eamag/protocols-with-steps huggingface dataset:
TITLE: 2009 Deep Soil Core Protocol
AUTHORS: Test McTester

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Describes the method of analyzing Deep Soil Cores</div></div>

[STEPS]
?. Mark cores at top of soil with marker around outside of cylinder, keeping the cores upright not to allow the soil to slide up the tube. Measure the overall length of the sample (cm) and enter on data sheet.
?. Place piece of tape on side of template and mark segment sizes on it, Lay tube in PVC template and cut tube in half length wise, , then cut sample into segmented lengths with a spatula 0-5, 5-30, 30-60, 60-70, 70-80, 80-100 putting individual segments in paper bags and labeling each bag, then place in green house to let dry. NOTE:  At this time, it may be easier to break up the clumps rather than after they have dried.
?. Weigh each sample and enter on data sheet, weigh 7 bags and average the weights to get average to use for bag weight to tare scale at before weighing samples
?. Grind samples separating stones and soil through a 2 mm sieve putting the stones and soil in separate containers, stones back in the paper bags, and soil in quart zip locks transcribing the tag information from the paper bags onto the zip locks.
?. After grinding samples, all stones collected (didn’t pass through a 2mm screen) must be saved from each individual tube and segment.  We just dumped the stones back into the original bag and saved until all the samples were ground.
?. After all samples are ground, the rocks must be washed free of soil and OM.  Using a 2mm screen, each rock sample was pre-soaked with water, scrubbed free of dirt, and placed in petri dish or aluminum pan for drying.  Also, the rock samples were submerged in a wash basin to float off any OM.  When washing the stones, a lot of the ‘stones’ were actually clay clumps so much of the sample is washed away.  A wash basin under the screen helps collect sediment rather than letting it go down the drain.  Samples were placed in a dryer at 50C.
?. Send the complete volume of soil labeled in a zip lock out for carbon analysis and ask the lab for the excess sample to be returned for archiving.
?. Calculate bulk density by taking roughly 75g of stones, the stone sample is dumped into a graduated cylinder with a known volume of water.  We used. 300ml of water.  Record the stone weight prior to adding to cylinder, the starting water volume, and the displaced water volume.  This process was repeated 3 times for each depth.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>This protocol was developed to use common wet lab device (Real Time PCR machine) to detect viral genome release and native viral particle conversion. We used temperature ramping for inducing genome uncoating and fluorescent probes for RNA/DNA and/or proteins, to detect genome and/or capsid changes.</p>

[GUIDELINES]
<p>Prepare a master mix (3.5X) with virus and probes in thermo stable buffer</p>
<p>Final volume 70 µL</p>
<p>Add replicates to 96-well PCR plate (Replicates 3 X 20 µL)</p>
<p>Seal the plate</p>
<p>Place the plate in Real Time PCR Equipment</p>
<p>Open the software and run a melting curve assay.</p>
<p> </p>

[STEPS]
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TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>Preparation of insect specimens for morphological studies classically employs chaotropic salts which can cause disruption of important structures. Also, extraction of nucleic acids for genetic studies leads to destruction of the specimen. Thus, in this paper is proposed a new technique, based on the use of proteinase K, which allows DNA extraction while keeping intact the entire morphology of insect specimens. <strong>The</strong> presented technique can contribute to taxonomic and systematic studies on different groups of arthropods. Also, with the global emergency and reemergence of diseases transmitted by arthropod vectors, genetic and morphological investigations performed in an individual-scale would unveil important aspects of environment and host-pathogen interactions.</p>

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TITLE: Vissentials Max BHB Canada:-Updated Results 2022 | Canada | Does It Works Or Scam?
AUTHORS: vissenmax  

[DESCRIPTION]
Vissentials Max BHB Reviews, Canada: Obesity issues are fatal, and if you have an obese body, it may provide you multiple negative effects if you do not get rid of it in time. If you have an obese body, you will know the struggle it comes with.

[STEPS]
TITLE: Astrocyte extraction from brain organoids
AUTHORS: gustavo.parfitt

[DESCRIPTION]
Protocol for astrocyte extraction from brain organoids.  

[STEPS]
1. Coat a 6 well plate coat with gelatin 0.1% or   1:100

2. Collect 10-20 spheres and place in a 6 well plate  (day 40+ spheres)

3. Wash in PBS twice 

4. Aspirate the  PBS
5. Add 1 mL  of  for  5 min 

6. Triturate using glass a pipette (2-3 up and down)

7. Transfer the cells and tissue (even the chunks, the trituration is more effective if you have chunks of tissue) to the coated 6 well plate 
8. Aspirate the extra TrypLe
9. Add 3 mL of astrocyte media (https://www.sciencellonline.com/astrocyte-medium.html)

10. Half media change media every 3 days or until it turns orange.
11. Keep changing media every 3d until you observe good amount of cell attached to the plate (may vary according to the patterning)
12. Passage the astrocytes to a gelatin or geltrex coated 15 cm plate in Astrocyte media once they reach 80% confluency
13. For the experimental protocols after passage cell will be incubated in maturation media (TBD)
TITLE: No Title
AUTHORS: 

[GUIDELINES]
References to 'DNA Extraction of Viruses using Wizard Prep Columns' protocol<br /><br />Needed:<br /><ul><li>Filters</li><li>Forceps (bleached)</li><li>Aluminum foil squares</li><li>50cc tube</li><li>Resuspension buffer (0.1M EDTA - 0.2M MgCl2 - 0.2M Ascorbate Buffer)</li><li>Sterile applicator sticks</li><li>20 mL filter</li><li>2x 10mL filter</li><li>20L seawater</li><li>Parafilm</li><li>Aluminum foil</li><li>Rotator</li><li>Rubber bands</li><li>5mL pipet</li><li>15mL or 50 mL sterile tube</li><li>Centrifuge @ 1000 rpm, 14rpm, 1,000g and 10,000g</li><li>Stock DNase</li><li>DNase buffer</li><li>EDTA</li><li>EGTA</li><li>Amicon Ultra 100kDa centrifugal concentrator</li><li>Wizard Prep Resin</li><li>Wizard Prep Column</li><li>3mL Luer Lock Syringe</li><li>5mL Snap-cap tube</li><li>Plunger</li><li>Syringe barrel</li><li>80% Isopropanol</li><li>1.5 mL centrifuge tube</li><li>50-100 &micro;L TE</li><li>Pico Green assay</li></ul>

[STEPS]
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TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>It is not always possible to isolate microalgae immediately after sample collection, for example on long cruises where no proper conditions are available (lack of culture chamber, sterile hoods) or on trips to remote locations. Therefore it is desirable to be able to preserve samples in such a way that microalgae can be isolated once the samples are brought back to the laboratory. One possible strategy is to use cryopreservation that is currently used to preserve live cultures of microalgae.</p>

[STEPS]
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TITLE: aCGH results extraction from TIFF file
AUTHORS: Hendrik F van Essen

[STEPS]
?. Copy TIFF file to “output folder”
?. Open “Feature Extraction” (Fe) program
?. File -> ‘Add extraction set’
?. Select TIFF files in "output folder"
?. Select under ‘project properties’ tab	the correct grid name* 4x44K* 2x105K* 4x180k
?. Under Project select ‘Start extracting’
TITLE: Cobia PCR of sex-specific markers
AUTHORS: Zhi Weng Josiah Poon

[DESCRIPTION]
PCR for sex-specific markers in Cobia (Rachycentron canadum)

[STEPS]
SECTION: Brazil population (Taq PCR Core Kit (QIAGEN))
2. (cephx1_1)
20 μL reaction containing:
- 2.08 µL of 10X Taq Buffer 
- 0.42 µl of dNTPs (10 µM) 
- 0.67 μL of each primer (10 µM)
- 0.17 μL of Taq DNA polymerase (5 units/μL) 
- 35 ng of extracted DNA
- made up to final volume with nuclease-free water

Thermal cycling:
- 3 mins at 94°C 
- 30 cycles of 1 min at 94°C, 1 min at 66°C (cephx1_1), and 1 min at 72°C
-  10 min at 72°C 

(cephx1_2)
20 μL reaction containing:
- 2.08 µL of 10X Taq Buffer 
- 0.42 µl of dNTPs (10 µM) 
- 0.67 μL of each primer (10 µM)
- 0.17 μL of Taq DNA polymerase (5 units/μL) 
- 20 ng of extracted DNA
- made up to final volume with nuclease-free water

Thermal cycling:
- 3 mins at 94°C 
- 20 cycles of 1 min at 94°C, 1 min at 65°C (cephx1_2), and 1 min at 72°C
-  10 mins at 72°C 
SECTION: Panama population (Taq PCR Core Kit (QIAGEN))
1. (cephx1_1) and (cephx1_2)
20 μL reaction containing:
- 2.08 µL of 10X Taq Buffer 
- 0.42 µl of dNTPs (10 µM) 
- 0.67 μL of each primer (10 µM)
- 0.17 μL of Taq DNA polymerase (5 units/μL) 
- 30 ng of extracted DNA
- made up to final volume with nuclease-free water

Thermal cycling:
- 3 mins at 94°C 
- 30 cycles of 1 min at 94°C, 1 min at 60°C (cephx1_1) and 61°C (cephx1_2), and 1 min at 72°C
-  10 mins at 72°C 


SECTION: Australia population (PlatinumTM Taq DNA Polymerase High Fidelity (Invitrogen))
3. 20μL reaction containing:
- 2 µL of 10X Buffer
- 0.4 µL of dNTPs (10 µM)
- 0.8 µl of MgSO4
- 0.4 µL of each primer (10 µM)
- 0.08 µL of Taq DNA polymerase
(5 units/μL) 
- 32 ng of extracted DNA
- made up to final volume with nuclease-free water


Thermal cycling:
- 2 mins at 94°C 
- 30 cycles of 15 secs at 94°C, 30 secs at 62°C (cephx1_1) and 62°C (cephx1_2), and 1 min at 72°C
-  10 mins at 72°C 
SECTION: Japan population (Q5 High-Fidelity 2X master Mix)
4. 25μL reaction containing:
- 12.5 µL of Q5
- 1 µL of each primer (10 µM)
- 15 ng of extracted DNA
- made up to final volume with nuclease-free water


Thermal cycling:
- 30 secs at 98°C 
- 30 cycles of 10 secs at 98°C, 30 secs at 61°C (cephx1_1 and cephx1_2), and 30 secs at 72°C
-  2 mins at 72°C
TITLE: Chemical Fixation and embedding of cultured cells for Transmission Electron Microscopy
AUTHORS: Marta Orlando

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol can be followed to fix primary cultured neurons (or cells in general) and embed them in epoxy resin. Later ultrathin sections can be obtained with an ultramicrotome for Transmission Electron Microscopy imaging.</div><div class = "text-block">The reagents used in this protocol are toxic!</div></div>

[STEPS]
?. Fix for 1 hr at RT in 1.25% glutaraldehyde in 66mM sodium cacodylate buffer
?. Wash 3 times with 0.1 M sodium cacodylate buffer
?. Postfix 1 hr in 1% OsO4 (optional: for better contrast add 1.5% K4Fe(CN)6 to the osmium solution) in 0.1M sodium cacodylate buffer
?. Wash 3x10' with 0.1 M sodium cacodylate buffer
?. Wash 3x10' with distilled H2O
?. En bloc stain for 45' in 1% uranyl acetate solution in distilled H2O
?. Wash 3x10' with distilled H2O
?. Dehydrate by incubating in increasing EtOH concentrations: 10 minutes in 70%, 10 minutes in 80%, 10 minutes in 96%, 2x15 minutes in 100%
?. Infiltrate in 30% Epoxy resin in EtOH
?. 10.  Infiltrate in 70% Epoxy resin in EtOH
?. 11.  Infiltrate in 90% Epoxy resin in EtOH
?. 12.  Incubate in 100% Epoxy resin
?. 13.  Flat embed in Epoxy resin
?. 14.  Bake for 48 hrs at 65°C
?. 15.  Remove the glass coverslip from the resin block by thermal shock
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
Modified after Gl&ouml;ckner et al. 1999

[GUIDELINES]
Needed:<br />
<ul>
<li>PFA Fixative</li>
<li>Water sample</li>
<li>Formaldehyde (optional)</li>
<li>Moistened support filter (0.45 µm pore size, cellulos nitrate, 47 mm diameter)</li>
<li>Membrane filter (0.2 µm pore size, white polycarbonate (GTTP), 47 mm diameter)</li>
<li>Filtration tower</li>
<li>Vacuum</li>
<li>Moistened support filter (0.45 µm pore size, cellulose nitrate, 25 mm diameter)</li>
<li>Membrane filter (0.2 µm pore size, white polycarbonate (GTTP), 25 mm diameter)</li>
<li>Sterile H2O</li>
<li>Petri dish lid</li>
<li>Parafilm</li>
</ul>

[STEPS]
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TITLE: UT Southwestern - Staining Melanoma Cells for Flow Cytometry
AUTHORS: Arin Aurora, Sean Morrison

[STEPS]
?. [STAINING CELLS FOR FLOW CYTOMETRY]
Adjust staining volume and antibody concentration to the number of cells. Concentrations listed are for 5x106 cells in a 50ml reaction. Do not exceed 106 cells/10ml.- mLin APC: Ter119 (1/100), CD31(1/100), CD45(1/200) - HLA FITC: HLA-ABC (1/5)
?. [STAINING CELLS FOR FLOW CYTOMETRY]
Add antibodies to tube and incubate covered on ice for
?. [STAINING CELLS FOR FLOW CYTOMETRY]
Wash 1x with  staining medium and spin down . Aspirate supernatant
1 mL
Centrifuge: 220 33, 4 min, 4 10
?. [STAINING CELLS FOR FLOW CYTOMETRY]
DAPI staining: resuspend samples in DAPI 1:2000 to gate out dead cells. Stock in made in water (1mg/ml)
?. [FACS]
Adjust final sample volume to run at 6000 events/sec at maximum and then run. If clogging becomes an issue, then filter through cut pieces of filter  ABC1Xenograft stain (50ml volume) 1x  5x 2HLA- PE or FITC (1/5)10ml50ml3mCD45 APC (1/200)0.3ml1.5ml4mCD31 APC (1/100)0.5ml2.5ml5mTer119 APC (1/100)0.5ml2.5ml  ABC1Human stain (50ml volume)1x5x2HLA- FITC (1/5)10ml50ml3ISO PE or P75 PE (1/5)10ml50ml4Glyc-A APC (1/2000)0.025ml0.125ml5hu-CD31 APC (1/800)0.063ml0.315ml6hu-CD45 APC (1/5)10ml50ml
ABC1Xenograft stain (50ml volume) 1x  5x 2HLA- PE or FITC (1/5)10ml50ml3mCD45 APC (1/200)0.3ml1.5ml4mCD31 APC (1/100)0.5ml2.5ml5mTer119 APC (1/100)0.5ml2.5ml
ABC1Human stain (50ml volume)1x5x2HLA- FITC (1/5)10ml50ml3ISO PE or P75 PE (1/5)10ml50ml4Glyc-A APC (1/2000)0.025ml0.125ml5hu-CD31 APC (1/800)0.063ml0.315ml6hu-CD45 APC (1/5)10ml50ml
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p><em>Diatraea</em> spp. (Lepidoptera: Crambidae) are a group of insects considered as an agriculture pest in many economically relevant crops such as sugarcane, sorghum, corn and rice. Currently, identification is based on the male genitalia. However, the availability of specimens collected from field and subjectivity on the character recognition can seriously hamper species identification, and therefore result in inadequate pest management. We described a protocol based on a fragment of the <em>cytochrome oxidase subunit</em> II (CO II) mitochondrial gene and Single-Strand Conformation Polymorphism (SSCP) methodology to properly recognizing each species and in consequence is proposed as an effective tool in <em>Diatraea</em> species identification.</p>

[GUIDELINES]
<ol>
<li>Simon C, Frati F, Beckenback A, Crespi B, Liu H, Flook P. Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved PCR primers. Ann Entomol Soc Am. 1994; 87: 651-701.</li>
<li>Lange CL, Scott KD, Graham GC, Sallam MN, Allsopp PG. Sugarcane moth borers (Lepidoptera: Noctuidae and Pyraloidea): phylogenetics constructed using COII and 16S mitochondrial partial gene sequences. Bull Entomol Res. 2004; <em>94</em>(5): 457-464</li>
<li>Palacio-Cortés AM., Zarbin PH, Takiya DM, Bento JM, Guidolin AS, Consoli FL. Geographic variation of sex pheromone and mitochondrial DNA in <em>Diatraea saccharalis</em> (Fab., 1794) (Lepidoptera: Crambidae). J Insect Physiol. 2010; 56: 1624-1630.</li>
</ol>

[STEPS]
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TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>ACUITYAdvanced Biotin Free HRP<br />Polymer Detection System for Immunohistochemistry</p>

[GUIDELINES]
<p><img id="s-mce-img" class="s-mce-img" src="https://s3.amazonaws.com/pr-journal/dutecje.jpg" data-src="https://s3.amazonaws.com/pr-journal/dusecje.jpg" data-ofn="acuity1.JPG" /></p>

[STEPS]
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TITLE: No Title
AUTHORS: 

[GUIDELINES]
<strong>Reagent List:</strong><br />
<ul>
<li> Sterile PBS</li>
<li> Cell culture medium (RPMI 1640 supplemented with 10% FBS)</li>
<li> Sterile 12-well plate</li>
<li> RBC Lysis Buffer (Cat. No. 420301)</li>
<li> Anti-mouse CD3ε, clone 145-2C11 (LEAF™ format, Cat. No. 100314)</li>
<li> Anti-mouse CD28, clone 37.51, (LEAF™ format, Cat. No. 102112)</li>
<li> Recombinant mouse IL-2 (carrier-free) (Cat. No. 575402)</li>
<li> Recombinant human TGF-β1 (carrier-free) (Cat. No. 580702)</li>
</ul>

[STEPS]
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TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>Details of envrionmental sampling methodology of different production locations within a broiler production enterprise.</p>
<p>Specific details regarding the sampling methodology and samples collected are provided.</p>

[BEFORE_START]
<p><strong>Sampling Equipment</strong></p>
<p>All sampling equiement should be assembled and sterilised in single units for sampling prior to sampling.</p>
<p>Pre-label all sample bags with shed ID, sample ID and sample location</p>
<p> </p>
<p><strong>Boots and Boot swabs</strong></p>
<p>Clean dry sanitised boots should be used on entry to all sheds prior to sampling if using boot swabs to sample sheds.</p>
<p>To ensure cross contamination is minimised between sheds new boots must be worn prior to entry.</p>
<p> </p>
<p><strong>Personal protective equipment</strong></p>
<p>Appropriate personal protective equipment should be worn when sampling sheds, this should include coveralls, gloves for collecting samples, face mask (P2), and hairnet.</p>
<p> </p>

[GUIDELINES]
<p><strong>Sampling Protocol</strong></p>
<p>All sampling procedures in this protocol have been designed to be conducted in commercial production facilities while birds are housed.</p>
<p>No sampling at height is required to obtain sufficient samples representative of the house or the flock to be sampled.</p>
<p> </p>
<p><strong>Animal Welfare</strong></p>
<p>This prtocol is designed to minimise adverse interference with birds while they are housed.</p>
<p>Sampling is conducted at routine times when birds would be normally inspected by farm staff.</p>
<p>No birds are directly handled during the sampling procedure, however they will be walked through during sampling within sheds.</p>
<p>Walking pace should be maintained, and it is recommended that sampling be conducted when birds are being routinely checked to minimise flock disturbance.</p>
<p>Samples can be obtained by collection of materials that are routinely used or disposed of during production, such as hatch debris or chick papers.</p>
<p> </p>
<p><strong>Repeated Sampling</strong></p>
<p>Where sampling is to be conducted repeatedly in the same environment, it is recommended that sampling be conducted at the same time of the day on each sampling ocassion to eliminate sampling or operator bias.</p>
<p>To ensure repeatability between sampling events, select the same sites to be sampled on each sampling ocassion. </p>
<p>To ensure this, identify simple to access sampling locations prior to sampling.</p>
<p>Top ensure adequate sample is collected during sampling samples should be collected from sites dispersed evenly along the length of the shed or within the environment to be sampled. </p>
<p>To ensure repeatability within the shed, it is easier if the sampling sites are collected from the same site, the length of the equipment or at an easily identifiable site such as the end of a cage frame.</p>
<p>Avoid sampling at height if possible.</p>

[STEPS]
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TITLE: Two-step protocol: Preparation and extrusion of phospholipid liposomes
AUTHORS: James Collins, James R. Collins,  Krista Longnecker,  Helen F. Fredricks,  Benjamin A. S. Van Mooy

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The protocols in this collection were original created by </span><a style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">Krista Longnecker</span></a><span> and </span><a style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">Jamie Collins</span></a><span> for creating lipsomes to be used in lipid photo-oxidation experiments. The results of these experiments are detailed in:</span></div><div class = "text-block"><span>Collins, J. R, H. F. Fredricks, J. S. Bowman, C. P. Ward, C. Moreno, K. Longnecker, A. Marchetti, C. M. Hansel, H. W. Ducklow, and B. A. S. Van Mooy. 2018. The molecular products and biogeochemical significance of lipid photooxidation in West Antarctic surface waters. </span><span style = "font-style:italic;">Geochimica et Cosmochimica Acta</span><span style = "font-style:italic;font-weight:bold;"> </span><span style = "font-weight:bold;">232</span><span>:244–264; doi:</span><a style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">10.1016/j.gca.2018.04.030</span></a><span></span></div><div class = "text-block">and in Chapter 4 of:</div><div class = "text-block"><span>Collins, J. R. 2017. The remineralization of marine organic matter by diverse biological and abiotic processes. Ph.D. thesis. Cambridge, Massachusetts: Massachusetts Institute of Technology, 300 pp; doi:</span><a style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">10.1575/1912/8721</span></a></div></div>

[STEPS]
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p><strong>Objective:</strong> To evaluate the comparative efficacy and safety of antiplatelet agents, vitamin K antagonist (VKA) and non-VKA oral anticoagulants (NOACs) in patients with atrial fibrillation (AF) undergoing percutaneous coronary intervention (PCI).</p>
<p><strong>Methods:</strong> PubMed, EMBASE, and the Cochrane Central Register of Controlled Trials will be searched to identify clinical trials comparing antiplatelet drugs with VKA and NOACs or their combination in AF patients undergoing PCI with a mean/median follow-up of at least 12 months. A network meta-analysis will be conducted to directly and indirectly compare the efficacy and safety of competitive antithrombotic regimens with a Bayesian random-effects model.</p>

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TITLE: Vivarium Population Spenser: Fertility protocol
AUTHORS: Camila Rangel Smith

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Description of the steps followed by Vivarium Population Spenser library when running the Fertility module. </div></div>

[STEPS]
?. Divide the annual fertility rates for that local authority by the number of time steps existing in a year.
?. For each time step:
?. Select all women in the sample that appear as "alive" and  haven't had a child in at least one year.
?. For these selected women, get the fertility rate given their age, ethnicity and location and turn it into a probability.
?. Using random sampling and the fertility probability of the women, choose which individuals give birth in that time step. Update their information in the state table with the last time they gave birth.
?. If children were born in the previous step, add them to the state table and record who their mother is. Assign them the same ethnicity and location from their mother, assign their sex randomly.