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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31,443 | Isolation of Klebsiella strains from food samples | null | dx.doi.org/10.17504/protocols.io.baxtifnn | null | MedVetKlebs consortium | TITLE: Isolation of Klebsiella strains from food samples
AUTHORS: MedVetKlebs consortium
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is intended for isolation of </span><span style = "font-style:italic;">Klebsiella</span><span> strains from different food sources. It is deriv... | ["[Pre-treatment of sample]\nCut sample into small slivers to a final weight of 25g.", "[Pre-treatment of sample]\nDilute the 25g portion in 225ml of Buffered Peptone Water (BPW) broth (1:10 dilution).", "[Pre-treatment of sample]\nMix the sample using a stomacher for 30 seconds or pulse using a blender.", "[Pre-treatm... |
40,490 | Binding of avian immunoglobulins to peroxidase-labeled anti-chicken IgY conjugate by double immunodiffusion (Ouchterlony) technique. | 4 | dx.doi.org/10.17504/protocols.io.bjsiknce | https://www.protocols.io/view/binding-of-avian-immunoglobulins-to-peroxidase-la-bjsiknce | Angel Justiz-Vaillant | TITLE: Binding of avian immunoglobulins to peroxidase-labeled anti-chicken IgY conjugate by double immunodiffusion (Ouchterlony) technique.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">In this experiment anti-chicken IgY developed in rabbit cross-reacts with a la... | ["The binding of avian immunoglobulins to a secondary antibody rabbit anti-chicken IgY antibody was investigated by the Ouchterlony technique.", "Briefly, 1% agarose gels are prepared and wells cut into the gel using a template.", "Initially, aliquots of 25 µl each of rabbit anti-IgY antibody at 1 µg/µl are applied to... |
38,380 | Dialysis using D-Tubes | 1 | dx.doi.org/10.17504/protocols.io.bhqkj5uw | https://www.protocols.io/view/dialysis-using-d-tubes-bhqkj5uw | Neilier Junior | TITLE: Dialysis using D-Tubes
AUTHORS: Neilier Junior
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Sample preparation is crucial for successful biomolecule analysis. For this, the method must be individually chosen, based on the characteristics of the sample and the analyte. How some strategies c... | ["[Material preparation]\nChoose the cutting mass (3.5 to 14 kDa) of the dialysis D-Tube based on the biomolecule to be purified.", "[Procedure]\nComplete the dialysis D-Tube with Milli-Q water and let it equilibrate for 15 min", "[Procedure]\nRemove the water and weigh the dialysis tube", "[Procedure]\nAdd the sample ... |
20,022 | Mammalian Cell Nucleus Staining | null | dx.doi.org/10.17504/protocols.io.xswfnfe | null | Kenneth Schackart, Kattika Kaarj | TITLE: Mammalian Cell Nucleus Staining
AUTHORS: Kenneth Schackart, Kattika Kaarj
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Introductory protocol for cell nucelus staining using and imaging. This protocol uses Invitrogen™ NucBlue™ LiveReady Probes™.</div></div>
[STEPS]
?. [Stain Cells]
Using m... | ["[Stain Cells]\nUsing micropipette, remove cell culture media from each well.", "[Stain Cells]\nWash each well twice with DPBS.\n100 µl", "[Stain Cells]\nAdd NucBlue™ solution to each well.\n100 µl", "[Stain Cells]\nCover with aluminum foil.\nThe aluminum foil is simply to prevent photobleaching of the fluorescent dye... |
45,931 | Expression and Purification of Thermostable Proteins Expressed in E. coli | 1 | dx.doi.org/10.17504/protocols.io.bq4jmyun | https://www.protocols.io/view/expression-and-purification-of-thermostable-protei-bq4jmyun | Michael Van Dyke | TITLE: Expression and Purification of Thermostable Proteins Expressed in E. coli
AUTHORS: Michael Van Dyke
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Our laboratory studies putative transcription regulatory proteins from the extreme thermophile, </span><span style = "font-style:italic;">T... | ["[Protein expression]\nInoculate 1 mL LB:50 µg/mL kanamycin culture in a 5 mL Falcon snap-cap tube with a ~1 cm swatch from a streak. Repeat for a second clone. Incubate tubes in a rack at 37 °C, 240 rpm, 30 min. Cultures will appear slightly cloudy when well dissociated.", "[Protein expression]\nUse each 1 mL culture... |
99,956 | Sequencing dMDA Products on the MinION using Oxford Nanopore's Rapid Barcoding Kit | 0 | dx.doi.org/10.17504/protocols.io.kxygxy9odl8j/v1 | https://www.protocols.io/view/sequencing-dmda-products-on-the-minion-using-oxfor-dduu26ww | Dominic Horner, Ester Kalef-Ezra, Marco Toffoli, Christos Proukakis | TITLE: Sequencing dMDA Products on the MinION using Oxford Nanopore's Rapid Barcoding Kit
AUTHORS: Dominic Horner, Ester Kalef-Ezra, Marco Toffoli, Christos Proukakis
[DESCRIPTION]
Using Oxford Nanopore MinION and the Rapid Barcoding library preparation kit, we perform long read sequencing on droplet multiple disp... | ["[Prepare Samples and Reagents] Remove Ampure XP beads from fridge and allow them to equilibrate to Room temperature for approximately 30 min. Mix well by vortexing prior to use, ensure beads are resuspended and appear homogenous.", "[dMDA product purification] Add Ampure XP beads in a 0.8X ratio by volume to each sa... |
78,833 | Viral purification from faecal sample | 4 | dx.doi.org/10.17504/protocols.io.81wgbywbovpk/v1 | https://www.protocols.io/view/viral-purification-from-faecal-sample-cq8rvzv6 | sarah.schulz | TITLE: Viral purification from faecal sample
AUTHORS: sarah.schulz
[DESCRIPTION]
Protocol for the purification of viral particles from a faecal sample
[STEPS]
1. Homogenise 200 mg of faecal sample in 30 ml of SM buffer (50 mM Tris-HCl pH 7.5, 100 mM NaCl, 8 mM MgSO4)
2. Centrifuge sample at 4000 rpm for 20 min, then ... | ["Homogenise 200 mg of faecal sample in 30 ml of SM buffer (50 mM Tris-HCl pH 7.5, 100 mM NaCl, 8 mM MgSO4)", "Centrifuge sample at 4000 rpm for 20 min, then filter through a 0.2 μm filter", "Add filtrate to a 100-kDa-molecular-mass Amicon Ultra-15 Centrifugal Filter", "Centrifuge filter tube at 4000 rpm for 3 min to c... |
null | null | null | dx.doi.org/10.17504/protocols.io.smkec4w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is used to dissociate adult (8-10 week) mouse testis into a single cell suspension. The entire procedure is carried out 'on ice', reducing artifact gene expression changes. The yield is 5.4 million cells from 25 mg tissue and the viability is ~99%. </p>
[GUIDE... | [] |
65,254 | Pioneer Woman CBD Gummies Reviews: Best Gummy Bears In USA | 1 | dx.doi.org/10.17504/protocols.io.261gen1dyg47/v1 | https://www.protocols.io/view/pioneer-woman-cbd-gummies-reviews-best-gummy-bears-cbyespte | pioneerwomangummireviews | TITLE: Pioneer Woman CBD Gummies Reviews: Best Gummy Bears In USA
AUTHORS: pioneerwomangummireviews
[DESCRIPTION]
Pioneer Woman CBD Gummies Reviews: Best Gummy Bears In USA
[STEPS]
1. Pioneer Woman CBD Gummies Reviews: Best Gummy Bears In USA
Pressure, despair, concern, and a variety of other internal issues face ... | ["Pioneer Woman CBD Gummies Reviews: Best Gummy Bears In USA\nPressure, despair, concern, and a variety of other internal issues face people with a lot of liabilities, and they must be dealt with on time and in a natural way. The brain is vital to a person’s overall physical well- being, but when neurodegenerative ails... |
82,377 | 11. Taxon Group: Polychaeta | 4 | dx.doi.org/10.17504/protocols.io.8epv5jw7nl1b/v1 | https://www.protocols.io/view/11-taxon-group-polychaeta-cuphwvj6 | Patrick Adkins, Chris Fletcher, Inez Januszczak | TITLE: 11. Taxon Group: Polychaeta
AUTHORS: Patrick Adkins, Chris Fletcher, Inez Januszczak
[DESCRIPTION]
This is part of the collection "DToL Taxon-specific Standard Operating Procedures (SOPs) for Marine Metazoa", lead by the Other Metazoa Working Group. The SOP collection contains guidance on how to process the var... | [] |
25,221 | CRISPR-Cas9 Genome Editing in Human Primary T Cells | null | dx.doi.org/10.17504/protocols.io.4vdgw26 | null | STEMCELL Technologies | TITLE: CRISPR-Cas9 Genome Editing in Human Primary T Cells
AUTHORS: STEMCELL Technologies
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">CRISPR-Cas9, an RNA-guided genome editing technology, is revolutionizing cell biology due to the ease and efficiency by which it enables genetic manipulation of m... | ["[T Cell Isolation and Activation]\nIsolate human T cells from peripheral blood using EasySep™ Human T Cell Isolation Kit. Refer to the Product Information Sheet for details.", "[T Cell Isolation and Activation]\nCount cells and adjust to 1 x 106 cells/mL in ImmunoCult™-XF T Cell Expansion Medium supplemented with:2 m... |
null | null | null | dx.doi.org/10.17504/protocols.io.qxhdxj6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This workflow described how to download RNA-seq raw data from NCBI or EBI and to process them to quantify transcript abundance.</p>
[STEPS]
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58,383 | Inducing gemmulation in the freshwater sponge Ephydatia muelleri in culture using theophylline | 4 | dx.doi.org/10.17504/protocols.io.n92ldzprnv5b/v1 | https://www.protocols.io/view/inducing-gemmulation-in-the-freshwater-sponge-ephy-b49pqz5n | Shunsuke Sogabe, Taitum Cornish, April Hill, Ana Riesgo, Sally P Leys | TITLE: Inducing gemmulation in the freshwater sponge Ephydatia muelleri in culture using theophylline
AUTHORS: Shunsuke Sogabe, Taitum Cornish, April Hill, Ana Riesgo, Sally P Leys
[DESCRIPTION]
Freshwater sponges produce overwintering cysts called gemmules that are full of stem cells, allowing them to survive harsh w... | ["[Hatching and growing sponges] Hatch and grow sponges using the protocol - \"Hatching and freezing gemmules from the freshwater sponge Ephydatia muelleri\" by Sally P Leys, Lauren Grombacher, and April Hill (dx.doi.org/10.17504/protocols.io.863hzgn).", "[Treating sponges with theophylline] After sponges have reached ... |
null | null | null | dx.doi.org/10.17504/protocols.io.h97b99n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Please contact Dr. Steven Wilhelm (wilhelm@utk.edu) for additional information regarding this protocol.</p>
<p> </p>
<p>Modified from Bold 1949, Bischoff and Bold 1963</p>
<p> </p>
<p> </p>
[STEPS]
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null | null | null | dx.doi.org/10.17504/protocols.io.kcecste | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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93,506 | Easy tracking of unstained cells in ImageJ | 5 | dx.doi.org/10.17504/protocols.io.261ged7rov47/v1 | https://www.protocols.io/view/easy-tracking-of-unstained-cells-in-imagej-c7jazkie | Isabella Gregorski, Henrike Rebl | TITLE: Easy tracking of unstained cells in ImageJ
AUTHORS: Isabella Gregorski, Henrike Rebl
[DESCRIPTION]
This protocol shows how stained and especially unstained cells can be tracked in ImageJ without much effort.
The aim was to establish a reproducible setup for electrical stimulation and to perform live tracking ... | ["[Image Processing] Process → Noise → 2x Despecle", "[Image Processing] Image → Adjust → Brightness/Contrast \n\nMove the sliders for Brightness and Contrast to the right until an evenly coloured background is created.\n\nBrightness is set to around 80 % and Contrast to 100 %.", "[Image Processing] Select \"Yes\" to ... |
null | null | null | dx.doi.org/10.17504/protocols.io.cjqumv | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is the protocol for Protein Expression Using BL21(DE3) Competent E. coli (C2527). For large scale, please follow <a href="https://protocols.io/view/Protein-Expression-Using-BL21-DE3-Large-Scale-C252-imsum5" target="_blank">this</a> protocol variant.
[GU... | [] |
99,083 | A Prospective Randomized Placebo-Controlled Double Blind Clinical Trial to Evaluate the Safety and Efficacy of CLBS03 (Autologous Ex Vivo Expanded Polyclonal CD4+CD25+CD127lo/-FOXP3+ Regulatory T-cells [Tregs]) in Adolescents with Recent Onset Type 1 Diabe | 0 | dx.doi.org/10.17504/protocols.io.n92ld8zb7v5b/v1 | https://www.protocols.io/view/a-prospective-randomized-placebo-controlled-double-dczj2x4n | Stephen Gitelman, Kurt Griffin | TITLE: A Prospective Randomized Placebo-Controlled Double Blind Clinical Trial to Evaluate the Safety and Efficacy of CLBS03 (Autologous Ex Vivo Expanded Polyclonal CD4+CD25+CD127lo/-FOXP3+ Regulatory T-cells [Tregs]) in Adolescents with Recent Onset Type 1 Diabe
AUTHORS: Stephen Gitelman, Kurt Griffin
[DESCRIPTION]
T... | ["[BACKGROUND AND SIGNIFICANCE] Summary", "[BACKGROUND AND SIGNIFICANCE] It is hypothesized that CLBS03 or autologous ex vivo expanded, polyclonal CD4+CD25+CD127lo/-FOXP3+ regulatory T-cells (Tregs) administered to participants with recent onset Type 1 Diabetes Mellitus (T1DM) will be safe and effective in preserving β... |
66,312 | https://www.facebook.com/GrownMDCBDGummiesOrder/ | 3 | dx.doi.org/10.17504/protocols.io.yxmvmn4kog3p/v1 | https://www.protocols.io/view/https-www-facebook-com-grownmdcbdgummiesorder-cczgsx3w | leedmoeller | TITLE: https://www.facebook.com/GrownMDCBDGummiesOrder/
AUTHORS: leedmoeller
[DESCRIPTION]
All Joy Organics merchandise are evaluated by an unbiased, 0.33-birthday party laboratory, which means that you are now not simply getting the organization's seal of approval.
[STEPS] | [] |
106,665 | Human post-mortem nuclei preparation and single-nucleus multiome DNA/RNA sequencing by ResolveOME | 0 | dx.doi.org/10.17504/protocols.io.3byl498bzgo5/v1 | https://www.protocols.io/view/human-post-mortem-nuclei-preparation-and-single-nu-dkeh4tb6 | Ester Kalef-Ezra, George Morrow, Yanping Guo, Christos Proukakis | TITLE: Human post-mortem nuclei preparation and single-nucleus multiome DNA/RNA sequencing by ResolveOME
AUTHORS: Ester Kalef-Ezra, George Morrow, Yanping Guo, Christos Proukakis
[DESCRIPTION]
Here we describe a protocol for nuclei isolation, immunostaining and sorting (FANS: Fluorescence-activated nuclear sorting) fo... | ["[Nuclei extraction from human post-mortem brain tissue] Experimental steps:\n\n \n\n \n\nDay 1", "[Nuclei extraction from human post-mortem brain tissue] Clean pestles provided in the Nuclei Isolation Minute kit the day before with 0.2 Molarity (M) NAOH, 10% Presept and place them in a falcon tube containing RNase AW... |
null | null | null | dx.doi.org/10.17504/protocols.io.j4icque | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>We describe a method to evaluate bacterial tolerance to air desiccation at 30 °C and 50% relative humidity.</p>
[STEPS] | [] |
92,287 | Western blotting of XK and VPS13A | 1 | dx.doi.org/10.17504/protocols.io.3byl4qb6zvo5/v1 | https://www.protocols.io/view/western-blotting-of-xk-and-vps13a-c6c7zazn | Chase Amos, Pietro De Camilli | TITLE: Western blotting of XK and VPS13A
AUTHORS: Chase Amos, Pietro De Camilli
[DESCRIPTION]
This protocol describes collection of protein from cultured cells and immunoblotting.
[STEPS]
SECTION: Cell culture and treatments
1. Culture K562 or COS-7 (ATCC) at 37 °C and 5% CO2, using RPMI for K562 or DMEM for COS-7 c... | ["[Cell culture and treatments] Culture K562 or COS-7 (ATCC) at 37 °C and 5% CO2, using RPMI for K562 or DMEM for COS-7 containing 10% FBS, 1 millimolar (mM) sodium pyruvate, 100 U/mL penicillin, 100 μg/mL streptomycin, 2 millimolar (mM) L-glutamine, 1 x non-essential amino acids, (all from Gibco) and 2.5 μg/mL pla... |
80,692 | Consent Form | 3 | dx.doi.org/10.17504/protocols.io.kqdg39z5pg25/v1 | https://www.protocols.click/view/consent-form-cs2uwgew | Christopher Hawthorne, Keenan Smith, Matthew Sheridan, Eric Jackson, Shona McKay, Malcolm Watson, Martin Shaw, Jonathan Cavanagh | TITLE: Consent Form
AUTHORS: Christopher Hawthorne, Keenan Smith, Matthew Sheridan, Eric Jackson, Shona McKay, Malcolm Watson, Martin Shaw, Jonathan Cavanagh
[DESCRIPTION]
Consent form for Predicting Cognitive Decline After Spinal Surgery (PROTECT).
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.vrhe536 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Integrated Whole Exome Sequencing (WES) analysis pipline using various tools and databases, developed as part of the Accelerator program for Discovery in Brain disorders using Stem cells (ADBS) program at National Centre for Biological Sciences (NCBS), Bangalore.
[STEPS]
SECTIO... | ["[Define paths and directories] {\"blocks\":[{\"key\":\"a3khf\",\"text\":\"\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]},{\"key\":\"75q51\",\"text\":\"\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]},{\"key\":\"1ti4a\",\"tex... |
50,562 | Integration of a control brick | 4 | dx.doi.org/10.17504/protocols.io.bvman42e | https://www.protocols.io/view/integration-of-a-control-brick-bvman42e | Carolyn Bayer, Maja Rennig, Anja Ehrmann, Morten Norholm | TITLE: Integration of a control brick
AUTHORS: Carolyn Bayer, Maja Rennig, Anja Ehrmann, Morten Norholm
[DESCRIPTION]
<div class = "text-blocks"><br/><div class = "text-block">SEGA, the Standardized Genome Engineering Architecture, is a comprehensive strain collection that enables genome engineering by combining onl... | ["[preculture and DNA fragment- Day 1]\nPrepare a PCR product of the control elements that need to be integrated and purify it from an agarose gel.", "[preculture and DNA fragment- Day 1]\nSetup a preculture of the strain harbouring pSIM19 in LB medium supplemented with Spectinomycin . Incubate overnight at\n30 33", "[... |
null | null | null | dx.doi.org/10.17504/protocols.io.ma4c2gw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is a protocol for extraction and purification of anthocyanin from potato.</p>
<h1> </h1>
[STEPS]
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39,209 | Preparing EV-depleted media | 1 | dx.doi.org/10.17504/protocols.io.biihkcb6 | https://www.protocols.io/view/preparing-ev-depleted-media-biihkcb6 | Aizea Morales Kastresana, Bryce Killingsworth, Joshua Welsh, Tim Traynor, Jennifer Jones | TITLE: Preparing EV-depleted media
AUTHORS: Aizea Morales Kastresana, Bryce Killingsworth, Joshua Welsh, Tim Traynor, Jennifer Jones
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes a method to prepare bovine EV-depleted 10% FBS cell culture media by ultracentrifugation of 20%... | ["[Setting up the centrifugation]\nPlace 80 mL of FBS and one new 500 mL bottle of media in the 37 ˚C water bath and allow FBS to thaw.", "[Setting up the centrifugation]\nTurn on and log into the ultracentrifuge using the account and password specific to the device.", "[Setting up the centrifugation]\nWrite your infor... |
85,734 | KAPP-Sen TMC: Tissue Section Preparation and H&E Staining | 1 | dx.doi.org/10.17504/protocols.io.6qpvr3653vmk/v1 | https://www.protocols.io/view/kapp-sen-tmc-tissue-section-preparation-and-h-amp-cxyexpte | Juliana Alcoforado Diniz, Paul Robson, Elaine Bechtel | TITLE: KAPP-Sen TMC: Tissue Section Preparation and H&E Staining
AUTHORS: Juliana Alcoforado Diniz, Paul Robson, Elaine Bechtel
[DESCRIPTION]
To perform imaging analysis of the whole pancreas the FFPE blocks were submitted to hematoxylin and eosin stain. Initially FFPE blocks were shipped from the Joslin Diabetes ... | ["[Preparation of the Workspace] Prepare workspace according to https://dx.doi.org/10.17504/protocols.io.36wgq37polk5/v1", "[Routine H&E Protocol: Leica AutoStainer XL] Step\n \n \n Station\n \n \n Reagent\n \n \n Time\n \n \n Exact\n \n \n \n 1\n \n \n 1\n \n \n Xylene\n \n \n 3:00\n \n ... |
25,369 | Sequencing open chromatin of single cell nuclei: snATAC-seq | null | dx.doi.org/10.17504/protocols.io.4zzgx76 | https://www.protocols.io/view/sequencing-open-chromatin-of-single-cell-nuclei-sn-4zzgx76 | Sebastian Preissl, Xinxin Wang, Bing Ren | TITLE: Sequencing open chromatin of single cell nuclei: snATAC-seq
AUTHORS: Sebastian Preissl, Xinxin Wang, Bing Ren
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for applying the TN5-based ATAC-seq method to the analysis of the chromatin of single cell nuclei isolated from brain tissue, ... | [] |
37,789 | Standard RNA Synthesis (E2050) | 1 | dx.doi.org/10.17504/protocols.io.bg55jy86 | https://www.protocols.io/view/standard-rna-synthesis-e2050-bg55jy86 | New England Biolabs | TITLE: Standard RNA Synthesis (E2050)
AUTHORS: New England Biolabs
[DESCRIPTION]
This is the synthesis protocol using the HiScribe™ T7 Quick High Yield RNA Synthesis Kit (E2050)
[BEFORE_START]
We strongly recommend wearing gloves and using nuclease-free tubes and reagents to avoid RNase contamination. Reactions ar... | ["Thaw the necessary kit components.", "Mix and pulse-spin in microfuge to collect solutions to the bottoms of tubes. Keep on ice.", "Assemble the reaction at Room temperature in the following order: \nNuclease-free water X µlNTP Buffer Mix10 µl (10 mM each NTP final)Template DNAX µl (1 µg)T7 RNA Polymerase Mix2 µlTot... |
37,709 | Protocol for characterization of morphology, electrophysiology, and synaptology of mouse stellate ganglion neurons | 1 | dx.doi.org/10.17504/protocols.io.bg3mjyk6 | https://www.protocols.io/view/protocol-for-characterization-of-morphology-electr-bg3mjyk6 | Amit Tsanhani, Youngjin Cho, Aidan Sullivan, Susan Tappan, John Tompkins | TITLE: Protocol for characterization of morphology, electrophysiology, and synaptology of mouse stellate ganglion neurons
AUTHORS: Amit Tsanhani, Youngjin Cho, Aidan Sullivan, Susan Tappan, John Tompkins
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The stellate is a thoracic sympathetic ganglion ... | ["[Stellate Isolation]\nAdult mice (M/F; 12±2 weeks of age) are sacrificed under deep isoflurane (5%) anesthesia by cervical dislocation and exsanguination.", "[Stellate Isolation]\nThe thorax is removed and placed in ice-cold physiologic salt solution (PSS) containing in mM: 121 NaCl, 5.9 KCl, 1.2 NaH2PO4, 1.2 MgCl2, ... |
null | null | null | dx.doi.org/10.17504/protocols.io.hpab5ie | null | null | TITLE: No Title
AUTHORS:
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82,490 | In Situ Imaging of N-Glycans by MALDIImaging Mass Spectrometry of Formalin-Fixed Paraffin-Embedded Tissue | 1 | null | https://www.protocols.click/view/in-situ-imaging-of-n-glycans-by-maldiimaging-mass-cus2wwge | Xiaowei Lu, Richard R. Drake, Thomas W. Powers, Kim Norris-Caneda, Anand S. Mehta, Peggi M. Angel, Sean C. Bendall, Michael Angelo | TITLE: In Situ Imaging of N-Glycans by MALDIImaging Mass Spectrometry of Formalin-Fixed Paraffin-Embedded Tissue
AUTHORS: Xiaowei Lu, Richard R. Drake, Thomas W. Powers, Kim Norris-Caneda, Anand S. Mehta, Peggi M. Angel, Sean C. Bendall, Michael Angelo
[DESCRIPTION]
Glycosylation of cell surface, secreted, and circula... | ["[Dewax] You can either use MIBI staining dewax_protocol or the protocol in Drake's published protocol. Here we adapted Drake's protocol into our oven settings in R139.", "[Antigen Retrieval (AR)] The purpose of antigen retrieval is to breakup the cross linking between the amino side chain of lysines and make the tiss... |
95,126 | Comprehensive Protocol for Total Protein Extraction, Precipitation, and BCA Assay Measurement from Plankton Samples | 4 | null | https://www.protocols.io/view/comprehensive-protocol-for-total-protein-extractio-c85wzy7e | Ying-Yu Hu | TITLE: Comprehensive Protocol for Total Protein Extraction, Precipitation, and BCA Assay Measurement from Plankton Samples
AUTHORS: Ying-Yu Hu
[DESCRIPTION]
This protocol outlines an optimized method for extracting total protein from plankton samples, encompassing both phytoplankton and zooplankton. The procedure invo... | ["[Sample collection] Microalgae samples", "[Sample collection] Filter microalgae in liquid media onto polycarbonate filters, using gentle vacuum pressure (130 mmHg).", "[Sample collection] Place folded filter in 2 mL cryogenic vial.", "[Reagent] 100 mM pH 7 Tris buffer\n\nDilute 1 part with 9 part MilliQ.", "[Protei... |
76,693 | Preparation and transformation of chemically competent Escherichia coli | 4 | null | https://www.protocols.io/view/preparation-and-transformation-of-chemically-compe-cn5vvg66 | Andreas Sagen | TITLE: Preparation and transformation of chemically competent Escherichia coli
AUTHORS: Andreas Sagen
[DESCRIPTION]
Calcium chloride (CaCl2) transformation is a laboratory technique in prokaryotic (bacterial) cell biology. The addition of calcium chloride to a cell suspension promotes the binding of plasmid DNA to lip... | ["[Preparation of Calcium chloride transformation buffer] In a sterile flask, add 200 mL distilled water", "[Transformation] Quickly thaw a single reaction tube with 100 µL hyper-competent cells in Inoue-DMSO", "[Preparation of Calcium chloride transformation buffer] Measure 25 mL (1 Molarity (M)) Calcium chloride\n\nM... |
67,160 | S-Trap™ column digestion protocol (Protifi) of proteins for LC-MS / proteomics | 1 | dx.doi.org/10.17504/protocols.io.yxmvmn6q9g3p/v1 | https://www.protocols.io/view/s-trap-column-digestion-protocol-protifi-of-protei-cdtys6pw | ronan.ocualain, Jamesallsey, Davidknight, Staceywarwood, Emmakeevill | TITLE: S-Trap™ column digestion protocol (Protifi) of proteins for LC-MS / proteomics
AUTHORS: ronan.ocualain, Jamesallsey, Davidknight, Staceywarwood, Emmakeevill
[DESCRIPTION]
This protocol details the in-house BioMS procedure of S-Trap™ protein clean-up and subsequent column digestion/conversion of protein to pepti... | ["[Sample preparation] To the reduced and alkylated sample of volume either of 25 µL or 50 µL, add a volume of 2.5 µL or 5.0 µL respectively of 12 % (v/v) aqueous phosphoric acid at a ratio of 1:10 for a final concentration of 1.2 % (v/v) phosphoric acid and vortex mix.", "[Sample preparation] Add 165 µL or 330 µL o... |
58,562 | Perfusion Live Microscopy of VEC-GFP HUVECs Using LSM780/980 for Junction Morphology Analysis | 4 | null | https://www.protocols.io/view/perfusion-live-microscopy-of-vec-gfp-huvecs-using-b5faq3ie | Emir Bora Akmeriç | TITLE: Perfusion Live Microscopy of VEC-GFP HUVECs Using LSM780/980 for Junction Morphology Analysis
AUTHORS: Emir Bora Akmeriç
[DESCRIPTION]
For live confocal microscopy with HUVEC VEC-GFP line
[STEPS]
SECTION: Cell Culture
1. Thaw a HUVEC-GFP tube (stored in liquid nitrogen tank, should be in F5, F6 or F7) in the ... | ["[Cell Culture] Thaw a HUVEC-GFP tube (stored in liquid nitrogen tank, should be in F5, F6 or F7) in the water bath. \n\nNOTICE: As of 21.02.22, there are only 4 tubes of VEC-GFP HUVEC line remaining. If there are no more tubes ready, early passage HUVECs have to be transduced with VEC-GFP lentiviruses", "[Cell Cultur... |
null | null | null | dx.doi.org/10.17504/protocols.io.je8cjhw | null | null | TITLE: No Title
AUTHORS:
[STEPS] | [] |
39,800 | Coral tissue and skeleton separation for downstream DNA and RNA extraction | 4 | dx.doi.org/10.17504/protocols.io.bi4ykgxw | https://www.protocols.io/view/coral-tissue-and-skeleton-separation-for-downstrea-bi4ykgxw | Molly Moynihan, Phyllis Yy Kho | TITLE: Coral tissue and skeleton separation for downstream DNA and RNA extraction
AUTHORS: Molly Moynihan, Phyllis Yy Kho
[STEPS]
?. [Preparation]
Prepare airbrush solution of with (Hester et al., 2016; ISME J, 10, 1157–1169)
[PBS]
[EDTA]
?. [Preparation]
Prepare airbrushing work space. Note: it is recommended to a... | ["[Preparation]\nPrepare airbrush solution of with (Hester et al., 2016; ISME J, 10, 1157–1169)\n[PBS]\n[EDTA]", "[Preparation]\nPrepare airbrushing work space. Note: it is recommended to airbrush in laboratory space that is removed from any molecular work-DNA/RNA extractions as aerosolized particles could be a sour... |
59,627 | A simple axial grafting method for Hydra | 1 | dx.doi.org/10.17504/protocols.io.14egn76emv5d/v1 | https://www.protocols.io/view/a-simple-axial-grafting-method-for-hydra-b6gjrbun | Gmakowski, Callen Hyland | TITLE: A simple axial grafting method for Hydra
AUTHORS: Gmakowski, Callen Hyland
[DESCRIPTION]
This protocol is a low cost and easy to implement method for axial grafting of Hydra. In 1742, Trembley first observed that tissues from two separate Hydra polyps can join when the cut edges are placed in contact (Lenhoff a... | ["[Prepare grafting slides] Working under the dissecting microscope, cut the fishing line into 10 mm segments using the razor blade or scalpel. Cut the fishing line at an angle to create a sharp point (Figure 1). We usually make slides with 10-12 fishing line \"skewers\" each.", "[Prepare grafting slides] Prepare the t... |
35,618 | Liquid Chromatography-Mass Spectrometry/Mass Spectrometry (LC-MS/MS) for Bulk Metabolomics | null | dx.doi.org/10.17504/protocols.io.be2ajgae | https://www.protocols.io/view/liquid-chromatography-mass-spectrometry-mass-spect-be2ajgae | Dusan Velickovic, Jessica Lukowski, Guanshi Zhang, Theodore Alexandrov, Chris Anderton, Kumar Sharma | TITLE: Liquid Chromatography-Mass Spectrometry/Mass Spectrometry (LC-MS/MS) for Bulk Metabolomics
AUTHORS: Dusan Velickovic, Jessica Lukowski, Guanshi Zhang, Theodore Alexandrov, Chris Anderton, Kumar Sharma
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Mass spectrometry imaging is an exciting tec... | ["[LC- MS/MS]\nVial is placed in autosampler of Waters H class LC.", "[LC- MS/MS]\nInject of sample onto a reversed phase Waters CSH column (3.0 mm x 150 mm x 1.7 μm particle size) with a 34 min gradient (mobile phase A: ACN/H2O (40:60) containing 10 mM ammonium acetate; mobile phase B: ACN/IPA (10:90) containing 10 ... |
36,417 | Growing overnight bacterial culture in 96WP | null | dx.doi.org/10.17504/protocols.io.bfs9jnh6 | https://www.protocols.io/view/growing-overnight-bacterial-culture-in-96wp-bfs9jnh6 | Priota Islam | TITLE: Growing overnight bacterial culture in 96WP
AUTHORS: Priota Islam
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Luria broth (LB) is a nutrient-rich media commonly used to culture bacteria in the lab. LB agar plates are frequently used to isolate individual (clonal) colonies of bacteria carr... | ["Obtain LB Broth from the Media kitchen LB Broth contents: 4gNaCl4 g Tryptone2 g Yeast Extract Add dH2O to 400 mL", "Wipe the work area with 70% ethanol and create a relatively sterile environment on the laboratory bench by using a simple gas-powered burner. Work under the hood if you have a large number of plates. Bo... |
74,843 | Fixation Protocol for Fresh Frozen Tissue Samples (post-MALDI) | 1 | dx.doi.org/10.17504/protocols.io.4r3l276d3g1y/v1 | https://www.protocols.io/view/fixation-protocol-for-fresh-frozen-tissue-samples-cmb3u2qn | Elizabeth Neumann, Jamie Allen, Jeff Spraggins | TITLE: Fixation Protocol for Fresh Frozen Tissue Samples (post-MALDI)
AUTHORS: Elizabeth Neumann, Jamie Allen, Jeff Spraggins
[DESCRIPTION]
Scope:
To provide a method for removal of MALDI matrix, fixation and preparation of tissue sections for Cell DIVE.
[GUIDELINES]
Special Notes:
1. Make sure no tissue drying, part... | ["After the tissue has been imaged via MALDI IMS, the slide should be placed in a coplin jar or glass petri dish with a solution of room temperature 4% paraformaldehyde in PBS (*must be room temperature).", "Place jar/dish on a shaker for 5 minutes.", "Discard the PFA (the MALDI IMS matrix will come off the slide in th... |
63,320 | K1 Keto Reviews (Scam or Legit) Worth Buying? | 3 | dx.doi.org/10.17504/protocols.io.kqdg3pbmql25/v1 | https://www.protocols.io/view/k1-keto-reviews-scam-or-legit-worth-buying-b93yr8pw | KKetocost | TITLE: K1 Keto Reviews (Scam or Legit) Worth Buying?
AUTHORS: KKetocost
[DESCRIPTION]
This thing deals with the ordinary elements of your body and gives you an unrivaled shape.
[STEPS] | [] |
52,299 | Keto Extreme Fat Burner South Africa - Does It Really Work Or Scam? | 1 | dx.doi.org/10.17504/protocols.io.bxbjpikn | https://www.protocols.io/view/keto-extreme-fat-burner-south-africa-does-it-reall-bxbjpikn | Keto Extreme Fat Burner South Africa | TITLE: Keto Extreme Fat Burner South Africa - Does It Really Work Or Scam?
AUTHORS: Keto Extreme Fat Burner South Africa
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">by</div><div style = "text-align :; float : ;"><img style = "" src = "https://s3.amazonaws.com/protocols-files/files/d67nbmtbx.jpg"... | ["[Keto Extreme Fat Burner South Africa]\nKeto Extreme Fat Burner South Africa: This is the weight reduction supplement for the purchasers through which they can get accomplishments in the get-healthy plan. As a matter of first importance, we should reveal to you one thing that weight reduction is definitely not a simp... |
57,797 | Preparing plasmids for nucleofection of hPSCs | 4 | dx.doi.org/10.17504/protocols.io.b4pdqvi6 | https://www.protocols.io/view/preparing-plasmids-for-nucleofection-of-hpscs-b4pdqvi6 | Hanqin Li, Oriol Busquets, Steven Poser, Dirk Hockemeyer, Frank Soldner | TITLE: Preparing plasmids for nucleofection of hPSCs
AUTHORS: Hanqin Li, Oriol Busquets, Steven Poser, Dirk Hockemeyer, Frank Soldner
[DESCRIPTION]
This protocol describes the standard procedure for the preparation of plasmids to be delivered into human pluripotent stem cells (hPSCs) using nucleofection.
General no... | ["Thaw plasmids on ice", "In each nucleofection, use 1 µg total of plasmid", "For prime editing PE2 strategy, use:\n 500 ng pCMV-PE2\n 500 ng pU6-pegRNA", "For prime editing PE3 strategy, use:\n 500 ng pCMV-PE2\n 330 ng pU6-pegRNA\n 170 ng pBPK1520-ngRNA", "Pipet the proper amount of each plasmid into a ... |
50,007 | Cell-free extract, 4x Wizard mix and CFPS reaction preparation- Haseloff Lab | 4 | null | https://www.protocols.io/view/cell-free-extract-4x-wizard-mix-and-cfps-reaction-bu3xnypn | Fernando Guzman Chavez, Jim Haseloff | TITLE: Cell-free extract, 4x Wizard mix and CFPS reaction preparation- Haseloff Lab
AUTHORS: Fernando Guzman Chavez, Jim Haseloff
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Following this recipe, you will cell-free extracts to perform Tx-TL reactions using plasmid or linear DNA based on P70a a... | ["[Preparing cell extracts]\n5 mL started culture (BL21 DE Star) were grown overnight at 37°C from a single colony in LB plate.", "[Preparing cell extracts]\nAt the next day 50 mL of LB medium were inoculated with 500 µL of the stationary culture from step 1 and grown at overnight at 37°C.", "[Preparing cell extracts]\... |
null | null | null | dx.doi.org/10.17504/protocols.io.ks9cwh6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Useful lab recipes such as common reagents, buffers, loading dye, etc. </p>
[STEPS] | [] |
94,903 | Descending Platform | 4 | null | https://www.protocols.io/view/descending-platform-c8wxzxfn | daniel.dautan, Per Svenningsson | TITLE: Descending Platform
AUTHORS: daniel.dautan, Per Svenningsson
[DESCRIPTION]
Behavioral test to assess motor function.
[STEPS]
1. Place the custom-made horizontal grid (0.5cm space between grid, 45cm long, 5cm wide) to have an angle of 45 degrees with the floor.
2. A clean cage was placed at the bottom of the gr... | ["Place the custom-made horizontal grid (0.5cm space between grid, 45cm long, 5cm wide) to have an angle of 45 degrees with the floor.", "A clean cage was placed at the bottom of the grid.", "Place a camera on top of the grid to allow recording of the time to descend.", "Naïve mice were placed on the horizontal end of ... |
null | null | null | dx.doi.org/10.17504/protocols.io.e9rbh56 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Protocol for digestion with NEBNext dsDNA Fragmentase (M0348)
[BEFORE_START]
Adequate mixing of NEBNext dsDNA Fragmentase is important for the success of this reaction. NEBNext dsDNA Fragmentase should be vortexed for 3 seconds prior to use.<br /><br />The protoc... | [] |
86,357 | 6-OHDA mouse model of Parkinson's disease | 1 | dx.doi.org/10.17504/protocols.io.81wgbxyjylpk/v1 | https://www.protocols.io/view/6-ohda-mouse-model-of-parkinson-39-s-disease-cyjvxun6 | Beatriz E Nielsen | TITLE: 6-OHDA mouse model of Parkinson's disease
AUTHORS: Beatriz E Nielsen
[DESCRIPTION]
This protocol describes the steps for generating a 6-hydroxy-dopamine (6-OHDA) mouse model of Parkinson's disease.
Low or high doses of 6-OHDA are injected into the medial forebrain bundle to induce a partial or a more comple... | ["[Drugs preparation] Preparation of low (1 µg/µL) and high dose (4 µg/µL) 6-OHDA solutions (freshly immediately before surgery):", "[Drugs preparation] For a final volume of 1 mL, weigh the appropriate amount of drug accounting for the weight of the salt component such that the following concentrations are achieved:\n... |
63,401 | Optimus GelРецензије - састав - *Прочитајте масти* Где купити! | 3 | dx.doi.org/10.17504/protocols.io.j8nlkk251l5r/v1 | https://www.protocols.io/view/optimus-gel-b96hr9b6 | Optimus Gel | TITLE: Optimus GelРецензије - састав - *Прочитајте масти* Где купити!
AUTHORS: Optimus Gel
[DESCRIPTION]
Оптимус Гел је нови квалитетан производ који обједињује најновија научна достигнућа која заувек ублажавају и отклањају болове у зглобовима, костима и мишићима! Наручите данас са 50% попуста!
https://www.digitalholi... | [] |
54,502 | Live Cell Quantification using Image Analysis | 1 | dx.doi.org/10.17504/protocols.io.bzgep3te | https://www.protocols.io/view/live-cell-quantification-using-image-analysis-bzgep3te | Minjung Song, Iman Mali, Venkat Pisupati, Florian T Merkle | TITLE: Live Cell Quantification using Image Analysis
AUTHORS: Minjung Song, Iman Mali, Venkat Pisupati, Florian T Merkle
[DESCRIPTION]
Purpose
This protocol describes image-based quantification of human pluripotent stem cells (hPSCs), which could be adapted for other cell populations that grow in a monolayer. It utili... | ["[Cell culture and staining: Cell plating] Coat plate with appropriate substrate to prepare cells for plating.", "[Cell culture and staining: Cell plating] When plating cells for culture, ensure that they are evenly distributed in the culture well by using a large enough volume of medium (e.g. 500 mL per well of a 24-... |
51,774 | Protocol for Generation of Pre-Formed Fibrils from Alpha-Synuclein Monomer | 2 | dx.doi.org/10.17504/protocols.io.bws6pehe | https://www.protocols.io/view/protocol-for-generation-of-pre-formed-fibrils-from-bws6pehe | The Michael J Fox Foundation Pff Standardization Consortium | TITLE: Protocol for Generation of Pre-Formed Fibrils from Alpha-Synuclein Monomer
AUTHORS: The Michael J Fox Foundation Pff Standardization Consortium
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a consensus protocol developed through discussions with Laura Volpicelli-Daley, Caryl Sortwel... | [] |
79,505 | Fixation and Embedding of Eyes at UAB | 1 | dx.doi.org/10.17504/protocols.io.8epv5jp75l1b/v1 | https://www.protocols.io/view/fixation-and-embedding-of-eyes-at-uab-crvrv656 | Jeffrey D. Messinger, David Anderson, Angela Kruse, Jamie Allen, Melissa Farrow, Jeff Spraggins, Kevin Schey, Christine Curcio | TITLE: Fixation and Embedding of Eyes at UAB
AUTHORS: Jeffrey D. Messinger, David Anderson, Angela Kruse, Jamie Allen, Melissa Farrow, Jeff Spraggins, Kevin Schey, Christine Curcio
[DESCRIPTION]
The accession and fixation of whole human eye specimens at University of Alabama Birmingham as part of the Human Biomo... | ["[Collection, dissection, and preservation of ocular tissue] Whole donor globes on wet ice were received within less than 6 hours time of death (TOD) from the Advancing Sight Network (500 Robert Jemison Rd Birmingham, AL 35209). Laterality was verified using extra ocular anatomy.", "[Optical coherence tomography (OCT)... |
null | null | null | dx.doi.org/10.17504/protocols.io.rmmd446 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Procedure to create an account, loging in and out of iMicrobe and exploring your dashboard.</p>
[STEPS]
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.gv2bw8e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Mapping metagenomic reads from <a href="https://github.com/MicroB3-IS/osd-analysis" target="_blank">Ocean Sampling Da</a>y (OSD) 2014 against NCBI's ViralRefSeq alongside viral sequences identified from the Tara Oceans survey using <a href="http://www.ncbi.nlm.nih.gov/pmc/articl... | [] |
95,966 | PURIFICATION OF PROTEINS FROM PFA FIXED SAMPLES BAK_WITH BIOTIN PULLDOWN FOR LC-MS/MS_2023 | 0 | dx.doi.org/10.17504/protocols.io.36wgq3xyylk5/v1 | https://www.protocols.io/view/purification-of-proteins-from-pfa-fixed-samples-ba-c9x6z7re | Bryan Killinger | TITLE: PURIFICATION OF PROTEINS FROM PFA FIXED SAMPLES BAK_WITH BIOTIN PULLDOWN FOR LC-MS/MS_2023
AUTHORS: Bryan Killinger
[DESCRIPTION]
This protocol details the purification of proteins from PFA fixed samples and extraction of proteins from formalin-fixed tissues. Also included, biotin pulldown prior to LC-MS/MS. Sa... | ["[Procedure Day 1 (Extract proteins and test concentration)] Wash sections in DM 3 X 10 min.", "[Procedure Day 1 (Extract proteins and test concentration)] Place sections in 1.5mL Eppendorf tube.", "[Procedure Day 1 (Extract proteins and test concentration)] Add 0.5 mL of reversal buffer.", "[Procedure Day 1 (Extract ... |
26,032 | SPARC Public Protocols | null | dx.doi.org/10.17504/protocols.io.5nqg5dw | null | SPARC Consortium, anita bandrowski | TITLE: SPARC Public Protocols
AUTHORS: SPARC Consortium, anita bandrowski
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a collection of protocols used by SPARC project investigators. </div></div>
[STEPS] | [] |
99,426 | Preparation and imaging of lipid bilayer-coated silica microspheres | 0 | dx.doi.org/10.17504/protocols.io.rm7vzjy2rlx1/v1 | https://www.protocols.io/view/preparation-and-imaging-of-lipid-bilayer-coated-si-ddca22se | Ezra Bruggeman | TITLE: Preparation and imaging of lipid bilayer-coated silica microspheres
AUTHORS: Ezra Bruggeman
[DESCRIPTION]
This protocol describes the preparation and imaging of lipid bilayer-coated micrometer-scale glass beads. This protocol was used to generate the data presented in Figure 2d-g in the following publication:
... | ["[Preparation of DPPC + 40% cholesterol lipid vesicles] Dissolve DPPC (850355C, Avanti Polar Lipids) in chloroform (366927, Sigma-Aldrich) to a concentration of 25 mg/mL in a glass vial with a PTFE (Teflon) lined cap (14-955-327, Fisher Scientific). You will need 23 µL per sample.", "[Preparation of DPPC + 40% cholest... |
94,675 | LIFEPLAN soil sampling | 1 | dx.doi.org/10.17504/protocols.io.5jyl8pw9rg2w/v2 | https://www.protocols.io/view/lifeplan-soil-sampling-c8ptzvnn | Gaia Giedre Banelyte, Arielle M Farrell, Hanna M.K. Rogers, Bess Hardwick, Deirdre Kerdraon | TITLE: LIFEPLAN soil sampling
AUTHORS: Gaia Giedre Banelyte, Arielle M Farrell, Hanna M.K. Rogers, Bess Hardwick, Deirdre Kerdraon
[DESCRIPTION]
Lifeplan is a global biodiversity monitoring project with the aim of assessing the current state of biodiversity worldwide, and using this knowledge to generate predictions o... | ["[Soil sampling] Remove any layer of live cryptogams (including moss, lichen or algae) and loose debris from the sampling area (such as dry or uncompacted leaves, branches, twigs, loose needles, etc.). Keep the litter layer, i.e. any layers which remain stuck to the ground. In habitats that have a lot of litter (such ... |
76,406 | All-oxide n-AZO/p-SnOx hetero-junction for flexible solar cells: A numerical approach | 1 | dx.doi.org/10.17504/protocols.io.261ge328jl47/v1 | https://www.protocols.io/view/all-oxide-n-azo-p-snox-hetero-junction-for-flexibl-cnuwvexe | MANOJ KUMAR, Syed Sadique Anwer Askari, BANOTH RAVI, BITTU KUMAR, SVS PRASAD, Santosh Kumar Choudhary, RAJESH SINGH, Shamsul Hassan, PURNENDU SHEKHAR PANDEY | TITLE: All-oxide n-AZO/p-SnOx hetero-junction for flexible solar cells: A numerical approach
AUTHORS: MANOJ KUMAR, Syed Sadique Anwer Askari, BANOTH RAVI, BITTU KUMAR, SVS PRASAD, Santosh Kumar Choudhary, RAJESH SINGH, Shamsul Hassan, PURNENDU SHEKHAR PANDEY
[DESCRIPTION]
Researcher needs to explore some metal oxide ... | ["[All-oxide n-AZO/p-SnOx hetero-junction for flexible solar cells: A numerical approach] Simulation studies on n-AZO/p-SnOx heterojunction thin film solar cells based on finite element analysis (FEA) using TCAD simulation software (Silvaco ATLAS TCAD tool, version 5.24.1.R) has been reported in this article.", "[All-o... |
105,359 | ClickSeq: Random-Primed Protocol with Single Indexing using ClickSeq Kit | 0 | null | https://www.protocols.io/view/clickseq-random-primed-protocol-with-single-indexi-di5p4g5n | Andrew Routh, Elizabeth Jaworski | TITLE: ClickSeq: Random-Primed Protocol with Single Indexing using ClickSeq Kit
AUTHORS: Andrew Routh, Elizabeth Jaworski
[DESCRIPTION]
ClickSeq is a simple, fragmentation-free method for the synthesis of Next-Generation Sequencing (NGS) libraries. ClickSeq derives its name by using ‘Click-Chemistry‘ in the place of c... | ["[Reverse Transcription and RNA Removal] In a 0.2ml tube, dilute 100 ng-1 µg of input RNA to 10 µL using nuclease free water.", "[Reverse Transcription and RNA Removal] Add 3 µL of ClickSeq Primer Mix (CPM) to the diluted RNA. Mix well.", "[Reverse Transcription and RNA Removal] Incubate the mixture at 65 °C for 5 min... |
96,872 | CMT-93 Cell Culture Protocol | 0 | dx.doi.org/10.17504/protocols.io.bp2l62k1dgqe/v1 | https://www.protocols.io/view/cmt-93-cell-culture-protocol-daug2etw | Laura Gómez | TITLE: CMT-93 Cell Culture Protocol
AUTHORS: Laura Gómez
[DESCRIPTION]
CMT-93 is a cell line exhibiting epithelial morphology that was isolated from the rectum of a mouse with polyploid carcinoma.
[BEFORE_START]
Clean and prepare the laminar flow cabinet, turn on the water bath and warm up the culture media.
[GUID... | ["[Preparation of complete growth medium (DMEM+)] Add 445 mL 1X DMEM, 50 mL FBS and 5 mLglutamine 200 millimolar (mM) to a sterile 500 mL bottle and homogenize", "[Preparation of complete growth medium (DMEM+)] Label the bottle with name, group, phone number, date and additions.", "[Preparation of complete growth mediu... |
90,859 | Sea Water - Blue Treasure | 4 | dx.doi.org/10.17504/protocols.io.36wgq36b5lk5/v2 | https://www.protocols.io/view/sea-water-blue-treasure-c4yjyxun | Willian Barela Costa | TITLE: Sea Water - Blue Treasure
AUTHORS: Willian Barela Costa
[DESCRIPTION]
Pt 🇧🇷
Produção de água do mar para cultivo de microalgas utilizando a marca Blue Treasure.
25 - 35 Salinidade
En
Sea water production for microalgae cultivation using the Blue Treasure supplier.
25 - 35 Salinity
27 mg/mL
[STEPS... | ["[Salting process - 1 liter] 0.027 g/mL -> 27 g Sea Sal to 1 L", "[Salting process - 1 liter] Shake until diluted", "[Salting process - 1 liter] Make sure the salinity is within the desired range using the salinity refractometer. In this protocol, the focus is 27 salinity.", "[Metodologia - 1 litro] 0.027 g/mL -> ... |
84,001 | Whole genome amplification and long read sequencing using ONT | 4 | dx.doi.org/10.17504/protocols.io.j8nlko5q5v5r/v1 | https://www.protocols.click/view/whole-genome-amplification-and-long-read-sequencin-cv99w996 | YiChien Lee, Huei-Mien Ke, Isheng Jason Tsai | TITLE: Whole genome amplification and long read sequencing using ONT
AUTHORS: YiChien Lee, Huei-Mien Ke, Isheng Jason Tsai
[DESCRIPTION]
A genome reference is a prerequisite for a complete understanding of the biology and evolution of a species. However, the major challenge remains to obtain high-quality DNA and RNA ... | ["[[Optional] extraction and denature of genomic DNA] Prepare DLB Lysis buffer: \n33 µL REPLI-g DLB buffer \n3 µL 1M DTT", "[Whole genome amplification] Prepare REPLI-g polymerase master mix\n9 µL Nuclease-free water\n29 µL REPLI-g Reaction Buffer\n2 µL REPLI-g DNA Polymerase", "[[Optional] extraction and denature of g... |
74,332 | QIAGEN DNeasy PowerSoil Pro Kit | 4 | dx.doi.org/10.17504/protocols.io.kxygx97mzg8j/v1 | https://www.protocols.io/view/qiagen-dneasy-powersoil-pro-kit-ckt4uwqw | QIAGEN | TITLE: QIAGEN DNeasy PowerSoil Pro Kit
AUTHORS: QIAGEN
[DESCRIPTION]
For the isolation of microbial genomic DNA from all soil types, including difficult samples such as compost, sediment, and manure.
The DNeasy PowerSoil Pro Kit comprises a novel and proprietary method for isolating microbial genomic DNA from environ... | ["[Sample preparation & cell lysis] SPIN the PowerBead Pro Tube briefly to ensure that the beads have settled at the bottom\n\nADD up to 0.25 g of soil sample to the PowerBead Pro Tube\n\nADD 800 µL of Solution CD1\n\nVORTEX briefly to mix", "[Sample preparation & cell lysis] HOMOGENIZE samples thoroughly usi... |
null | null | null | dx.doi.org/10.17504/protocols.io.mqfc5tn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.e2rbgd6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The cells targeted by the Streptavidin Nanobeads are either selected or depleted by incubating your sample with the magnetic particles after incubating with a biotin-conjugated antibody or antibody cocktail. The magnetically labeled fraction is retained by the use of a magnet... | [] |
52,149 | Enzymatic fragmentation of plant chromatin for Hi-C libraries | 4 | dx.doi.org/10.17504/protocols.io.j8nlk4pnxg5r/v1 | https://www.protocols.click/view/enzymatic-fragmentation-of-plant-chromatin-for-hi-bw6vphe6 | ignacio.carvajal, Elena Hilario | TITLE: Enzymatic fragmentation of plant chromatin for Hi-C libraries
AUTHORS: ignacio.carvajal, Elena Hilario
[DESCRIPTION]
The aim of this protocol is to learn how to prepare, evaluate and optimize a plant chromatin sample to produce a proximity ligated sample ready for NGS library preparation. We introduce several q... | ["[Nuclei isolation and integrity check] Add 20 mL to the ground tissue by gently dislodging it with an inoculation loop. Stir gently and drag the lump up against the tube wall until it is resuspended", "[Nuclei isolation and integrity check] Centrifuge 3500 rpm, 5 min, 10 °C. Pour off the supernatant into designated ... |
80,368 | The Evolution of the Tahitian Lexicon | 1 | dx.doi.org/10.17504/protocols.io.kqdg39o71g25/v1 | https://www.protocols.io/view/the-evolution-of-the-tahitian-lexicon-csqqwdvw | Ellinor Arzbaecher | TITLE: The Evolution of the Tahitian Lexicon
AUTHORS: Ellinor Arzbaecher
[DESCRIPTION]
The purpose of this research proposal is to analyze the changes to the Tahitian lexicon over time and connect these changes to the biocultural evolution of Polynesian communities on the island of Mo'orea in French Polynesia. Tahitia... | ["[COMMUNITY REVIEW & RESOURCE SYNTHESIS]", "[TAHITIAN LEXICON DATA CURATION] Develop a data extraction and curation plan.", "[TAHITIAN LEXICON DATA CURATION] Determine guiding review question. For this project, the review question is: what are the Tahitian words for flora and fauna?", "[TAHITIAN LEXICON DATA CURAT... |
35,969 | COPAS wormsorter | null | dx.doi.org/10.17504/protocols.io.bfc9jiz6 | https://www.protocols.io/view/copas-wormsorter-bfc9jiz6 | Ida Barlow | TITLE: COPAS wormsorter
AUTHORS: Ida Barlow
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for dispensing adult worms using the COPAS 500 flowpilot</div></div>
[STEPS]
?. [Prepare equipment]
Turn on the compressor at the wall – it should show a pressure of 40psi after switched on
?. [Prep... | ["[Prepare equipment]\nTurn on the compressor at the wall – it should show a pressure of 40psi after switched on", "[Prepare equipment]\nTurn on COPAS machine with switch on the left hand side", "[Prepare equipment]\nTurn on the lasers (488 laser sufficient if using unmarked animals). Add in picture of lasers.", "[Prep... |
37,726 | Türk solution and Trypan Blue | 3 | null | https://www.protocols.io/view/t-rk-solution-and-trypan-blue-bg36jyre | Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino | TITLE: Türk solution and Trypan Blue
AUTHORS: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This recepe is used in the following protocols:</div><div class = "text-block">- Separa... | [] |
26,448 | Mouse 2- Step Collagenase Liver Perfusion protocol | 1 | dx.doi.org/10.17504/protocols.io.53qg8mw | https://www.protocols.io/view/mouse-2-step-collagenase-liver-perfusion-protocol-53qg8mw | Michael Cheng, Xue-Zhong Ma, Chao Jiang, Ian McGilvray, Sonya Macparland | TITLE: Mouse 2- Step Collagenase Liver Perfusion protocol
AUTHORS: Michael Cheng, Xue-Zhong Ma, Chao Jiang, Ian McGilvray, Sonya Macparland
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Analyzing the mouse liver requires optimal cell recovery from the tissue in terms of quality (viability) and qu... | ["[Preparation]\nAnesthetize mouse with inhalational anesthesia (4-5% isofluorane) in the induction chamber", "[Laparotomy]\nMidline incision: cut open the abdomen from the pubic symphysis to the xiphoid process. Flip over the intestines to locate the liver and its portal vein.Please refer to Figure 14.4.1 of the follo... |
53,342 | Standard operating procedure of glassware cleaning | 1 | null | https://www.protocols.io/view/standard-operating-procedure-of-glassware-cleaning-byb6psre | Yingyu Hu | TITLE: Standard operating procedure of glassware cleaning
AUTHORS: Yingyu Hu
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">In our Marine Microbial Macroecology Lab, we focus on microalgae cultivation and macromolecule measurement. We expect all lab members to use the standard operating procedure o... | ["[Wash]\nDispose hazardous material in the appropriate waste location.", "[Wash]\nRemove filter or other items from the glassware.", "[Wash]\nPut small items, such as filter holder mesh, stir bar, cap…etc. in a beaker or container, so that they won’t get lost during washing.", "[Wash]\nRinse glassware with tap water t... |
62,868 | Standard Operating Procedure for collecting resting mosquitoes with pyrethrum spray catch | 1 | dx.doi.org/10.17504/protocols.io.kqdg3pb67l25/v1 | https://www.protocols.io/view/standard-operating-procedure-for-collecting-restin-b9mur46w | Tanya L Russell, Kyran Staunton, Thomas Burkot | TITLE: Standard Operating Procedure for collecting resting mosquitoes with pyrethrum spray catch
AUTHORS: Tanya L Russell, Kyran Staunton, Thomas Burkot
[DESCRIPTION]
The purpose of this SOP is to outline the materials and processes required to perform pyrethrum spray catches (PSCs) inside rooms or houses to collect ... | ["[Sampling procedure] Gather all equipment.\n\nA pyrethrum spray containing pyrethroid containing piperonyl butoxide (PBO) is preferred but permethin in a pump sprayer can also be used.", "[Sampling procedure] Identify the homes where the PSC will be conducted. Notify the head of the household and receive permission, ... |
50,559 | Measuring experience, including mistreatment, and satisfaction with newborn care: a scoping review of tools and indicators | 1 | dx.doi.org/10.17504/protocols.io.bvk7n4zn | https://www.protocols.io/view/measuring-experience-including-mistreatment-and-sa-bvk7n4zn | Nicole Minckas, Emma Sacks, Moise Muzigaba, Anayda Portela | TITLE: Measuring experience, including mistreatment, and satisfaction with newborn care: a scoping review of tools and indicators
AUTHORS: Nicole Minckas, Emma Sacks, Moise Muzigaba, Anayda Portela
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify"><s... | ["[INTRODUCTION]\nBACKGROUND Every woman and newborn has the right to high-quality health care, with evidence-based practices delivered in a humane, supportive environment. This quality of care should encompass clinical care as well as the experience of care of women, newborns, parents and their families, such as the r... |
92,326 | Flow cytometry for ex vivo stimulated pMacs | 4 | dx.doi.org/10.17504/protocols.io.rm7vzx9x4gx1/v1 | https://www.protocols.io/view/flow-cytometry-for-ex-vivo-stimulated-pmacs-c6eezbbe | Rebecca Wallings | TITLE: Flow cytometry for ex vivo stimulated pMacs
AUTHORS: Rebecca Wallings
[DESCRIPTION]
Flow cytometry for ex vivo stimulated pMacs
[STEPS]
1. Incubate cells for 30 minutes at 37 degrees in incubator in media containing 3mM EDTA at pH 6.2 to gently lift cells from plate. To encourage dissociation from plate, gentl... | ["Incubate cells for 30 minutes at 37 degrees in incubator in media containing 3mM EDTA at pH 6.2 to gently lift cells from plate. To encourage dissociation from plate, gently tap plate, or alternatively use a mini scraper", "Aliquot cells in to wells of v-bottom 96 well plate\n\nSpin cells at 300 x g at 4 degrees for ... |
50,839 | Protocol-RT-qPCR | 1 | dx.doi.org/10.17504/protocols.io.bvvxn67n | https://www.protocols.io/view/protocol-rt-qpcr-bvvxn67n | Klaus Hirschbühl | TITLE: Protocol-RT-qPCR
AUTHORS: Klaus Hirschbühl
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:center">Protocol-RT-qPCR to the paper:</div></div><div class = "text-block"><div class = "justify" style = "text-align:center"></div></div><div class = "text-b... | [] |
77,176 | Cryo_preservation_Synechocystis_PCC_6803 | 4 | dx.doi.org/10.17504/protocols.io.5jyl8jw38g2w/v1 | https://www.protocols.io/view/cryo-preservation-synechocystis-pcc-6803-cpkyvkxw | maurice.mager1808 | TITLE: Cryo_preservation_Synechocystis_PCC_6803
AUTHORS: maurice.mager1808
[DESCRIPTION]
Cryopreservation protocol used during the interlaboratory study published by Mager et al. 2023.
[STEPS]
SECTION: Precultures for Cryo conservation of Synechocystis PCC 6803
1. Starting from a BG11 agar plate with your strain of i... | ["[Precultures for Cryo conservation of Synechocystis PCC 6803] Starting from a BG11 agar plate with your strain of interest, inoculate a BG11 liquid culture", "[Cryo conservation of Synechocystis PCC 6803] Centrifuge cells at 12.000 g (fixed angle rotor) for 15 min and wash in the same volume of fresh BG11 medium", "[... |
46,639 | Advances in Hydrogen-deuterium Exchange Mass Spectrometry-A New Method for Protein Structure Analysis | 4 | null | https://www.protocols.io/view/advances-in-hydrogen-deuterium-exchange-mass-spect-brspm6dn | 181830691 , fe | TITLE: Advances in Hydrogen-deuterium Exchange Mass Spectrometry-A New Method for Protein Structure Analysis
AUTHORS: 181830691 , fe
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Hydrogen - deuterium exchange mass spectrometry is to study the spatial conformation of proteins. It is widely used in ... | [] |
37,213 | Feedstocks-to-Fuels Labman solid biomass dispensing protocol | 1 | dx.doi.org/10.17504/protocols.io.dm6gprm25vzp/v1 | https://www.protocols.io/view/feedstocks-to-fuels-labman-solid-biomass-dispensin-bgj5juq6 | Tad Ogorzalek, Jennifer Gin, Christopher J Petzold | TITLE: Feedstocks-to-Fuels Labman solid biomass dispensing protocol
AUTHORS: Tad Ogorzalek, Jennifer Gin, Christopher J Petzold
[DESCRIPTION]
This protocol details the steps necessary for aliquoting biomass for the Feedstocks-to-Fuels pipeline. Samples must be ground and put in scintillation or Sarstedt tubes prior to... | ["[Run Configuration - Process Parameters (middle left side)] Process Parameters:\n\nInput Filename - Input csv file\nManual Mapping Filename - manual mapping csv file\nOutput File Path - Output file path\nInput filename - The input file ('Input Filename' option) is a csv file that tells the robot where the source via... |
null | null | null | dx.doi.org/10.17504/protocols.io.ta7eihn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div>
<p>In the study we have used a standard Thermo Fisher Scientific Sanger sequencing protocol which can be found under this link:</p>
<p> </p>
<p>http://www.ramaciotti.unsw.edu.au/wp-content/uploads/2016/08/sequencing_handbook_FLR.pdf</p>
</div>
[STEPS]
?. | [] |
86,489 | Anatomical variations and dimensions of the popliteus muscle in cadaveric specimens | 4 | dx.doi.org/10.17504/protocols.io.3byl4qqk8vo5/v1 | https://www.protocols.io/view/anatomical-variations-and-dimensions-of-the-poplit-cypzxvp6 | Bv Murlimanju, Rajanigandha Vadgaonkar | TITLE: Anatomical variations and dimensions of the popliteus muscle in cadaveric specimens
AUTHORS: Bv Murlimanju, Rajanigandha Vadgaonkar
[DESCRIPTION]
Introduction
The popliteus muscle is located at the flexor aspect of
the leg and is supplied by the tibial nerve. This is the only muscle in the
back of leg... | [] |
23,271 | High quality DNA from Fungi for long read sequencing e.g. PacBio | null | dx.doi.org/10.17504/protocols.io.2yfgftn | null | Benjamin Schwessinger | TITLE: High quality DNA from Fungi for long read sequencing e.g. PacBio
AUTHORS: Benjamin Schwessinger
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Extraction of high quality DNA for long read sequencing e.g. PacBio</div><div class = "text-block">Optimized for DNA extraction from wheat stripe rus... | ["[Extraction I]\nMake lysis buffer by mixing buffer A+B+C (2.5:2.5:1 + 0.1%PVP final) and briefly heat to 64 °C. Let cool to room temperature for use in 50mL Falcon tubes.All following steps are based on 17.5ml lysis buffer as starting volume.", "[Extraction I]\nadd 10uL (10kU) RNAse T1 to lysis buffer", "[Extraction ... |
null | null | null | dx.doi.org/10.17504/protocols.io.un7evhn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
NS-Forest is an alogrithm that determines the minimum set of genes that are necessary and sufficient to define a cell type cluster derived from single cell RNAseq expression data.
Development and stable releases can be found at :
https://github.com/JCVenterInstitute/NSForest... | ["[Pre-analysis data preparation] 1. The script is a Jupyter notebook in python 2.7. Required libraries: Numpy, Pandas, Sklearn, graphviz, numexpr\n\n2. Build a Cell by Gene matrix where the values are either normalized or raw count expression values from a single cell RNAseq experiment (tsv or csv formats work by defa... |
20,152 | U Mass - Exercise model | null | dx.doi.org/10.17504/protocols.io.xwyfpfw | null | Jason Kim | TITLE: U Mass - Exercise model
AUTHORS: Jason Kim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">In-cage free running wheel is used to voluntarily induce exercise in awake mice. Exercise affects insulin sensitivity and... | ["Place running wheel inside mouse home cage.", "Monitor mouse health."] |
12,123 | RNA in situ hybridization | null | dx.doi.org/10.17504/protocols.io.p33dqqn | null | Nicholas Leigh, Garrett Dunlap, Kimberly Johnson, Rachelle Mariano, Rachel Oshiro, Alan Y. Wong, Donald M. Bryant, Bess Miller, Jessica L. Whited | TITLE: RNA in situ hybridization
AUTHORS: Nicholas Leigh, Garrett Dunlap, Kimberly Johnson, Rachelle Mariano, Rachel Oshiro, Alan Y. Wong, Donald M. Bryant, Bess Miller, Jessica L. Whited
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol provides details on tissue harvest and fixat... | ["[II. Probe Preparation]\nPerform PCR using OneTaq and with T7 and Sp6 primers using pGEM-T easy with probe inserted as template. Do 5+ reactions to ensure ample PCR product. Annealing temperature 40.5°C, extension time time appropriate for length of probe (typically around 30 seconds). AB1ReagentVolume (μL)25x OneT... |
77,692 | Alpha-synuclein immunochemistry on STC-1 cells using DAB | 4 | dx.doi.org/10.17504/protocols.io.kqdg39yjpg25/v1 | https://www.protocols.io/view/alpha-synuclein-immunochemistry-on-stc-1-cells-usi-cp44vqyw | Michael J Hurley | TITLE: Alpha-synuclein immunochemistry on STC-1 cells using DAB
AUTHORS: Michael J Hurley
[DESCRIPTION]
This protocol describes how to visualise alpha-synuclein in STC-1 cells by DAB immunohistochemistry. It also works for other antibodies (e.g. 5-HT, CCK, GLP).
[STEPS]
SECTION: Alpha-synuclein immunochemistry on STC... | ["[Alpha-synuclein immunochemistry on STC-1 cells using DAB] Thaw frozen 24-well plates containing fixed cells grown on glass coverslips", "[Alpha-synuclein immunochemistry on STC-1 cells using DAB] Wash cells with PBS 5 min", "[Alpha-synuclein immunochemistry on STC-1 cells using DAB] Quench with 0.3% H2O2 5 min", "[A... |
89,595 | Intestinal transit time | 1 | dx.doi.org/10.17504/protocols.io.eq2lyje1plx9/v1 | https://www.protocols.io/view/intestinal-transit-time-c3q3ymyn | Núria Peñuelas | TITLE: Intestinal transit time
AUTHORS: Núria Peñuelas
[DESCRIPTION]
Intestinal transit time measurement in mice
[STEPS]
1. Prepare red dye (Carminered dye, Sigma #C1022) in 0,5% methylcellulose (Sigma #M7027).
2. Take the animal and administer the red dye by oral gavage.
3. After oral gavage, individualize the anima... | ["Prepare red dye (Carminered dye, Sigma #C1022) in 0,5% methylcellulose (Sigma #M7027).", "Take the animal and administer the red dye by oral gavage.", "After oral gavage, individualize the animals in separate boxes without bedding.", "Monitor the animal boxes for a total time of 4h.", "Register the time when the anim... |
44,676 | Calf stretching | 3 | dx.doi.org/10.17504/protocols.io.bpvcmn2w | https://www.protocols.io/view/calf-stretching-bpvcmn2w | Masood Khan | TITLE: Calf stretching
AUTHORS: Masood Khan
[DESCRIPTION]
This time course study aimed to assess the acute effects of static stretching (SS) of different durations on the isometric maximum voluntary contraction force (MVCF) of the calf muscle. Ten male participants participated in three pretest-posttest experimental ... | [] |
40,921 | ELISA for quantification of human properdin in serum or plasma. | 6 | dx.doi.org/10.17504/protocols.io.bj7zkrp6 | https://www.protocols.io/view/elisa-for-quantification-of-human-properdin-in-se-bj7zkrp6 | Angel Justiz-Vaillant, Belkis Ferrer-Cosme | TITLE: ELISA for quantification of human properdin in serum or plasma.
AUTHORS: Angel Justiz-Vaillant, Belkis Ferrer-Cosme
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. An anti-human properdin coating antibody is adsorbed onto the microwells by incubation overnight at 4°C with carbonate-bicarbona... | ["An anti-human properdin coating antibody is adsorbed onto the microwells by incubation overnight at 4°C with carbonate-bicarbonate buffer.", "Add 50 µl of human serum or plasma. Human properdin present in the serum or plasma binds to antibodies adsorbed into the microwells.", "The microplate is blocked with 3% non-fa... |
91,810 | ssUMI: high-throughput long-read sequencing workflow for highly-accurate near full-length 16S rRNA genes on the ONT platform | 4 | dx.doi.org/10.17504/protocols.io.6qpvr3qkpvmk/v1 | https://www.protocols.io/view/ssumi-high-throughput-long-read-sequencing-workflo-c5way7ae | Xuan Lin, Katherine Waring, John Tyson, Ryan Ziels | TITLE: ssUMI: high-throughput long-read sequencing workflow for highly-accurate near full-length 16S rRNA genes on the ONT platform
AUTHORS: Xuan Lin, Katherine Waring, John Tyson, Ryan Ziels
[DESCRIPTION]
This is the online protocol for near full-length 16S rRNA amplicon sequencing with unique molecule identifiers (s... | ["[Sample pre-dilution and ddPCR quantification of starting material] Estimate the full-length 16S rRNA concentration in the DNA extract (e.g., sample), and dilute the sample to 20000 copies/μL with .", "[ssUMI-PCR1: UMI tagging and cleanup] In this step, the near full-length 16S rRNA gene primers containing UMIs are ... |
null | null | null | dx.doi.org/10.17504/protocols.io.d9q95v | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
In this protocol, we will merge the 20 profiled metagenomes in a table of relative abundances and visualize the table with a heatmap.
[BEFORE_START]
REQUIREMENTS: the <a href="http://matplotlib.org/" target="_blank">matplotlib</a> python library installed.
[GUIDELINES]
The com... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.gscbwaw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol show you how to create a sequence alignment with multiple sequences using CLUSTAL Omega and to futher modify it with Jalview and visualize it with Weblogo.</p>
[STEPS]
?.
?.
?.
?. | [] |
89,375 | Algaeorithm Classroom Guide: Analyzing Microscope Images | 5 | null | https://www.protocols.io/view/algaeorithm-classroom-guide-analyzing-microscope-i-c3h7yj9n | Ashwin Mukherjee, rohan chanani | TITLE: Algaeorithm Classroom Guide: Analyzing Microscope Images
AUTHORS: Ashwin Mukherjee, rohan chanani
[DESCRIPTION]
A guide to using Algaeorithm to analyze microscope images of algae.
[STEPS]
SECTION: Preparation
1. Before getting started, you'll want to ensure your photos meet the following criteria:
400x magnifi... | ["[Preparation] Before getting started, you'll want to ensure your photos meet the following criteria:\n400x magnification (typically through a 40x objective lens)\nclear/focused viewfinder\nhigh contrast between the viewfinder and the background\n\nsee examples of photos below:", "[Uploading Images] Once your images h... |
null | null | null | dx.doi.org/10.17504/protocols.io.jfncjme | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Here we present an efficient way to grow Tp colonies inside a 0.25% superclean agar matrix. This protocol could possibly be applicable to other marine microeukaryotes that are problematic to grow on fully solid support.</p>
[BEFORE_START]
<p><strong>1. Tp L1</strong></p>
<p>... | [] |
46,089 | Membrane challenge | 4 | null | https://www.protocols.io/view/membrane-challenge-bq9hmz36 | Elizabeth Fozo | TITLE: Membrane challenge
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Membrane Stress Challenge Protocol</div></div>
[STEPS]
?. [Protocol]
Prepare a 10 ml overnight of OG1RF in BHI. Grow at 37°C
?. [Protocol]
Prepare dilution tubes with 0.9% saline - autoclave dilution t... | ["[Protocol]\nPrepare a 10 ml overnight of OG1RF in BHI. Grow at 37°C", "[Protocol]\nPrepare dilution tubes with 0.9% saline - autoclave dilution tubes for 12 minutes", "[Protocol]\nIn a.m., dilute overnight to b 0.01 in x of BHI + 1.5mM CaCl2Prepare BHI +1.5mM CaCl2: Depending on how much BHI you need, you can take a ... |
null | null | null | dx.doi.org/10.17504/protocols.io.nx7dfrn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div>
<div>
<div>This is our standard brain tissue dissociation protocol for cell sorting (<a href="https://www.humancellatlas.org/" target="_blank" rel="noopener noreferrer">Human Cell Atlas</a>).</div>
</div>
</div>
[GUIDELINES]
<p><strong>NOTE</strong>: A critical component ... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.c4zyx5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
April 2000 chp<br /><br />Phage are best purified by a CsCl gradient. This is separated by density not sedimentation as in a sucrose gradient.<br /><br />This is a protocol for P22 like phage not T4 with delicate tail fibers.
[GUIDELINES]
This protocol is part of a larger colle... | [] |
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