... | ["Use one colony from a 5-10% blood agar plate.", "Add one drop (10l) of latex reagent on a glass slide.", "Apply 10l phosphate buffer saline next to the drop of latex and suspend one\ncolony from the agar plate into the drop of saline.", "Mix the two drops", "Spread to cover the area of the circle.", "Observe for ag... |
76,236 | 616.1 URMC HTC BSL2+ Formalin-Inflated, Paraffin-Embedded Human Lung Tissue | 4 | dx.doi.org/10.17504/protocols.io.kxygxejwdv8j/v2 | https://www.protocols.io/view/616-1-urmc-htc-bsl2-formalin-inflated-paraffin-emb-cnpkvdkw | Gloria S Pryhuber, Heidie Huyck, Lisa Rogers | TITLE: 616.1 URMC HTC BSL2+ Formalin-Inflated, Paraffin-Embedded Human Lung Tissue
AUTHORS: Gloria S Pryhuber, Heidie Huyck, Lisa Rogers
[DESCRIPTION]
Processing of Formalin Fixed Lung and Non-Lung Tissue for the LungMAP HTC
[GUIDELINES]
Scientific Principles or Validation of Procedures :
CDC. “COVID-19 Perso... | ["[Record Process] Record details of procedure in Worksheet or Directly in Inventory or ELN", "[Record Process] Keep photographic recording of inflation and all steps of sectioning and blocking of lung lobe and tissue", "[Inflation Fixed (Formalin) Lung Lobe] Inflation fixation procedure should be accomplished in a bio... |
97,032 | CRISPR/Cas9-Mediated Knockdown in LUHMES Cells: Nucleofection and Validation Protocol | 0 | null | https://www.protocols.io/view/crispr-cas9-mediated-knockdown-in-luhmes-cells-nuc-dazg2f3w | Mallory Wright, William J Buchser, Colin Kremitzki, Serena Elia, Graham Bachman, emanuel gerbi, Jason Waligorski, Nicholas Tu, Lina Mohammed Ali | TITLE: CRISPR/Cas9-Mediated Knockdown in LUHMES Cells: Nucleofection and Validation Protocol
AUTHORS: Mallory Wright, William J Buchser, Colin Kremitzki, Serena Elia, Graham Bachman, emanuel gerbi, Jason Waligorski, Nicholas Tu, Lina Mohammed Ali
[DESCRIPTION]
Utilizing a CRISPR RNP complex and nucleofection, this pro... | ["[Nucleofection Protocol] Maintain cell confluency between 70–85% to optimize Nucleofection efficiencies; optimal results typically occur with cells in the logarithmic growth phase.", "[Nucleofection Protocol] Coat a new 6-well plate freshly with poly-L-ornithine and fibronectin to facilitate LUHMES attachment.", "[Nu... |
77,801 | In vitro kinase assay: phosphorylation of PI3Kc1 by TBK1and ULK1 | 4 | dx.doi.org/10.17504/protocols.io.j8nlkwr51l5r/v1 | https://www.protocols.io/view/in-vitro-kinase-assay-phosphorylation-of-pi3kc1-by-cp8hvrt6 | Elias Adriaenssens | TITLE: In vitro kinase assay: phosphorylation of PI3Kc1 by TBK1and ULK1
AUTHORS: Elias Adriaenssens
[DESCRIPTION]
This protocol describes in vitro kinase assay, in which PI3Kc is tested for phosphorylation by TBK1 and ULK1 complex either by western blotting (S29 on ATG14L subunit) or mass spectrometry analysis.
[STEP... | ["[In vitro kinase assay: phosphorylation of ATG14 by TBK1] Prepare Kinase Buffer without ATP and MgCl2.", "[In vitro kinase assay: phosphorylation of ATG14 by TBK1] Prepare 100 μL of Master Mix I containing TBK1 at the final concentration of 50 nM and PI3Kc1 at the final concentration of 800 nM in the Kinase Buffer wi... |
43,487 | Cell cryopreservation | 4 | null | https://www.protocols.io/view/cell-cryopreservation-bnp7mdrn | PMAT0001 | TITLE: Cell cryopreservation
AUTHORS: PMAT0001
[STEPS]
?. Gently detach cells from the tissue culture flask in the following manner:
?. Aspirate media
?. Wash with PBS, then aspirate.
2 mL
?. Wash with trypsin.
2 mL
?. Incubate for at .
37 °C
?. Resuspend the cells in of DMEM with FBS. Aliquot into a centrifug... | ["Gently detach cells from the tissue culture flask in the following manner:", "Aspirate media", "Wash with PBS, then aspirate.\n2 mL", "Wash with trypsin.\n2 mL", "Incubate for at .\n37 °C", "Resuspend the cells in of DMEM with FBS. Aliquot into a centrifuge tube. Of course, if there is a T25 flask, resuspend i... |
101,116 | Purification of mCh-WIPI2d-IDR (364-426aa) | 0 | dx.doi.org/10.17504/protocols.io.5qpvokk8bl4o/v1 | https://www.protocols.io/view/purification-of-mch-wipi2d-idr-364-426aa-dey43fyw | Elias Adriaenssens | TITLE: Purification of mCh-WIPI2d-IDR (364-426aa)
AUTHORS: Elias Adriaenssens
[DESCRIPTION]
This protocol details the purification of mCherry WIPI2d-IDR.
[STEPS]
SECTION: Purification procedure
1. To purify mCherry-WIPI2d IDR (364-426aa) (available from Addgene), fuse the corresponding coding sequence of WIPI2d to a... | ["[Purification procedure] To purify mCherry-WIPI2d IDR (364-426aa) (available from Addgene), fuse the corresponding coding sequence of WIPI2d to a N-terminal 6xHis-TEV-mCherry-tag through cloning into a pET-DUET1 vector (available from Addgene).", "[Purification procedure] After the transformation of the pET-DUET1 ve... |
86,827 | Isolation of DNA from spots (smears) of old microscopic glass slides with mini column isolation kit for molecular analysis | 4 | dx.doi.org/10.17504/protocols.io.14egn331ql5d/v1 | https://www.protocols.io/view/isolation-of-dna-from-spots-smears-of-old-microsco-cy2jxycn | Sudhir Bhatia | TITLE: Isolation of DNA from spots (smears) of old microscopic glass slides with mini column isolation kit for molecular analysis
AUTHORS: Sudhir Bhatia
[DESCRIPTION]
Many institutes have old fixed slides for microbiological purposes. These slides have valuable material for a particular
pathogen, which can be used f... | ["1. Mark the spot from the glass slide from which DNA\nis to be isolated but from other side. This can be done with normal Edding pen.\n\nNow switch on the heating block and adjust the temperature to 56°C.", "Put the slide on heating block but the marked area must touch the heating block.", "Prepare a microtube with 3... |
88,497 | Buck Institute Morphology Microtome Protocol | 4 | dx.doi.org/10.17504/protocols.io.j8nlkodrdv5r/v1 | https://www.protocols.io/view/buck-institute-morphology-microtome-protocol-c2nrydd6 | Stella Breslin, Akos A Gerencser | TITLE: Buck Institute Morphology Microtome Protocol
AUTHORS: Stella Breslin, Akos A Gerencser
[DESCRIPTION]
Buck Institute Morphology uses automatic rotary microtomes to section paraffin embedded tissue.
Safety considerations must be followed to safely acquire paraffin sections on an automatic microtome. The followin... | ["[Microtome setup] Turn on microtome, make sure all locks are set and blade guard is in place.", "[Microtome setup] Have tools accessible - forceps, brushes, kimwipes, blades, ice water.\nPlace water bath near microtome. Water temperature 40-45 C", "[Microtome setup] Set up blade holder angle between 5 to 10 degrees. ... |
40,496 | Detection of anti- SpA antibodies in egg white tested by double immunodiffusion (Ouchterlony) technique. | 4 | dx.doi.org/10.17504/protocols.io.bjsqkndw | https://www.protocols.io/view/detection-of-anti-spa-antibodies-in-egg-white-test-bjsqkndw | Angel Justiz-Vaillant | TITLE: Detection of anti- SpA antibodies in egg white tested by double immunodiffusion (Ouchterlony) technique.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Keyhole limpet hemocyanin (KLH) is a cooper-containing protein comprising of subunits with MW of 400 kDa. T... | ["Detection of anti-keyhole limpet hemocynin antibodies by double immunodiffusion is carried out.", "Briefly, 1% agarose gels are prepared and wells cut into the gel using a template.", "Initially, aliquots of 25 µl each of KLH in concentration of 1 mg/ml are applied to the centre well.", "The peripheral wells are fill... |
58,237 | A Programmable DNA Roadblock System Using dCas9 and Multivalent Target Sites | 1 | dx.doi.org/10.17504/protocols.io.b445qyy6 | https://www.protocols.io/view/a-programmable-dna-roadblock-system-using-dcas9-an-b445qyy6 | priceal , ekmatozel , parzialest | TITLE: A Programmable DNA Roadblock System Using dCas9 and Multivalent Target Sites
AUTHORS: priceal , ekmatozel , parzialest
[DESCRIPTION]
A protein roadblock forms when a protein binds DNA and hinders translocation of other DNA binding proteins. These roadblocks can have significant effects on gene expression an... | ["[PCR Preparation] Gather the materials used in Step 1 (See Materials section). Thaw components before use. Keep all on ice.", "Dilute the primers for (See Materials) to 10 uM before using.", "[PCR reaction] Combine the components from Step 1 into PCR tube(s) in order, for the desired final volume. Use Table 1 for ref... |
28,734 | Podocyte Counting and Density Analysis | null | dx.doi.org/10.17504/protocols.io.8a6hshe | null | Frank Brosius | TITLE: Podocyte Counting and Density Analysis
AUTHORS: Frank Brosius
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">This protocol describes the procedures for quantifying the podocyte count and density in the glomerul... | ["[Procedure:]\n1) Stain the Perfusion-fixed paraffin embedded sections (3.9 and 10.2 microns thick) with WT-1 antibody and immunoperoxidase and then take photograph at 40x by using Spot Advanced Software Camera.\n2) Photograph 50 consecutive glomerular cross-sections moving systematically from outer cortex to inner ... |
28,370 | MojoSort™ Mouse anti-PE Nanobeads Protocol | null | dx.doi.org/10.17504/protocols.io.7xshpne | null | Sam Li | TITLE: MojoSort™ Mouse anti-PE Nanobeads Protocol
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Product description and procedure summary:</span><span> Target cells are positively selected or depleted by incubating the sample with an anti-human PE ... | ["Prepare cells from your tissue of interest or blood without lysing erythrocytes.", "In the final wash of your sample preparation, resuspend the cells in MojoSort™ Buffer by adding up to 4 mL in a 5 mL (12 x 75 mm) polypropylene tube.Note: Keep MojoSort™ Buffer on ice throughout the procedure.", "Filter the cells with... |
52,925 | MicroCT protocols for scanning egg capsules of Hexaplex trunculus | 4 | dx.doi.org/10.17504/protocols.io.bxw5ppg6 | https://www.protocols.io/view/microct-protocols-for-scanning-egg-capsules-of-hex-bxw5ppg6 | Eva Chatzinikolaou, Kleoniki Keklikoglou | TITLE: MicroCT protocols for scanning egg capsules of Hexaplex trunculus
AUTHORS: Eva Chatzinikolaou, Kleoniki Keklikoglou
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Micro-computed tomography (micro-CT) is a high-resolution 3D-imaging technique which is now increasingly applied in biolog... | ["[Sample preparation]\nFixation of egg capsules of Hexaplex trunculus in 5% formaldehyde buffered with seawater.", "[Sample preparation]\nWash egg capsules with distilled water and dehydrated them with ethanol in gradually increasing concentrations (20%, 50%, 70%, 96%).", "[Sample preparation]\nPlacement of samples in... |
36,179 | CRISPR-based RNA proximity proteomics (CBRPP) | null | dx.doi.org/10.17504/protocols.io.bfjtjknn | https://www.protocols.io/view/crispr-based-rna-proximity-proteomics-cbrpp-bfjtjknn | Yunfei Li, Shengde Liu, Lili Cao, Yujie Luo, Hongqiang Du, Fuping You | TITLE: CRISPR-based RNA proximity proteomics (CBRPP)
AUTHORS: Yunfei Li, Shengde Liu, Lili Cao, Yujie Luo, Hongqiang Du, Fuping You
[STEPS]
?. [Construction of inducibly expressing dPspCas13b-BioID2 cell line.]
Construction of inducibly expressing dPspCas13b-BioID2 cell line. The two consecutive manipulation steps are... | ["[Construction of inducibly expressing dPspCas13b-BioID2 cell line.]\nConstruction of inducibly expressing dPspCas13b-BioID2 cell line. The two consecutive manipulation steps are necessary to generate Tet-on cell line with inducible expression of dPspCas13b-BioID2. The first step is generation of cells stably expressi... |
40,785 | ELISA for quantification of IL-22 in human serum. | 6 | dx.doi.org/10.17504/protocols.io.bj3rkqm6 | https://www.protocols.io/view/elisa-for-quantification-of-il-22-in-human-serum-bj3rkqm6 | Angel Justiz-Vaillant | TITLE: ELISA for quantification of IL-22 in human serum.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Interleukins (IL) are a type of cytokine first thought to be expressed by leukocytes alone but have later been found to be produced by many other body cells. ... | ["An anti-human IL-22 coating antibody is adsorbed onto the microwells by incubation overnight at 4°C.", "Add 50 µl of human serum. Human IL-22 present in the serum sample binds to antibodies adsorbed to the microwells.", "The microplate is blocked with 3% non-fat milk-PBS buffer and later wash to remove unbound protei... |
null | null | null | dx.doi.org/10.17504/protocols.io.rtad6ie | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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?. | ["Female third instar wandering larvae were weighed, and methanol was added to make up each sample to 20 mg/ ml.", "Metabolites were extracted using an ultrasonic probe (30 s), 1 h incubation at 4° C and then centrifugation to remove particulates", "100 µl aliquots of the supernatant were derivatised [200] before mass ... |
47,732 | Glutathione reductase (GR) activity assessment for zebrafish brain tissue | 6 | dx.doi.org/10.17504/protocols.io.bsuuneww | https://www.protocols.io/view/glutathione-reductase-gr-activity-assessment-for-z-bsuuneww | Adrieli Sachett, Matheus Gallas-Lopes, Greicy M M Conterato, Ana Herrmann, Angelo Piato | TITLE: Glutathione reductase (GR) activity assessment for zebrafish brain tissue
AUTHORS: Adrieli Sachett, Matheus Gallas-Lopes, Greicy M M Conterato, Ana Herrmann, Angelo Piato
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Zebrafish are being increasingly used as a model animal in neuroscience re... | ["[Preparing the reagents]\nThe first step is to prepare the reagents to be used in the assessment of glutathione reductase activity;", "[Preparing the reagents]\nPotassium phosphate buffer : 1.1.1 Weigh of monobasic potassium phosphate (KH2PO4) in a beaker of appropriate size; 1.1.2 Dissolve the salt with of u... |
null | null | null | dx.doi.org/10.17504/protocols.io.krbcv2n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Separation of reovirus particles by gel electrophoresis</p>
[BEFORE_START]
<p><strong>Materials and Reagents</strong></p>
<p> </p>
<p>-1M Tris Acetate pH 7.2</p>
<ul>
<li>MW = 121.1g/mol</li>
<li>Add 60.5 g Tris base to 300 ml ddH<sub>2</sub>O</li>
<li>pH to 7.2 with glacial... | [] |
94,391 | Parallel rapid expression and purification of proteins for crystallography (PREPX): large scale 1 L cultures | 1 | dx.doi.org/10.17504/protocols.io.4r3l22jkxl1y/v1 | https://www.protocols.io/view/parallel-rapid-expression-and-purification-of-prot-c8exztfn | michael.fairhead | TITLE: Parallel rapid expression and purification of proteins for crystallography (PREPX): large scale 1 L cultures
AUTHORS: michael.fairhead
[DESCRIPTION]
This protocol details the parallel rapid expression and purification of proteins for crystallography (PREPX) at a 1 L culture scale. Recombinant proteins are expre... | ["[Expression] Either transform BL21 (DE3) with the appropriate plasmid OR streak from glycerol stock onto agar plate and incubate 240 min 37 °C*.", "[Expression] Grow 10 mL 240 min in 50 mL tube of each clone in superbroth + 1 % glucose + the appropriate antibiotics.", "[Expression] Use 10 mL to inoculate 1 L AIM-TB (... |
null | null | null | dx.doi.org/10.17504/protocols.io.tqcemsw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
An alternative protocol for isolated astrocyte cell culture preparation. Dissociation, preparation and plating of mice cortex neurons and glia cells on flasks. Isolatioin process of the culture from neurons, to obtain an isolated astrocyte culture. Plating isolated astrocytes on... | ["[Sample collection] Dissect and place on ice cortices from pups (post natal day 0 or 1 mice).", "[Cell lysis] {\"blocks\":[{\"key\":\"8g4h9\",\"text\":\"1. Chopp with scissors in a papain-based dissociation buffer (2.5 mM CaCl2, 0.83 mM EDTA, 137 U papain (Sigma-Aldrich)), 100 \\u03bcl DNAse (Sigma-Aldrich), 3\\u2013... |
47,508 | Polymer-brush-bilayers-equilibrium | 1 | dx.doi.org/10.17504/protocols.io.bsmunc6w | https://www.protocols.io/view/polymer-brush-bilayers-equilibrium-bsmunc6w | Mike Edwards | TITLE: Polymer-brush-bilayers-equilibrium
AUTHORS: Mike Edwards
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">By means of statistical mechanics of polymers and density functional theory (DFT), polymer brush bilayers are investigated at thermal equilibrium. Density profiles show how brushes balan... | [] |
20,843 | UC Davis - Gut Microbiome Analysis (454-10K reads) | null | dx.doi.org/10.17504/protocols.io.ykjfuun | null | Trina Knotts | TITLE: UC Davis - Gut Microbiome Analysis (454-10K reads)
AUTHORS: Trina Knotts
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span><span style = "font-weight:bold;"> </span></div><div class = "text-block"><span>The work of Gordon and colleagues (i.e., Na... | ["Mice are singly housed in clean cages with fresh food and water and low bedding.", "Weigh mouse and “food-in” (grams of rodent diet provided at start of experiment).", "Save several pellets of rodent diet for analysis (e.g., for energy or macronutrient content)-Store at 4ºC in airtight container.", "At 24h, weigh mou... |
29,473 | Intaspecific aggression assay for Nylanderia fulva | null | dx.doi.org/10.17504/protocols.io.8z9hx96 | null | Edward LeBrun | TITLE: Intaspecific aggression assay for Nylanderia fulva
AUTHORS: Edward LeBrun
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for conducting intraspecific aggression assays with the tawny crazy,</div><div class = "text-block"><span style = "font-style:italic;">Nylanderia fulva</span><spa... | [] |
18,431 | Obtaining of NK cell clones using IL-2 and gene-modified K562 cells expressing membrane-bound IL-21 | null | dx.doi.org/10.17504/protocols.io.v87e9zn | null | Maria Streltsova, Sofya Erokhina, Leonid Kanevskiy, Dean Lee, William Telford, Elena Kovalenko | TITLE: Obtaining of NK cell clones using IL-2 and gene-modified K562 cells expressing membrane-bound IL-21
AUTHORS: Maria Streltsova, Sofya Erokhina, Leonid Kanevskiy, Dean Lee, William Telford, Elena Kovalenko
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Here we present the simple and effe... | ["[NK cell isolation]\nResuspend PBMC with ice-cold separation buffer in 15 or 50 ml Falcon™ tube. Determine cell number.\nAll further steps should be done in sterile conditions and as fast as possible. Keeping cells cold and using pre-cooled solutions is needed to prevent capping of antibodies and non-specific labelli... |
63,379 | Glucotrust Ingredients: Does It Really Work? Must Read Before Buy | 3 | dx.doi.org/10.17504/protocols.io.q26g746zkgwz/v1 | https://www.protocols.io/view/glucotrust-ingredients-does-it-really-work-must-re-b95tr86n | healthodiet | TITLE: Glucotrust Ingredients: Does It Really Work? Must Read Before Buy
AUTHORS: healthodiet
[DESCRIPTION]
Glucotrust Ingredients: Does It Really Work? Must Read
[STEPS] | [] |
82,529 | Protocol for surgical implantation of chronic cecal cannula in pigs | 1 | dx.doi.org/10.17504/protocols.io.8epv5jwx5l1b/v1 | https://www.protocols.io/view/protocol-for-surgical-implantation-of-chronic-ceca-cut9wwr6 | Muriel Larauche, Karim Atmani, Yushan Wang, Zach Weitzner, Sandra Duarte-Vogel, Wentai Liu, Mulugeta Million, Justin Wagner | TITLE: Protocol for surgical implantation of chronic cecal cannula in pigs
AUTHORS: Muriel Larauche, Karim Atmani, Yushan Wang, Zach Weitzner, Sandra Duarte-Vogel, Wentai Liu, Mulugeta Million, Justin Wagner
[DESCRIPTION]
Gastroduodenal and ileal cannulas in pigs are commonly used to evaluate food digestibility and n... | ["[Surgical cannula implantation through laparotomy] Pre-operative diet regimen for intestine preparation\n\nFive days prior to surgery, the animals were started on a low residue diet consisting of 2 cups of low residue food (Hill's Prescription Diet i/d Dry Dog Food or LabDiet Advanced \nProtocol 0043639 (594K)) plus ... |
40,659 | Direct ELISA for investigating the binding of Peptostreptococcal Protein-L to immunoglobulins. | 6 | dx.doi.org/10.17504/protocols.io.bjxtkpnn | https://www.protocols.io/view/direct-elisa-for-investigating-the-binding-of-pep-bjxtkpnn | Angel Justiz-Vaillant, Monica F. Smikle | TITLE: Direct ELISA for investigating the binding of Peptostreptococcal Protein-L to immunoglobulins.
AUTHORS: Angel Justiz-Vaillant, Monica F. Smikle
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Peptostreptococcal protein L is an immunoglobulin-binding protein that interacts with the Fab reg... | ["This ELISA is used to study the interaction of Peptostreptococcal protein-L (SpL) with diverse immunoglobulins.", "The 96 well microtitre plate is coated overnight at 4°C with 1 µg/µl per well of purified immunoglobulins or 50 µl of any animal sera in carbonate-bicarbonate buffer pH 9.6.", "Then plate is treated with... |
40,795 | Copy of ELISA for quantification of IL-30 in human serum. | 6 | dx.doi.org/10.17504/protocols.io.bj33kqqn | https://www.protocols.io/view/copy-of-elisa-for-quantification-of-il-30-in-human-bj33kqqn | Angel Justiz-Vaillant | TITLE: Copy of ELISA for quantification of IL-30 in human serum.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Interleukins (IL) are a type of cytokine first thought to be expressed by leukocytes alone but have later been found to be produced by many other bod... | ["An anti-human IL-31 coating antibody is adsorbed onto the microwells by incubation overnight at 4°C with carbonate-bicarbonate buffer.", "Add 50 µl of human serum. Human IL-31 present in the serum sample binds to antibodies adsorbed into the microwells.", "The microplate is blocked with 3% non-fat milk-PBS buffer and... |
36,531 | SPARC_Duke_PelotGrill_OT2-OD025340_PigVagusNerve_FibronectinIF_Morphology | 1 | dx.doi.org/10.17504/protocols.io.bfwtjpen | https://www.protocols.io/view/sparc-duke-pelotgrill-ot2-od025340-pigvagusnerve-f-bfwtjpen | Nicole A. Pelot, J. Ashley Ezzell, Gabriel B. Goldhagen, Kara A. Clissold, Warren M. Grill | TITLE: SPARC_Duke_PelotGrill_OT2-OD025340_PigVagusNerve_FibronectinIF_Morphology
AUTHORS: Nicole A. Pelot, J. Ashley Ezzell, Gabriel B. Goldhagen, Kara A. Clissold, Warren M. Grill
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The protocol describes immunohistochemistry with anti-claudin-1, imagin... | ["[Immunofluorescence]\nBake slides with sections of paraffin-embedded vagus nerve overnight at 50oC and then cool overnight.", "[Immunofluorescence]\nDeparaffinize the slides and hydrate them to distilled water: xylene (2x 6 min), 100% ethanol (5 min), 95% ethanol (4 min), 70% ethanol (3 min), deionized water (2x 1 mi... |
32,513 | A Typical DNase I Reaction (M0303) | 1 | dx.doi.org/10.17504/protocols.io.bby9ipz6 | https://www.protocols.io/view/a-typical-dnase-i-reaction-m0303-bby9ipz6 | New England Biolabs | TITLE: A Typical DNase I Reaction (M0303)
AUTHORS: New England Biolabs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a protocol for a typical DNase I Reaction, using the M0303 RNase-free DNase I.</div></div>
[STEPS]
?. Set up the following reaction : AB1COMPONENTS100 μl REACTION2RNA~ 10... | ["Set up the following reaction : AB1COMPONENTS100 μl REACTION2RNA~ 10 μg RNA3DNase I Reaction Buffer (10X)10 μl (1X)4DNAse I (RNase-free)1 μl (2 units)5Nuclease-free H2Oto 100 μl\non ice\nAB1COMPONENTS100 μl REACTION2RNA~ 10 μg RNA3DNase I Reaction Buffer (10X)10 μl (1X)4DNAse I (RNase-free)1 μl (2 units)5Nuclease-fr... |
null | null | null | dx.doi.org/10.17504/protocols.io.kkscuwe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>A real-time PCR method for the detection of Molluscum contagiosum virus from human samples. This assay targets the MC021L gene and detects both subtype 1 and 2 of the virus.</p>
[BEFORE_START]
<ul>
<li>If using a different brand or model of real-time thermocycler, check the ... | [] |
12,444 | Terminal restriction fragment length polymorphism (T-RFLP) | 1 | dx.doi.org/10.17504/protocols.io.kqdg3jy7l25z/v1 | https://www.protocols.io/view/terminal-restriction-fragment-length-polymorphism-qd4ds8w | Eva Petrova, Roey Angel | TITLE: Terminal restriction fragment length polymorphism (T-RFLP)
AUTHORS: Eva Petrova, Roey Angel
[DESCRIPTION]
Optimized protocol for T-RFLP analysis of complex bacteria and archea communities.
[STEPS]
1. Extract and purify DNA from the sample. DNA should be at about 10-20 ng/µl.
2. Amplify the sample using PCR (re... | ["Extract and purify DNA from the sample. DNA should be at about 10-20 ng/µl.", "Amplify the sample using PCR (refer to PCR conditions and mixes.doc). Primers need to be fluorescently labeled at their 5'. Labeling should be of at least one of the primers though both can be labeled (in which case the two primers should ... |
71,967 | Microwave Synthesis of Lanthanum-Doped Carbon Dots | 6 | null | https://www.protocols.io/view/microwave-synthesis-of-lanthanum-doped-carbon-dots-cih7ub9n | Samuel Holberg, Addy Cullen, Chih-Yu (Jill) Lee, Destiny Caulder, Geisianny AM Moreira, Eric S McLamore | TITLE: Microwave Synthesis of Lanthanum-Doped Carbon Dots
AUTHORS: Samuel Holberg, Addy Cullen, Chih-Yu (Jill) Lee, Destiny Caulder, Geisianny AM Moreira, Eric S McLamore
[DESCRIPTION]
This protocol describes the synthesis of lanthanum-doped carbon dots using microwave irradiation. The complete process requires approx... | ["[SECTION 1) Preparation] Prepare Solution 1 (200 mM D-glucose)\nPrepare a sealed plastic or glass container that has at least 10 mL of capacity and label as 200mM D-glucose\nWeigh 0.721 g of D-glucose and solvate in 200 mL of DI/nano-pure water\nMix solution and look carefully to ensure there are no precipitates\nCov... |
58,228 | PEPPI-MS | 5 | null | https://www.protocols.io/view/peppi-ms-b44uqyww | David S. Butcher, Ayako Takemori | TITLE: PEPPI-MS
AUTHORS: David S. Butcher, Ayako Takemori
[DESCRIPTION]
This protocol is derived from the version originally published in the Journal of Proteome Research (https://doi.org/10.1021/acs.jproteome.0c00303).
Ayako Takemori was instrumental in developing the original PEPPI-MS protocol, but not involved in ... | ["Prepare a volume of protein solution (e.g. whole cell lysate) sufficient to load 10 gel lanes with 11 µg of protein in a volume no greater than 18.75 µL per lane (e.g. 110 µg of protein in ≤187.5 µL) in a 1.5 mL microcentrifuge tube.", "Add DTT stock solution to protein sample to a final concentration of 1 mM (e.g. 1... |
87,586 | Multiplex Cyclical Immunofluorescence on Fresh Frozen Tissue-V3 | 1 | dx.doi.org/10.17504/protocols.io.81wgb1m3yvpk/v3 | https://www.protocols.io/view/multiplex-cyclical-immunofluorescence-on-fresh-fro-czsax6ae | Maya Brewer, Liz McDonough, Yuantee Zhu, Elizabeth Neumann, Danielle Gutierrez, Jeff Spraggins, Mark De Caestecker | TITLE: Multiplex Cyclical Immunofluorescence on Fresh Frozen Tissue-V3
AUTHORS: Maya Brewer, Liz McDonough, Yuantee Zhu, Elizabeth Neumann, Danielle Gutierrez, Jeff Spraggins, Mark De Caestecker
[DESCRIPTION]
Scope:
To obtain multiple cycles of immunofluorescence on fresh frozen human kidney tissue embedded in carboxy... | ["[Immunofluorescence] Place frozen slides from the -80˚C freezer directly into the formalin, and post-fix for 5 minutes.", "[Immunofluorescence] Pour used formalin into the appropriate waste container, then fill jar with 1X PBS and wash sections for 5 minutes four times.", "[Immunofluorescence] Using a hydrophobic pen... |
null | null | null | dx.doi.org/10.17504/protocols.io.e29bgh6 | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<p><strong>SOLUTIONS & BUFFERS:</strong></p>
<p> </p>
<p><em>Note: Do not use sodium azide in any buffers or solutions as sodium azide inactivates</em><br /><em>the horseradish-peroxidase enzyme.</em></p>
<p><br /><strong>Phosphate Buffered Saline (PBS):</strong><br />80.0 g ... | [] |
67,392 | https://www.facebook.com/ViaKetoAppleGummiesinCA/ | 3 | dx.doi.org/10.17504/protocols.io.kqdg3pjeel25/v1 | https://www.protocols.io/view/https-www-facebook-com-viaketoapplegummiesinca-cd28s8hw | Kaylie Diteman | TITLE: https://www.facebook.com/ViaKetoAppleGummiesinCA/
AUTHORS: Kaylie Diteman
[DESCRIPTION]
Likewise, you will likewise track down garcinia Cambogia in this extremely solid item.
[STEPS] | [] |
75,844 | PhageFISH for DIG-labelled bacterial probes | 4 | dx.doi.org/10.17504/protocols.io.kqdg3931pg25/v1 | https://www.protocols.io/view/phagefish-for-dig-labelled-bacterial-probes-cnbcvaiw | Line Jensen Ostenfeld, Saria Otani | TITLE: PhageFISH for DIG-labelled bacterial probes
AUTHORS: Line Jensen Ostenfeld, Saria Otani
[DESCRIPTION]
This protocol details about PhageFISH for DIG-labelled bacterial probes.
[STEPS]
SECTION: Fix liquid samples to glass slides
1. Place liquid sample in a 30-50 µL droplet on poly-L-lysine coated slide.
SECTION... | ["[Fix liquid samples to glass slides] Place liquid sample in a 30-50 µL droplet on poly-L-lysine coated slide.", "[Fix liquid samples to glass slides] Dry in warm incubator for approx. 30 min or until the droplet has dried out.", "[Fix liquid samples to glass slides] OPTIONAL: if sample is very dilute add several drop... |
null | null | null | dx.doi.org/10.17504/protocols.io.e5jbg4n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>ThI high sensitivity miRNA library generation for the Illumina sequencing platform. Our enhanced reagent kit enables the discovery and profiling of small RNAs from a variety of sources including FFPE, exosome, serum, and whole blood. The TailorMix workflow is designed for eas... | [] |
65,244 | Prodentim Reviews: Does Prodentim advanced oral probiotics Works For Gums& Teeth? | 1 | dx.doi.org/10.17504/protocols.io.kqdg3pnx7l25/v1 | https://www.protocols.io/view/prodentim-reviews-does-prodentim-advanced-oral-pro-cbx4spqw | tryProDentim | TITLE: Prodentim Reviews: Does Prodentim advanced oral probiotics Works For Gums& Teeth?
AUTHORS: tryProDentim
[DESCRIPTION]
Beware Of Fake Website
[STEPS]
1.
==> Official Website "Click Here" <==
Prodentim is an innovative oral health product which keeps your gums and teeth as well-maintained as they cou... | ["==> Official Website \"Click Here\" <==\n\n\nProdentim is an innovative oral health product which keeps your gums and teeth as well-maintained as they could be and makes them more white. The quality of this product is guaranteed because of the ingredients used to create Prodentim. \n \n\n\n\nProdentim Reviews Int... |
65,089 | Generation of full-length circRNA libraries for Oxford Nanopore long-read sequencing | 1 | dx.doi.org/10.17504/protocols.io.rm7vzy8r4lx1/v2 | https://www.protocols.io/view/generation-of-full-length-circrna-libraries-for-ox-cbs9snh6 | Steffen Fuchs, Loélia Babin, Elissa Andraos, Chloé Bessiere, Semjon Willier, Johannes H. Schulte, Christine Gaspin, Fabienne Meggetto | TITLE: Generation of full-length circRNA libraries for Oxford Nanopore long-read sequencing
AUTHORS: Steffen Fuchs, Loélia Babin, Elissa Andraos, Chloé Bessiere, Semjon Willier, Johannes H. Schulte, Christine Gaspin, Fabienne Meggetto
[DESCRIPTION]
Circular RNA (circRNA) is a noncoding RNA class with broad implication... | ["[1) Ribodepletion] Ribodepletion", "[1) Ribodepletion] Hybridization and RNaseH treatment\nPrepare the following: thaw 7 µg total RNA on ice", "[1) Ribodepletion] Thaw one aliquot of rRNA depletion oligos on ice", "[1) Ribodepletion] Bring one aliquot of Agencourt RNA Clean XP beads to Room temperature at least 30 mi... |
41,447 | Minimization of protein structures using refineD | 1 | null | https://www.protocols.io/view/minimization-of-protein-structures-using-refined-bkqfkvtn | Chris Berndsen | TITLE: Minimization of protein structures using refineD
AUTHORS: Chris Berndsen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Sometimes structural issues can be corrected with energy minimization. In this process, the weak interactions are optimized in order to produce a more thermodynamically sta... | ["[Uploading structure]\nNavigate to refineD (http://watson.cse.eng.auburn.edu/refineD/)", "[Uploading structure]\nUpload your structure to the interface.", "[Uploading structure]\nSelect “conservative” for refinement mode and provide your email. Then press submit.\nThe server takes 24 to 72 hours to run typically. I r... |
91,873 | Immunofluorescence Multi-label Protocol for Free-floating Fixed Tissue | 1 | dx.doi.org/10.17504/protocols.io.j8nlkorn5v5r/v1 | https://www.protocols.io/view/immunofluorescence-multi-label-protocol-for-free-f-c5x9y7r6 | Jeffrey Kordower, Yaping Chu | TITLE: Immunofluorescence Multi-label Protocol for Free-floating Fixed Tissue
AUTHORS: Jeffrey Kordower, Yaping Chu
[DESCRIPTION]
Immunofluorescence multi-label protocol for staining free-floating fixed tissue in the Kordower Laboratory.
[GUIDELINES]
HISTO- NOTES:
Primate tissue staining dishes use 100 mLsolution per... | ["[DAY 1 (4 hrs)] Wash sections (6 x 10 min) in Dilution Media (DM) (0.2 Molarity (M)TBS plus 0.05 % volumeTriton X-100).", "[DAY 1 (4 hrs)] Endogenous peroxidase inhibition (20 min). 0.1 Molarity (M) Sodium meta-periodate in TBS. \n \n\n100 mL 0.2 Molarity (m)Tris-buffered saline (TBS)\n2.13 g Sodium meta-periodate", ... |
78,512 | [Modified] DNeasy PowerSoil Pro Kit_Increased Sediment Volume & Inhibitor Removal Pre-Extraction | 1 | dx.doi.org/10.17504/protocols.io.yxmvm2be9g3p/v1 | https://www.protocols.io/view/modified-dneasy-powersoil-pro-kit-increased-sedim-cqwqvxdw | Grayson Huston | TITLE: [Modified] DNeasy PowerSoil Pro Kit_Increased Sediment Volume & Inhibitor Removal Pre-Extraction
AUTHORS: Grayson Huston
[DESCRIPTION]
Protocol (wash buffer plus modified extraction) unsuccessful at detecting fish sedDNA from lakes in Maine, USA
Protocol successful at detecting fish sedDNA collected from st... | ["[Wash buffer reagents] CREATE 0.5M EDTA, pH 8.0; final volume: 250mL", "[Wash buffer reagents] CREATE 1M Tris-HCl, pH 8.0; final volume: 500mL", "[Wash buffer reagents] CREATE a batch of 0.5M Na2PO4*7H2O, pH 8.0; final volume: 250mL", "[Wash buffer reagents] CREATE 10N NaOH; final volume: 40mL", "[Wash buffer reagent... |
37,425 | Amplicon clean-up using SPRI beads for RAPID nanopore kit RBK004 | null | dx.doi.org/10.17504/protocols.io.bgsrjwd6 | https://www.protocols.io/view/amplicon-clean-up-using-spri-beads-for-rapid-nanop-bgsrjwd6 | Muhammad Faisal, Olin Silander, Nikki Freed | TITLE: Amplicon clean-up using SPRI beads for RAPID nanopore kit RBK004
AUTHORS: Muhammad Faisal, Olin Silander, Nikki Freed
[STEPS]
?. Vortex SPRI beads thoroughly to ensure they are well resuspended, the solution should be a homogenous brown colour.
?. [Ampure XP bead clean up]
Add an equal volume (1:1) of SPRI bead... | ["Vortex SPRI beads thoroughly to ensure they are well resuspended, the solution should be a homogenous brown colour.", "[Ampure XP bead clean up]\nAdd an equal volume (1:1) of SPRI beads to the sample tube and mix gently by either flicking or pipetting. For example add room temperature SPRI beads to a reaction.\n5... |
67,880 | ChatGPT step-by-step comparison protocol | 1 | dx.doi.org/10.17504/protocols.io.kxygxz6dwv8j/v1 | https://www.protocols.click/view/chatgpt-step-by-step-comparison-protocol-ceigtcbw | Francesco Varrato | TITLE: ChatGPT step-by-step comparison protocol
AUTHORS: Francesco Varrato
[DESCRIPTION]
Protocol helpful to compare two products or items of any sort with ChatGPT or similar tool. It needs to be able to accept and gather information from external web links: at the time of writing, the GPT-4 version is the one that al... | ["Go to https://chat.openai.com and insert the text from protocol step 2, replacing the [LINK*] parts with web links pointing to reviews or informational webpage of two products or items.", "Hereby I provide you with a series of references to two products I would like for you to compare:\n • [LINK 1]\n • [LINK 2]\n • [... |
30,670 | Doubting what you already know: uncertainty regarding state transitions is associated with obsessive compulsive symptoms | null | dx.doi.org/10.17504/protocols.io.97nh9me | null | Isaac Fradkin, Casimir Ludwig, Eran Eldar, Jonathan D. Huppert | TITLE: Doubting what you already know: uncertainty regarding state transitions is associated with obsessive compulsive symptoms
AUTHORS: Isaac Fradkin, Casimir Ludwig, Eran Eldar, Jonathan D. Huppert
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Obsessive compulsive (OC) symptoms involve exc... | ["[Instructions and training]\nParticipants read instructions explaining that they will see three cues (with example given) pointing either left or right. Then they will see a black circle appearing at one side of the screen. They are told that their task is to predict the location of the circle by using the arrow keys... |
23,790 | FAA MEDIA (FASTIDIOUS ANAEROBES AGAR) | 1 | null | https://www.protocols.io/view/faa-media-fastidious-anaerobes-agar-3gngjve | Roey Angel, Ana Lara-Rodriguez, Eva Petrova | TITLE: FAA MEDIA (FASTIDIOUS ANAEROBES AGAR)
AUTHORS: Roey Angel, Ana Lara-Rodriguez, Eva Petrova
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">For the growing and maintance of Clostridium sp. </div><div class = "text-block">Fastidious Anaerobe Agar is used for the cultivation of anaerobic microor... | ["Prepare stock solutions:L-cystein hydrochloride solution (50 g/l): Dissolve of Cysteine HCl Monohydrate in a distilled water and filter sterilize. Store refrigerated. HEMIN solution (10 g/l) : Dissolve in ; make up to with distilled water and filter sterilize. Store refrigerated. VITAMIN K1 solution (10 g/l): D... |
57,818 | Nerve Sample Preparation for MicroCT Scanning | 4 | dx.doi.org/10.17504/protocols.io.b4p2qvqe | https://www.protocols.io/view/nerve-sample-preparation-for-microct-scanning-b4p2qvqe | Nicole Thompson, Svetlana Mastitskaya, Enrico Ravagli, Kirill Aristovich, David Holder | TITLE: Nerve Sample Preparation for MicroCT Scanning
AUTHORS: Nicole Thompson, Svetlana Mastitskaya, Enrico Ravagli, Kirill Aristovich, David Holder
[DESCRIPTION]
This protocol describes the preparation and staining process of pig vagus nerves for microCT scanning.
[STEPS]
SECTION: Vagus nerve dissection and fixat... | ["[Vagus nerve dissection and fixation] Following euthanasia, dissect the left vagi of the pigs carefully from cervical region (with both the stimulating and EIT electrodes attached) down to the branching regions of cardiac, recurrent laryngeal and pulmonary branches, with all the branches left attached to the main tru... |
null | null | null | dx.doi.org/10.17504/protocols.io.eq4bdyw | 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]
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.n9pdh5n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Notes from HAB OOS meeting, April 4 2018, SCCRWP. </p>
[STEPS]
?. | [] |
21,811 | Contact testing protocol | null | dx.doi.org/10.17504/protocols.io.zitf4en | null | Monika Hassan | TITLE: Contact testing protocol
AUTHORS: Monika Hassan
[STEPS] | [] |
42,754 | Efficacy of metformin in patients with breast cancer receiving chemotherapy or endocrine therapy：Systematic review and meta-analysis (protocol) | 1 | dx.doi.org/10.17504/protocols.io.bmzak72e | https://www.protocols.io/view/efficacy-of-metformin-in-patients-with-breast-canc-bmzak72e | Kayoko Morio, Yasuko Kurata, Nobuko Kawaguchi-Sakita, Akihiro Shiroshita, Yuki Kataoka | TITLE: Efficacy of metformin in patients with breast cancer receiving chemotherapy or endocrine therapy：Systematic review and meta-analysis (protocol)
AUTHORS: Kayoko Morio, Yasuko Kurata, Nobuko Kawaguchi-Sakita, Akihiro Shiroshita, Yuki Kataoka
[STEPS]
?.
?. | [] |
70,997 | Standard Operating Procedure for Determination of the Minimum Inhibitory Concentration (MIC) of Different Antimicrobial Agents Against Different Bacteria | 1 | dx.doi.org/10.17504/protocols.io.j8nlkw4owl5r/v1 | https://www.protocols.io/view/standard-operating-procedure-for-determination-of-chjvt4n6 | Alanoud T Aljasham, Mashal M. Almutairi | TITLE: Standard Operating Procedure for Determination of the Minimum Inhibitory Concentration (MIC) of Different Antimicrobial Agents Against Different Bacteria
AUTHORS: Alanoud T Aljasham, Mashal M. Almutairi
[DESCRIPTION]
This standard operating procedure (SOP) describes the standardized laboratory procedure for per... | ["[Antimicrobial Agents Stock Solution Preparation] Set the electronic balance to mg unit", "[Antimicrobial Agents Stock Solution Preparation] Add the desired amount of the antimicrobial powder into the Eppendorf tube.", "[Antimicrobial Agents Stock Solution Preparation] Add 1 mL of the recommended solvent (depending o... |
null | null | null | dx.doi.org/10.17504/protocols.io.ertbd6n | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<p><strong>MATERIALS:</strong></p>
<p> </p>
<p> 1) <em>E. coli</em>, strain ____, containing plasmid</p>
<p> 2) LB media</p>
<p> 1.0% Bacto-tryptone</p>
<p> 0.5% Bacto-yeast extract</p>
<p> ... | [] |
104,648 | USDA LTAR Common Experiment measurement: Crop scouting for pests and diseases | 0 | dx.doi.org/10.17504/protocols.io.bp2l62mzdgqe/v1 | https://www.protocols.io/view/usda-ltar-common-experiment-measurement-crop-scout-difg4bjw | Brook J. Wilke | TITLE: USDA LTAR Common Experiment measurement: Crop scouting for pests and diseases
AUTHORS: Brook J. Wilke
[DESCRIPTION]
Measuring pest and disease frequency and abundance can be cumbersome but contributes to important knowledge for research and management of cropland sites. Most LTAR Sites are assumed to lack the c... | ["[Sample collection, processing, and analysis] Hire a professional crop scout to observationally scout all treatments every other week throughout the growing season. \n\nDuring each visit, include one replication at the plot and field scale for all treatments and rotation entry points. Rotate to a different replicatio... |
71,928 | Midbrain astrocyte and co-culture | 4 | dx.doi.org/10.17504/protocols.io.5jyl8j9yrg2w/v1 | https://www.protocols.io/view/midbrain-astrocyte-and-co-culture-cigyubxw | gustavo.parfitt | TITLE: Midbrain astrocyte and co-culture
AUTHORS: gustavo.parfitt
[DESCRIPTION]
Midbrain astrocyte and co-culture for mix-genetic experiments.
[STEPS]
SECTION: Intro
1. Midbrain NPC were generated following the publish protocol https://www.protocols.io/view/midbrain-organoid-differentiation-in-spinner-flask-rm7vzbnr4... | ["[Intro] Midbrain NPC were generated following the publish protocol https://www.protocols.io/view/midbrain-organoid-differentiation-in-spinner-flask-rm7vzbnr4vx1/v1 with modifications listed bellow.", "[NPC generation] From a 80% confluent plate of iPSCs in a 10 cm plate.", "[NPC generation] Wash with 5ml of PBS", "[N... |
91,299 | Pudendal Nerve Mapping in Humans | 1 | dx.doi.org/10.17504/protocols.io.14egn3jezl5d/v1 | https://www.protocols.io/view/pudendal-nerve-mapping-in-humans-c5eby3an | Amador C Lagunas, Po-Ju Chen, Priyanka Gupta, Tim Bruns | TITLE: Pudendal Nerve Mapping in Humans
AUTHORS: Amador C Lagunas, Po-Ju Chen, Priyanka Gupta, Tim Bruns
[DESCRIPTION]
The goal of this study is to map the pudendal nerve with imaging and electrophysiology by gathering additional data from patients receiving an implanted neurostimulator as part of their normal clinica... | ["[Stage 1 Intraoperative Testing] After multicontact lead has been placed next to the pudendal nerve as described in Peters 2013, connect the external pulse generator to electrode 0 and a surface patch electrode placed on the ankle.", "Change pulse width to 210 microseconds.", "Change stimulation frequency of the exte... |
108,929 | Outcomes of Total Hip Replacement in Septic Arthritis of the Native Hip Joint Amongst the Adult Population: A Systematic Review | 0 | dx.doi.org/10.17504/protocols.io.8epv5r415g1b/v1 | https://www.protocols.io/view/outcomes-of-total-hip-replacement-in-septic-arthri-dnk95cz6 | Teddy Cheong, Surya Varma Selvakumar, Ryan Kwang Jin Goh, Ing How Moo | TITLE: Outcomes of Total Hip Replacement in Septic Arthritis of the Native Hip Joint Amongst the Adult Population: A Systematic Review
AUTHORS: Teddy Cheong, Surya Varma Selvakumar, Ryan Kwang Jin Goh, Ing How Moo
[DESCRIPTION]
Background: Septic arthritis is a debilitating condition that results in joint destruction ... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.kg2ctye | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes the transformation of Synechococcus sp. PCC7002 with linear DNA fragments with homologous regions. </p>
[GUIDELINES]
<p>Work as sterile as possible.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
26,213 | Retro-orbital injection of virus or dye in mice | null | dx.doi.org/10.17504/protocols.io.5udg6s6 | null | Boaz Mohar | TITLE: Retro-orbital injection of virus or dye in mice
AUTHORS: Boaz Mohar
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is following:</div></div>
[STEPS]
?. [Injection]
Prepare either virus dilution (5.0e11-1.0e12) with PBS prepare or a dye aliquot. Injection is up to 200ul per mou... | ["[Injection]\nPrepare either virus dilution (5.0e11-1.0e12) with PBS prepare or a dye aliquot. Injection is up to 200ul per mouse.", "[Injection]\nTake one mouse from the cage into an induction chamber and start isoflurane at 3% with flow rate of ~1L/min", "[Injection]\nAfter the mouse has slow breathing (~1/s) move t... |
null | null | null | dx.doi.org/10.17504/protocols.io.dmb42m | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Filtering protocol adapted from SangHoon Lee
[GUIDELINES]
Filtering protocol adapted from SangHoon Lee<strong><br /><br />Materials needed for cruise:</strong> <br />4 acid washed 20L cubitainers <br />8 60cm pieces of acid washed tubing <br />Gloves <br />Sharpie <br />2 coole... | [] |
21,863 | Rabbit calicivirus capsid Taqman RT-qPCR | 1 | dx.doi.org/10.17504/protocols.io.zkff4tn | https://www.protocols.io/view/rabbit-calicivirus-capsid-taqman-rt-qpcr-zkff4tn | Robyn Hall, Lily Tran, Nina Huang, Ina Smith, Tanja Strive | TITLE: Rabbit calicivirus capsid Taqman RT-qPCR
AUTHORS: Robyn Hall, Lily Tran, Nina Huang, Ina Smith, Tanja Strive
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">To improve the sensitivity and throughput of molecular testing for rabbit caliciviruses we have developed a multiplex TaqMan RT-qPCR ass... | ["[Plate set-up]\nABCDEFGHIJKL1GI.1GI.1RNA 6RNA 6RNA 15RNA 15RNA 24RNA 24RNA 33RNA 33RNA 41RNA 412GI.2GI.2RNA 7RNA 7RNA 16RNA 16RNA 25RNA 25RNA 34RNA 34RNA 42RNA 423GI.1aGI.1aRNA 8RNA 8RNA 17RNA 17RNA 26RNA 26RNA 35RNA 35RNA 43RNA 434 NTC NTC RNA 9RNA 9RNA 18RNA 18RNA 27RNA 27RNA 36RNA 36RNA 44RNA 445RNA 1RNA 1RNA... |
null | null | null | dx.doi.org/10.17504/protocols.io.p98dr9w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>connect to localhost ip: 127.0.0.1</p>
<p>get deafult ip getway</p>
<p>Get access to root </p>
<p>get permmision </p>
<p>create dump file </p>
<p>run as administrator</p>
<p>open=start adb server </p>
<p>start=exit user </p>
<p> </p>
[STEPS] | [] |
69,606 | Treatment and staining of iPSC-derived neurons for lysosomal phenotype analysis | 1 | dx.doi.org/10.17504/protocols.io.261ge3pmdl47/v1 | https://www.protocols.io/view/treatment-and-staining-of-ipsc-derived-neurons-for-cf8etrte | Jessica Chedid, Adahir Labrador-Garrido, Nicolas Dzamko | TITLE: Treatment and staining of iPSC-derived neurons for lysosomal phenotype analysis
AUTHORS: Jessica Chedid, Adahir Labrador-Garrido, Nicolas Dzamko
[DESCRIPTION]
This protocol describes the preparation and treatment of neuronal cultures to be imaged for its analysis using the Opera Phenix high-content screening sy... | ["[Live cells experimental outline] Prepare: DQ-red-BSA 1:100, Cytopainter green cell proliferation reagent 1:500 and Hoechst 1:100 in complete cell culture media.", "[Live cells experimental outline] Alternatively prepare: Mitotracker 1:10.000, Lysosomal staining 1:500, Cytopainter 1:500 and Hoechst 1:100 in complete ... |
37,792 | 2D and 3D Electron Microscopy (EM) Imaging of Tissue Biopsies and Resections | 1 | dx.doi.org/10.17504/protocols.io.bg58jy9w | https://www.protocols.io/view/2d-and-3d-electron-microscopy-em-imaging-of-tissue-bg58jy9w | Jessica Riesterer, Erin Stempinski, Claudia S Lopez | TITLE: 2D and 3D Electron Microscopy (EM) Imaging of Tissue Biopsies and Resections
AUTHORS: Jessica Riesterer, Erin Stempinski, Claudia S Lopez
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Recent developments in large format electron microscopy have enabled generation of images that provide deta... | ["[Toluidine blue (TB) screening]\nOnce the samples have been processed for 3DEM using a preferred protocol, sections from the resin block can be stained with Toluidine Blue. Our preferred protocol is published here:This step allows researchers and pathologists to decide if more sectioning is needed to expose areas of ... |
18,296 | qPCR | null | dx.doi.org/10.17504/protocols.io.v4ye8xw | null | Lele Sun, Xiujun Cheng, Hong Liu, Furen Zhang | TITLE: qPCR
AUTHORS: Lele Sun, Xiujun Cheng, Hong Liu, Furen Zhang
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS] | [] |
79,821 | Luminex-Based Multiplex Cytokine Analysis | 4 | dx.doi.org/10.17504/protocols.io.ewov1ob7plr2/v1 | https://www.protocols.click/view/luminex-based-multiplex-cytokine-analysis-cr7mv9k6 | michela.deleidi, Bianca Marchetti, Federico Bertoli, Carmela Giachino | TITLE: Luminex-Based Multiplex Cytokine Analysis
AUTHORS: michela.deleidi, Bianca Marchetti, Federico Bertoli, Carmela Giachino
[DESCRIPTION]
Multiplexed kit "Mouse High Sensitivity T Cell Magnetic Bead Panel" allows a Simultaneous analyze low levels of cytokine and chemokine biomarker with the High Sensitivity Bead-B... | ["[Luminex-Based Multiplex Cytokine Analysis] Measure Cytokines from murine plasma samples, including IFN-γ, IL-1β, IL-2, IL-4, IL-6, IL-10, IL-17A, and TNF-α simultaneously using the multiplexed kit \"Mouse High Sensitivity T Cell Magnetic Bead Panel\" (MHSTCMAG-70K, MILLIPLEX, EMD Millipore Corp., Billerica, MA, USA)... |
71,839 | Library clean up and quality control for Illumina sequencing | 4 | dx.doi.org/10.17504/protocols.io.n2bvj861ngk5/v1 | https://www.protocols.io/view/library-clean-up-and-quality-control-for-illumina-cid7ua9n | Katherine Smollett, Lily Tong, Kyriaki Nomikou, Jenna Nichols, Kirsty Kwok, Ma. Jowina Galarion, Daniel Mair, Ana Filipe | TITLE: Library clean up and quality control for Illumina sequencing
AUTHORS: Katherine Smollett, Lily Tong, Kyriaki Nomikou, Jenna Nichols, Kirsty Kwok, Ma. Jowina Galarion, Daniel Mair, Ana Filipe
[DESCRIPTION]
There are many different ways of preparing libraries for Illumina sequencing but when it comes to the post... | ["[Library clean up] Equilibrate Ampure XP beads to Room temperature for 30 min and vortex well to mix.", "[Library clean up] If needed make libraries up to 50 µL with 10mM Tris pH8.", "[Library clean up] Add 45 µL to the samples (ratio 0.9:1) and mix well.", "[Library clean up] Incubate at Room temperature room tempe... |
67,541 | Nuclease Test (OpenVent polymerase, PCR Master Mix, DNA loading dye) | 4 | dx.doi.org/10.17504/protocols.io.j8nlkk1xwl5r/v2 | https://www.protocols.io/view/nuclease-test-openvent-polymerase-pcr-master-mix-d-cd7vs9n6 | Nadine Mowoh, Stephane Fadanka | TITLE: Nuclease Test (OpenVent polymerase, PCR Master Mix, DNA loading dye)
AUTHORS: Nadine Mowoh, Stephane Fadanka
[DESCRIPTION]
Quality control and nuclease test involves incubating the enzymes or reagents in reconstituted recombination assays to eliminate the possibility of relevant protein or nucleic aci... | ["[Nuclease activity]", "[Nuclease activity] Pipetting\n\nPipette the following reagents into 0.2 mL PCR reaction tubes as shown in the table below, while working on ice.", "[Nuclease activity] Checking and interpreting results:\n\nAfter the incubation period, prepare a 1.5% agarose gel, run and visualized as described... |
15,831 | Nuclei isolation from snap frozen human pancreatic tissue using a citric acid buffer | 1 | dx.doi.org/10.17504/protocols.io.tpxempn | https://www.protocols.io/view/nuclei-isolation-from-snap-frozen-human-pancreatic-tpxempn | Luca Tosti, Christian Conrad | TITLE: Nuclei isolation from snap frozen human pancreatic tissue using a citric acid buffer
AUTHORS: Luca Tosti, Christian Conrad
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A protocol to isolate nuclei from snap-frozen pancreatic tissue and protect RNA from RNAse-mediated degradation</div></div... | ["Incubate the tissue for 5 min on ice\n[on ice]\n[incubation]", "Crush the tissue with 5 more strokes of the loose pestle and leave to incubate for 5 minutes\n[on ice]\n[incubation]", "Homogenize the tissue with 3 more strokes of the loose pestle and 5 more strokes with the tight pestle", "Filter through a FACS-tube w... |
86,480 | origamiFISH (Cell Culture) | 4 | dx.doi.org/10.17504/protocols.io.kxygx33pwg8j/v1 | https://www.protocols.io/view/origamifish-cell-culture-cypqxvmw | Wendy Wang | TITLE: origamiFISH (Cell Culture)
AUTHORS: Wendy Wang
[DESCRIPTION]
This is the origamiFISH protocol for cell culture work, as outlined in the associated paper "Universal, label-free, single-molecule visualization of DNA origami nanodevices across biological samples using origamiFISH" (PMID: 37500778; Nat. Nanotechnol... | ["[DNA origami (DN) Uptake] NOTE: DN uptake can occur in any vessel of choice to fit experimental needs. We typically perform DN uptake in a 24-well plate containing 12mm PDL-treated #1.5 glass coverslips. PDL treatment ensures cell adherence, and #1.5 glass coverslips ensure compatibility with downstream confocal micr... |
42,089 | DNA functionalization on oxide | 1 | null | https://www.protocols.io/view/dna-functionalization-on-oxide-bmchk2t6 | hnyein | TITLE: DNA functionalization on oxide
AUTHORS: hnyein
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">DNA functionalization</div></div>
[STEPS]
?. [Glass slide cleaning]
Clean glass slides in acetone, IPA by sonicating (2 times each) and put in water and dry under N2. Acetone, IPA in cabinet under... | ["[Glass slide cleaning]\nClean glass slides in acetone, IPA by sonicating (2 times each) and put in water and dry under N2. Acetone, IPA in cabinet under fumehood.After cleaning, put under UV for 60 mins. Check the marked level to be consistent every time.", "[Silanization]\nPut glass slides in a dessicator. Put APTMS... |
40,599 | Implantation of a pelvic nerve array in rats | 1 | dx.doi.org/10.17504/protocols.io.bjvxkn7n | https://www.protocols.io/view/implantation-of-a-pelvic-nerve-array-in-rats-bjvxkn7n | James Fallon, Sophie Payne, Janet Keast, Peregrine Osborne | TITLE: Implantation of a pelvic nerve array in rats
AUTHORS: James Fallon, Sophie Payne, Janet Keast, Peregrine Osborne
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A pelvic nerve array is custom designed for implantation onto the pelvic nerve of male rats. This device is used for long-term (reco... | ["[Surgical Preparation]\nPrior to surgery, pelvic nerve arrays are sterilised through a sonication process and autoclaving.", "[Surgical Preparation]\nSonication cycles: 15 mins in 5% Pyroneg, 5 mins distilled water, 5 mins in distilled water, 10 mins in 96% ethanol, 5 mins in distilled water, 5 mins in distilled wate... |
42,980 | BSCI:414 Lab 6 and Lab 7--Analyze RT-qPCR Results from COVID-19 Test | 1 | null | https://www.protocols.io/view/bsci-414-lab-6-and-lab-7-analyze-rt-qpcr-results-f-bm8ck9sw | Harley King | TITLE: BSCI:414 Lab 6 and Lab 7--Analyze RT-qPCR Results from COVID-19 Test
AUTHORS: Harley King
[STEPS]
?. [Review Experiment]
Watch and discuss experimental video.https://youtu.be/9s5sACRqkZ8
?. [Review Results]
Download screenshots and "Human.sample.chart.results.JPG" in our class folder, "Files>Lab Results>Lab 6 ... | ["[Review Experiment]\nWatch and discuss experimental video.https://youtu.be/9s5sACRqkZ8", "[Review Results]\nDownload screenshots and \"Human.sample.chart.results.JPG\" in our class folder, \"Files>Lab Results>Lab 6 qPCR Data\".", "[Review Results]\nCalculate the concentration of plasmid DNA used to generate the stan... |
98,505 | Spinal cord epidural stimulation to control bladder in spinal cord injury patients | 1 | dx.doi.org/10.17504/protocols.io.8epv5x2w6g1b/v2 | https://www.protocols.io/view/spinal-cord-epidural-stimulation-to-control-bladde-dcfh2tj6 | Daniel Medina Aguinaga, April N. Herrity, Sevda C. Aslan, Samineh Mesbah, Ricardo Siu, Karthik Kalvakuri, Beatrice Ugiliweneza, Ahmad Mohamed, Charles H. Hubscher, Susan J. Harkema | TITLE: Spinal cord epidural stimulation to control bladder in spinal cord injury patients
AUTHORS: Daniel Medina Aguinaga, April N. Herrity, Sevda C. Aslan, Samineh Mesbah, Ricardo Siu, Karthik Kalvakuri, Beatrice Ugiliweneza, Ahmad Mohamed, Charles H. Hubscher, Susan J. Harkema
[DESCRIPTION]
Aim was to investigate ... | ["[Clinical Evaluation] The patients’ injuries were classified by two independent clinicians using the ASIA (American Spinal Injury Association) Impairment Scale (AIS)1.", "[Clinical Evaluation] The patients underwent a physical examination for medical clearance, ensuring participation safety using the following inclus... |
80,353 | Modified NEBNext® VarSkip Long SARS-CoV-2 Enrichment and library prep (Native Barcoding Kit V14 Oxford Nanopore Technologies)- adapted for wastewater samples | 4 | dx.doi.org/10.17504/protocols.io.8epv5jqb6l1b/v1 | https://www.protocols.io/view/modified-nebnext-varskip-long-sars-cov-2-enrichmen-csp9wdr6 | Kathryn Judy, Padmini Ramachandran, Amanda Windsor, Tamara Walsky, Chris Grim, Maria Hoffmann | TITLE: Modified NEBNext® VarSkip Long SARS-CoV-2 Enrichment and library prep (Native Barcoding Kit V14 Oxford Nanopore Technologies)- adapted for wastewater samples
AUTHORS: Kathryn Judy, Padmini Ramachandran, Amanda Windsor, Tamara Walsky, Chris Grim, Maria Hoffmann
[DESCRIPTION]
This protocol details methods for t... | ["[Before you start]", "[Targeted cDNA Amplification]", "[Targeted cDNA Amplification] Prepare master mixes fresh immediately before performing cDNA amplification. \n\nQ5 Hot Start High-Fidelity Polymerase should stay on ice at all times. Do not vortex.\nThaw Q5 Reaction Buffer, MgCl2, dNTPs, and water.\nMix thawed tub... |
23,845 | LB Media | null | dx.doi.org/10.17504/protocols.io.3idgka6 | null | William Brydon, Sricharan Kadimi | TITLE: LB Media
AUTHORS: William Brydon, Sricharan Kadimi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">LB (Luria-Bertani) media is commonly used for bacterial culture. We use it for overnight cultures after transformations.</div></div>
[STEPS]
?. [Creating the Broth]
In a large glass bottle (at ... | ["[Creating the Broth]\nIn a large glass bottle (at least 1L), add the following:Component AmountDeoinized Water Tryptone Yeast Extract NaCl (You do not have to add the exact amoun... |
22,265 | 1M Potassium Phosphate Buffer, pH 6.0 | 1 | null | https://www.protocols.io/view/1m-potassium-phosphate-buffer-ph-6-0-zyzf7x6 | Adrien Assie, Buck Samuel | TITLE: 1M Potassium Phosphate Buffer, pH 6.0
AUTHORS: Adrien Assie, Buck Samuel
[DESCRIPTION]
Potassium Phosphate buffer recipe
[STEPS]
1. Start with700 mL
2. 108.3 g KH2PO4
3. 35.6 g K2HPO4
4. Adjust to 1000 mL
5. Autoclave | ["Start with700 mL", "108.3 g KH2PO4", "35.6 g K2HPO4", "Adjust to 1000 mL", "Autoclave"] |
58,489 | Additional information for the manual annotation of the terpene synthase gene family in Melaleuca alternifolia (tea tree) | 5 | dx.doi.org/10.17504/protocols.io.3byl4bjr2vo5/v1 | https://www.protocols.io/view/additional-information-for-the-manual-annotation-o-b5czq2x6 | Julia Voelker | TITLE: Additional information for the manual annotation of the terpene synthase gene family in Melaleuca alternifolia (tea tree)
AUTHORS: Julia Voelker
[DESCRIPTION]
This protocol was created to be read in conjunction with the publication about the manual annotation of the terpene synthase (TPS) gene family in Melaleu... | ["[Manual terpene synthase (TPS) annotation] The genome of the tea tree reference genotype SCU01 (BioProject PRJNA702189) was used for the manual TPS annotation. Genes in the tea tree genome sequence were automatically predicted with Fgenesh++ v7.2.2 (RRID:SCR_018928) and GenemarkET+ v4.59 (RRID:SCR_011930). The method... |
26,560 | Preparation of Adult Human Kidney Tissue for Single Nucleus RNA-seq and Other Multiomics Studies | null | dx.doi.org/10.17504/protocols.io.568g9hw | null | sanjay jain, Masato Hoshi, Amanda Knoten, Diane Salamon | TITLE: Preparation of Adult Human Kidney Tissue for Single Nucleus RNA-seq and Other Multiomics Studies
AUTHORS: sanjay jain, Masato Hoshi, Amanda Knoten, Diane Salamon
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Critical to generating robust single cell or tissue gene expression data is ensurin... | ["[FrozenTissue embedding and OCT Block Preparation]\nLabel one cryomold with specimen number and place it on powdered dry ice. This will be the cassette in which tissue will be embedded.", "[FrozenTissue embedding and OCT Block Preparation]\nTake the second cryomold and fill it with O.C.T.\nTissue will be bathed in it... |
51,252 | Whole Genome Bi-sulphite Sequencing (WGBS) | 4 | dx.doi.org/10.17504/protocols.io.bwaupaew | https://www.protocols.io/view/whole-genome-bi-sulphite-sequencing-wgbs-bwaupaew | Klaus H. Kaestner Lab, Suzanne Shapira | TITLE: Whole Genome Bi-sulphite Sequencing (WGBS)
AUTHORS: Klaus H. Kaestner Lab, Suzanne Shapira
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">The molecular mechanisms that underlie islet dysfunction in Type 1 (autoimmune) and Type 2</span></div><div class = "tex... | ["[Fragmentation]\n1. Covaris Fragmented gDNA: 55ng. Fragmentation program: 200bp as the Covaris recommended in in the low TE buffer by using snap-cap microtube (Covaris, cat#520045)\n130 µl", "[Bisulfite by using Ultralow Methylation-seq with TrueMethl oxBS (NuGEN, CAT#0541) Only use the indicated mock-oxidation step... |
51,933 | Immunostaining | 1 | dx.doi.org/10.17504/protocols.io.bwx5pfq6 | https://www.protocols.io/view/immunostaining-bwx5pfq6 | Jamie Verheyden | TITLE: Immunostaining
AUTHORS: Jamie Verheyden
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for immunofluorescent staining of lung tissue embedded in paraffin or OCT.</div></div>
[STEPS]
?. See attached protocol. | ["See attached protocol."] |
43,985 | High-throughput microbial metabarcoding amplification Protocol sequenced by DNBSEQ-G400 | 4 | dx.doi.org/10.17504/protocols.io.bn7rmhm6 | https://www.protocols.io/view/high-throughput-microbial-metabarcoding-amplificat-bn7rmhm6 | Xiaohuan Sun, Yuehua Hu, Zewei Song | TITLE: High-throughput microbial metabarcoding amplification Protocol sequenced by DNBSEQ-G400
AUTHORS: Xiaohuan Sun, Yuehua Hu, Zewei Song
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used for bacteral 16S V4 and fungal ITS amplification following sequencing characterizaiton u... | ["Amplify the 16SV4 region and ITS region from samples using a pair of primers with unique barcodes. X refers to 6bp artificial DNA oligos as first-barcode. N refers to the 0-3 bases random nuclear acid, which used to shift sequences in template DNA to avoid synchronal signals caused by conserved DNA regions in amplico... |
30,940 | Lactophenol-aniline blue solution | null | dx.doi.org/10.17504/protocols.io.baf4ibqw | null | Andrea Sweigart | TITLE: Lactophenol-aniline blue solution
AUTHORS: Andrea Sweigart
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Lactophenol-aniline blue recipe</div></div>
[STEPS]
?. [Make Lactophenol]
To make of stock Lactophenol:Combine:
100 ml
20 ml
40 ml
20 ml
20 ml
?. [Lactophenol-aniline blue recipe]
To... | ["[Make Lactophenol]\nTo make of stock Lactophenol:Combine:\n100 ml\n20 ml\n40 ml\n20 ml\n20 ml", "[Lactophenol-aniline blue recipe]\nTo prepare working solution, combine: stock Lactophenol to\n100 ml\n100 ml\n1 ml\n5 ml"] |
84,265 | Protocols for "Characterizing the diversity of enteric neurons using Dopamine Transporter (DAT)-Cre reporter mice". | 2 | dx.doi.org/10.17504/protocols.io.3byl4q792vo5/v1 | https://www.protocols.click/view/protocols-for-34-characterizing-the-diversity-of-e-cwihxcb6 | sherilyn.recinto, Shobina Premachandran, Sriparna Mukherjee, Adam Macdonald | TITLE: Protocols for "Characterizing the diversity of enteric neurons using Dopamine Transporter (DAT)-Cre reporter mice".
AUTHORS: sherilyn.recinto, Shobina Premachandran, Sriparna Mukherjee, Adam Macdonald
[DESCRIPTION]
Dopaminergic neurons (DA) are the predominant cell type in the midbrain that synthesize d... | [] |
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