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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30,503 | Loop L2 (even level) SapI type IIS cloning into pCs vectors | null | dx.doi.org/10.17504/protocols.io.92fh8bn | null | Eftychis Frangedakis, Susana Sauret-Gueto, Anthony West, marta tomaselli, Nicola Patron, Marius Rebmann, Jim Haseloff | TITLE: Loop L2 (even level) SapI type IIS cloning into pCs vectors
AUTHORS: Eftychis Frangedakis, Susana Sauret-Gueto, Anthony West, marta tomaselli, Nicola Patron, Marius Rebmann, Jim Haseloff
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol based on</div><div class = "text-block"><a href="... | ["[Protocol for assembly of L1 constructs into a L2 device]\nDetermine the concentration of each DNA plasmid needed (L1 plasmids and pCs acceptor plasmid)with spectrophotometry (Nanodrop).In the example in step 2, determine concentration of plasmids L1_001-Ck1, L1_002-Ck2, L1_003-Ck3, L1_004-Ck4 and pCsA", "[Protocol f... |
11,100 | NEBNext Ultra II FS DNA Module E7810 | null | dx.doi.org/10.17504/protocols.io.n34dgqw | null | New England Biolabs | TITLE: NEBNext Ultra II FS DNA Module E7810
AUTHORS: New England Biolabs
[DESCRIPTION]
<p>The NEBNext Ultra II FS DNA Module contains the enzymes and buffers required to convert a broad range of input amounts of intact DNA into fragmented DNA with 5´ phosphorylated 3´ dA-tailed ends. The module is optimized for use w... | ["[Fragmentation/End Prep]\nFragmentation occurs during the 37°C incubation step. Use the chart below to determine the incubation time required to generate the desired fragment sizes. Incubation time may need to be optimized for individual samples. See Figure 1 for a typical fragmentation pattern. ABC1Fragmentation Si... |
100,054 | Phenocycler-Fusion Staining Protocol For Bone Marrow Tissue | 1 | dx.doi.org/10.17504/protocols.io.5jyl8pzodg2w/v2 | https://www.protocols.io/view/phenocycler-fusion-staining-protocol-for-bone-marr-ddxw27pe | Kyung J Ahn, Shovik Bandyopadhyay, Anusha Thadi, Kai Tan | TITLE: Phenocycler-Fusion Staining Protocol For Bone Marrow Tissue
AUTHORS: Kyung J Ahn, Shovik Bandyopadhyay, Anusha Thadi, Kai Tan
[DESCRIPTION]
This protocol describes the method for antibody staining of FFPE bone marrow tissue on slides using CODEX barcoded antibodies. The Akoya Phenocycler-Fusion user manual was... | ["[Tissue Pre-treatment] Bake sample slide/s in an incubator at 65°C for 1-3 hours until paraffin thoroughly melts.", "[Tissue Deparaffinization and Hydration] Immerse sample slide/s in a coplin jar containing the following reagents for 5 minutes each: \n\na.Histochoice \nb.Histochoice\nc.100% Ethanol\nd.100% Ethanol\n... |
80,143 | Synthesis and preparation of DOPA pheomelanin and eumelanin | 1 | dx.doi.org/10.17504/protocols.io.4r3l27j4qg1y/v1 | https://www.protocols.io/view/synthesis-and-preparation-of-dopa-pheomelanin-and-cshpwb5n | Kazumasa Wakamatsu | TITLE: Synthesis and preparation of DOPA pheomelanin and eumelanin
AUTHORS: Kazumasa Wakamatsu
[DESCRIPTION]
This is the protocol for synthesizing and preparing DOPA pheomelanin and DOPA eumelanin using tyrosinase.
[STEPS]
1. As precursor(s) of melanin, 1) l-dopa, 2) DHI, 3) a mixture of DHI and DHICA, 4) DHICA, 5) a... | ["As precursor(s) of melanin, 1) l-dopa, 2) DHI, 3) a mixture of DHI and DHICA, 4) DHICA, 5) a mixture of l-dopa and l-cysteine, and 6) 5SCD in the presence of l-dopa is used.", "To a solution of the precursor(s) (1 mmol) in 0.1 M sodium phosphate buffer, pH 6.8 (98 ml), add a solution of mushroom tyrosinase in the sam... |
null | null | null | dx.doi.org/10.17504/protocols.io.e7sbhne | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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31,664 | Archival preservation of cell suspensions for scRNA-Seq | 1 | null | https://www.protocols.io/view/archival-preservation-of-cell-suspensions-for-scrn-ba6qihdw | Linas Mazutis, Ignas Masilionis | TITLE: Archival preservation of cell suspensions for scRNA-Seq
AUTHORS: Linas Mazutis, Ignas Masilionis
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The inability to archive cells for subsequent high-quality single-cell analysis has hampered the interrogation of complex sample collections, such ... | ["[Preparation of single-cell suspension ]", "[DAPI staining]\nResuspend the dissociated cells in 400 µl cell culture media (e.g RPMI, DMEM) supplemented with 2.5% FBS and 0.1 mg/ml DAPI dye. Aim for dilution of 500-2000 cells/µl.Incubate on ice for 5 min.", "[FACS sorting]\nAdd 400 µl of Bambanker preservation media i... |
49,596 | Tertiary Lymphoid Structures in Mouse Models of Lung Cancer: From Induction to Imaging | 4 | dx.doi.org/10.17504/protocols.io.bun4nvgw | https://www.protocols.io/view/tertiary-lymphoid-structures-in-mouse-models-of-lu-bun4nvgw | Wendy Memishian, Teresa McGee, Julie Wells, Carol Bult | TITLE: Tertiary Lymphoid Structures in Mouse Models of Lung Cancer: From Induction to Imaging
AUTHORS: Wendy Memishian, Teresa McGee, Julie Wells, Carol Bult
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Tertiary lymphoid structures (TLSs) are a recently-described immune response that occurs when ... | ["[Perfusion and Harvest of Lungs]\nEuthanize mouse using an IACUC-approved method, such as carbon dioxide, until it no longer responds to toe pinches.", "[Perfusion and Harvest of Lungs]\nWeigh mouse before dunking completely in soapy water.", "[Perfusion and Harvest of Lungs]\nPin down limbs and cut open abdomen from... |
94,146 | Analysis of glycosphingolipids from cell lines | 1 | dx.doi.org/10.17504/protocols.io.x54v9pn14g3e/v1 | https://www.protocols.io/view/analysis-of-glycosphingolipids-from-cell-lines-c77azrie | David A Priestman, Yuzhe Weng, Marya Sabir, Reuben Bush, Danielle te Vruchte, Kerri-Lee Wallom, María E Fernández-Suárez, Frances M Platt | TITLE: Analysis of glycosphingolipids from cell lines
AUTHORS: David A Priestman, Yuzhe Weng, Marya Sabir, Reuben Bush, Danielle te Vruchte, Kerri-Lee Wallom, María E Fernández-Suárez, Frances M Platt
[DESCRIPTION]
Interest in the role of cellular glycosphingolipids (GSLs) in health and disease led to us developing a ... | ["[GSL preparation from cell lines] Lyse and homogenise cell pellet (≥ 1 ⋅ 106 cells) in 200 µL ddH2O through three cycles of freeze-thawing with vortexing after each cycle.", "[GSL preparation from cell lines] Using determined protein concentrations, prepare sample as 200 µg protein in 200 µL ddH2O in a 1.5 ml scre... |
57,045 | Annotation of the Albula glossodona Genome using MAKER | 5 | dx.doi.org/10.17504/protocols.io.b3xvqpn6 | https://www.protocols.io/view/annotation-of-the-albula-glossodona-genome-using-m-b3xvqpn6 | Brandon D Pickett, Sheena Talma, Jessica R. Glass, Daniel Ence, Timothy P. Johnson, Paul D. Cowley, Perry G. Ridge, John S. K. Kauwe | TITLE: Annotation of the Albula glossodona Genome using MAKER
AUTHORS: Brandon D Pickett, Sheena Talma, Jessica R. Glass, Daniel Ence, Timothy P. Johnson, Paul D. Cowley, Perry G. Ridge, John S. K. Kauwe
[DESCRIPTION]
The Roundjaw Bonefish (Albula glossodonta) genome assembly was annotated following the MAKER pipeline... | ["[Prepare for MAKER] Prepare for MAKER\nCreate a working directory for MAKER and then create the initial control files. Edit them to match your environment using your favorite text editor, e.g., we had to set use_rapsearch to 0 and blast_type to ncbi+ in maker_bopts.ctl. Take a careful look at maker_exe.ctl to ensure ... |
52,938 | Qiagen AllPrep 96 DNA/RNA protocol for bee abdomens (FFAR) | 4 | null | https://www.protocols.io/view/qiagen-allprep-96-dna-rna-protocol-for-bee-abdomen-bxxippke | Jocelynz | TITLE: Qiagen AllPrep 96 DNA/RNA protocol for bee abdomens (FFAR)
AUTHORS: Jocelynz
[DESCRIPTION]
Qiagen AllPrep 96 DNA/RNA protocol for bee abdomens (FFAR)
[STEPS]
SECTION: Before beginning protocol
1. must be added tobbefore use. Add 20 µL20 Molarity (M) per 1 mL . Stock solution of should be prepared fr... | ["[Before beginning protocol] must be added tobbefore use. Add 20 µL20 Molarity (M) per 1 mL . Stock solution of should be prepared fresh or frozen in single use aliquots. containing can be stored at room temperature for up to 1 month.", "[Prepare samples] UV sterilize supplies for 2 96 well plates: stainles... |
47,436 | Benchmarking protocol for plant genomes | 5 | null | https://www.protocols.io/view/benchmarking-protocol-for-plant-genomes-bsjknckw | Vidya S Vuruputoor, Daniel Monyak, Karl C Fetter, Akriti Bhattarai, Bikash Shrestha, Sumaira Zaman, Jeremy Benett, Susan L McEvoy, Madison Caballero, Jill L Wegrzyn, Cynthia Webster | TITLE: Benchmarking protocol for plant genomes
AUTHORS: Vidya S Vuruputoor, Daniel Monyak, Karl C Fetter, Akriti Bhattarai, Bikash Shrestha, Sumaira Zaman, Jeremy Benett, Susan L McEvoy, Madison Caballero, Jill L Wegrzyn, Cynthia Webster
[DESCRIPTION]
This is the protocol we used to benchmark several plant genomes. We... | ["Download/gather genome resources\n\nUnmasked genome (for MAKER-P) pipeline\nSoft-masked genome (if available)\ngff, gtf files\ncDNA and pep files", "Filter genome\n\n1. filtersubmit.sh removes sequences less than 500 bp \n - The script filtersubmit.sh calls filterLen.py (custom script, no version no.)\n\n\n\n ... |
52,913 | FindingNemo: A Toolkit of CoHex- and Glass Bead-based Protocols for Ultra-Long Sequencing on ONT Platforms | 1 | dx.doi.org/10.17504/protocols.io.bxwrppd6 | https://www.protocols.io/view/findingnemo-a-toolkit-of-cohex-and-glass-bead-base-bxwrppd6 | Inswasti Cahyani, John Tyson, Nadine Holmes, Josh Quick, Nicholas Loman, Matthew Loose | TITLE: FindingNemo: A Toolkit of CoHex- and Glass Bead-based Protocols for Ultra-Long Sequencing on ONT Platforms
AUTHORS: Inswasti Cahyani, John Tyson, Nadine Holmes, Josh Quick, Nicholas Loman, Matthew Loose
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This collection of protocols is designed t... | ["[UHMW DNA Extraction]\nA DNA extraction protocol that yields clean and homogeneous UHMW DNA is essential for good UL sequencing output. The choice of protocol should be based on achieving these parameters.We provide alternatives to achieve this by following kit-based or kit-free extraction protocols as follows:Kit-fr... |
94,384 | TE buffer | 3 | dx.doi.org/10.17504/protocols.io.yxmvm346bl3p/v1 | https://www.protocols.io/view/te-buffer-c8eqztdw | Anna Schmidt, Sarah Nagel, Matthias Meyer | TITLE: TE buffer
AUTHORS: Anna Schmidt, Sarah Nagel, Matthias Meyer
[DESCRIPTION]
TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8.0) is used in various steps of sample preparation by the Ancient DNA Core Unit of the MPI-EVA.
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ht6b6re | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<p><strong>Training Requirements</strong></p>
<p><strong> </strong></p>
<p>Able to accurately pipet load gel and dilute tissue samples and use Licor Odyssey Imaging Software</p>
[STEPS]
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101,676 | Enterovirus coxsackievirus A16 2A protease small scale expression and purification protocol | 1 | dx.doi.org/10.17504/protocols.io.rm7vzj3y5lx1/v2 | https://www.protocols.io/view/enterovirus-coxsackievirus-a16-2a-protease-small-s-dfik3kcw | Korvus Wang, michael fairhead, Eleanor Williams | TITLE: Enterovirus coxsackievirus A16 2A protease small scale expression and purification protocol
AUTHORS: Korvus Wang, michael fairhead, Eleanor Williams
[DESCRIPTION]
This protocol details the expression and purification of coxsackievirus A16 2A protease construct bearing a N-terminal His-SUMO tag at small scale (<... | ["[Plasmid Transformation] Transform the coxsackievirus A16 2A protease plasmid into BL21(DE3) and store a glycerol stock of this at -80 °C\nThe coxsackievirus A16 2A protease plasmid encodes the 2A protease with an N-terminal His6-SUMO tag on a kanamycin resistant backbone with a T7 promoter.", "[Protein expression] W... |
null | null | null | dx.doi.org/10.17504/protocols.io.rbjd2kn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol enriches holobiont <em>Exaiptasia pallida</em> tissue for <em>Symbiodinium</em>, removing more than 99% of host tissue while maintaining high RNA integrity (RIN > 7). The symbiont-enriched fraction is subsequently lysed via bead beating and rna isolated using... | [] |
99,784 | Cloning with Golden Gate | 0 | dx.doi.org/10.17504/protocols.io.yxmvme22bg3p/v1 | https://www.protocols.io/view/cloning-with-golden-gate-ddpg25jw | Raining Wang, Melinda Wheelock | TITLE: Cloning with Golden Gate
AUTHORS: Raining Wang, Melinda Wheelock
[DESCRIPTION]
This protocol details the cloning and transformation.
[STEPS]
SECTION: Wild-type target assembly
1. Golden Gate assembly:
If the wild-type insert is obtained from PCR amplification, ensure the PCR product is cleaned.
SECTION: Wi... | ["[Wild-type target assembly] Golden Gate assembly:\n\nIf the wild-type insert is obtained from PCR amplification, ensure the PCR product is cleaned.", "[Wild-type target assembly] Made additional digestion mix.", "[Wild-type target assembly] Aliquot 5 µL of digestion mix to each of the golden gate reactions.", "[Wild-... |
36,651 | Imaging Mass Cytometry Compensation Slide Acquisition | null | dx.doi.org/10.17504/protocols.io.bf2jjqcn | https://www.protocols.io/view/imaging-mass-cytometry-compensation-slide-acquisit-bf2jjqcn | Michelle Daniel, Marda Jorgensen | TITLE: Imaging Mass Cytometry Compensation Slide Acquisition
AUTHORS: Michelle Daniel, Marda Jorgensen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This SOP describes the slide acquisition for spill-over correction of Imaging Mass</div><div class = "text-block">Cytometry experiments. The protocol... | ["[Set-Up]\n1. Attach the flat-bed scanner to a computer and take an image of the compensation slide.2. Create a folder on the CyTOF computer on the “E” drive.3. Save the image of the compensation slide in that folder with the same name as the compensationslide.4. Insert the compensation slide into the Hyperion.5. Unde... |
46,671 | Protocols for " Efficient and stable metabarcoding sequencing data using DNBSEQ-G400 sequencer validated by comprehensive community analyses" | 2 | dx.doi.org/10.17504/protocols.io.brtpm6mn | https://www.protocols.io/view/protocols-for-34-efficient-and-stable-metabarcodin-brtpm6mn | Xiaohuan Sun, Yuehua Hu, Zewei Song | TITLE: Protocols for " Efficient and stable metabarcoding sequencing data using DNBSEQ-G400 sequencer validated by comprehensive community analyses"
AUTHORS: Xiaohuan Sun, Yuehua Hu, Zewei Song
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Sequencing in DNBSEQ-G400 of this study was carried out ... | [] |
66,880 | Preparation of ATP13A2 microsomes from Sf9 cells | 6 | dx.doi.org/10.17504/protocols.io.kxygxzde4v8j/v1 | https://www.protocols.io/view/preparation-of-atp13a2-microsomes-from-sf9-cells-cdi8s4hw | Sue Sim, eunyong_park | TITLE: Preparation of ATP13A2 microsomes from Sf9 cells
AUTHORS: Sue Sim, eunyong_park
[DESCRIPTION]
Isolate microsomes from Sf9 cells expressing ATP13A2
[STEPS]
1. Thaw Sf9 cell pellets at room temperature (typical size around 5g for 0.4 L of culture)
2. All subsequent steps should be carried out at 4 °C
3. Was... | ["Thaw Sf9 cell pellets at room temperature (typical size around 5g for 0.4 L of culture)", "All subsequent steps should be carried out at 4 °C", "Wash pellet twice with 15 mL of Phosphate-buffered Saline, centrifuge at 1000 x g, 7 min, 4 °C in between washes", "Gently resuspend by inverting tube and pipetting", "Colle... |
70,789 | big redesign protocol Version-2 | 1 | null | https://www.protocols.io/view/big-redesign-protocol-version-2-chddt226 | Maria Gul, katarina | TITLE: big redesign protocol Version-2
AUTHORS: Maria Gul, katarina
[DESCRIPTION]
abstract
Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Integer in sapien. Praesent id justo in neque elementum ultrices. Cras elementum. Sed ac dolor sit amet purus malesuada congue. Nunc auctor. Quis autem vel eum iure re... | ["[section 1] Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Integer in sapien. Praesent id justo in neque elementum ultrices. Cras elementum. Sed ac dolor sit amet purus malesuada congue. Nunc auctor. Quis autem vel eum iure reprehenderit qui in ea voluptate velit esse quam nihil molestiae consequatur, vel ... |
56,537 | Transcardial Perfusion in Mouse | 4 | dx.doi.org/10.17504/protocols.io.dm6gpbrw1lzp/v1 | https://www.protocols.io/view/transcardial-perfusion-in-mouse-b3fzqjp6 | Michael Henderson | TITLE: Transcardial Perfusion in Mouse
AUTHORS: Michael Henderson
[DESCRIPTION]
This protocol details about the transcardial perfusion in mouse.
[STEPS]
SECTION: Transcardial Perfusion
1. Make mixture of ketamine:xylazine:acepromazine (4:2:1) sufficient for anesthesia of all mice (~30 µL/ 20 gmouse). Record ketamine ... | ["[Transcardial Perfusion] Make mixture of ketamine:xylazine:acepromazine (4:2:1) sufficient for anesthesia of all mice (~30 µL/ 20 gmouse). Record ketamine used in controlled substance log book.", "[Transcardial Perfusion] Apply anesthesia to one mouse via intraperitoneal injection, and place mouse in bucket long enou... |
22,438 | Unsucessful atemps on transfromation of the Icthyosporean Sphaeroforma artica | null | dx.doi.org/10.17504/protocols.io.z6ef9be | null | Elena Casacuberta, Cristina Aresté, Omaya Dudin , Elena Casacuberta | TITLE: Unsucessful atemps on transfromation of the Icthyosporean Sphaeroforma artica
AUTHORS: Elena Casacuberta, Cristina Aresté, Omaya Dudin , Elena Casacuberta
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Testing electroporation on Spaheroforma artica with two different electroporators</div><di... | ["Cells were seeded 24 hours prior transfection", "200.000 cells per transfecion condition were tested", "Tested techniques and settings are as follows (with 1 to 5 micrograms of DNA endogenous promoter (actin) plus fluorescent reporter (venus or mCherry) ABCD1S.arcticaNeon1000-2500V, 10-40 ms, 1-3 pulsesn/a (not suc... |
94,665 | Extraction and analysis of primary metabolites during Xanthomonas-Barley interaction | 4 | dx.doi.org/10.17504/protocols.io.5qpvo36wdv4o/v2 | https://www.protocols.io/view/extraction-and-analysis-of-primary-metabolites-dur-c8phzvj6 | Veronica Roman-Reyna, Nathaniel Heiden, Jules Butchacas, Hannah Toth, Jessica L. Cooperstone, Jonathan M. Jacobs | TITLE: Extraction and analysis of primary metabolites during Xanthomonas-Barley interaction
AUTHORS: Veronica Roman-Reyna, Nathaniel Heiden, Jules Butchacas, Hannah Toth, Jessica L. Cooperstone, Jonathan M. Jacobs
[DESCRIPTION]
Intercellular host-associated bacteria shape the chemistry of the living eukaryotic environ... | ["[Sample preparation] For sample preparation you need:\n- Barley cv. Morex seeds\n- Xanthomonas translucens pv. undulosa strain UPB513, \n- Xanthomonas translucens pv. translucent strain UPB886", "[Bacterial and mock inoculation] The youngest fully expanded leaf of the three-week-old plants was used for inoculations. ... |
27,614 | Simulation of a 6300 year intergalactic journey | null | dx.doi.org/10.17504/protocols.io.676hhre | null | Thorsten Sommer | TITLE: Simulation of a 6300 year intergalactic journey
AUTHORS: Thorsten Sommer
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes a possible implementation of a simulation of a 6300 year journey from Earth to Proxima Centauri b. It is based on the description of Frédéric Marin ... | ["[Setup]\nReset: Reset i.e. clear the entire simulation.", "[Setup]\nPens: Initialize all pens of both diagrams. This is necessary so that the user can choose between a simulation on a daily or monthly basis.", "[Setup]\nCapacity: Define the capacity of the spaceship so that a maximum of 500 people can live on it.", "... |
89,425 | Rodent brain processing for histological analyses (update) | 4 | dx.doi.org/10.17504/protocols.io.e6nvwj61wlmk/v3 | https://www.protocols.io/view/rodent-brain-processing-for-histological-analyses-c3jrykm6 | Miquel Vila | TITLE: Rodent brain processing for histological analyses (update)
AUTHORS: Miquel Vila
[DESCRIPTION]
Protocol for rat brain processing in order to perform histological analyses
[STEPS]
SECTION: Rat perfusion
1. Deeply anesthetize animals with sodium pentobarbital (50 mg/kg, i.p.)
SECTION: Rat perfusion
2. Perfuse thr... | ["[Rat perfusion] Deeply anesthetize animals with sodium pentobarbital (50 mg/kg, i.p.)", "[Rat perfusion] Perfuse through the left ventricle with saline [0.9% (wt/vol)] at room temperature (RT)", "[Rat perfusion] Perfuse again with ice-cold formaldehyde solution 4% in PBS buffered for histology", "[Postfixation] Remov... |
19,470 | Octopus social tolerance experiment | 1 | dx.doi.org/10.17504/protocols.io.w9nfh5e | https://www.protocols.io/view/octopus-social-tolerance-experiment-w9nfh5e | Eric Edsinger, Reuven Pnini, Natsumi Ono, Ryoko Yanagisawa, Kathryn Dever, Jonathan Miller | TITLE: Octopus social tolerance experiment
AUTHORS: Eric Edsinger, Reuven Pnini, Natsumi Ono, Ryoko Yanagisawa, Kathryn Dever, Jonathan Miller
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Culturing]
Octopus laqueus juveniles and adults can be housed in any stable recirculating or flow-through seawater ... | ["[Culturing]\nOctopus laqueus juveniles and adults can be housed in any stable recirculating or flow-through seawater aquarium at densities of up to 1 animal per 15 liters seawater. Medium or large clay pots can serve as dens, at least one per animal when not part of a housing experiment. Ideally, light cycles will m... |
30,014 | Steps to Create FASTQ of CCS Overlapping Control SSR - CCS ROI | null | dx.doi.org/10.17504/protocols.io.9i6h4he | null | Gregory Harhay | TITLE: Steps to Create FASTQ of CCS Overlapping Control SSR - CCS ROI
AUTHORS: Gregory Harhay
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The virulence and pathogenicity of bacterial pathogens are related to their adaptability to changing environments. One process enabling adaptation is ba... | ["[Software Requirements]\nFor those without Matlab licences, Matlab code can be run in CodeOcean at this Matlab Compute CapsuleGeneious was used to as wrapper for running sequence mappers, phobos, and sequence extraction", "[Workflow Summary]", "[Acquire Annotated Control SSR Sequences and Genome For Mapping Refere... |
86,819 | U54 SCENT Immunohistochemistry (IHC) Protocol | 1 | dx.doi.org/10.17504/protocols.io.4r3l222z3l1y/v1 | https://www.protocols.io/view/u54-scent-immunohistochemistry-ihc-protocol-cy2bxyan | Carolyn Glass | TITLE: U54 SCENT Immunohistochemistry (IHC) Protocol
AUTHORS: Carolyn Glass
[DESCRIPTION]
This document outlines the Immunohistochemistry (IHC) protocol at Duke University
[STEPS]
SECTION: Protocol
1. EZH2
SECTION: Protocol
2. H3K-HDAC2
| ["[Protocol] EZH2", "[Protocol] H3K-HDAC2"] |
18,754 | ChIP on BJ infected by HSV-1 | null | dx.doi.org/10.17504/protocols.io.wjafcie | null | Patrick Lomonte, Camille COHEN | TITLE: ChIP on BJ infected by HSV-1
AUTHORS: Patrick Lomonte, Camille COHEN
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">ChIP-seq and ChIP-qPCR are powerful tools that allows the specific matching of proteins or histone modifications to regions of the genome. Chromatin is isolated and antibodies ... | ["[A. Fixation and Sonication]\nCrosslink cells by adding in the media 16% formaldehyde methanol free solution to a final concentration of 1% during 5 min at room temperature. Place cells on a shaking platform Quench the crosslonking reaction by adding the appropriate volume of Glycine 2,5M to fixed cells for an additi... |
19,951 | Western blotting of hypothalamic proteins | null | dx.doi.org/10.17504/protocols.io.xqpfmvn | null | Kira V. Derkach, Irina O. Zakharova, Inna I. Zorina, Andrey A. Bakhtyukov, Irina V. Romanova, Liubov V. Bayunova, Alexander Shpakov | TITLE: Western blotting of hypothalamic proteins
AUTHORS: Kira V. Derkach, Irina O. Zakharova, Inna I. Zorina, Andrey A. Bakhtyukov, Irina V. Romanova, Liubov V. Bayunova, Alexander Shpakov
[STEPS]
?. [Sample preparation:]
Homogenize a piece of hypothalamus tissue (½ of hypothalamus) in the 1X Tissue Lysis Buffer in t... | ["[Sample preparation:]\nHomogenize a piece of hypothalamus tissue (½ of hypothalamus) in the 1X Tissue Lysis Buffer in the ratio of 1:10.", "[Sample preparation:]\nKeep homogenate on ice for 30 min.", "[Sample preparation:]\nCentrifuge the homogenate at 14 000g for 10 minutes (4 °C).", "[Sample preparation:]\nTransfer... |
107,168 | Electrolysis agarose gel preparation | 0 | dx.doi.org/10.17504/protocols.io.kqdg32d4qv25/v1 | https://www.protocols.io/view/electrolysis-agarose-gel-preparation-dkv84w9w | UM ILT team, Mar Roca Cugat | TITLE: Electrolysis agarose gel preparation
AUTHORS: UM ILT team, Mar Roca Cugat
[DESCRIPTION]
This is how students at Maastricht University's Biomedical Sciences bachelor are instructed to prepare agarose gel for electrolysis.
[STEPS]
1. Prepare the casting tray by putting the sides together.
2. The silicon coated ... | ["Prepare the casting tray by putting the sides together.", "The silicon coated site should point towards the inside.", "Apply the elastic band around the extruding parts in the middle of the sides to hold everything in place.", "Flip the assembled tray in the correct position and press it lightly on the table to ensur... |
45,468 | SEM User Protocol | 4 | null | https://www.protocols.io/view/sem-user-protocol-bqm4mu8w | Elizabeth Fozo | TITLE: SEM User Protocol
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">How to use the Auriga Scanning Electron Microscope at JIAM</div></div>
[STEPS]
?. [How to:]
After samples have been prepped, and the silicon chip is placed on carbon tape sticking it to the aluminum stu... | ["[How to:]\nAfter samples have been prepped, and the silicon chip is placed on carbon tape sticking it to the aluminum stub, grab a sample holder in the desiccator vessel usually on the backbench in the Auriga room. The sample holder has 3 screw holes on one side and what looks like a bracket on the base. Use the fa... |
73,622 | Cichlid genome modification | 4 | dx.doi.org/10.17504/protocols.io.x54v9d2nzg3e/v1 | https://www.protocols.io/view/cichlid-genome-modification-cj5wuq7e | Scott Juntti | TITLE: Cichlid genome modification
AUTHORS: Scott Juntti
[DESCRIPTION]
Here we provide a microinjection protocol for the modification of cichlid fish via CRISPR or transgenesis.
[STEPS]
SECTION: General considerations
1. Obtaining viable embryos can be the most trying part of generating transgenic fish. Putting in t... | ["[General considerations] Obtaining viable embryos can be the most trying part of generating transgenic fish. Putting in time up front to maximize survival, and to be able to get embryos on demand will be well worth your time!\nIf your cichlid species of choice is not a year-round spawner, get to know the conditions t... |
18,565 | HCR-FISH for Choanoflagellate Cultures | 1 | null | https://www.protocols.io/view/hcr-fish-for-choanoflagellate-cultures-wddfa26 | Kayley Hake | TITLE: HCR-FISH for Choanoflagellate Cultures
AUTHORS: Kayley Hake
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is a fluorescent </span><span style = "font-style:italic;">in situ </span><span>hybridization (FISH) technique for labeling 16S rRNA from specific bacteria in choano... | ["[FIX Choanoflagellate culture]", "[FILTER Choanoflagellate culture]\nUsing a 15ml glass microanalysis filter holder (Millipore Sigma), filter 250-1000µl of fixed culture onto a filter. To capture all choanoflagellate and free-living bacteria, use a 0.2µm pore size 25mm filter (GTTP02500, Millipore Sigma). To capture ... |
44,563 | Large Volume Immunostaining for Cleared Samples | 1 | dx.doi.org/10.17504/protocols.io.bprtmm6n | https://www.protocols.io/view/large-volume-immunostaining-for-cleared-samples-bprtmm6n | Seth Currlin, Marda Jorgensen, Jerelyn Nick | TITLE: Large Volume Immunostaining for Cleared Samples
AUTHORS: Seth Currlin, Marda Jorgensen, Jerelyn Nick
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This is a guide for immunostaining CLARITY-processed samples. </span><a href="https://dx.doi.org/10.17504/protocols.io.8jihuke" style = "t... | ["[Immunohistochemistry for large (5 mm3) tissue volumes]\nWash out residual clearing solutionThree washes in PBST, 24 hours each, 37ºC with gentle agitation. Large wash volumes are best, a 50 ml conical tube with 50 ml fresh PBST is recommended for each wash step.", "[Immunohistochemistry for large (5 mm3) tissue volu... |
19,658 | UC Davis - Acquisition/Acclimation/Quarantine | null | dx.doi.org/10.17504/protocols.io.xfifjke | null | K.C. Kent Lloyd | TITLE: UC Davis - Acquisition/Acclimation/Quarantine
AUTHORS: K.C. Kent Lloyd
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;font-style:italic;">Summary</span></div><div class = "text-block">The purpose of this standard operating procedure (SOP) is to provide steps f... | ["1.1 Laboratory rodents must be purchased from vendors that have been approved by the MBP veterinary staff; e.g., Harlan Sprague Dawley, Inc., Charles River Laboratories, The Jackson Laboratory, Taconic, etc. 1.1.1 Vendor approval is based on vendor health surveillance data generated by either the vendor or co... |
106,074 | Automated Bar-Seq Library Preparation and Pooling | 0 | dx.doi.org/10.17504/protocols.io.3byl49qdjgo5/v3 | https://www.protocols.io/view/automated-bar-seq-library-preparation-and-pooling-djt24nqe | David Ross, Nina Alperovich | TITLE: Automated Bar-Seq Library Preparation and Pooling
AUTHORS: David Ross, Nina Alperovich
[DESCRIPTION]
Protocol for automated Bar-Seq Library preparation
This protocol prepares 96 DNA samples, representing 24 samples from 4 different timepoints, for multiplexed Illumina sequencing. The process starts with two r... | ["[Transfer Plasmid DNA to PCR Plate and Dilute with DI water] Pre-heat the on deck thermocycler (ODTC) for 1st PCR step", "[Transfer Plasmid DNA to PCR Plate and Dilute with DI water] Remove lids from PCR-Plate 1, Sample-Plate, and Reagent Plate", "[Transfer Plasmid DNA to PCR Plate and Dilute with DI water] Transfer ... |
37,752 | Fragment Analyzer Operation for PCR Products | 1 | dx.doi.org/10.17504/protocols.io.bg4yjyxw | https://www.protocols.io/view/fragment-analyzer-operation-for-pcr-products-bg4yjyxw | Allen Institute for Brain Science | TITLE: Fragment Analyzer Operation for PCR Products
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes fragment analyzer operation for polymerase chain reaction (PCR) products. The Fragment Analyzer by Advanced Analytical is used as a q... | [] |
71,962 | Wastewater Sequencing using the EasySeq™ RC-PCR SARS CoV-2 (Nimagen) V3.0 | 4 | dx.doi.org/10.17504/protocols.io.81wgb7bx3vpk/v3 | https://www.protocols.io/view/wastewater-sequencing-using-the-easyseq-rc-pcr-sar-cih2ub8e | Harry T Child, Paul A O'Neill, Karen Moore, Hubert Denise, Matthew Loose, Steve Paterson, Ronny van Aerle, Aaron Jeffries | TITLE: Wastewater Sequencing using the EasySeq™ RC-PCR SARS CoV-2 (Nimagen) V3.0
AUTHORS: Harry T Child, Paul A O'Neill, Karen Moore, Hubert Denise, Matthew Loose, Steve Paterson, Ronny van Aerle, Aaron Jeffries
[DESCRIPTION]
This SOP describes the procedure for generating cDNA libraries from SARS-CoV-2 viral nuc... | ["[Cleanup of RNA extract] Aim: Reduction of any PCR inhibitors and potential concentration of RNA. Starting volume is 20 µl but this can be increased if further concentration is required (although for the latter tests on whether inhibitors are also concentrated have not been undertaken).\nNotes: Use either AMPure RNA ... |
42,262 | tomato hypocotyl grafting | 4 | dx.doi.org/10.17504/protocols.io.bmhwk37e | https://www.protocols.io/view/tomato-hypocotyl-grafting-bmhwk37e | hengliu | TITLE: tomato hypocotyl grafting
AUTHORS: hengliu
[STEPS]
?. Tomato (Solanum lycopersicum) cultivar Zhongshu No.4 seeds were surface sterilized with 75% ethanol for 1 min, and in sterilization solution containing 35% commercial bleach solution (5.25% [w/v] sodium hypochlorite) and 0.1% Tween-20 (Bio-Rad, Shanghai, Ch... | ["Tomato (Solanum lycopersicum) cultivar Zhongshu No.4 seeds were surface sterilized with 75% ethanol for 1 min, and in sterilization solution containing 35% commercial bleach solution (5.25% [w/v] sodium hypochlorite) and 0.1% Tween-20 (Bio-Rad, Shanghai, China) for 6 min.", "The seeds were placed in 1/2strength MS me... |
null | null | null | dx.doi.org/10.17504/protocols.io.p44dqyw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is a simple PCR-SSP for amplification of the rs6656401, located in intron 4 (CR1 gene).</p>
[BEFORE_START]
<p>1- Wear clean gloves;<br />2- Clean pipettes and stand with hypochlorite and 70% alcohol;<br />3- Defreeze DNA samples and reagents (exception: Taq polymerase);... | [] |
91,304 | IgA Metagenomic Immunoglobulin Sequencing (MIG-Seq) | 4 | dx.doi.org/10.17504/protocols.io.5jyl8pk6dg2w/v1 | https://www.protocols.io/view/iga-metagenomic-immunoglobulin-sequencing-mig-seq-c5egy3bw | Matthew R Olm, Sean Spencer | TITLE: IgA Metagenomic Immunoglobulin Sequencing (MIG-Seq)
AUTHORS: Matthew R Olm, Sean Spencer
[DESCRIPTION]
IgA, the most highly produced human antibody, is continually secreted into the gut to shape the intestinal microbiota. Methodological limitations have critically hindered defining which microbial strains are t... | ["[Preparation of fecal samples] Weigh out 300 mg of thawed in 2 mL centrifuge tube", "[Preparation of fecal samples] Rehydrate sample with 1.25 mL cold . Incubate 5 min on ice", "[Preparation of fecal samples] Vigorously vortex and mix samples via pipetting to ensure homogenization", "[Preparation of fecal samples]... |
70,223 | Dual staining for gamma delta and alpha beta T cell detection in formalin-fixed, paraffin-embedded (FFPE) pig tissues | 4 | null | https://www.protocols.io/view/dual-staining-for-gamma-delta-and-alpha-beta-t-cel-cgtptwmn | Jayne E Wiarda | TITLE: Dual staining for gamma delta and alpha beta T cell detection in formalin-fixed, paraffin-embedded (FFPE) pig tissues
AUTHORS: Jayne E Wiarda
[DESCRIPTION]
A combined staining protocol for CD3e immunohistochemistry (IHC) and TRDC RNA in-situ hybridization (RNA-ISH) created for in-situ identification of porcine ... | ["[Baking] Before baking slides:\nPreheat a dry oven to 60℃\nLoad slides for assay into vertical slide rack\n\nBake slides 30 min 60℃\nOptional stopping point: store slides in a dry place & use within 1 week\n\nWhile slides bake:\nPrepare 0.05% PBS-T (can store at RT up to 1 month)\nPrepare 1X Co-Detection Target Retri... |
33,468 | Start or STop Anticoagulants Randomised Trial (SoSTART) after spontaneous intracranial haemorrhage | null | dx.doi.org/10.17504/protocols.io.bcw4ixgw | null | Rustam Al-Shahi Salman, Martin S. Dennis, Kasia Adamczuk, Karen Innes, Ruth Fraser, Jonathan Drever, Lynn Dinsmore, Carol Williams, Steff Lewis, Philip M. White, David E. Newby, Gregory Y.H. Lip, Adrian Parry-Jones, Dan Lasserson, Colin Oliver, Joanna Wardlaw, John Norrie | TITLE: Start or STop Anticoagulants Randomised Trial (SoSTART) after spontaneous intracranial haemorrhage
AUTHORS: Rustam Al-Shahi Salman, Martin S. Dennis, Kasia Adamczuk, Karen Innes, Ruth Fraser, Jonathan Drever, Lynn Dinsmore, Carol Williams, Steff Lewis, Philip M. White, David E. Newby, Gregory Y.H. Lip, Adrian Pa... | [] |
91,353 | Generation of hiPSC derived cortical astrocytes | 4 | dx.doi.org/10.17504/protocols.io.8epv5xmmng1b/v1 | https://www.protocols.io/view/generation-of-hipsc-derived-cortical-astrocytes-c5fzy3p6 | Minee-Liane Choi | TITLE: Generation of hiPSC derived cortical astrocytes
AUTHORS: Minee-Liane Choi
[DESCRIPTION]
This is a modified protocol that describes how to generate cortical region-specific astrocytes based on Gupta et al., 2012, Serio et al., 2013 and Seto-Salvia et al., 2021
[STEPS]
SECTION: hiPSC culture
1. hiPSC... | ["[hiPSC culture] hiPSCs are maintained on Geltrex in mTeSR (Stem Cell) and passaged using 0.5mM EDTA, as followed by Virdi et al., 2022.", "[Differentiation of hiPSC into Cortical astrocytes] Differentiation of cortical region-specific astrocytes is performed using a modified protocol based on Gupta et al., 2012, Seri... |
71,302 | Live-imaging of axonal cargoes in human iPSC-derived neurons or mouse primary neurons | 1 | dx.doi.org/10.17504/protocols.io.rm7vzb3r4vx1/v1 | https://www.protocols.io/view/live-imaging-of-axonal-cargoes-in-human-ipsc-deriv-chvet63e | Dan Dou, C. Alexander Boecker, Erika L.F. Holzbaur | TITLE: Live-imaging of axonal cargoes in human iPSC-derived neurons or mouse primary neurons
AUTHORS: Dan Dou, C. Alexander Boecker, Erika L.F. Holzbaur
[DESCRIPTION]
Here, we describe procedure and equipment used for live-imaging of axonal cargoes. This was performed both using primary mouse cortical neurons and huma... | ["[Live-imaging of axonal cargoes in human iPSC-derived neurons or mouse primary neurons] Image primary mouse cortical neurons on DIV7. Image human iNeurons on DIV21.", "[Live-imaging of axonal cargoes in human iPSC-derived neurons or mouse primary neurons] Replace culture media with low fluorescence imaging media.", "... |
77,088 | Midbrain viral injections for striatal fiber photometry in mice | 4 | dx.doi.org/10.17504/protocols.io.5qpvor8zxv4o/v1 | https://www.protocols.io/view/midbrain-viral-injections-for-striatal-fiber-photo-cph8vj9w | Maite Azcorra | TITLE: Midbrain viral injections for striatal fiber photometry in mice
AUTHORS: Maite Azcorra
[DESCRIPTION]
This protocol describes how to:
- Inject AAV viruses into the midbrain (SNc: substantia nigra pars compacta, or VTA: ventral tegmental area) of mice
- Train mice for head-fixed running on a cylindrical treadmill... | ["[Injection pipette pulling and beveling] Pull glass pipettes using program 28 on Shutter Instrument Co. laser puller model P-2000 using the following program. This program might have to be adjusted for each puller’s characteristics, with the goal of pulling a pipette with a narrow shaft about 6 mm long (5 mm will go ... |
27,678 | MojoSort™ Mouse CD4 Nanobeads Column Protocol | null | dx.doi.org/10.17504/protocols.io.696hh9e | null | Sam Li | TITLE: MojoSort™ Mouse CD4 Nanobeads Column Protocol
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>BioLegend MojoSort™ nanobeads work in commonly used separation columns, based on our internal research as well as validation by external testing by academic labs. This simple pr... | ["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... |
91,083 | Culturing iPSC cells in Essential 8 medium | 1 | dx.doi.org/10.17504/protocols.io.n92ldmj99l5b/v1 | https://www.protocols.io/view/culturing-ipsc-cells-in-essential-8-medium-c47jyzkn | rachel.bates, Matthew Gegg | TITLE: Culturing iPSC cells in Essential 8 medium
AUTHORS: rachel.bates, Matthew Gegg
[DESCRIPTION]
Culturing of iPSC lines in essential 8 medium, thawing and passaging techniques.
[STEPS]
SECTION: Preparing plates and medium for cells
1. Essential 8 media (Thermo, Cat # A1517001). This consists of 500 mL of basal ... | ["[Preparing plates and medium for cells] Essential 8 media (Thermo, Cat # A1517001). This consists of 500 mL of basal medium and 10 mL of supplement. Media with supplement has a shelf life at 4 °C for 2 weeks. Unless culturing large numbers of cells it is best to make up 100 mL aliquots (or whatever volume you thi... |
15,169 | f/2 medium with soil extract | null | dx.doi.org/10.17504/protocols.io.s29egh6 | null | Roscoff Culture Collection | TITLE: f/2 medium with soil extract
AUTHORS: Roscoff Culture Collection
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Medium to grow phytoplankton species in particular dinoflagellates which often require soil extract.</div></div>
[STEPS]
?. [Prepare f/2 medium]
{"blocks":[{"key":"fhe99","text":"... | ["[Prepare f/2 medium]\n{\"blocks\":[{\"key\":\"fhe99\",\"text\":\"Medium to grow\\u00a0most phytoplankton species in particular diatoms.\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]}],\"entityMap\":[]}", "[Add soil extract]\n{\"blocks\":[{\"key\":\"e5mbp\",\"text\":\"How... |
78,761 | Protocol for DNA extraction from saliva samples, used for shotgun microbiome analysis.pdf | 1 | dx.doi.org/10.17504/protocols.io.dm6gpjm11gzp/v1 | https://www.protocols.io/view/protocol-for-dna-extraction-from-saliva-samples-us-cq6hvzb6 | Aymeric David, christian.morabito | TITLE: Protocol for DNA extraction from saliva samples, used for shotgun microbiome analysis.pdf
AUTHORS: Aymeric David, christian.morabito
[DESCRIPTION]
Protocol for DNA extraction from saliva samples, used for shotgun microbiome analysis
[STEPS] | [] |
50,500 | Restriction Digest - OpenPlast | 1 | null | https://www.protocols.io/view/restriction-digest-openplast-bvjcn4iw | yasoo , New England Biolabs | TITLE: Restriction Digest - OpenPlast
AUTHORS: yasoo , New England Biolabs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The following is a "typical" restriction endonuclease reaction. Please see the "guidelines" tab below for the NEB tips on optimizing restriction digests.</div></div>
[STEPS]
?.... | ["Set up the following reaction (total reaction volume 20µl). AB1Restriction Enzyme0.5µl2DNA0.5 - 1 µg310X NEBuffer2 µl (1X)4Total Reaction Volume20 µl5Incubation Time1 hour6Incubation TemperatureEnzyme dependent\nAB1Restriction Enzyme0.5µl2DNA0.5 - 1 µg310X NEBuffer2 µl (1X)4Total Reaction Volume20 µl5Incubation Time... |
24,046 | in situ hybridization performed on the peri-rhopalial tissue of a scyphozoan jellyfish | null | dx.doi.org/10.17504/protocols.io.3qngmve | null | Christelle Bouchard | TITLE: in situ hybridization performed on the peri-rhopalial tissue of a scyphozoan jellyfish
AUTHORS: Christelle Bouchard
[STEPS]
?.
?.
?. Fix tissue 2 h, RT, in freshly prepared 4% PF in 0.1 M PB (pH 9.5) + 0.42M NaCl + 2 mM MgSO4
?. Wash 3X 5’ in PBST, pH 7.5
?. Dehydration in PBS/methanol 3:1 → 1:1 → 1:3 10 min ... | ["Fix tissue 2 h, RT, in freshly prepared 4% PF in 0.1 M PB (pH 9.5) + 0.42M NaCl + 2 mM MgSO4", "Wash 3X 5’ in PBST, pH 7.5", "Dehydration in PBS/methanol 3:1 → 1:1 → 1:3 10 min each then 100% methanol 5 min to ON in -20C.", "Rehydration in PBS/methanol 1:3 → 1:1 → 3:1 10 min each then PBST, 10 min.", "Heat treatment ... |
91,274 | Freezing of hPSC | 4 | dx.doi.org/10.17504/protocols.io.rm7vzx278gx1/v1 | https://www.protocols.io/view/freezing-of-hpsc-c5diy24e | Valeria Fernandez Vallone, Lyn Healy, Nathalie Lefort, Katarzyna Ludwik, Tamer Onder, Lisa Pavinato, Fatma Visal FVO OKUR, Harald Stachelscheid | TITLE: Freezing of hPSC
AUTHORS: Valeria Fernandez Vallone, Lyn Healy, Nathalie Lefort, Katarzyna Ludwik, Tamer Onder, Lisa Pavinato, Fatma Visal FVO OKUR, Harald Stachelscheid
[DESCRIPTION]
This protocol describes cryopreservation of hPSC as clumps or single cells.
[BEFORE_START]
Prepare labelled or barcoded cryo-vi... | ["[Clump freezing] Aspirate and discard medium from the vessel.", "[Clump freezing] Add required volume of non-enzymatic dissociation reagent to the culture vessel, refer to Table 1 for recommended volumes.", "[Clump freezing] Gently aspirate non-enzymatic dissociation reagent gently without disturbing the cells and di... |
94,808 | Gene set enrichment analysis | 4 | dx.doi.org/10.17504/protocols.io.kxygx3d2wg8j/v1 | https://www.protocols.io/view/gene-set-enrichment-analysis-c8tyzwpw | Peter Kilfeather | TITLE: Gene set enrichment analysis
AUTHORS: Peter Kilfeather
[DESCRIPTION]
Gene set enrichment analysis from Kilfeather, Khoo et al., 2024
[STEPS]
SECTION: Protocol
1. No statistical methods were used to predetermine sample sizes, but our sample sizes for TRAP analyses surpass those reported in previous publications... | ["[Protocol] No statistical methods were used to predetermine sample sizes, but our sample sizes for TRAP analyses surpass those reported in previous publications23,28,87 and our sample sizes for Stereo-seq samples are comparable with or exceed those of similar spatial transcriptomic datasets11. All statistical analyse... |
69,904 | ONT Flongle Flowcell Loading with Q20+ (V12) Chemistry | 4 | dx.doi.org/10.17504/protocols.io.ewov1nm5pgr2/v3 | https://www.protocols.io/view/ont-flongle-flowcell-loading-with-q20-v12-chemistr-cghqtt5w | Stephen Douglas Russell | TITLE: ONT Flongle Flowcell Loading with Q20+ (V12) Chemistry
AUTHORS: Stephen Douglas Russell
[DESCRIPTION]
Overview: This protocol describes the steps used to load a Flongle flowcell utilizing the Q20+ (V12) Ligation Sequencing Kit from ONT.
This protocol has been tested with Flongle R9.4.1 flowcells.
Time ... | ["[Starting out] Before starting, watch the first 13 minutes of this video: https://vimeo.com/651243660\n\nIt covers all of the vital aspects of this protocol.", "[Starting out] Begin by restarting your computer. This will help to ensure there are no performance issues during your run or other programs running that may... |
93,472 | Photometry Acquisition in Freely Moving Mice | 1 | dx.doi.org/10.17504/protocols.io.bp2l6xwxzlqe/v1 | https://www.protocols.io/view/photometry-acquisition-in-freely-moving-mice-c7h8zj9w | Katerina Rademacher, Ken Nakamura | TITLE: Photometry Acquisition in Freely Moving Mice
AUTHORS: Katerina Rademacher, Ken Nakamura
[DESCRIPTION]
This protocol describes the steps for acquiring photometry data for freely moving mice.
[STEPS]
SECTION: Habituation
1. Habituate the mouse to tethering and the behavioral chamber for 10 minutes/day for two da... | ["[Habituation] Habituate the mouse to tethering and the behavioral chamber for 10 minutes/day for two days prior to starting testing sessions.", "[Habituation] Scruff the mouse and attach the optical fiber patch cable to the mouse’s implant.", "[Habituation] Place mouse in the behavioral chamber (a clear acrylic cylin... |
20,478 | Neural Rosette Formation and Selection | null | dx.doi.org/10.17504/protocols.io.x86frze | null | Celeste Karch, Rita Martinez, Jacob Marsh | TITLE: Neural Rosette Formation and Selection
AUTHORS: Celeste Karch, Rita Martinez, Jacob Marsh
[STEPS]
?. On Day 5 of neural aggregate formation, remove media (by pipetting) and carefully wash spheres with of pre-warmed DMEM/F12. Repeat 2 times.
100 µl
Do not break apart spheres. Neural spheres are very delicate at ... | ["On Day 5 of neural aggregate formation, remove media (by pipetting) and carefully wash spheres with of pre-warmed DMEM/F12. Repeat 2 times.\n100 µl\nDo not break apart spheres. Neural spheres are very delicate at this stage. An alternative approach is to remove of spent media and wash with . Add . Transfer of s... |
47,868 | NEBNext® ARTIC SARS-CoV-2 Library Prep Kit (Illumina®) (NEB #E7650S/L) | 1 | dx.doi.org/10.17504/protocols.io.bsy4nfyw | https://www.protocols.io/view/nebnext-artic-sars-cov-2-library-prep-kit-illumina-bsy4nfyw | Isabel Gautreau | TITLE: NEBNext® ARTIC SARS-CoV-2 Library Prep Kit (Illumina®) (NEB #E7650S/L)
AUTHORS: Isabel Gautreau
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is about the NEBNext® ARTIC SARS-CoV-2 Library Prep Kit (Illumina®).</div></div>
[STEPS]
?. [cDNA Synthesis]
Gently mix and spin down ... | ["[cDNA Synthesis]\nGently mix and spin down the LunaScript RT SuperMix reagent. Prepare the cDNA synthesis reaction as described below:COMPONENT VOLUMERNA Sample8 µl(lilac) LunaScript RT SuperMix2 µlTotal Volume10 µlFor no template controls, mix the following components:COMPONENTVOLUME(white) Nuclease-free Water8 µl(l... |
81,546 | Mycrowave synthesis of low molecular weigth deacylated chitosan | 6 | dx.doi.org/10.17504/protocols.io.x54v9d6w4g3e/v1 | https://www.protocols.io/view/mycrowave-synthesis-of-low-molecular-weigth-deacyl-ctviwn4e | Maria J Torres, Eric S McLamore, Geisianny AM Moreira | TITLE: Mycrowave synthesis of low molecular weigth deacylated chitosan
AUTHORS: Maria J Torres, Eric S McLamore, Geisianny AM Moreira
[DESCRIPTION]
This protocol describes the synthesis of low molecular weight deacylated chitosan using microwave irradiation. The process requires approximately 2.5 hours (including base... | ["[SECTION 1) Materials and solution preparation] Prepare reaction vials\n\nCheck the vial cap and Teflon liner to make sure neither is damageddamage to the cap and both are clean (Fig 1A-B)", "[SECTION 1) Materials and solution preparation] Add solution to the reaction vial.\n\nPipette 8000 µL of 1% deacylated chitosa... |
54,201 | SDS-PAGE gel electrophoresis | 4 | dx.doi.org/10.17504/protocols.io.by6zpzf6 | https://www.protocols.io/view/sds-page-gel-electrophoresis-by6zpzf6 | Steven J Burgess, Lynn Doran | TITLE: SDS-PAGE gel electrophoresis
AUTHORS: Steven J Burgess, Lynn Doran
[DESCRIPTION]
SDS-PAGE gel electrophoresis protocol for analyzing samples from plant leaf tissue via immunofluorescence. In this protocol no Coomassie blue is added to samples, the reason is that this interferes with the fluorescent signal du... | ["[Prepare gel tank and buffers] Create a 1X working dilution of Tris/Glycine/SDS buffer (~1 L is required per gel tank) by diluting 10X stock 1:10 with distilled H2O.", "[Prepare gel tank and buffers] Carefully remove the comb from the precast gel and the tape across the bottom.", "[Prepare gel tank and buffers] Ass... |
null | null | null | dx.doi.org/10.17504/protocols.io.vgje3un | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Este é um guia de como deverá ser a consulta anestésica para eletroconvulsoterapia.
Nossa equipe exige um padrão mínimo de qualidade destas consultas, que devem incluir informações específicas e muito relevantes para a realização de anestesias com o máximo de segurança no nosso ... | ["Identificação\n\nSão dados exigidos:\nNome completo\nSexo biológico\nNúmero de identificação único (CPF, RG, etc)\nTelefone para contato\nNome de acompanhante responsável\nTelefone de acompanhante responsável\nData da avaliação", "Idade e dados antropométricos\n\nData de nascimento e idade\nPeso\nAltura\nIMC\nCircunf... |
null | null | null | dx.doi.org/10.17504/protocols.io.kv4cw8w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Paraffin sections (4 μm thickness) of formalin-fixed human pancreases were treated with heat/citrate buffer for antigen retrieval. Hpse was detected immunohistochemically using HP130 mouse anti-human Hpse mAb (Insight), with biotinylated anti-mouse IgG (1/250) (PK-2200, Vecto... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.eywbfxe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The following is a general procedure guide for preparation and staining of acetone-fixed <strong>frozen</strong> tissues using a purified, unconjugated primary antibody, biotinylated secondary antibody and streptavidin-horseradish peroxidase (Sav-HRP) and DAB detection system... | [] |
56,567 | Modular automated bottom-up proteomic sample preparation for high-throughput applications | 2 | dx.doi.org/10.17504/protocols.io.b3gxqjxn | https://www.protocols.io/view/modular-automated-bottom-up-proteomic-sample-prepa-b3gxqjxn | Yan Chen, Nurgul Kaplan Lease, Jennifer Gin, Tad Ogorzalek, Paul D. Adams, Nathan Hillson, Christopher J Petzold | TITLE: Modular automated bottom-up proteomic sample preparation for high-throughput applications
AUTHORS: Yan Chen, Nurgul Kaplan Lease, Jennifer Gin, Tad Ogorzalek, Paul D. Adams, Nathan Hillson, Christopher J Petzold
[DESCRIPTION]
Manual proteomic sample preparation methods limit sample throughput and often lea... | [] |
53,808 | SHORT: a human brain tissue clearing and labeling protocol for 3D recostruction with LSFM | 1 | dx.doi.org/10.17504/protocols.io.kxygxp6nkl8j/v1 | https://www.protocols.io/view/short-a-human-brain-tissue-clearing-and-labeling-p-bysqpwdw | Luca Pesce, Marina Scardigli, Vladislav Gavryusev, Annunziatina Laurino, Giacomo Mazzamuto, Giuseppe Sancataldo, Ludovico Silvestri, Christophe Destrieux, Patrick R. Hof, Irene Costantini, Francesco S. Pavone | TITLE: SHORT: a human brain tissue clearing and labeling protocol for 3D recostruction with LSFM
AUTHORS: Luca Pesce, Marina Scardigli, Vladislav Gavryusev, Annunziatina Laurino, Giacomo Mazzamuto, Giuseppe Sancataldo, Ludovico Silvestri, Christophe Destrieux, Patrick R. Hof, Irene Costantini, Francesco S. Pavone
[DE... | [] |
39,202 | Derivation of organoids from frozen tumour material | 1 | dx.doi.org/10.17504/protocols.io.biiakcae | https://www.protocols.io/view/derivation-of-organoids-from-frozen-tumour-materia-biiakcae | Hazel Rogers, Laura Letchford, Sara Vieira, Maria Garcia-Casado, Mya Fekry-Troll, Charlotte Beaver, Rachel Nelson, Hayley Francies, Mathew Garnett | TITLE: Derivation of organoids from frozen tumour material
AUTHORS: Hazel Rogers, Laura Letchford, Sara Vieira, Maria Garcia-Casado, Mya Fekry-Troll, Charlotte Beaver, Rachel Nelson, Hayley Francies, Mathew Garnett
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the cryoprese... | ["[Process Diagram]", "[Cryopreservation of primary tissue]\nPour or pipette tissue, and media sample has been transported in, into a glass petri dish.\nIf tissue has unknown infection status, only open the container the sample has been transported in within a microbiological safety cabinet.\nWe recommend using glass r... |
100,780 | ConA Cover Slide Preparation | 0 | dx.doi.org/10.17504/protocols.io.kxygxy3rzl8j/v1 | https://www.protocols.io/view/cona-cover-slide-preparation-denk3dcw | Mathias Hammer, Ammeret Rossouw, Azra Lari, Ben Montpetit, David Grunwald | TITLE: ConA Cover Slide Preparation
AUTHORS: Mathias Hammer, Ammeret Rossouw, Azra Lari, Ben Montpetit, David Grunwald
[DESCRIPTION]
Concanavalin A is used to attach yeast cell to surfaces. This protocol describes the preparation of cover slides for high resolution fluorescence microscopy.
[BEFORE_START]
Have the fol... | ["[Cover slide preconditioning] Rinse a 25mm cover slide No. 1.5 or No. 1.5H. \nDry with Kim wipe, remove leftover driplet with optical tissue.", "[Cover slide preconditioning] Plasma clean the cover slide to a hydrophilic negative charged surface.\nQuorum Emitech K100X glow discharger at 25 mA 45 s", "[Cover slide pre... |
null | null | null | dx.doi.org/10.17504/protocols.io.gzwbx7e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>A protocol for yeast colony PCR, starting with intact cells. Can be used to analyze genomic and plasmid DNA, with PCR products up to 2 kb being no problem. It doesn't get easier than this: pick a small amount of cells from a plate into water, lyse cells at 99C for 5 min. Use ... | [] |
42,439 | SARS-CoV-2 Genomic Variation - African perspective | 4 | dx.doi.org/10.17504/protocols.io.bmpfk5jn | https://www.protocols.io/view/sars-cov-2-genomic-variation-african-perspective-bmpfk5jn | Olabode Omotoso | TITLE: SARS-CoV-2 Genomic Variation - African perspective
AUTHORS: Olabode Omotoso
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines the methodology for the acquisition and analysis of SARS-CoV-2 genomic sequences.</div></div>
[STEPS]
?. [Data Acquisition]
Mine and analyze SARS... | ["[Data Acquisition]\nMine and analyze SARS-CoV-2 genomic sequences from the Global Initiative on Sharing All Influenza Data (GISAID) database (epicov.org). Use sequences filtered as “high coverage only, Homo sapiens, complete, all clades and low coverage excl”, with patient’s status, \"Africa\".", "[Data Acquisition]\... |
41,439 | RT-LAMP Reaction | 4 | dx.doi.org/10.17504/protocols.io.bkp7kvrn | https://www.protocols.io/view/rt-lamp-reaction-bkp7kvrn | Noah Toppings | TITLE: RT-LAMP Reaction
AUTHORS: Noah Toppings
[STEPS]
?. Add 9.5 µL extracted RNA + 15 µL resuspension buffer + 0.5 µL of dye to a lyophilized reaction pellet.
?. Mix reaction by pipetting.
?. Add 30 µL mineral oil on top of reaction.
?. Spin down the strip of tubes.
?. Incubate at 61 ºC for 45 minutes.
?. Visualize ... | ["Add 9.5 µL extracted RNA + 15 µL resuspension buffer + 0.5 µL of dye to a lyophilized reaction pellet.", "Mix reaction by pipetting.", "Add 30 µL mineral oil on top of reaction.", "Spin down the strip of tubes.", "Incubate at 61 ºC for 45 minutes.", "Visualize reactions under a transilluminator."] |
70,526 | CLINICAL CHARACTERISTICS, PATTERNS OF USE, AND INCIDENCE OF ADVERSE EVENTS IN PATIENTS WITH NONVALVULAR ATRIAL FIBRILLATION TREATED WITH ORAL ANTICOAGULANTS | 1 | dx.doi.org/10.17504/protocols.io.rm7vzb852vx1/v1 | https://www.protocols.io/view/clinical-characteristics-patterns-of-use-and-incid-cg46tyze | Jorge Machado Alba | TITLE: CLINICAL CHARACTERISTICS, PATTERNS OF USE, AND INCIDENCE OF ADVERSE EVENTS IN PATIENTS WITH NONVALVULAR ATRIAL FIBRILLATION TREATED WITH ORAL ANTICOAGULANTS
AUTHORS: Jorge Machado Alba
[DESCRIPTION]
Purpose: The aim was to analyze the characteristics, treatment patterns, persistence, and clinical outcome... | [] |
74,349 | Activation of Simvastatin | 6 | dx.doi.org/10.17504/protocols.io.j8nlkwd5xl5r/v1 | https://www.protocols.io/view/activation-of-simvastatin-ckumuwu6 | Dennis Juarez, dfruman | TITLE: Activation of Simvastatin
AUTHORS: Dennis Juarez, dfruman
[DESCRIPTION]
Activation of simvastatin lactone to active simvastatin acid by hydrolysis of lactone ring with NaOH.
[STEPS]
SECTION: Preparation
1. For every 8.4 mg of simvastatin sodium salt, dissolve in 0.2 mL of 100% ethanol.
SECTION: Preparation
2. ... | ["[Preparation] For every 8.4 mg of simvastatin sodium salt, dissolve in 0.2 mL of 100% ethanol.", "[Preparation] Add 30 uL of 1N NaOH for every 8.4 mg of simvastatin sodium salt.", "[Preparation] Heat the solution for at 50 °C for 2 hours.", "[Preparation] Neutralize the solution to pH 7.2 with 1N HCl.", "[Preparation... |
62,612 | Limitless Glucose 1 Reviews: Limitless Glucose 1 Supplement Scam or Legit? (Is Reducing Sugar And Glucose The Same?) | 3 | dx.doi.org/10.17504/protocols.io.yxmvmn5b6g3p/v1 | https://www.protocols.io/view/limitless-glucose-1-reviews-limitless-glucose-1-su-b9dur26w | Limitless Glucose | TITLE: Limitless Glucose 1 Reviews: Limitless Glucose 1 Supplement Scam or Legit? (Is Reducing Sugar And Glucose The Same?)
AUTHORS: Limitless Glucose
[DESCRIPTION]
Limitless Glucose 1
[STEPS] | [] |
47,140 | Making E8 medium for ES/iPS culture | 1 | dx.doi.org/10.17504/protocols.io.bsacnaaw | https://www.protocols.io/view/making-e8-medium-for-es-ips-culture-bsacnaaw | Jiuchun Zhang, Harper JW | TITLE: Making E8 medium for ES/iPS culture
AUTHORS: Jiuchun Zhang, Harper JW
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is about making E8 medium for ES/iPS culture.</div></div>
[STEPS]
?. [Preparation of Recombinant Human TGF-beta 1 ]
**Most temperature sensitive, work fast***Th... | ["[Preparation of Recombinant Human TGF-beta 1 ]\n**Most temperature sensitive, work fast***This is for large number of aliquots. Change volume according to your own scale.\nOrder 1 mg but have them provide it in 2 x 500 μg aliquots plus a sample for testing if theywill do this. 1000X = 1.745 μg/mLFor 500 μg protein: b... |
18,379 | Caspase activity assays | null | dx.doi.org/10.17504/protocols.io.v7je9kn | null | Kiichi Hirota, Yoshiyuki Matsuo | TITLE: Caspase activity assays
AUTHORS: Kiichi Hirota, Yoshiyuki Matsuo
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. Cells were seeded into 96-well plates and incubated overnight.
?. The following day, cells were treated with reagents for varying lengths of time.
?. 100 μl of Apo-ONE® Caspase-3/7 Reagen... | ["Cells were seeded into 96-well plates and incubated overnight.", "The following day, cells were treated with reagents for varying lengths of time.", "100 μl of Apo-ONE® Caspase-3/7 Reagent was added to each well.", "Cells were incubated at room temperature for 1 h.", "The luminescence of each well was measured using ... |
100,772 | Prevalence of Thiamine Deficiency in Hospitalized Non-Alcoholic Veterans | 0 | null | https://www.protocols.io/view/prevalence-of-thiamine-deficiency-in-hospitalized-denc3daw | Elisabeth Mates | TITLE: Prevalence of Thiamine Deficiency in Hospitalized Non-Alcoholic Veterans
AUTHORS: Elisabeth Mates
[DESCRIPTION]
In this protocol we will measure the prevalence of thiamine deficiency in hospitalist Veterans without alcohol use disorder. In addition to measuring blood levels of thiamine, we will interview partic... | ["[Abbreviations] ADL’s Activities of Daily Living \nAIC Acute inflammatory condition\nCIC Chronic inflammatory condition\nCOVID-19 Coronavirus disease 2019\nGI Gastrointestinal\nhs-CRP Highly sensitive C-reactive protein\nIADLs ... |
null | null | null | dx.doi.org/10.17504/protocols.io.e5fbg3n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is for the ProteSEEKER™ kit, designed to identify the specific type of proteases present in cell or tissue lysates, and allows determining the minimal number of individual protease inhibitors required for a sample. </p>
[GUIDELINES]
<p><strong>INTRODUCTION </st... | [] |
81,986 | CXCR4 CXCR7 effects in melanoma & melanocytes | 3 | dx.doi.org/10.17504/protocols.io.e6nvwjwb9lmk/v1 | https://www.protocols.io/view/cxcr4-cxcr7-effects-in-melanoma-amp-melanocytes-cubawsie | Maria Elena de Bellard | TITLE: CXCR4 CXCR7 effects in melanoma & melanocytes
AUTHORS: Maria Elena de Bellard
[DESCRIPTION]
Chemokines are small signaling proteins released by cells in response to chemical stimuli in their environment. The chemokine stromal cell-derived factor-1 (SDF1/CXCL12) plays a role in the growth and metastasis of ... | [] |
32,646 | Isolation of high-molecular weight (HMW) DNA from Diplonema papillatum | null | dx.doi.org/10.17504/protocols.io.bb5eiq3e | null | Matus Valach | TITLE: Isolation of high-molecular weight (HMW) DNA from Diplonema papillatum
AUTHORS: Matus Valach
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>A simple protocol for high-molecular weight (HMW) DNA extraction from </span><span style = "font-style:italic;">Diplonema papillatum</span><span>.... | ["Prepare the cell lysis buffer: A1100 mM Tris-HCl pH8.02100 mM EDTA pH8.031.15 % polyvinylpyrrolidone (PVP)45 mM spermidine\nA1100 mM Tris-HCl pH8.02100 mM EDTA pH8.031.15 % polyvinylpyrrolidone (PVP)45 mM spermidine\nIf highly quality HMW DNA is required, prepare the buffer freshly before use.", "Harvest ~150 mg wet... |
88,985 | Confirmation of Gene Knockdown with RT-qPCR | 4 | dx.doi.org/10.17504/protocols.io.dm6gp3yo1vzp/v1 | https://www.protocols.io/view/confirmation-of-gene-knockdown-with-rt-qpcr-c25zyg76 | Megan Lee, Neal Bennett, Ken Nakamura | TITLE: Confirmation of Gene Knockdown with RT-qPCR
AUTHORS: Megan Lee, Neal Bennett, Ken Nakamura
[DESCRIPTION]
This protocol confirms knockdown of individual genes from CRISPRi sgRNAs using RT-qPCR. Details below specifically validate gene knockdown of complex subunits within the electron transport chain in K562 cell... | ["[Prepare Cell Lysis] Collect cell pellet, wash cells in cold PBS (For K562 cells, optimized cell number is 100.000). Place cells on ice.", "[Prepare Cell Lysis] For each reaction, prepare 0.5 μL DNase I with 49.5 μL of Lysis solution.", "[Prepare Cell Lysis] Add 50 μL of Lysis solution containing DNase I to cell pell... |
93,093 | ECIS Data Analysis for Stimulation of Human Pulmonary Microvascular Endothelial Cells (HPMECs) with Human Serum | 4 | dx.doi.org/10.17504/protocols.io.bp2l69erklqe/v3 | https://www.protocols.io/view/ecis-data-analysis-for-stimulation-of-human-pulmon-c66dzha6 | Michael Bokoch | TITLE: ECIS Data Analysis for Stimulation of Human Pulmonary Microvascular Endothelial Cells (HPMECs) with Human Serum
AUTHORS: Michael Bokoch
[DESCRIPTION]
Sera from patients in our UCSF Liver Transplant Biobank are used to stimulate human pulmonary microvascular endothelial cells (HPMECs) grown to confluency on ECIS... | ["[ECIS Data Analysis for HPMEC stimulation by Liver Biobank Sera] Determine Difference in Area-under-the-Curve (Normalized Resistance at 4000 Hz)\nTo be calculated after recording full ECIS curve after stimulation with human serum from liver transplant (LT) patients.\n\nGoal: To calculate the difference in AUC between... |
107,456 | FruitRescue! - Apple phenotyping | 0 | null | https://www.protocols.io/view/fruitrescue-apple-phenotyping-dk684zhw | Mathieu Brisson, Amandine Cornille | TITLE: FruitRescue! - Apple phenotyping
AUTHORS: Mathieu Brisson, Amandine Cornille
[DESCRIPTION]
The FruitRescue project aims to create a pipeline to predict fruit trees' genomic offset. To confirm the pipeline predictions, tree fitness parameters are measured in crop and wild tree orchards along a longitudinal gradi... | ["[Trunk diameter] The trunk diameter is an indicator of the tree vigor (Waring 1987). Genetic information as well as environmental cues including abiotic and biotic stresses can modify the source-sink relationships and therefore modify the trunk growth during the year. Tree adaptation to its location can thus be asses... |
80,327 | Cell DIVE Platform | Accessing HuBMAP Datasets and Analysis on Globus | 1 | dx.doi.org/10.17504/protocols.io.14egn2qwpg5d/v1 | https://www.protocols.io/view/cell-dive-platform-accessing-hubmap-datasets-and-a-cspfwdjn | Liz McDonough, Christine Surrette | TITLE: Cell DIVE Platform | Accessing HuBMAP Datasets and Analysis on Globus
AUTHORS: Liz McDonough, Christine Surrette
[DESCRIPTION]
This method describes navigating to Globus from the HuBMAP data portal to access Cell DIVE data and analysis.
[STEPS]
1. Click on the DOI link provided, or alternatively navigate to h... | ["Click on the DOI link provided, or alternatively navigate to http://dx.doi.org, enter the DOI in the text box, and click Go.", "If the DOI takes you to a Collection on the HuBMAP Data Portal, click on a HuBMAP ID of interest, located under the Dataset heading.", "On the Dataset page, scroll down to the Files heading ... |
102,532 | Test share with Gabriel | 4 | null | https://www.protocols.io/view/test-share-with-gabriel-dgdc3s2w | Lenny Teytelman | TITLE: Test share with Gabriel
AUTHORS: Lenny Teytelman
[DESCRIPTION]
test
[STEPS]
1. 3000 rpm
Second test | ["3000 rpm \nSecond test"] |
71,084 | Comparison of measured LDL cholesterol with calculated LDL-cholesterol using the Friedewald and Martin-Hopkins formulae in diabetic adults at Charlotte Maxeke Johannesburg Academic Hospital/NHLS Laboratory | 1 | dx.doi.org/10.17504/protocols.io.yxmvm2ky6g3p/v1 | https://www.protocols.io/view/comparison-of-measured-ldl-cholesterol-with-calcul-chnkt5cw | Mogomotsi Dintshi, Ngalulawa Kone, Siyabonga Khoza | TITLE: Comparison of measured LDL cholesterol with calculated LDL-cholesterol using the Friedewald and Martin-Hopkins formulae in diabetic adults at Charlotte Maxeke Johannesburg Academic Hospital/NHLS Laboratory
AUTHORS: Mogomotsi Dintshi, Ngalulawa Kone, Siyabonga Khoza
[DESCRIPTION]
Background
National Cholesterol... | [] |
70,149 | Staphilococcus Aureus Sampling | 4 | dx.doi.org/10.17504/protocols.io.81wgb6pk1lpk/v7 | https://www.protocols.io/view/staphilococcus-aureus-sampling-cgrdtv26 | Mar Roca Cugat, Olga Sánchez | TITLE: Staphilococcus Aureus Sampling
AUTHORS: Mar Roca Cugat, Olga Sánchez
[DESCRIPTION]
This protocol is intended to study the affectation of Staphylococcus Aureus, including the MRSA, VISA and VRSA variants, even if it makes the test more difficult to perform. It outlines the basic protocol for a multi-subject stud... | ["[Preparation] Wash your hands with soap. Put on your lab coat, your mask, and your goggles or face shield. Make sure your mask is airtight and air cannot escape through the sides.", "[Preparation] Prepare the area where you are going to work. Disinfect the surfaces with the bleach solution.\nThe subjects should not b... |
74,213 | Kompetitive Allele Specific PCR (KASP) with BioRad Software | 1 | dx.doi.org/10.17504/protocols.io.dm6gpj9njgzp/v1 | https://www.protocols.click/view/kompetitive-allele-specific-pcr-kasp-with-biorad-s-ckqduvs6 | Olivia E Todd, Eric L Patterson | TITLE: Kompetitive Allele Specific PCR (KASP) with BioRad Software
AUTHORS: Olivia E Todd, Eric L Patterson
[DESCRIPTION]
A short guide to primer design with HEX/FAM tags and a basic KASP protocol using LGC Genomics KASP master mix and BioRad analyzation software.
[STEPS]
SECTION: Primer Design
1. Design regular prim... | ["[Primer Design] Design regular primers over the mutation you wish to test.", "[Primer Design] Copy and paste the FAM and HEX tags to your wild type and mutant alleles. Pay attention to which tag is which.\n\nFAM tag: GAAGGTGACCAAGTTCATGCT\nHEX tag: GAAGGTCGGAGTCAACGGATT", "[Example: IAA16 GG to RR mutation Primers in... |
54,033 | MIBI staining | 1 | dx.doi.org/10.17504/protocols.io.byzrpx56 | https://www.protocols.io/view/mibi-staining-byzrpx56 | Marc MB Bosse, Sean Bendall, Mike Angelo | TITLE: MIBI staining
AUTHORS: Marc MB Bosse, Sean Bendall, Mike Angelo
[DESCRIPTION]
This protocol is the standard FFPE tissue staining procedure recommended for Multiplex Ion Beam Imaging Time of Flight instrument (MIBI_TOF) developed in the Sean C. Bendall and Michael R. Angelo labs. The protocol has been successf... | ["[Slide for MIBI] FFPE or frozen sections should be deposited on special conductive slides for MIBI\nIt is recommended to use freshly cut tissue sections. Otherwise tissue section slides should be stored properly using different state of the art methods (vacuum chamber, nitrogen chamber or vacuum sealed bags)", "[Sli... |
54,749 | Neural activation of the GI tract | 4 | dx.doi.org/10.17504/protocols.io.bzp5p5q6 | https://www.protocols.io/view/neural-activation-of-the-gi-tract-bzp5p5q6 | Bryan Yoo, Jessica Griffiths, Sarkis Mazmanian | TITLE: Neural activation of the GI tract
AUTHORS: Bryan Yoo, Jessica Griffiths, Sarkis Mazmanian
[DESCRIPTION]
Protocol for neural activation of the GI tract used in Yoo et al 2021
[STEPS]
1. TH-Cre and ChAT-Cre mice are used for these experiments.
2. “Activated” mice are infected with AAV-PHP.S:hSYN1-DIO-hM3Dq-... | ["TH-Cre and ChAT-Cre mice are used for these experiments.", "“Activated” mice are infected with AAV-PHP.S:hSYN1-DIO-hM3Dq-mRuby2 and “Control Mice” are infected with AAV-PHP.S:hSYN1-DIO-mRuby2. This is to control for both AAV-PHP.S-mediated expression and the effects of Compound 21 dihydrochloride (C21) (HelloBio, Pri... |
38,116 | High-Throughput gDNA Extraction of Mosquito Tissues using QIAcube HT | 4 | dx.doi.org/10.17504/protocols.io.bhgcj3sw | https://www.protocols.io/view/high-throughput-gdna-extraction-of-mosquito-tissue-bhgcj3sw | Jack Dorman, Ilinca Ciubotariu, Maria Levy, Abebe Fola, Giovanna Carpi | TITLE: High-Throughput gDNA Extraction of Mosquito Tissues using QIAcube HT
AUTHORS: Jack Dorman, Ilinca Ciubotariu, Maria Levy, Abebe Fola, Giovanna Carpi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Genomic DNA (gDNA) is crucial to the study of many important aspects of vector-parasite in... | ["[Sample Homogenization]\nUsing clean tweezers, separate the head and abdomen of a mosquito from the thorax on a sterile petri dish. Move either the thorax or abdomen (depending on which will be used for extraction) to the 2 mL RB tube with a 5mm stainless steel bead in it. Store the other 2 segments in the other 2 RB... |
null | null | null | dx.doi.org/10.17504/protocols.io.e9sbh6e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The Non-Interfering™ Protein Assay is a colorimetric assay for determining protein concentrations in protein loading buffer (Laemmli buffer), high β-mercaptoethanol concentrations, and in lipid and vesicle preparations.</p>
[BEFORE_START]
<p><em><strong>Prepare Reagent-II -<... | [] |
80,234 | Sakata et al. Fish SedDNA Extraction Protocol | 1 | dx.doi.org/10.17504/protocols.io.6qpvr4n8ogmk/v1 | https://www.protocols.io/view/sakata-et-al-fish-seddna-extraction-protocol-cskiwcue | Masayuki K. Sakata | TITLE: Sakata et al. Fish SedDNA Extraction Protocol
AUTHORS: Masayuki K. Sakata
[DESCRIPTION]
Variations of this standardised protocol have been used by Masayuki K. Sakata and colleagues to successfully extract fish eDNA from modern and historic Japanese lake and river sediments.
The method has been used to recover... | ["[Alkaline extraction] VORTEX samples to mix\n\nINCUBATE samples at 94 °C for 50 min", "[Alkaline extraction] ALLOW samples to cool to Room temperature \n\nCENTRIFUGE at 5000 x g for 30 s", "[Alkaline extraction] PLACE 9.0 g of sediment sample into a 50 mL tube\n\nADD 6 mL NaOH\n\nADD 3 mL TE buffer\n\nADD 500 µL G2 e... |
92,279 | Protocol for Neuronal Live-imaging of primary cultures | 1 | dx.doi.org/10.17504/protocols.io.q26g7pn4qgwz/v1 | https://www.protocols.io/view/protocol-for-neuronal-live-imaging-of-primary-cult-c6cxzaxn | Camila Pulido, Timothy A. Ryan | TITLE: Protocol for Neuronal Live-imaging of primary cultures
AUTHORS: Camila Pulido, Timothy A. Ryan
[DESCRIPTION]
Neurons stand out as remarkably intricate cells. The development of live-imaging techniques on primary neurons expressing genetically engineered biosensor has proven pivotal in advancing our comprehensio... | ["[Mounting the coverslip to recording chamber] Add 2 mL of ‘Imaging Solution’ into a P35 dish.", "[Mounting the coverslip to recording chamber] Cut a piece of a new coverslip and fix it with some grease into the ‘Stimulator insert’ (Figure 1).", "[Mounting the coverslip to recording chamber] Add a drop of grease to ev... |
null | null | null | dx.doi.org/10.17504/protocols.io.p88drzw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol to use ACCEL-NGS® METHYL-SEQ DNA LIBRARY KIT (NGS Prep with Bisulfite-Converted DNA Capability; Cat. No. DL-ILMMS-12/48) to perform MethylC-sequencing in Arabidopsis.</p>
<p> </p>
<p>Code used to analyse raw sequencing data can be found: Please see https://github.com... | [] |
66,635 | Coverage of DOAJ journals' citations through OpenCitations - Protocol | 1 | dx.doi.org/10.17504/protocols.io.n92ldz598v5b/v5 | https://www.protocols.io/view/coverage-of-doaj-journals-39-citations-through-ope-cdbjs2kn | Constance Dami, Alessandro Bertozzi, Chiara Manca, Umut Kucuk | TITLE: Coverage of DOAJ journals' citations through OpenCitations - Protocol
AUTHORS: Constance Dami, Alessandro Bertozzi, Chiara Manca, Umut Kucuk
[DESCRIPTION]
This is the protocol for the research of the coverage of DOAJ journals' citations through OpenCitations.
Our goal is to find out:
about the coverage o... | ["[Data Gathering: DOAJ] Collecting data from DOAJ: we download data about journals and articles from the DOAJ website, and then refine it excluding all information that we are not interested in.", "[Data Gathering: DOAJ] We download the data dumps from DOAJ in .tar.gz. format.\n \n\n \nBoth datasets contain metadata t... |
37,389 | Pelvic nerve implantation, testing and processing in awake rats | 2 | dx.doi.org/10.17504/protocols.io.bgrmjv46 | https://www.protocols.io/view/pelvic-nerve-implantation-testing-and-processing-i-bgrmjv46 | James Fallon, Sophie Payne, Peregrine Osborne, Janet Keast | TITLE: Pelvic nerve implantation, testing and processing in awake rats
AUTHORS: James Fallon, Sophie Payne, Peregrine Osborne, Janet Keast
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This collection describes the procedures required to implant a pelvic nerve array and bladder catheter into male ... | [] |
99,704 | Phage screening - colorimetric test | 0 | dx.doi.org/10.17504/protocols.io.5jyl82jmdl2w/v1 | https://www.protocols.io/view/phage-screening-colorimetric-test-ddky24xw | Kesia da Silva, Jason Andrews | TITLE: Phage screening - colorimetric test
AUTHORS: Kesia da Silva, Jason Andrews
[DESCRIPTION]
Phage Screening - Colorimetric Test protocol involves a series of steps designed to detect the presence of specific bacteriophages through a colorimetric assay. This comprehensive procedure aims to provide a robust method f... | ["[Day 1] Prepare LB-agar plates.", "[Day 1] Prepare LB-broth.", "[Day 1] To recover bacteria from stock open the tube and use a sterile loop, toothpick or pipette tip to scrap off some bacteria and streak on appropriate media plates using the overnight culture and grow at37 °C.", "[Day 2] Next, start overnight culture... |
null | null | null | dx.doi.org/10.17504/protocols.io.m9sc96e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>One of the challenges to describing the human liver on a single cell level is the process of cell dissociation. Cell dissociation methods can be quite damaging to the cells and can lead to a biasing of the transcriptome. We have developed gentle surgical and perfusion techniq... | [] |
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