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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93,470 | Striatal injection of 6-OHDA or Saline and post-operative care (Mendonça et al 2024) | 1 | dx.doi.org/10.17504/protocols.io.x54v9p4pzg3e/v1 | https://www.protocols.io/view/striatal-injection-of-6-ohda-or-saline-and-post-op-c7h6zj9e | Marcelo D Mendonça | TITLE: Striatal injection of 6-OHDA or Saline and post-operative care (Mendonça et al 2024)
AUTHORS: Marcelo D Mendonça
[DESCRIPTION]
Striatal injection of 6-OHDA or Saline and post-operative care procedure from Mendonça et al 2024
[BEFORE_START]
Mice were kept in deep anesthesia using 1-3% isoflurane and oxygen (at ... | ["[Stereotaxic Surgery] Place the anesthetized mouse in the stereotaxic apparatus then stabilize the head.", "[Stereotaxic Surgery] Make a skin incision to expose the skull.", "[Stereotaxic Surgery] Carefully remove any connective and muscle tissue from the exposed area.", "[Stereotaxic Surgery] Level the skull surface... |
null | null | null | dx.doi.org/10.17504/protocols.io.djf4jm | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
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null | null | null | dx.doi.org/10.17504/protocols.io.c29yh5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol consists of several methods for the preservation of seawater samples to later perform various techniques in the lab. It is meant as a sampling treatment in the field and is written as comprehensive; however, depending on needs and scientific questions, any or all o... | [] |
64,437 | True KetoGenics [BETTER OUT COME] Does It Really Work? Don’t Buy Before Read | 3 | dx.doi.org/10.17504/protocols.io.dm6gpbqnplzp/v1 | https://www.protocols.io/view/true-ketogenics-better-out-come-does-it-really-wor-ca6vshe6 | H Douglas Morris | TITLE: True KetoGenics [BETTER OUT COME] Does It Really Work? Don’t Buy Before Read
AUTHORS: H Douglas Morris
[DESCRIPTION]
Thus, click any picture or button on this page to check whether you can guarantee a FREE TRIAL OFFER of the top selling keto pills before provisions are gone!
[STEPS] | [] |
50,987 | Role of Soap Boxes in Cosmetic Products | 1 | dx.doi.org/10.17504/protocols.io.bv2jn8cn | https://www.protocols.io/view/role-of-soap-boxes-in-cosmetic-products-bv2jn8cn | soap boxes | TITLE: Role of Soap Boxes in Cosmetic Products
AUTHORS: soap boxes
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Cosmetic boxes are the trend in today’s market where cosmetic products are sold. These boxes are perfectly able to ensure your commercial success. Your wise decisions can help you expan... | ["The presentation has a vital role in promoting a certain product. Talking specifically about Soap Boxes, they are the most important presentation product that enhances the beauty of the soap. Soaps are used excessively and the presentation is everything that the products’ marketing depends on. In cosmetic products, t... |
28,336 | MojoSort™ Human CD45 Nanobeads Protocol 2 - CD45 greater than 50% | null | dx.doi.org/10.17504/protocols.io.7wqhpdw | null | Sam Li | TITLE: MojoSort™ Human CD45 Nanobeads Protocol 2 - CD45 greater than 50%
AUTHORS: Sam Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Product description and procedure summary:</span></div><div class = "text-block"><span style = "font-weight:bold;">If the percent... | ["Prepare cells from your tissue of interest or blood without lysing erythrocytes. Kits for human samples have been optimized for PBMCs, please prepare the cells using a suitable method.", "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) ... |
84,976 | Golden Gate Cloning - Loop and MoClo - part and primerdesign guidelines | 4 | dx.doi.org/10.17504/protocols.io.5jyl8p568g2w/v1 | https://www.protocols.io/view/golden-gate-cloning-loop-and-moclo-part-and-primer-cw8qxhvw | is Sparrow | TITLE: Golden Gate Cloning - Loop and MoClo - part and primerdesign guidelines
AUTHORS: is Sparrow
[DESCRIPTION]
This protocol is largely based on the original Loop and uLoop protocol dx.doi.org/10.17504/protocols.io.yxnfxmeby the corresponding authors. This protocol provides general guidelines for primer design for ... | ["[Designing L-1 parts] If you are not familiar with Golden Gate, please read description for Golden Gate summary. \n\nPurchase your primers to create a L-1 part through PCR or synthesize the part. See below for guidelines on designing primers and synthesis parts to ensure system compatibility.", "[Designing L-1 parts]... |
23,335 | Prospective cohort of AIDS patients screened for cryptococcal antigenaemia, pre-emptively treated and followed in Midwest Brazil | null | dx.doi.org/10.17504/protocols.io.22fggbn | null | Moara Borges, João Alves de Araújo Filho, Marília Dalva Turchi | TITLE: Prospective cohort of AIDS patients screened for cryptococcal antigenaemia, pre-emptively treated and followed in Midwest Brazil
AUTHORS: Moara Borges, João Alves de Araújo Filho, Marília Dalva Turchi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a study carried out in partnership w... | ["Inclusion Criteria:Laboratory confirmed diagnosis of HIV-1 infectionCD4Age ≥18 yearsWith or without neurological symptomsHospitalized or outpatientRegardless of antiretroviral therapy (ARV) experience or adherence", "Study Type: Prospective cohort", "Exclusion Criteria:Prior known history of cryptococcal diseaseCurre... |
63,381 | Stamena 10RX Reviews {LEGIT DIET 2022} Best Mens Pills? Scam Alert | 3 | dx.doi.org/10.17504/protocols.io.81wgb69d3lpk/v1 | https://www.protocols.io/view/stamena-10rx-reviews-legit-diet-2022-best-mens-pil-b95vr866 | H Douglas Morris | TITLE: Stamena 10RX Reviews {LEGIT DIET 2022} Best Mens Pills? Scam Alert
AUTHORS: H Douglas Morris
[DESCRIPTION]
help diabetics maintain their blood glucose levels. And a teaspoon of grated organic orange peel added to food can reduce cholesterol.
[STEPS] | [] |
66,101 | Rapid extraction of total lipids from microalgae | 1 | dx.doi.org/10.17504/protocols.io.dm6gpr9jdvzp/v5 | https://www.protocols.io/view/rapid-extraction-of-total-lipids-from-microalgae-ccsvswe6 | Yingyu Hu, Zoe V Finkel | TITLE: Rapid extraction of total lipids from microalgae
AUTHORS: Yingyu Hu, Zoe V Finkel
[DESCRIPTION]
In this protocol, total lipids from miroalgae is extracted with a mixture of water and Folch solvent (2:1 chloroform-methanol v/v). Filter and cell debris is commonly removed by filtration, which is laborious and t... | ["[Collect microalgae samples] Precombust GFF filter at 450 °C for 240 min", "[Collect microalgae samples] Rinse forceps with 95% ethanol, air-dry.", "[Collect microalgae samples] Filter microalgae in liquid media onto precombusted GFF filters, using gentle vacuum pressure (130 mm Hg).", "[Collect microalgae samples] ... |
null | null | null | dx.doi.org/10.17504/protocols.io.hg8b3zw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>To develop broadly useful methods for the genetic manipulation of Labyrinthulomycetes, it is essential to understand the similarities and differences in regulation of gene expression among them. Toward this end we have used FIMO from the MEME suite (http://meme-suite.org/doc/... | [] |
96,475 | Refined Protocol for the Isolation and Purification of BETALAINS Pigment from Celosia argentea y Beta vulgaris | 0 | dx.doi.org/10.17504/protocols.io.14egn3pmql5d/v1 | https://www.protocols.io/view/refined-protocol-for-the-isolation-and-purificatio-daf32bqn | Antonino Michel Lecona Jiménez, Kalpana Nanjareddy, Manoj-Kumar Arthikala | TITLE: Refined Protocol for the Isolation and Purification of BETALAINS Pigment from Celosia argentea y Beta vulgaris
AUTHORS: Antonino Michel Lecona Jiménez, Kalpana Nanjareddy, Manoj-Kumar Arthikala
[DESCRIPTION]
Betalains, a group of secondary metabolites exclusive to the Caryophyllales order, are particularly abun... | ["[Purification process] The samples are transferred into a LH-20 separation column measuring 100 x 2.5 cm in diameter. The separation process is achieved through elution using water adjusted to a pH between 5 and 6 with formic acid.", "[Extraction process] The frozen samples should be ground thoroughly in a mortar unt... |
70,613 | Quantify photophysiology of endosymbiotic dinoflagellates (Symbiodiniaceae) using the Guava Flow Cytometer | 4 | null | https://www.protocols.io/view/quantify-photophysiology-of-endosymbiotic-dinoflag-cg7vtzn6 | Colin J Anthony, Colin Lock, Bastian Bentlage | TITLE: Quantify photophysiology of endosymbiotic dinoflagellates (Symbiodiniaceae) using the Guava Flow Cytometer
AUTHORS: Colin J Anthony, Colin Lock, Bastian Bentlage
[DESCRIPTION]
This protocol quantifies light-harvesting complex (LHC) and antioxidant pigments, while simultaneously determining cell density of endos... | ["[Sample Preservation] Sample tissue from cnidarian\nIf calcifying coral, we suggest 3 pieces at around 2 cm3 sampled with wire cutters or hammer and chisel \nIf gelatinous cnidarian, 0.05 - 0.1 g of tissue sampled with sterile scissors works well", "[Sample Preservation] Store tissue in bag or tube\nFor calcifiers, W... |
52,311 | Protocol for RNA isolation and RT‐PCR confirmation for Neomycin gene expression in transformed Bodo saltans | 1 | dx.doi.org/10.17504/protocols.io.bxbxpipn | https://www.protocols.io/view/protocol-for-rna-isolation-and-rt-pcr-confirmation-bxbxpipn | Fatma Gomaa, Zhu-Hong Li, Roberto Docampo, Virginia Edgcomb | TITLE: Protocol for RNA isolation and RT‐PCR confirmation for Neomycin gene expression in transformed Bodo saltans
AUTHORS: Fatma Gomaa, Zhu-Hong Li, Roberto Docampo, Virginia Edgcomb
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Developing transfection protocol for </span><span style = "fon... | ["-Total RNA was isolated from 4 months old transformed clones and wild type Bodo saltans cultures using the Quick-RNA Miniprep Kit (Zymo Research) according to the manufacturer’s instructions.", "-RNA underwent two rounds of DNAse treatments. First, we performed an on-column DNAse digestion, following the protocol of ... |
88,808 | ddRADseq for animal population genomics/phylogenomics | 1 | dx.doi.org/10.17504/protocols.io.kxygx3nzwg8j/v1 | https://www.protocols.io/view/ddradseq-for-animal-population-genomics-phylogenom-c2ygyftw | Tomasz Suchan, Christophe Dufresnes, Robin Schmidt, Johanna Ambu, Sven Gippner, Miguel Vences | TITLE: ddRADseq for animal population genomics/phylogenomics
AUTHORS: Tomasz Suchan, Christophe Dufresnes, Robin Schmidt, Johanna Ambu, Sven Gippner, Miguel Vences
[DESCRIPTION]
Restriction-site Associated DNA sequencing (RADseq) offers a simple, affordable, and versatile approach to swiftly genotype thousands of gene... | ["[Preparation] Before starting the protocol, it is necessary to prepare the SbfI and MseI adapters as follows:", "[Restriction Reaction] In this section of the protocol, the restriction digestion reaction of samples will be carried out.", "[Purification (short fragment removal)] Purify the ligation reaction product us... |
40,949 | Bench top CUT&RUN with antibodies-online™ CUT&RUN Sets | 1 | dx.doi.org/10.17504/protocols.io.kqdg3557pv25/v6 | https://www.protocols.io/view/bench-top-cut-run-with-antibodies-online-cut-run-s-bj8vkrw6 | Antibodies Online Gmbh | TITLE: Bench top CUT&RUN with antibodies-online™ CUT&RUN Sets
AUTHORS: Antibodies Online Gmbh
[DESCRIPTION]
CUT&RUN (Cleavage Under Targets and Release Using Nuclease) offers a novel approach
to pursue epigenetics. The method is designed to map genome wide transcription factor
binding sites, chromatin-associated c... | ["[REAGENT SETUP (for 12 samples)] » Wash buffer (165 mL)\n \n\n» Binding Buffer (45 mL)\n \n\n» Digitonin Wash Buffer (82.5 mL)\n \n\n\n\n» Antibody Buffer (1.5 mL)\n \n\n\n » Low Salt Rinse Buffer (27 mL)\n \n\n\n» Low Salt Incubation Buffer (3 mL)\n \n\n» Low Salt Stop Buffer (3 mL)", "[I.Cell Harvest – at room temp... |
39,409 | protocol_template_for_intervention_review | 3 | dx.doi.org/10.17504/protocols.io.biqrkdv6 | https://www.protocols.io/view/protocol-template-for-intervention-review-biqrkdv6 | Yuki Kataoka, Yasushi Tsujimoto, Masahiro Banno, Shunsuke Taito, Ryuhei So, Jun Watanabe, Akihiro Shiroshita | TITLE: protocol_template_for_intervention_review
AUTHORS: Yuki Kataoka, Yasushi Tsujimoto, Masahiro Banno, Shunsuke Taito, Ryuhei So, Jun Watanabe, Akihiro Shiroshita
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.sn7edhn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Histones are a family of basic proteins that associate with DNA in the nucleus and help condense it into chromatin, they are alkaline (basic pH) proteins, and their positive charges allow them to associate with DNA. They are found inside the nucleus of eukaryotic cells. DNA a... | [] |
57,715 | Visualization and Enumeration of Ostreococcus via Kohler Transmitted Light/Dark-Field on the Axio A1 Imager Microscope and AxioCam HrC | 4 | dx.doi.org/10.17504/protocols.io.b4ktquwn | https://www.protocols.io/view/visualization-and-enumeration-of-ostreococcus-via-b4ktquwn | Lynn Doran | TITLE: Visualization and Enumeration of Ostreococcus via Kohler Transmitted Light/Dark-Field on the Axio A1 Imager Microscope and AxioCam HrC
AUTHORS: Lynn Doran
[DESCRIPTION]
Basic setup and usage instructions for visualization of Ostreococcus species on the Axio A1 Imager Microscope using the AxioCam HrC and Ax... | ["[Prepare organisms] Sterilize a laminar flow hood or biological safety cabinet, pipettes, and gloves. Autoclave pipette tips. Sterilize the outside of the culture vial, especially the lid.", "[Prepare organisms] Gently rock culture vial to evenly suspend organisms. Using aseptic technique, pipette 10 µLof culture ... |
null | null | null | dx.doi.org/10.17504/protocols.io.i2mcgc6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Frost formation on solid surfaces is ubiquitous in nature when the water vapor droplets contact surfaces with low temperature. The protocol is for carrying out the frost on the butterfly wing surface and analyzing the hydrophobic durability mechanism of butterfly wing surface... | [] |
20,549 | Isolation of endothelial cells from umbillical vessels | null | dx.doi.org/10.17504/protocols.io.ybdfsi6 | null | Thomas Mudersbach, Daniel Siuda, Karin Kohlstedt, Ingrid Fleming | TITLE: Isolation of endothelial cells from umbillical vessels
AUTHORS: Thomas Mudersbach, Daniel Siuda, Karin Kohlstedt, Ingrid Fleming
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Reagents]
Hank's Balanced Salt Solution (HBSS) (H6648-500ml, Sigma-Aldrich)Enzymatic digestion with Dispase II (29585300, ... | ["[Reagents]\nHank's Balanced Salt Solution (HBSS) (H6648-500ml, Sigma-Aldrich)Enzymatic digestion with Dispase II (29585300, Roche) (2.4 U/ml) in Ham's F12Ham's F12 with 10% fetal calf serum (FCS), penicillin (50 U/ml) and streptomycin (50 µg/ml) for centrifugationEndothelial cell culture medium: MCDB131 (10372-019, G... |
85,866 | Nuclei Isolation for FACS | 4 | dx.doi.org/10.17504/protocols.io.kxygx9jk4g8j/v4 | https://www.protocols.io/view/nuclei-isolation-for-facs-cx4ixque | Lakme Caceres | TITLE: Nuclei Isolation for FACS
AUTHORS: Lakme Caceres
[DESCRIPTION]
This protocol is for purifying nuclei for downstream 10X sequencing.
[GUIDELINES]
Keep tissue/nuclei on ice as much as possible.
[STEPS]
SECTION: Prepare Fresh Solutions
4. Make 3 mL Homogenization Buffer by adding 2.9 mL Nuclear Isolation Media (... | ["[Prepare Fresh Solutions] Make 3 mL Homogenization Buffer by adding 2.9 mL Nuclear Isolation Media (filtered via syringe) to a 5 mL eppendorf. Then add 3 μL 100 mM DTT and 30 μL 10% Triton X-100.", "[Prepare Stock Solutions] Make 20 mL 10% BSA by combining 2 mL of BSA with 18 mL of MilliQ water in a 50 mL falcon tube... |
82,455 | 14. Taxon Group: Sipuncula | 4 | dx.doi.org/10.17504/protocols.io.q26g7yq89gwz/v1 | https://www.protocols.click/view/14-taxon-group-sipuncula-curxwv7n | Patrick Adkins, Inez Januszczak | TITLE: 14. Taxon Group: Sipuncula
AUTHORS: Patrick Adkins, 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 various marine Meta... | [] |
89,964 | F-4 FECES TESTING | 4 | dx.doi.org/10.17504/protocols.io.5qpvo37b7v4o/v1 | https://www.protocols.io/view/f-4-feces-testing-c34kyquw | REDI-NET Consortium | TITLE: F-4 FECES TESTING
AUTHORS: REDI-NET Consortium
[DESCRIPTION]
This protocol details standard operating procedure for feces testing.
[BEFORE_START]
BEFORE START
Check the DNA and RNA concentrations in each sample of total nucleic acid (TNA) extraction.
If the concentrations are detectable, choose the sequencin... | ["[gDNA PREPARATION] When the RNA concentration of the sample is lower than the detectable range of the Qubit High Sensitivity Assay (<0.01 ng/µl), the sample is subjected to gDNA sequencing. The cDNA synthesis can be skipped.", "[gDNA PREPARATION] When the DNA concentration >10 ng/ul, calculate the required volume of ... |
48,400 | Calcium phosphate transfection mammalian cells | 4 | dx.doi.org/10.17504/protocols.io.bthqnj5w | https://www.protocols.io/view/calcium-phosphate-transfection-mammalian-cells-bthqnj5w | Karla Feijs | TITLE: Calcium phosphate transfection mammalian cells
AUTHORS: Karla Feijs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is our calcium phosphate transfection protocol. It always works with HEK293T cells, for other lines the transfection efficiency depends on their source: some HeLa and U2OS ... | ["[Day 1]\nSeed cells: density depends on cell line and dish used. For example in a 10cm dish seed 0.8x106 HeLa or 1.5 x106 HEK293T cells; in a 6-well plate seed 0.3 x106 HEK293T cells or 0.15x106 HeLa cells.", "[Day 2]\nObserve the cells under the microscope.Prepare the transfection mix. The amounts given here are for... |
37,957 | HTAPP_NST- Nuclei isolation from frozen tissue | 1 | dx.doi.org/10.17504/protocols.io.bhbdj2i6 | https://www.protocols.io/view/htapp-nst-nuclei-isolation-from-frozen-tissue-bhbdj2i6 | Eugene Drokhlyansky, Nicholas Van Wittenberghe, Michal Slyper, Julia Waldman, Asa Segerstolpe, Orit Rozenblatt-Rosen, Aviv Regev | TITLE: HTAPP_NST- Nuclei isolation from frozen tissue
AUTHORS: Eugene Drokhlyansky, Nicholas Van Wittenberghe, Michal Slyper, Julia Waldman, Asa Segerstolpe, Orit Rozenblatt-Rosen, Aviv Regev
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes a nuclei isolation method for ... | ["[Nuclei isolation]\nUsing forceps, place tissue in the pre-filled well of the 6-well plate on ice (containing the 1 ml of NST; Step 1) and chop tissue for 10 minutes in the buffer using spring scissors.\n[On ice]", "[Nuclei isolation]\nWith a 1 ml pipette transfer the suspension from the 6-well plate to a 40 µm filte... |
92,522 | Immunohistochemistry data processing | 4 | null | https://www.protocols.io/view/immunohistochemistry-data-processing-c6kizcue | Tae-Un Han | TITLE: Immunohistochemistry data processing
AUTHORS: Tae-Un Han
[DESCRIPTION]
This protocol has been used for high throughput quantification of immunohistochemistry data of mouse brain sections
[STEPS]
1. Widefield fluorescent images are collected for GFP and DAPI fluorescent channels using a Zeiss AxioScan.Z1 slide ... | ["Widefield fluorescent images are collected for GFP and DAPI fluorescent channels using a Zeiss AxioScan.Z1 slide scanning microscope system with a Plan-Apochromat 20x/0.8 objective lens.", "All images are acquired using a Hamamatsu Orca flash 4.0 camera with an average tile count of 165 tiles per brain section.", "Th... |
58,490 | Preparation of Biological Tissues for Serial Block Face Scanning Electron Microscopy (SBEM) | 1 | dx.doi.org/10.17504/protocols.io.36wgq7je5vk5/v1 | https://www.protocols.io/view/preparation-of-biological-tissues-for-serial-block-b5c2q2ye | Thomas J. Deerinck, Eric A. Bushong, Mark H. Ellisman, Andrea Thor | TITLE: Preparation of Biological Tissues for Serial Block Face Scanning Electron Microscopy (SBEM)
AUTHORS: Thomas J. Deerinck, Eric A. Bushong, Mark H. Ellisman, Andrea Thor
[DESCRIPTION]
This protocol was designed to enhance signal for backscatter electron imaging of epoxy embedded mammalian tissue at low accelerati... | ["Animals are anesthetized and perfused with normal Ringer’s solution containing xylocaine (0.2 mg/ml) and heparin (20 units/ml) for 2 minutes at 35°C followed by 0.15M cacodylate buffer (Ted Pella Inc., Redding, CA) pH 7.4 containing 2.5% glutaraldehyde (Electron Microscopy Sciences, Hartfield, PA), 2% formaldehyde (f... |
52,557 | Intracardial perfusion for electrophysiology in rat | 4 | null | https://www.protocols.io/view/intracardial-perfusion-for-electrophysiology-in-ra-bxjmpkk6 | Alicia Avelar | TITLE: Intracardial perfusion for electrophysiology in rat
AUTHORS: Alicia Avelar
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is to use for clearing blood from the brain and helping to maintain viable cells for electrophysiology experiments. No PFA or any tools that have had conta... | ["[Anesthesia]\nanesthetize rat with isoflurane anesthesia machine.", "[Anesthesia]\nwhen rat is lying down immobile, doesn’t right it’s position when moved, and is breathing slowly put isoflurane nose cone on rat and test for pain with forceps toe pinch of both feet", "[Surgery and intracranial perfusion]\nopen rat th... |
58,172 | Making slip | 1 | null | https://www.protocols.io/view/making-slip-b424qygw | Amber York | TITLE: Making slip
AUTHORS: Amber York
[DESCRIPTION]
Rough procedure for making slip including colored slip.
[STEPS]
1. Bone dry clay (small chunks/trimmings are better). Drying clay first allows it to break down and mix better than using wet recycled clay.
2. Cover with water. Soak overnight at least.
3. Blend. I... | ["Bone dry clay (small chunks/trimmings are better). Drying clay first allows it to break down and mix better than using wet recycled clay.", "Cover with water. Soak overnight at least.", "Blend. I used an old blender. Adding water as needed to keep it moving.", "Add colorants.", "Blend", "If using as slip, keep it ... |
null | null | null | dx.doi.org/10.17504/protocols.io.jr3cm8n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The immunostaining detection of isolated lymphoid follicles (ILFs) was performed according to the method of McDonald and Newberry [BioTechniques. 2007; 43(1): 50-56], with some modifications. Instead of mounting the tissue samples on a mounting plate, each segment was treated... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.h99b996 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p style="text-align: justify;">Ancient DNA research has been revolutionized following the development of ‘Next Generation’ Sequencing platforms. Although a number of such platforms have been applied to ancient DNA samples, the Illumina series are the dominant choice today, main... | [] |
28,222 | Atherosclerotic Morphometry in Pigs | null | dx.doi.org/10.17504/protocols.io.7s6hnhe | null | Tim Nichols, Dave Clemmons | TITLE: Atherosclerotic Morphometry in Pigs
AUTHORS: Tim Nichols, Dave Clemmons
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span><span style = "font-weight:bold;"> </span></div><div class = "text-block">These assays are performed on all the pig models s... | ["En face abdominal aorta total area\nEn face abdominal aorta lesion area\nEn face abdominal aorta lesion percent\nThe abdominal aorta is opened longitudinally, immersion fixed with 10% buffered paraformaldehyde, and photographed for measuring the percent surface area with raised lesions when macroscopically present (s... |
44,771 | Salmonella spp. detection and isolation | 4 | dx.doi.org/10.17504/protocols.io.bpybmpsn | https://www.protocols.io/view/salmonella-spp-detection-and-isolation-bpybmpsn | Enrique Delgado | TITLE: Salmonella spp. detection and isolation
AUTHORS: Enrique Delgado
[STEPS]
?. [1.1 Pre-enrichment of surface water samples]
Close to a gas burner, open the plastic bag containing the modified Moore Swab (MMS) and aseptically take out the cheesecloth from inside the MMS.
?. [1.1 Pre-enrichment of surface water sa... | ["[1.1 Pre-enrichment of surface water samples]\nClose to a gas burner, open the plastic bag containing the modified Moore Swab (MMS) and aseptically take out the cheesecloth from inside the MMS.", "[1.1 Pre-enrichment of surface water samples]\nPlace the cheesecloth inside a 500-mL Whirl-pak bag, previously identified... |
98,521 | A Systematic Comparison of Protocols for Recovery of High-Quality RNA from Human Islets Extracted by Laser Capture Microdissection | 4 | dx.doi.org/10.17504/protocols.io.n2bvjx16xlk5/v2 | https://www.protocols.io/view/a-systematic-comparison-of-protocols-for-recovery-dcfz2tp6 | Chiara M. A. Cefalo, Teresa Mezza, Andrea Giaccari, Rohit N. Kulkarni | TITLE: A Systematic Comparison of Protocols for Recovery of High-Quality RNA from Human Islets Extracted by Laser Capture Microdissection
AUTHORS: Chiara M. A. Cefalo, Teresa Mezza, Andrea Giaccari, Rohit N. Kulkarni
[DESCRIPTION]
The isolation of high-quality RNA from endocrine pancreas sections represents a consider... | ["[Materials and Methods] To compare the efficiency of different RNA extraction protocols in frozen human islet samples, we used LCM to collect a mean of 100 islets from pancreatic surgical specimens, obtained from non-diabetic or diabetic patients who had undergone partial pancreatectomy for an extra-pancreatic tumor.... |
93,752 | Nuclei Isolation for HMBA FACS | 4 | dx.doi.org/10.17504/protocols.io.kxygx35ywg8j/v2 | https://www.protocols.io/view/nuclei-isolation-for-hmba-facs-c7syznfw | Lakme Caceres | TITLE: Nuclei Isolation for HMBA FACS
AUTHORS: Lakme Caceres
[DESCRIPTION]
This protocol is for purifying nuclei for downstream 10X sequencing.
[GUIDELINES]
Keep tissue/nuclei on ice as much as possible.
[STEPS]
SECTION: Prepare Fresh Solutions
4. Make 3 mL Homogenization Buffer by adding 2.892 mL Nuclear Isolation ... | ["[Prepare Fresh Solutions] Make 3 mL Homogenization Buffer by adding 2.892 mL Nuclear Isolation Media to a 5 mL eppendorf. Then add 60 uL protease inhibitor, 30 μL 10% Triton X-100, 15 uL RNase inhibitor, and 3 μL 100 mM DTT.", "[Prepare Stock Solutions] Make 50 mL Nuclear Isolation Media by filling a 100 mL bottle wi... |
22,921 | A simple, accurate, low cost method for starch quantification in green microalgae | null | dx.doi.org/10.17504/protocols.io.2mhgc36 | null | Tze Ching Yong, Chia-Sheng Chiu, Ching-Nen Nathan Chen | TITLE: A simple, accurate, low cost method for starch quantification in green microalgae
AUTHORS: Tze Ching Yong, Chia-Sheng Chiu, Ching-Nen Nathan Chen
[STEPS]
?. Harvest microalgal cells from 10 mL culture using swing bucket centrifugation (2600 g for 3 min).
?. Transfer the cells to a 2-mL screw cap microtube. Spi... | ["Harvest microalgal cells from 10 mL culture using swing bucket centrifugation (2600 g for 3 min).", "Transfer the cells to a 2-mL screw cap microtube. Spin briefly and get rid of the medium using a pippet. Freeze the cells immediately at -15 °C in an ice-crude sea salt mix.", "Add 1 mL methanol/tetrahydrofuran mix (... |
28,875 | Isolation of rodent eyes for analysis of diabetic retinopathy | null | dx.doi.org/10.17504/protocols.io.8fjhtkn | null | Timothy Kern | TITLE: Isolation of rodent eyes for analysis of diabetic retinopathy
AUTHORS: Timothy Kern
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">This protocol describes the procedure used by the DiaComp to isolate rodent eye... | ["What we want: Both eyes in formalin from at least 5 animals per experimental group. The longer the duration of diabetes, the better (C57BL/6 mice require at least 6 months diabetes before we can detect retinal microvascular lesions). Include also age-matched nondiabetic animals and diabetic controls for comparison.",... |
82,827 | Differentiation of RGC Induced Neurons (RGC-iNs) | 4 | null | https://www.protocols.click/view/differentiation-of-rgc-induced-neurons-rgc-ins-cu5jwy4n | Devansh Agarwal, Karl Wahlin | TITLE: Differentiation of RGC Induced Neurons (RGC-iNs)
AUTHORS: Devansh Agarwal, Karl Wahlin
[DESCRIPTION]
This protocol is designed to create induced retinal ganglion cells neurons (RGC-iNs) using a doxycycline-inducible polycistronic transcription factor cassette containing NEUROG2, ATOH7, ISL1, and POU4F2 and TetO... | ["[PSC expansion step] Grow iPSCs in hypoxia (5 % (v/v) O2/10 % (v/v) CO2) or normoxia (20 % (v/v) O2/5 % (v/v) CO2) at 37 °C.\n12-well plate (3.5 cm2): Plate 5,000 iPSCs into each well of 12 well plates in the presence of blebbistatin. Feed daily in mTeSR1 and grow for ~4 more days. Typically, we can get 200,00 – 500,... |
null | null | null | dx.doi.org/10.17504/protocols.io.g4dbys6 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
93,931 | Slot-blot analysis of recombinant α-synuclein fibrils | 4 | dx.doi.org/10.17504/protocols.io.q26g7pkrkgwz/v1 | https://www.protocols.io/view/slot-blot-analysis-of-recombinant-synuclein-fibril-c7yjzpun | Arpine Sokratian | TITLE: Slot-blot analysis of recombinant α-synuclein fibrils
AUTHORS: Arpine Sokratian
[DESCRIPTION]
This protocol aims to provide an accurate analysis of aggregated species of α-synuclein. The method involves the immunoblotting of protein samples via low vacuum-induced filtration, followed by the blocking of the memb... | ["[Sample preparation] Dilute samples to the final concentration of fibrils - 1 ug/mL.", "[Bio-dot slot format microfiltration apparatut assembly] Clean and dry the Bio-Dot apparatus and gasket prior to assembly", "[Immunnoblotting] Place the membrane into the rack with 20 mL of TBS with 5% non-fat milk \nBlock for ... |
44,534 | CuPCR SARS-Cov-2 | 1 | dx.doi.org/10.17504/protocols.io.bpqwmmxe | https://www.protocols.io/view/cupcr-sars-cov-2-bpqwmmxe | B Ronacher, Christoph Reschreiter | TITLE: CuPCR SARS-Cov-2
AUTHORS: B Ronacher, Christoph Reschreiter
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">RNA based diagnostic test of different human samples (nasopharyngeal swabs, saliva) to detect SARS-Cov-2. The test requires RNA/DNA extraction and a follow-up RT-PCR (reverse transc... | ["[RT-PCR test]\nRNA / DNA extraction\n100µl eluation buffer (e.g. water) containing RNA / DNA from the sample", "[RT-PCR test]\nRT-PCR\nPrepare mastermix: 5µl of primer mix + 5µl of enzyme mix (per sample)Put mastermix and sample into PCR tube:10µl of mastermix + 10µl of sample (eluate)Select (or program) RT-PCR proto... |
null | null | null | dx.doi.org/10.17504/protocols.io.vnee5be | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
MALDI-TOF MS specimen preparation for rapid identification of Australian mosquitoes
[GUIDELINES]
<p>There are 3 main steps involved with preparing and launching a mosquito sample for MALDI-TOF analysis:</p>
<ul>
<li>Preparing the matrix</li>
</ul>
<p>The matrix solution ionises... | ["[Preparing the matrix] {\"blocks\":[{\"key\":\"a9ti\",\"text\":\"Using a small spatula, put approx. in the Eppendorf tube and return the stock powder to the fridge immediately.\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[{\"offset\":35,\"length\":1,\"key\":0}],\"data\":[]},{\"key\... |
72,528 | Conflict of interest and funding in health communication on social media: a systematic review | 1 | dx.doi.org/10.17504/protocols.io.5jyl8jj4rg2w/v1 | https://www.protocols.io/view/conflict-of-interest-and-funding-in-health-communi-ci3qugmw | Vanessa Helou, Fatima Mouzahem, Hussein A. Noureldine, Adham Makarem, Rayane Al Khoury, Dana Al Oweini, Razan Halak, Layal Hneiny, Joanne Khabsa, Elie A Akl | TITLE: Conflict of interest and funding in health communication on social media: a systematic review
AUTHORS: Vanessa Helou, Fatima Mouzahem, Hussein A. Noureldine, Adham Makarem, Rayane Al Khoury, Dana Al Oweini, Razan Halak, Layal Hneiny, Joanne Khabsa, Elie A Akl
[DESCRIPTION]
Objective: To synthesize the availabl... | ["[Title: Conflict of interest and funding in health communication on social media: a systematic review] Authors’ List: \nVanessa Helou\nFatima Mouzahem\nHussein Noureldine\nAdham Makarem \nJoanne Khabsa \nLayal Hneiny \nRayane Al Khoury \nDana Al Oweini \nRazan Hala \nElie A. Akl\n\nCorresponding author: \nElie A. Akl... |
27,337 | “O-map/way method-site”: A sampling method for complete plant site inventories in large forests in the moderate/colline zone using orienteering maps or maps of similar quality | null | dx.doi.org/10.17504/protocols.io.6xhhfj6 | null | André Strauss | TITLE: “O-map/way method-site”: A sampling method for complete plant site inventories in large forests in the moderate/colline zone using orienteering maps or maps of similar quality
AUTHORS: André Strauss
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">“O-map/way m... | ["Making 3 complete inspection rounds in the season, when the given plant species can be best recognized, in the same year, ideally carried out by different persons, in the forest target area using an orienteering map or a map of similar quality (in paper or in an electronic device; ideally at a scale of 1: 5 000) with... |
58,069 | HyDrop-ATAC v1.0 | 1 | dx.doi.org/10.17504/protocols.io.b4xvqxn6 | https://www.protocols.io/view/hydrop-atac-v1-0-b4xvqxn6 | Florian De Rop, Suresh Poovathingal, Stein Aerts | TITLE: HyDrop-ATAC v1.0
AUTHORS: Florian De Rop, Suresh Poovathingal, Stein Aerts
[DESCRIPTION]
Step-by-step protocol for execution of HyDrop-ATAC.
[STEPS]
SECTION: Preparation Stage
1. User manual sheet
The sheet below should streamline your execution of the protocol. It contains adaptive tables for all buffers a... | ["[Preparation Stage] User manual sheet\nThe sheet below should streamline your execution of the protocol. It contains adaptive tables for all buffers and mixes. The tables will change depending on the parameters you enter at the start of the sheet, such as number of cells and total volume of emulsion you want to make.... |
null | null | null | dx.doi.org/10.17504/protocols.io.fcdbis6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Purpose:</strong> To evaluate the influence of nutrient availability on cellular elemental composition (quotas and stoichiometry) in marine picoeukaryotes.</p>
<p><strong>Summary:</strong> Elemental quotas and ratios are assessed under nutrient replete and deplete con... | [] |
99,521 | Native Nanobleach of native nanodiscs | 0 | dx.doi.org/10.17504/protocols.io.ewov19nbklr2/v1 | https://www.protocols.io/view/native-nanobleach-of-native-nanodiscs-dde923h6 | Caroline Brown, Gerard Walker, Snehasish Ghosh, Kallol Gupta, Moitrayee Bhattacharyya | TITLE: Native Nanobleach of native nanodiscs
AUTHORS: Caroline Brown, Gerard Walker, Snehasish Ghosh, Kallol Gupta, Moitrayee Bhattacharyya
[DESCRIPTION]
This is a protocol to conduct Native Nanobleach of native nanodiscs.
[STEPS]
1. Note, this method is adapted from Walker, Brown, et al. (DOI: 10.1038/s41565-023-015... | ["Note, this method is adapted from Walker, Brown, et al. (DOI: 10.1038/s41565-023-01547-4)", "Prepare flow chamber by treating with poly-L-lysine (PLL) PEG and PEG-biotin.", "Add streptavidin to flow chamber.", "Add biotinylated GFP-nanobody to flow chamber.", "Add native nanodiscs to the flow chamber for immobilizati... |
104,114 | T cell purification and activation | 0 | dx.doi.org/10.17504/protocols.io.81wgbz431gpk/v2 | https://www.protocols.io/view/t-cell-purification-and-activation-dhws37ee | Moustafa Nouh Elemeery, Salix Boulet, louis-eric.trudeau, Nathalie Labrecque | TITLE: T cell purification and activation
AUTHORS: Moustafa Nouh Elemeery, Salix Boulet, louis-eric.trudeau, Nathalie Labrecque
[DESCRIPTION]
This protocol details the purification and activation of Mouse Naïve CD8+ T Cell using an isolation kit from STEMCELL. This kit is designed to isolate naïve CD62L+CD44-CD8+ T ce... | ["[Purification and activation] Dilute CD3 antibody (145-2C11) (clone KT3 can also be used) to 1 1621 in PBS.", "[Purification and activation] Coat plates with anti-CD3 antibody.", "[Purification and activation] Use 24 or 96 wells flat bottom suspension plates. If these plates are not used, there is a risk of partial s... |
40,443 | How to Design a Primer | 1 | dx.doi.org/10.17504/protocols.io.bjq3kmyn | https://www.protocols.io/view/how-to-design-a-primer-bjq3kmyn | Addgene The Nonprofit Plasmid Repository | TITLE: How to Design a Primer
AUTHORS: Addgene The Nonprofit Plasmid Repository
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes how to design a primer. To see the full abstract and additional resources, visit </span><a href="https://www.addgene.org/protocols/primer-desi... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.jekcjcw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol aims to assess:</p>
<p>- the interaction between two proteins harboring two parts of the gaussia luciferase (Glu1 and Glu2)</p>
<p>- in presence of a third protein co-expressed</p>
<p>- in presence of a rabies virus</p>
[STEPS]
?.
?.
?.
?.
?. | [] |
90,002 | The culture-independent Bcc NAD method for the rapid detection and quantification of Bcc in water | 4 | dx.doi.org/10.17504/protocols.io.rm7vzxox8gx1/v1 | https://www.protocols.io/view/the-culture-independent-bcc-nad-method-for-the-rap-c35syq6e | Huong Thu Duong, Shannon Fullbrook, Kate Reddington, Elizabeth Minogue, Thomas Barry | TITLE: The culture-independent Bcc NAD method for the rapid detection and quantification of Bcc in water
AUTHORS: Huong Thu Duong, Shannon Fullbrook, Kate Reddington, Elizabeth Minogue, Thomas Barry
[DESCRIPTION]
Here we present a rapid (<4 hours from sample in to result out) culture-independent Bcc NAD method, incor... | ["[WATER FILTRATION] Water preparation:\nWater is collected in a sterile container containing sterile 0.1% v/v sodium thiosulfate pentahydrate solution to inactivate any residual disinfectant chlorine (if needed) and immediately used for experimental analysis upon arrival in the laboratory (within approximately 2 hours... |
null | null | null | dx.doi.org/10.17504/protocols.io.j66crhe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Introduction: This study was conducted to describe the repeat multiparametric MRI (mpMRI)<br />changes occurring in prostate cancer (PCa) patients during active surveillance (AS), and to study<br />possible associations between mpMRI-related parameters in predicting prostate ... | [] |
84,620 | Chromosomal DNA extraction from Gram-positive bacteria, V3 | 4 | dx.doi.org/10.17504/protocols.io.5jyl85119l2w/v3 | https://www.protocols.click/view/chromosomal-dna-extraction-from-gram-positive-bact-cwvkxe4w | Anders Kiledal, Julia A Maresca | TITLE: Chromosomal DNA extraction from Gram-positive bacteria, V3
AUTHORS: Anders Kiledal, Julia A Maresca
[DESCRIPTION]
Extraction of high-molecular-weight DNA from Gram-positive bacterial species, with optional steps for removing surfactants. This DNA is suitable for sequencing and the protocol can be scaled up at l... | ["[Grow culture] Inoculate 10 mL rich medium from a fresh overnight culture, and incubate at appropriate temperature on shaker. At OD600 of ~0.8-1.0, harvest cells by centrifugation (10 min., 5000 rpm).", "[Cell lysis] Resuspend cell pellet in 2 mL TEN (10 mM Tris-HCl, pH 8.0, 10 mM EDTA, 150 mM NaCl).", "[Cell lysis] ... |
73,253 | CRISPR-Cas9 screen in NIH-3T3 cells to identify modulators of LRRK2 function | 4 | dx.doi.org/10.17504/protocols.io.8epv5jr9jl1b/v1 | https://www.protocols.io/view/crispr-cas9-screen-in-nih-3t3-cells-to-identify-mo-cjsduna6 | Herschel Dhekne, Ebsy Jaimon, Wondwossen Yeshaw, Suzanne R Pfeffer | TITLE: CRISPR-Cas9 screen in NIH-3T3 cells to identify modulators of LRRK2 function
AUTHORS: Herschel Dhekne, Ebsy Jaimon, Wondwossen Yeshaw, Suzanne R Pfeffer
[DESCRIPTION]
Activating mutations in the LRRK2 gene represent the most common cause of inherited Parkinson’s disease, and modifiers of LRRK2 kinase activity a... | ["[CRISPR-Cas9 screen in NIH-3T3 cells to identify modulators of LRRK2 function] See our related protocol entitled, Creating pooled CRISPR-Cas9 knock-outs in NIH-3T3 cells \n(dx.doi.org/10.17504/protocols.io.eq2ly7wpmlx9/v1)", "[CRISPR-Cas9 screen in NIH-3T3 cells to identify modulators of LRRK2 function] Large scale p... |
null | null | null | dx.doi.org/10.17504/protocols.io.ebnbame | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Quick crude protein extraction from budding or fission yeast.
[BEFORE_START]
Cool NaOH on ice before use.
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
84,518 | Quantitative multi-target amplicon sequencing workflow | 4 | dx.doi.org/10.17504/protocols.io.36wgq351ylk5/v1 | https://www.protocols.io/view/quantitative-multi-target-amplicon-sequencing-work-cwsexebe | Mateusz Buczek, Monika Prus-Frankowska, Piotr Łukasik | TITLE: Quantitative multi-target amplicon sequencing workflow
AUTHORS: Mateusz Buczek, Monika Prus-Frankowska, Piotr Łukasik
[DESCRIPTION]
High-throughput sequencing of marker gene amplicons is a powerful tool for the discovery of biodiversity, at different levels. However, the method has multiple caveats.
Here, we d... | ["[A. DNA extraction] Sample homogenization\n\nMaterial: \n • Lysis buffer „Vesterinen” [0.4M NaCl, 10mM Tris-HCl, 2mM EDTA, 2% SDS] – before use, place\nin a container with warm water to help dissolve any precipitate\n • Proteinase K (stored frozen at -20oC) \n • Ceramic beads: 2,8mm and 0,5mm \n • 2 ml screw-cap tube... |
101,944 | Human Ganglia and Spinal Cord Tissue Procurement from Organ Donors and Tissue Quality Assessment | 0 | dx.doi.org/10.17504/protocols.io.kqdg32qr1v25/v1 | https://www.protocols.io/view/human-ganglia-and-spinal-cord-tissue-procurement-f-dfsy3nfw | Stephanie Shiers, Muhammad Saad Yousuf, Juliet Mwirigi, Anna Cervantes, Theodore Price | TITLE: Human Ganglia and Spinal Cord Tissue Procurement from Organ Donors and Tissue Quality Assessment
AUTHORS: Stephanie Shiers, Muhammad Saad Yousuf, Juliet Mwirigi, Anna Cervantes, Theodore Price
[DESCRIPTION]
Purpose
Describe the human nervous tissue removal, preservation, storage, and transportation procedures d... | ["[HSG Recovery Notification] OPO staff notifies the UTD Recovery Teams of a donor for HSG Study Enrollment via email and provides the following information:\n1) Donor ID\n2) Seros report\n3) Medication history\n4) Travel history\n5) COVID-19 test results\n6) Age\n7) Sex\n8) COD\n9) Tissue recovery site\n10) OR time\n1... |
62,866 | Standard Operating Procedure for animal baited tent traps to sample host-seeking mosquitoes | 1 | dx.doi.org/10.17504/protocols.io.36wgq7e4ovk5/v1 | https://www.protocols.io/view/standard-operating-procedure-for-animal-baited-ten-b9msr46e | Tanya L Russell, Kyran Staunton, Thomas Burkot | TITLE: Standard Operating Procedure for animal baited tent traps to sample host-seeking mosquitoes
AUTHORS: Tanya L Russell, Kyran Staunton, Thomas Burkot
[DESCRIPTION]
This Standard Operating Procedure (SOP) outlines the materials and processes required to deploy animal baited traps to collect host-seeking adult mos... | ["[Sampling procedure] Before setting up the animal-baited trap, the owner of each animal must be asked for permission to participate in the experiment. It is generally good to hire the animal’s owner to collect mosquitoes need the animal to avoid unnecessarily stressing the animal.", "[Sampling procedure] Erect the ou... |
39,168 | TAP agar plate preparation | 4 | null | https://www.protocols.io/view/tap-agar-plate-preparation-big8kbzw | Joao Vitor Molino | TITLE: TAP agar plate preparation
AUTHORS: Joao Vitor Molino
[STEPS]
?. Always follow aseptic techniquesAutoclavate freshly prepared TAP media with with a magnetic bar insideMix the flask using a magnetic stirrer to evenly dissolve the agar in the solutionFor antibiotic containing plates, cool down the flask tempera... | ["Always follow aseptic techniquesAutoclavate freshly prepared TAP media with with a magnetic bar insideMix the flask using a magnetic stirrer to evenly dissolve the agar in the solutionFor antibiotic containing plates, cool down the flask temperarute until - or until it is possible to hold it without hurting t... |
19,270 | Immunohistochemical analysis of ganglion neurons innervating the lower urinary tract [keast-001-stage03] | null | dx.doi.org/10.17504/protocols.io.w3efgje | null | Janet Keast, Peregrine Osborne | TITLE: Immunohistochemical analysis of ganglion neurons innervating the lower urinary tract [keast-001-stage03]
AUTHORS: Janet Keast, Peregrine Osborne
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used for studies of neurons containing retrograde tracer dye in adult rat dorsal ro... | ["[Preparation of cryosections]\nCryoprotect tissues in phosphate-buffered saline (PBS; 0.1 M, pH7.2) containing 30% sucrose. This should be performed at 4C, 24-72h prior to cutting.", "[Preparation of cryosections]\nEmbed tissues in cryomold using OCT, freeze in cryostat and cut sections (14 µm), distributing sections... |
95,263 | Consensus Sequence Generation Protocol: Leveraging Variant Analysis in Mulberry Genotypes | 5 | dx.doi.org/10.17504/protocols.io.n2bvj37dnlk5/v1 | https://www.protocols.io/view/consensus-sequence-generation-protocol-leveraging-c897zz9n | Vidya Niranjan, Lavanya C, Shri Ganapathi, Spoorthi R Kulkarni | TITLE: Consensus Sequence Generation Protocol: Leveraging Variant Analysis in Mulberry Genotypes
AUTHORS: Vidya Niranjan, Lavanya C, Shri Ganapathi, Spoorthi R Kulkarni
[DESCRIPTION]
This research investigates four distinct Mulberry genotypes, each offering valuable traits essential for sericulture and broader agricul... | ["[SAMPLE COLLECTION AND REFERENCE GENOME] Collection of the Whole genome sequences and the Reference genome for Morus Indica (Mulberry)\n\nThe high-depth sequencing of multiple mulberry accessions were sequenced via Illumina platform and the fastq files were retrieved from MindGP an Indian repository of Mulberry data.... |
91,012 | INJECTION MOLDING TECHNIQUE: CORRECTING THE DREADED "BLACK TRIANGLE". | 4 | dx.doi.org/10.17504/protocols.io.5qpvo35obv4o/v3 | https://www.protocols.io/view/injection-molding-technique-correcting-the-dreaded-c45cyy2w | Álvaro Ferrando Cascales DDS,PhD., Antonio Mendoza Rodriguez DDS,MSc., Rubén Agustín-Panadero DDS,MSc,PhD., José Amengual Lorenzo DDS,PhD., Salvatore Sauro PhD, Raúl Ferrando Cascales DDS,MSc,PhD., Ronaldo Hirata DDS,MSc,PhD., David Clark DDS,MSc. | TITLE: INJECTION MOLDING TECHNIQUE: CORRECTING THE DREADED "BLACK TRIANGLE".
AUTHORS: Álvaro Ferrando Cascales DDS,PhD., Antonio Mendoza Rodriguez DDS,MSc., Rubén Agustín-Panadero DDS,MSc,PhD., José Amengual Lorenzo DDS,PhD., Salvatore Sauro PhD, Raúl Ferrando Cascales DDS,MSc,PhD., Ronaldo Hirata DDS,MSc,PhD.,... | ["[Description of the technique] Pre-treatment analysis of the gingival embrasure area and selection of the corresponding bioclear black triangle (BT) matrix.", "[Description of the technique] Smoothing and relief of the interdental contact points.", "[Description of the technique] This second step consists of checking... |
null | null | null | dx.doi.org/10.17504/protocols.io.erzbd76 | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<strong>MATERIALS:</strong> <br /><br />1) 60-65°C heat block or water bath <br />2) Microfuge <br />3) 1.5 and 2.0 mL microfuge tubes (screw-cap) <br />4) 50 mM Tris-HCl, pH 7.5, 10 mM MgCl<sub>2</sub> <br />5) 10% NP-40 or Triton X-100 <br />6) DNAse I, 2.0 mg/mL in 50 mM Tris-... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.nxmdfk6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Loess (decayed limestone) topsoil based soil and water media concentrate for use with RO/DI water. NOT for use with treated tap or spring water! Intended for use in filamentous algae, volvox and euglenoid culture.</p>
[BEFORE_START]
<p>Collect 5 to 10kg of loess soil. Break ... | [] |
45,318 | 3.4 Genome Editing with CRISPR/Cas9 | 1 | dx.doi.org/10.17504/protocols.io.bqhemt3e | https://www.protocols.io/view/3-4-genome-editing-with-crispr-cas9-bqhemt3e | Evelyn J. Sauter, Lisa K. Kutsche, Simon D. Klapper, Volker Busskamp | TITLE: 3.4 Genome Editing with CRISPR/Cas9
AUTHORS: Evelyn J. Sauter, Lisa K. Kutsche, Simon D. Klapper, Volker Busskamp
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This is part 3.4 of the "</span><a href="https://www.protocols.io/private/C65DB81838BC11EBA61A0A58A9FEAC2A/protocols" style =... | ["[3.4 Genome Editing with CRISPR/Cas9]\nDesign a sgRNA for the locus of interest using designing tools (such as http://crispr.mit.edu/, see Note 23) [12].", "[3.4 Genome Editing with CRISPR/Cas9]\nOrder two oligos representing the sgRNA with a design as follows: top oligo—CACC(G)[20 N of sgRNA], bottom oligo—AAAC[20 N... |
28,013 | Recipe for standard BG-11 media | null | dx.doi.org/10.17504/protocols.io.7kmhku6 | null | Anna Behle | TITLE: Recipe for standard BG-11 media
AUTHORS: Anna Behle
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Stanier RY, Deruelles J, Rippka R, Herdman M, Waterbury JB: </span><span style = "font-weight:bold;">Generic Assignments, Strain Histories and Properties of Pure Cultures of Cyanobacteria... | ["[100 x BG11 stock:]\nCaCl2 2H2O (3.6 g · L-1)Citric acid (0.6 g · L-1)NaNO3 (149.58 g · L-1)MgSO4 · 7 H2O (7.49 g · L-1)0.25 M Na2-EDTA, pH 8.0 (0.56 ml · L-1) For 100x BG11 Stock -N: Omit NaNO3.For 100x BG11 Stock -N:", "[Supplemental stocks for standard media:]\n1000x Na2CO3: 20 mg mL-1100x TES-buffer, pH 8.0 (1M)... |
106,673 | Methods and instruments used in the literature to quantitatively analyze the acceptability of pharmaceutical interventions for the prevention and treatment of neglected tropical diseases: a systematic review | 0 | dx.doi.org/10.17504/protocols.io.j8nlk81k1l5r/v1 | https://www.protocols.io/view/methods-and-instruments-used-in-the-literature-to-dker4td6 | Claudia Duguay, Katarina Ost, Alison Krentel | TITLE: Methods and instruments used in the literature to quantitatively analyze the acceptability of pharmaceutical interventions for the prevention and treatment of neglected tropical diseases: a systematic review
AUTHORS: Claudia Duguay, Katarina Ost, Alison Krentel
[DESCRIPTION]
Acceptability is one of the four cor... | ["[Review question] How is the acceptability of pharmaceutical interventions for the prevention and treatment of neglected tropical diseases quantitatively measured and analyzed in the literature.", "[Searches] MEDLINE, Embase, SCOPUS, Global health, CINAHL", "[Condition or domain being studied] Acceptability is one of... |
29,677 | Improving pneumonia diagnoses using pulse oximetry at rural health institutions in southern Ethiopia: Protocol for a cluster-randomized controlled trial | null | dx.doi.org/10.17504/protocols.io.88mhzu6 | null | Solomon Hailemariam1, 2, 3*, Yabibal Gebeyehu4, Eskinder Loha1, 5, Kjell Arne Johansson2, Bernt Lindtjørn1, 2 | TITLE: Improving pneumonia diagnoses using pulse oximetry at rural health institutions in southern Ethiopia: Protocol for a cluster-randomized controlled trial
AUTHORS: Solomon Hailemariam1, 2, 3*, Yabibal Gebeyehu4, Eskinder Loha1, 5, Kjell Arne Johansson2, Bernt Lindtjørn1, 2
[DESCRIPTION]
<div class = "text-blocks"... | [] |
46,831 | Preparation of LRRK2 RCKW trimer cryo-EM grids | 4 | null | https://www.protocols.io/view/preparation-of-lrrk2-rckw-trimer-cryo-em-grids-brypm7vn | Mariusz Matyszewski | TITLE: Preparation of LRRK2 RCKW trimer cryo-EM grids
AUTHORS: Mariusz Matyszewski
[DESCRIPTION]
This protocol has been adapted from Deniston et al (https://doi.org/10.1038/s41586-020-2673-2)
Original protocol by Colin Deniston. Adapted to protocol.io by Mariusz Matyszewski.
This protocol describes how to create cry... | ["[Preparing Sample] Dialyze purified LRRK2 RCKW into the final LRRK2 buffer (see Materials)", "[Preparing Sample] Dilute the protein to the desired final concentration.", "[Freezing Grids] Glow discharge grids.\nWe used UltrAuFoil Holey Gold 1.2/1.3 300 mesh grids and glow discharged them at 20 mA for 20 s in a K100 i... |
90,983 | An NGS amplicon tiling protocol for HIV-1 drug resistance detection using Illumina® COVIDSeq™ Assay Kit. | 4 | dx.doi.org/10.17504/protocols.io.n92ldmq4ol5b/v1 | https://www.protocols.io/view/an-ngs-amplicon-tiling-protocol-for-hiv-1-drug-res-c44fyytn | Noah C. Hull, Eugene Yeboah, laura.j.tsaknaridis, Vanda Makris | TITLE: An NGS amplicon tiling protocol for HIV-1 drug resistance detection using Illumina® COVIDSeq™ Assay Kit.
AUTHORS: Noah C. Hull, Eugene Yeboah, laura.j.tsaknaridis, Vanda Makris
[DESCRIPTION]
Summary
Human immunodeficiency virus (HIV) is the pathogen responsible for acquired immunodeficiency syndrome (AIDS) an... | ["Sample Extraction\n\nHIV-1 subtype B positive culture\ncontrol ZeptoMetrix (Part #v0801032CF), was extracted via the Qiagen Advanced XL DSP kit on the EZ1 extractor and serially diluted to the following concentration: 10ᶺ(-1), 10ᶺ(-2), 10ᶺ(-3), 10ᶺ(-4), 10ᶺ(-5), and 10ᶺ(-6), Undiluted control (1.74*10^10 IU/mL or 2.0... |
81,589 | Imaging cleared mouse brains on SmartSPIM | 1 | dx.doi.org/10.17504/protocols.io.3byl4jo1rlo5/v1 | https://www.protocols.io/view/imaging-cleared-mouse-brains-on-smartspim-ctwvwpe6 | John Rohde | TITLE: Imaging cleared mouse brains on SmartSPIM
AUTHORS: John Rohde
[DESCRIPTION]
The SmartSPIM is an axially swept lightsheet microscope that produces uniform axial resolution across the entire imaging volume of large biological samples, such as whole mouse brains. Acquiring these datasets requires well prepared sam... | ["[Mounting Samples:] Mounting agarose-embedded and unembedded brain samples. A small drop of super glue is sufficient to hold a brain for >24 hrs when submerged in the imaging bath (see figure (a) below). Placing the glue along one edge makes it easier to remove the brain after imaging.", "[Configuring the microscope ... |
82,115 | 10x Genomics Multiome ATAC+GEX | 1 | dx.doi.org/10.17504/protocols.io.n2bvj8kqpgk5/v1 | https://www.protocols.io/view/10x-genomics-multiome-atac-gex-cufbwtin | Andrew Houston | TITLE: 10x Genomics Multiome ATAC+GEX
AUTHORS: Andrew Houston
[DESCRIPTION]
Link to 10x Genomics Multiome protocol to assess chromatin accessibility and gene expression from a dissociated sample
[STEPS]
1. Protocol can be found here:
https://cdn.10xgenomics.com/image/upload/v1666737555/support-documents/CG000338_Chr... | ["Protocol can be found here:\nhttps://cdn.10xgenomics.com/image/upload/v1666737555/support-documents/CG000338_ChromiumNextGEM_Multiome_ATAC_GEX_User_Guide_RevF.pdf\n\nTransposition through cDNA pgs. 28-57\nATAC library construction pgs. 49-52\nGEX library construction pgs. 59-67"] |
83,917 | siRNA-mediated knockdown of TFE3 | 4 | dx.doi.org/10.17504/protocols.io.3byl4q26rvo5/v1 | https://www.protocols.click/view/sirna-mediated-knockdown-of-tfe3-cv7mw9k6 | Narayana Yadavalli, Shawn M. Ferguson | TITLE: siRNA-mediated knockdown of TFE3
AUTHORS: Narayana Yadavalli, Shawn M. Ferguson
[DESCRIPTION]
This protocol details siRNA-mediated knockdown of TFE3.
[STEPS]
SECTION: siRNA-mediated knockdown of TFE3
1. On the day before transfection, plate 100,000 cells per well in a 6 well dish.
SECTION: siRNA-mediated knock... | ["[siRNA-mediated knockdown of TFE3] On the day before transfection, plate 100,000 cells per well in a 6 well dish.", "[siRNA-mediated knockdown of TFE3] Change media 60 min before transfection (2 mL with no antibiotics).", "[siRNA-mediated knockdown of TFE3] The next day, assemble the siRNA transfection reaction by co... |
null | null | null | dx.doi.org/10.17504/protocols.io.jz4cp8w | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
44,016 | Differentiation of hPSCs to hypothalamic neurons | 1 | dx.doi.org/10.17504/protocols.io.bn8qmhvw | https://www.protocols.io/view/differentiation-of-hpscs-to-hypothalamic-neurons-bn8qmhvw | Cortina Chen, Iman Mali, Florian T Merkle | TITLE: Differentiation of hPSCs to hypothalamic neurons
AUTHORS: Cortina Chen, Iman Mali, Florian T Merkle
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is about Differentiation of hPSCs to hypothalamic neurons.</div></div>
[STEPS]
?. [Thawing of human pluripotent stem cell (hPSC) l... | ["[Thawing of human pluripotent stem cell (hPSC) lines:]\nThaw an aliquot of 1:10 diluted Geltrex or in the fridge.\non ice", "[Thawing of human pluripotent stem cell (hPSC) lines:]\nAspirate Geltrex and rinse the dish/plate 1x with an equal volume of DPBS.\nNote: do not let the dish/plate dry out.", "[Thawing of huma... |
63,898 | martha maccallum cbd gummies | 3 | dx.doi.org/10.17504/protocols.io.rm7vzy245lx1/v1 | https://www.protocols.io/view/martha-maccallum-cbd-gummies-cam2sc8e | EricRaiey | TITLE: martha maccallum cbd gummies
AUTHORS: EricRaiey
[DESCRIPTION]
<!--td {border: 1px solid #ccc;}br {mso-data-placement:same-cell;}-->martha maccallum cbd gummies Is 100% Clinically Tested Its Beneficial Gummy Reduces Pain!
[STEPS] | [] |
27,130 | Depending on Proteomics, Precision Medicine is Coming | null | dx.doi.org/10.17504/protocols.io.6q2hdye | null | susan wind | TITLE: Depending on Proteomics, Precision Medicine is Coming
AUTHORS: susan wind
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">On the last day of February 2019, the British "Nature" magazine published a Chinese scholar's paper "Molecular typing of e... | [] |
94,368 | SOP88v1_TGD_Lentivirus transduction in EndoC-bH1 | 4 | null | https://www.protocols.io/view/sop88v1-tgd-lentivirus-transduction-in-endoc-bh1-c8d8zs9w | Yunkyeong Lee | TITLE: SOP88v1_TGD_Lentivirus transduction in EndoC-bH1
AUTHORS: Yunkyeong Lee
[DESCRIPTION]
For lentivirus transduction in EndoC-bH1 cells
[STEPS]
1. After generating lentivirus (Virus core facility), keep them at -80C.
2. Seed 4x10^6 cells in T25 flask or 7x10^6 cells in T75 flask (EndoC-bH1 cells).
3. The next d... | ["After generating lentivirus (Virus core facility), keep them at -80C.", "Seed 4x10^6 cells in T25 flask or 7x10^6 cells in T75 flask (EndoC-bH1 cells).", "The next day, calculate MOI and left the appropriate amount of lentivirus (MOI must be tested to ensure appropriate before transduction) on the cells for 8 days.",... |
null | null | null | dx.doi.org/10.17504/protocols.io.jsecnbe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><span style="font-weight: 400;">This protocol describes the procedure to obtain single bacterial colonies composed of multiple sectors of different strains. Each sector is originated from different founder cells (situated in close proximity to each other at the moment of plat... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.fpfbmjn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div style="left: 279.287px; top: 275.557px; font-size: 15.4212px; font-family: serif; transform: scaleX(1.02067); text-align: left;" data-canvas-width="54.1293365688">This protocol is designed to allow you to clean large numbers of 15 mL vials to the highest standards of cleanl... | [] |
45,943 | Chemically competent cells transformation | 4 | null | https://www.protocols.io/view/chemically-competent-cells-transformation-bq4xmyxn | Elizabeth Fozo | TITLE: Chemically competent cells transformation
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Chemically competent cells transformation protocol</div></div>
[STEPS]
?. [Preparation for competent cells]
Inoculate a single colony into 5 mL appropriate media containing appro... | ["[Preparation for competent cells]\nInoculate a single colony into 5 mL appropriate media containing appropriate antibiotics", "[Preparation for competent cells]\nIncubate overnight using appropriate temperature and shaking conditions", "[Preparation for competent cells]\nDilute overnight culture to an optical density... |
null | null | null | dx.doi.org/10.17504/protocols.io.e24bggw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Cell Fixation and Permeabilization Protocol Using 70% Ethanol</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?. | [] |
37,200 | Acropora DNA extraction with Qiagen DNeasy tissue kit | null | null | https://www.protocols.io/view/acropora-dna-extraction-with-qiagen-dneasy-tissue-bgjqjumw | Iliana Baums, Sheila Kitchen | TITLE: Acropora DNA extraction with Qiagen DNeasy tissue kit
AUTHORS: Iliana Baums, Sheila Kitchen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>DNA extraction protocol for Acropora or other coral tissue based on Qiagen DNAeasy kit. This extraction protocol works well for the Acropora SNPchi... | ["[Sample preparation]\nUse sterile technique to cut 3-4 polyps (skeleton with tissue) off the coral fragment with a razor blade.", "[Sample preparation]\nTransfer the pieces to a 1.5 ml tube/96-well plate.", "[Sample preparation]\nAdd 180 ul of Buffer ATL and 20 ul of proteinase K (from Qiagen kit) to each tube/well."... |
83,949 | Analysis of ER Flux in Cultured Induced Neurons using Keima ER reporters | 4 | null | https://www.protocols.click/view/analysis-of-er-flux-in-cultured-induced-neurons-us-cv8mw9u6 | Melissa Hoyer, Harper JW, Vinay Eapen | TITLE: Analysis of ER Flux in Cultured Induced Neurons using Keima ER reporters
AUTHORS: Melissa Hoyer, Harper JW, Vinay Eapen
[DESCRIPTION]
The endoplasmic reticulum (ER) has a vast proteomic landscape to preform many diverse functions including protein and lipid synthesis, calcium ion flux, and inter-organelle commu... | ["[Electroporation of PB vectors. Use ThermoFisher kit and ThermoFisher Neon Electroporator to electroporate ES cells with PB vector and PB helper vector.] Add 10ml buffer R to a sterile 1.5ml tube. Add 0.5µg of pAC150 ER Keima vector and 0.5µg of pCMV-hyPBase hyperactive piggyBac vector. Pipet up and down to mix. Let ... |
null | null | null | dx.doi.org/10.17504/protocols.io.ruud6ww | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Mitochondrial viability is determined through 2,3,5-triphenyltetrazolium chloride (TTC) conversion to insoluble formazan. TTC reduction depends on the mitochondrial respiratory activity and is proportional to the number of viable cells.</p>
[STEPS]
?. | [] |
51,291 | SCoPE2 | 1 | dx.doi.org/10.17504/protocols.io.bwb3paqn | https://www.protocols.io/view/scope2-bwb3paqn | Harrison Specht, Edward Emmott, Aleksandra A. Petelski, R. Gray Huffman, David H. Perlman, Antonius Koller, Nikolai Slavov | TITLE: SCoPE2
AUTHORS: Harrison Specht, Edward Emmott, Aleksandra A. Petelski, R. Gray Huffman, David H. Perlman, Antonius Koller, Nikolai Slavov
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Protocol for preparing single cells for mass-spec analysis by SCoPE2 as described by Specht et al., ... | ["[Prepare 384-well plate(s) for sorting single cells]\nAdd 1uL of 25 fmol/uL Waters MassPrep (dissolved in HPLC-grade water) to each well of a 384-well thermalcycler plate (ThermoFisher AB1384).", "Seal plate with adhesive foil (Thermo Fisher Scientific; cat. no: AB0626)", "[Cell sorting]\nCRITICAL: Ensure that cell s... |
null | null | null | dx.doi.org/10.17504/protocols.io.hnwb5fe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is a standard polymerase chain reaction, optimized to amplify a () bp gene flanked by two loxP sites. (?)</p>
<p> </p>
<p>Refer to page 32, April 5, 2017 entry in Miguel's laboratory notebook for the original document.</p>
<p> </p>
[STEPS]
?.
?.
?. | [] |
19,145 | IP Glucose Tolerance Test in Mouse | null | dx.doi.org/10.17504/protocols.io.wxhffj6 | https://www.protocols.io/view/ip-glucose-tolerance-test-in-mouse-wxhffj6 | Nancy Smith, Mourad Ferdaoussi, Haopeng Lin, Patrick Macdonald | TITLE: IP Glucose Tolerance Test in Mouse
AUTHORS: Nancy Smith, Mourad Ferdaoussi, Haopeng Lin, Patrick Macdonald
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details the IP glucose tolerance test in mice. This is performed on C57Bl6, transgenic SENP1 KO and ZMIZ1 KO mouse models. ... | ["[Fasting]\nFasting begins first thing in the morning (around 9am). Fast mice for 4-6 hours before IPGTT begins. Transfer mice to clean cage and wire top. Keep water bottles in cages during the fasting period.\nIf using High Fat diet (HFD), save food to give back at the end of the IPGTT.Mark tails with a sharpie fo... |
18,885 | ITS and LSU nrDNA analyses | null | dx.doi.org/10.17504/protocols.io.wpdfdi6 | null | Maria P Martin, Thiago Accioly, Julieth O. Sousa, Melanie Roy , Monique Gardes, Iuri G. Baseia | TITLE: ITS and LSU nrDNA analyses
AUTHORS: Maria P Martin, Thiago Accioly, Julieth O. Sousa, Melanie Roy , Monique Gardes, Iuri G. Baseia
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">After DNA extraction, the ITS regions were amplified and sequenced using the primer pair ITS1F/ITS4. Part of the L... | [] |
47,741 | LC-MS/MS Label-Free Proteomic Data Analysis Parameters | 1 | dx.doi.org/10.17504/protocols.io.bsu5ney6 | https://www.protocols.io/view/lc-ms-ms-label-free-proteomic-data-analysis-parame-bsu5ney6 | Danielle Gutierrez, Jamie Allen, Zach Jenkins, Jeff Spraggins | TITLE: LC-MS/MS Label-Free Proteomic Data Analysis Parameters
AUTHORS: Danielle Gutierrez, Jamie Allen, Zach Jenkins, Jeff Spraggins
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">List of parameters and settings for searching label free proteomic data in MaxQuant version 1.6.17.</div></div>
[STEPS... | ["Label-free proteomic samples were searched using MaxQuant version 1.6.17.", "Group Specific Parameter settings included: StandardMultiplicity = 1Variable modifications: Oxidation (M); Acetylation (Protein N-term), Carbamidomethyl (C)Fixed modifications: Carbamidomethyl (C)Max number of modifications per peptide: 5Ins... |
62,298 | Monitoring of Citrobacter rodentium shed from infected mice using luminometry and viable counts | 4 | dx.doi.org/10.17504/protocols.io.rm7vzyo3rlx1/v1 | https://www.protocols.io/view/monitoring-of-citrobacter-rodentium-shed-from-infe-b832ryqe | Hannah Read, Priyali Patel, Siouxsie Wiles | TITLE: Monitoring of Citrobacter rodentium shed from infected mice using luminometry and viable counts
AUTHORS: Hannah Read, Priyali Patel, Siouxsie Wiles
[DESCRIPTION]
Citrobacter rodentium is a Gram-negative bacterium which infects laboratory mice in a similar way to how enteropathogenic Escherichia coli (EPEC) and ... | ["[Stool collection] Place each mouse in a clean pipette tip box which has had the insert removed.", "[Stool collection] Once a mouse has produced 1-3 individual stools, transfer these to a sterile labelled microfuge tube of known weight using a pair of clean tweezers. \n\nDepending on the mouse strain, stools can beco... |
84,147 | SDS-PAGE and western blot analysis | 4 | dx.doi.org/10.17504/protocols.io.eq2lyj33plx9/v1 | https://www.protocols.io/view/sds-page-and-western-blot-analysis-cwetxben | Elias Adriaenssens | TITLE: SDS-PAGE and western blot analysis
AUTHORS: Elias Adriaenssens
[DESCRIPTION]
This protocol describes SDS-PAGE and western blot analysis.
[STEPS]
SECTION: SDS-PAGE and western blot analysis
1. For SDS-PAGE and western blot analysis, collect cells by trypsinization and subsequent centrifugation at 300 x g, 5 min... | ["[SDS-PAGE and western blot analysis] For SDS-PAGE and western blot analysis, collect cells by trypsinization and subsequent centrifugation at 300 x g, 5 min, 4 °C.", "[SDS-PAGE and western blot analysis] Wash the cell pellets in PBS and centrifuge once more at 300 x g, 5 min, 4 °C.", "[SDS-PAGE and western blot analy... |
37,910 | Thermolabile Proteinase K Typical Reaction Protocol | 1 | dx.doi.org/10.17504/protocols.io.bg9wjz7e | https://www.protocols.io/view/thermolabile-proteinase-k-typical-reaction-protoco-bg9wjz7e | New England Biolabs | TITLE: Thermolabile Proteinase K Typical Reaction Protocol
AUTHORS: New England Biolabs
[DESCRIPTION]
Thermolabile Proteinase K is an engineered, subtilisin-related serine protease that will hydrolyze a variety of peptide bonds and is frequently used to cleanup enzymatic reactions or cell lysates.
Heat inactivated ... | ["Reactions may be scaled-up linearly to accommodate larger amounts of substrate and larger reaction volumes. Optimal buffering reagents, enzyme quantity, incubation temperatures and times may vary for particular substrates. Typical restriction enzyme cleanup conditions are as follows:\n\nTo a 50 µL containing 1 µg and... |
71,112 | Open-field blast (OFB) model in mice | 1 | dx.doi.org/10.17504/protocols.io.yxmvm2kwog3p/v1 | https://www.protocols.io/view/open-field-blast-ofb-model-in-mice-chpgt5jw | Catherine Johnson, Jiankun Cui, Amitai Zuckerman, Hailong Song, Graham K. Hubler, Ralph G. DePalma, Ibolja Cernak, Zezong Gu | TITLE: Open-field blast (OFB) model in mice
AUTHORS: Catherine Johnson, Jiankun Cui, Amitai Zuckerman, Hailong Song, Graham K. Hubler, Ralph G. DePalma, Ibolja Cernak, Zezong Gu
[DESCRIPTION]
This is a protocol to describe the materials and methods utilized by the submitter to perform preclinical traumatic brain injur... | ["[Open-Field Blast Setup] The open-field blast experimental site is located within the well-equipped Energetics Research Facility at Missouri University of Science & Technology, on the University Experimental Mine in Rolla.", "[Open-Field Blast Setup] Set the blast conditions for calculated peak overpressure using a b... |
12,870 | Inoculating and harvesting fungal isolates on cellophane overlay | 1 | dx.doi.org/10.17504/protocols.io.qtedwje | https://www.protocols.io/view/inoculating-and-harvesting-fungal-isolates-on-cell-qtedwje | Jana U'Ren, Lilly Moore | TITLE: Inoculating and harvesting fungal isolates on cellophane overlay
AUTHORS: Jana U'Ren, Lilly Moore
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Some fungal isolates will embed into the solid media during growth, which makes it difficult to harvest agar-free mycelium for downstream applicat... | ["[Preparing Cellophane]\nWipe down bench top and scissors with RNase away solution.", "[Preparing Cellophane]\nCut cellophane into approximately 1 inch squares, taking care to measure squares to ensure they will fit in a 60mm Petri dish.", "[Preparing Cellophane]\nPlace ~75 pieces into a 250mL glass beaker.", "[Prepar... |
47,270 | Expression and purification protocol of PI3KC3-C1 complex | 4 | dx.doi.org/10.17504/protocols.io.bseenbbe | https://www.protocols.io/view/expression-and-purification-protocol-of-pi3kc3-c1-bseenbbe | Chunmei Chang | TITLE: Expression and purification protocol of PI3KC3-C1 complex
AUTHORS: Chunmei Chang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines the procedure for expression and purification of the PI3KC3-C1 complex.</div></div>
[STEPS]
?. [Plasmid amplification]
Amplify the plasmid.
... | ["[Plasmid amplification]\nAmplify the plasmid.\nconstructs: pCAG-VPS15, pCAG-TSF-VPS34, pCAG-TSF-BECN1, pCAG-GST-TEVs- A TG14All of the constructs are Amp resistant and high copy, could be amplified in normal XL10 strain.", "[Transfection in HEK GnTI cells]\nGrow HEK293 GnTI suspension cells to 1.5-2 million cells/ml ... |
62,779 | Seawater eDNA extraction for Sterivex - rocky intertidal habitats | 1 | dx.doi.org/10.17504/protocols.io.q26g74dqkgwz/v1 | https://www.protocols.io/view/seawater-edna-extraction-for-sterivex-rocky-intert-b9i3r4gn | Mary McElroy | TITLE: Seawater eDNA extraction for Sterivex - rocky intertidal habitats
AUTHORS: Mary McElroy
[DESCRIPTION]
This protocol describes DNA extractions from filtered 1-L seawater samples from rocky intertidal habitats for environmental DNA (eDNA) metabarcoding. Optimized for samples collected from rocky intertidal monito... | ["[Sample preparation] SXTUBE\nTransfer the Longmire’s buffer from the Sterivex filter capsule and into a 2mL sterile LoBind tube using a 5 mL Luer-Lock syringe. Be careful not to apply too much pressure. The extractions from the buffers are hereafter referred to as SXTUBE. Spin at 6,000 ∗ g (8,000 rpm) for 30-45 min i... |
41,424 | Using the Tecan Infinite M200 Pro plate reader for Symbiodiniaceae Biomass/Growth Estimates | 1 | dx.doi.org/10.17504/protocols.io.bkpqkvmw | https://www.protocols.io/view/using-the-tecan-infinite-m200-pro-plate-reader-for-bkpqkvmw | Samantha Coy | TITLE: Using the Tecan Infinite M200 Pro plate reader for Symbiodiniaceae Biomass/Growth Estimates
AUTHORS: Samantha Coy
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a protocol for estimating Symbiodiniaceae biomass and growth based on fluorescence (chlorphyll-a). This is not directly com... | ["Turn the Tecan Infinite M200 Pro plate reader on. There is a switch on the back of the big plate reader box. You should see a green light turn on or electronic dialogue pop up, letting you know both components are on. **the box on top is a specialized option used for controlling gas for growth experiments done in the... |
59,658 | Plant assemble - Plant de novo genome assembly: assembly | 5 | dx.doi.org/10.17504/protocols.io.dm6gpbr1jlzp/v2 | https://www.protocols.io/view/plant-assemble-plant-de-novo-genome-assembly-assem-b6hirb4e | Scott Ferguson, Ashley Jones, Justin Borevitz | TITLE: Plant assemble - Plant de novo genome assembly: assembly
AUTHORS: Scott Ferguson, Ashley Jones, Justin Borevitz
[DESCRIPTION]
With the advancement of long-read sequencing technologies and associated bioinformatics tools, it has now become possible to de novo assemble complex plant genomes with unrivalled con... | ["[Data Input] De novo genome assembly works best if long-read sequencing has been performed. For best results, optimise a high-molecular weight DNA extraction, for example we use: High-molecular weight DNA extraction, clean-up and size selection for long-read sequencing (https://journals.plos.org/plosone/article?id=10... |
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