eamag/protocols-with-steps huggingface dataset:
TITLE: U Mass - Cholesterol (LDL)
AUTHORS: Jason Kim

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">This experiment involves a spectrophotometric measurement using Roche Cobas Clinical Chemistry Analyzer. Serum levels of LDL-cholesterol reflect cholesterol metabolism and are associated with cardiovascular disease.</div></div>

[STEPS]
?. Perform daily quality control assessment of instrumentation before analysis.
?. Load each sample into a specialized micro-sample cup for the clinical chemistry analyzer.
?. Select Cholesterol (LDL) test on display and run the analysis.
?. Collect and analyze the data.
TITLE: Planting Tobacco Seeds in the Greenhouse
AUTHORS: Lynn Doran

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for planting, germinating, and growing tobacco seedlings in the UIUC RIPE greenhouse.  Has been verified on Petite Havana and Samson cultivars.  </div><div class = "text-block">For additional information on growing tobacco for research purposes refer to UIUC RIPE greenhouse guide "Growing Tobacco (Nicotiana tabacum) under Greenhouse Conditions, RIPE Project UIUC Field and Greenhouse, 2020"</div></div>

[STEPS]
?. Fill an 8" azalea pot completely full with Berger BM6 HP Myco Organic Fertilized Peat Moss Mix soil.
?. Tamp the soil down firmly with your hands. Trying to make as level of a surface as possible.
?. Using the super fine (0.5 GPM @ 40 PSI) fogg-IT drench nozzle, soak the soil until saturated to remove any air bubbles.
?. Tamp the soil lightly and relevel.  If the soil settles more than about an inch, add additional soil and rewet.  Do not overpack the soil.
A level surface is important because tobacco seeds are tiny and round.  If surface is not level, seeds will roll towards each other or the sides of the pot and cause overcrowding during germination.
?. Pour 50-300 seeds from stock vial into a pour boat.  Using the pour boat, carefully sprinkle the seeds on top of the soil.  Sprinkling them in a spiral shape starting on the outside and working in to ensure even coverage across the pot and even spacing of seeds. Seed 5 to 10x more seeds than will be transplanted. Do not cover seeds with soil.
Nicotiana tabacum seed requires light in order to germinate. The seeds are very miniscule and need to be scattered on the soil surface in order to avoid being covered.
?. Label pot twice. Once with sharpie on a plastic stake in the pot and once on the exterior of the pot using a sharpie and labelling tape or a laser printed label.
Laser printed labels are more robust.  Handwritten sharpie labels tend to fade over the growing season.
?. Place azalea pots in a propagation tray with no drain holes.
?. Fill the tray with approximately 1 inch of water.
?. Cover with a humidity dome. Leave the vents on the humidity dome half open, half closed.
?. Grow at  ,  , 300-750PAR, and light cycle 12 hours on/12 hours off. Check daily and add water to keep tray filled with approximately 1" water.
23 °C
Do not allow soil to dry out during germination. The water level can be maintained at 1” of water in the tray without any disease/damping off issues.
?. Transplant seedlings when they have one to two true leaves.
Seedling will be ready to transplant in approximately 10 to 14 days.  Do not wait too long to transplant. The root system begins to develop rapidly after the first true leaves.  When the true leaves first appear, there is typically one branch in the root system making it easy to remove from the initial media if care is taken. Damaging roots during transplant will drastically affect development and result in non-uniform plants.
TITLE:  Rotina de Manutenção e Infecção de Células C6/36_v2
AUTHORS: Fabio Gomes

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocolo de Manutenção de Infecção (DENV e ZIKV) de Células C6/36 - PLO</div></div>

[STEPS]
?. [Tripsinização Cultura]
Pre-aquecer o meio e PBS 1x
?. [Tripsinização Cultura]
De uma garrafa (25cm2) com 90% de confluência, remover o meio e lavar com 5 mL PBS (2)
?. [Tripsinização Cultura]
Acrescentar 1 mL tripsina
?. [Tripsinização Cultura]
Deixar agir por 1 min e acompanhe em microscopio
?. [Tripsinização Cultura]
Paralisar a reação adicionando 7 mL meio
?. [Preparo de Garrafas para Infecção]
Contar células e passar em diluição 1:10 para garrafar de 225cm2
?. [Preparo de Garrafas para Infecção]
Deixar crescer até 50-70% de confluência (48-72h)
?. [Infecção]
Adicionar o inóculo do vírus em meio L15 (sem soro), completando volume em 10 mL
?. [Infecção]
Manter a 28oC por 1 hora,
?. [Infecção]
A cada 15 min, mexa a garrafa de cultura para banhar a camada de células
?. [Infecção]
Descartar o meio com vírus e acrescentar 15mL meio (2% FBS, PenStrep, L15)
?. [Infecção]
Manter a cultura na estufa a 28oC por até 9 dias. Não mover as garrafas!
?. [Processamento Vírus]
Recolher o meio e ajustar o pH usando 7,5% bicarbonato de sódio
?. [Processamento Vírus]
Centrifuga 300g por 10 min
?. [Processamento Vírus]
Aliquotar (500 µl) e manter em -80oC
?. [Preparo de Garrafas para Infecção]
Remover meio de cultura e lavar com 10 mL PBS
?. [Preparo de Garrafas para Infecção]
Adicionar 10mL 0.25% Tripsina
?. [Preparo de Garrafas para Infecção]
Contar células e calcular para infecção com MOI-0.1
?. [Processamento Vírus]
Adicionar FBS até a concentração final 20%
?. [Processamento Vírus]
Filtrar com membrana de 0.22 µm
TITLE: Workflow for human fallopian tube and uterine endomyometrium bulk ATACseq
AUTHORS: Scott   Lindsay-Hewett, Valentina  Stanley, Mana   Parast, Louise Laurent

[DESCRIPTION]
Described here is the workflow used by the Female Reproductive Tissue Mapping Center at UCSD to generate bulk ATACseq data from human fallopian tube and uterine endomyometrium.

[STEPS]
SECTION: Tissue preparation
1. As soon as possible after sterilization (salpingectomy or tubal ligation), prepare fallopian tube tissue according to the following protocol:

Human Pregnant Fallopian Tube Tissue Collection and Preservation Methods - UCSD Female Reproductive TMC

At the time of C-section, prepare uterine endomyometrium tissue according to the following protocol:

Human Pregnant Uterine Myometrium Tissue Collection and Preservation Methods - UCSD Female Reproductive TMC

For this protocol, use tissue that has been snap-frozen.
SECTION: Nuclei isolation
2. Isolate nuclei from 4 samples at a time according to the following protocol:

Nuclei isolation from snap-frozen human placental tissue for bulk ATACseq

Proceed to tagmentation immediately.
 

SECTION: Tagmentation and library generation
3. Perform tagmentation and library generation according to the following protocol:


Tagmentation and library generation for human placental bulk ATACseq


After passing quality control, proceed to sequencing.
 

SECTION: Sequencing
4. For HuBMAP bulk ATACseq samples, the multiplexed pool was sequenced on a NovaSeq 6000 S4 lane using a 100bp paired-end run configuration. Alignment and peak-calling were performed using the ATAC-seq pipeline within the bcbio Python package.
TITLE: Effects of hypolipemic drugs on psoriasis
AUTHORS: Mateusz Matwiejuk, Hanna Mysliwiec, Olivia Jakubowicz-Zalewska, Adrian Chabowski, Iwona Flisiak

[DESCRIPTION]
Psoriasis is a chronic, systematic, inflammatory disease in which, multiple metabolic and immunologic disturbances lead to lipid abnormalities, impaired glucose tolerance, metabolic syndrome, diabetes mellitus, atherosclerosis, hypertension, ischemic heart disease, and numerous metabolic disorders. In clinical practice, the most commonly used drugs in treatment of lipid abnormalities are statins and fibrates. Statins are characterized by pleiotropic effects, such as antioxidant, anti-inflammatory, anticoagulant, antiproliferative. They work by reducing concentration of low-density lipoprotein (LDL), total cholesterol, triglycerides, and stabilize atherosclerotic plaque. Fibrates are medications, which help to lower triglycerides, LDL, very low-density lipoprotein (VLDL) levels and increase lower high-density lipoprotein (HDL). In recent years, many new drugs were found to normalize lipid profile in patients with psoriasis: glitazones (pioglitazone, troglitazone), and glucagon-like peptide-1 (GLP-1) receptor agonists. Pioglitazone improves lipid profile including decrease of triglicerydes, fatty acids, LDL, and increase of HDL.Glucagon-like peptide 1 (GLP-1) analogues decrease modestlylow-density lipoprotein cholesterol (LDL-C), total cholesterol and triglycerides. The purpose of this study is to assess the current state of knowledge on the effect of different hypolipemic treatments on the course of psoriasis. The study includes literature from medical databases: Pubmed and Google Scholar. We were browsing the PubMed and Google Scholar untill the beginning of December. The systematic review includes 41 eligible original articles. 

[STEPS]
1.
TITLE: protocol_CPG
AUTHORS: juanruanoruiz , fjgg79 ,  Pedro J Gómez Arias,  Jesús Gay-Mimbrera,  Macarena Aguilar-Luque,  Salvador Peiró Moreno,  Beatriz Isla-Tejera

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Hypothesis</span></div><div class = "text-block">The degree of transparency and reproducibility of economic health analyses, whether primary studies or systematic reviews and meta-analysis, which are used for development could condition the usefulness of clinical practice guidelines in which they are included regardless of the methodological quality of them. </div><div class = "text-block"><span style = "font-weight:bold;">Objectives</span></div><div class = "text-block"><span style = "font-style:italic;">Primary objective</span></div><div class = "text-block">Analyze the relationship between the methodological quality of clinical practice guides published in Spain and the current state of reproducibility and transparency of the health economic assessment studies included in them, both primary studies or systematic reviews and meta-analysis. </div><div class = "text-block"><span style = "font-style:italic;">Secondary objectives </span></div><div class = "text-block"><ol style = "list-style-type: decimal;"><li style = "counter-reset:ol0;">Evaluate the quality of CFCs produced in Spain in the period 2000-2020. </li><li style = "counter-reset:ol0;">Evaluate the methodological quality of the economic assessment studies included in the GPCs produced in Spain in the period 2000-2020. </li><li style = "counter-reset:ol0;">Describe the transparency and reproducibility of the selected economic assessment studies. </li><li style = "counter-reset:ol0;">Analyse whether there are differences in transparency and reproducibility of economic assessment studies depending on the quality of the GPCs that include them. </li><li style = "counter-reset:ol0;">Analyse whether there have been improvements in the transparency and reproducibility of economic assessment studies by comparing the GPCs containing them that have been produced in 2000-2012 vs 2013-2020.</li></ol></div></div>

[STEPS]
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>Dinoflagellates are unicellular algae that can have photosynthetic or nonphotosynthetic lifestyles. Dinoflagellates in the genus <em>Symbiodinium</em> can enter endosymbiotic associations with corals, providing the metabolic basis for the highly productive and biologically diverse coral-reef ecosystems (Hoegh-Guldberg, 1999), as well as with other cnidarians, including sea anemones and jellyfish, and noncnidarian hosts (Trench, 1993; Lobban <em>et al.</em>, 2002; Mordret <em>et al.</em>, 2016).</p>
<p> </p>
<p>Here I describe a protocol for isolating total DNA from <em>Symbiodinium</em> cells.</p>

[BEFORE_START]
<p>Prepare 2X lysis buffer in this composition:</p>
<p>2% SDS,</p>
<p>400mM NaCl,</p>
<p>40 mM EDTA,</p>
<p>100mM Tris-HCl, pH 8.0</p>
<p> </p>
<p>Keep the buffer at room temperature, SDS will precipitate in the coldness. Warm up the buffer in advance at 37ºC into clear liquid if it was precipiated. </p>

[GUIDELINES]
<p>Prepare the lysis buffer before you start.</p>

[STEPS]
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
Concentrate phytoplankton samples about 100-fold typically from 5L down to 20 mL.&nbsp; Takes about 1 hour&nbsp;per sample. &nbsp;Samples can be used for flow cytometry sorting or for cultures.&nbsp; Enrichment by TFF usually keep growing for a longer time than unconcentrate samples.<br /><br /><strong>Reference<br /></strong><a href=".https://www.researchgate.net/publication/42254387_Use_of_flow_cytometric_sorting_to_better_assess_the_diversity_of_small_photosynthetic_eukaryotes_in_the_English_Channel" target="_blank">Marie, D., Shi, X.L., Rigaut-Jalabert, F. &amp; Vaulot, D. (2010). Use of flow cytometric sorting to better assess the diversity of small photosynthetic eukaryotes in the English Channel. <em>FEMS Microbiology Ecology</em>. 72. p.pp. 165&ndash;178<strong>.<br /></strong></a>

[BEFORE_START]
<p><a href="https://s3.amazonaws.com/pr-journal/qqchcw.jpg" target="_blank"><img src="https://s3.amazonaws.com/pr-journal/qqchcw.jpg" alt="" /></a><br /><strong>Necesssary equipement</strong><br />•    Vivaflow Cartridge 100,000 MWCO (Regenerated Cellulose - RC) VF20C4  for viruses<br />•    Vivaflow Cartridge  0.2 μm (PES) VF20P7 for plankton<br />•    Masterflex Pump 6-600 rpm (ref Bioblock F39671) - It is critical to have a 600 rpm pump, lower speed will not work.  The rate of the pump must be adjustable.<br />•    Rotor 3 “galets” (ref  F39110)<br />•    1 Head high throughput (ref F40103) (Can be replaced with quick load head)<br />•    Replace tube provided by stronger tube with two connectors (see picture)<br />•    Bottle 6 L<br />•    Bottle 1 L<br />•    Conical tube 50 mL (Falcon tube)<br />•    Masterflex Tygon tubing size 16<br />•    Plastique pipettes (1 mL) - this is used to plunge in the sample<br />•    Clamps with screw (to control retentate speed)</p>
<p> </p>
<p><strong>Solutions</strong></p>
<ul>
<li>MilliQ water : 1L</li>
<li>NaOH 0.1 N : 500 mL</li>
<li>EtOJ 10% : 500 mL</li>
</ul>

[GUIDELINES]
In order to estimate actual concentration efficiency measure Synechoccus, pico, and nanoeularyote concentration before and after TFF.

[STEPS]
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
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?. 
?. 
?. 
?. 
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?. 
?. 
?. 
?. 
?. 
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?. 
?.
TITLE: Chlamydomonas reinhardtii cell wall proteins recrystallization 
AUTHORS: Joao Vitor Molino

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocols describe the steps required for the recrystalization of cell wall proteins from </span><span style = "font-style:italic;">Chlamydomonas reinhardtii </span><span>from perchlorate extractions. </span></div><div class = "text-block">Protocol based on:</div></div>

[STEPS]
?. [Before start]
Check the protocol "Chlamydomonas reinhardtii cell wall extraction with perchlorate"The amount of recrystalized material varies, but in some results I was able to obtain 1% of the inicial cell mass as cell wall material. Recrystalization can be performed by diafiltration of dialysis.
?. [By Diafiltration]
Prepare of cell wall proteins extract by perchlorate treatment of   with  of   sodium perchlorateAdd   of sample in centrifugal filters with a 30 KDa cutoff (e.g. Amicon Ultra 0.5 Centrifugal filters)Centrifuge at Remove the flow-through and add enought sample to the max capacity of the filter. Repeat until all sample processedConcentrate the sample until   Add 400 uL of ddH20Centrifuge at  Repeat 4-7Collect the precipitated material by inverting the membrane in a new collecting tube and centrifuge at  Proceed to planned experiments. Concentrate the sample until Add 400 uL of ddH20Centrifuge at  Repeat 4-7Collect the precipitated material by inverting the membrane in a new collecting tube and centrifuge at  Proceed to planned experiments. Centrifuge at Repeat 4-7Collect the precipitated material by inverting the membrane in a new collecting tube and centrifuge at  Proceed to planned experiments. Collect the precipitated material by inverting the membrane in a new collecting tube and centrifuge at
1 mL
1
1 mL
500 µl
Centrifuge: 14000 1324, 20 min, 25 10
100 µl
Centrifuge: 14000 1324, 20 min, 25 10
Centrifuge: 1000 1324, 1 min, 25 10
?. [By Dialsysis ]
Prepare membranes with 30 Kda for dialysis, by cutting a segment larger enough to hold  of sample, and rehydrating it in ddH20   prior to usePrepare of cell wall proteins extract by perchlorate treatment of   with  of   sodium perchlorate,Add the extract to the membrane adn close itPlace the membrane inside a vessel containig   of ddH20. (A magnetic stirring can be used, making sure the membrane is not hit by the magnet bar)Incubate for   Change the   of ddH20 and incubate   Retrieve the liquid inside the tube, ressuspending any precipitate material by pipetting and transfering it to a clean microcentrifugal tube. Spin   , a precipitate should be visibleProceed to planned experiments. Place the membrane inside a vessel containig  of ddH20. (A magnetic stirring can be used, making sure the membrane is not hit by the magnet bar)Incubate for Change the  of ddH20 and incubate Retrieve the liquid inside the tube, ressuspending any precipitate material by pipetting and transfering it to a clean microcentrifugal tube. Spin   , a precipitate should be visibleProceed to planned experiments. Spin  , a precipitate should be visible
1 mL
1 mL
1
1 mL
1 L
1 L
Centrifuge: 20000 1324, 1 min, 25 10
TITLE: Tracing long-term demographic changes: The issue of spatial scales
AUTHORS: Johannes Mueller, Aleksandr Diachenko

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The protocol concerns estimations of the population density in prehistory at different spatial scales. The following issues are addressed: chronological resolution of demographic changes, estimation of the weight of values for population density in order to transform the initial values included in the sample into the values that may be compared with each other at the regional scale, calibration of the transformed values into real population densities, and the estimation of the weight of values for population density at the scales of macro-regions and for the density of metapopulations. </div></div>

[STEPS]
?. The coefficient representing the ‘weight’ of regions was estimated one time for each of regions, while the number of times a region was considered in different chronological periods is not taken into account. The relative sizes of the regions, as parts of the constant territory, are obtained as the result of the division of their real area by the total area of the macro-region. These contributions are then summed. Therefore, the related product of multiplication at this stage of the research does not represent the actual regional population density, but its ‘contribution’ to the macro-regional population density.
?. Consideration of the most precise estimations possible in terms of original archaeological records, temporal resolution, etc.
?. 
?. An estimation of the population density for a macro-region must consider the regional densities calculated for both agriculturalists and hunter-gatherers. This linearization follows the logic of estimating the macro-regional population density from several differently sized regions as discussed above. This is made possible by an introduction of the coefficient ‘k’ that weights the size of areas that are inhabited by populations with these subsistence strategies.
?. Densities of metapopulations are estimated according to the same logic. However, instead of densities estimated for agriculturalists and hunter-gatherers, the weighting of population densities for macro-regions is considered.
TITLE: Simpli Acv Keto Gummies Reviews | Simpli Acv Keto Gummies Shark Tank | Simpli Acv Keto Gummies Reviews for Weight Loss
AUTHORS: christinealez  

[DESCRIPTION]
The main ingredient in Simpli Acv Keto Gummies is acai berry extract, which has been proven to help in weight loss by suppressing appetite and preventing food cravings. It also helps in reducing body fat and burning fat faster than other diets or programs.

[STEPS]
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
This protocol is part of the VERVE holiday drive to collect exotic off-the-shelf laboratory recipes. More details <a href="https://www.protocols.io/g/verve-net/news/call-for-recipes" target="_blank">here</a>.

[GUIDELINES]
<img id="s-mce-img" class="s-mce-img" src="https://s3.amazonaws.com/pr-journal/bydcz36.png" alt="" data-src="https://s3.amazonaws.com/pr-journal/bydcz36.png" data-ofn="Screen Shot 2015-12-16 at 3.51.39 PM.png" /><br /><strong>Buffer and Reagents for 20-25 people</strong>
<table>
<tbody>
<tr>
<td><strong>Reagent</strong></td>
<td><strong>Amount</strong></td>
</tr>
<tr>
<td>Fresh limes</td>
<td>approximately 40 depending on size and juiciness</td>
</tr>
<tr>
<td>Triple Sec</td>
<td>1 liter</td>
</tr>
<tr>
<td>Tequila</td>
<td>1.5 -1.75 liters</td>
</tr>
<tr>
<td>Crushed ice</td>
<td>7 lbs. "crystal clear"</td>
</tr>
<tr>
<td>Salt</td>
<td> </td>
</tr>
</tbody>
</table>
<br /><strong>Equipment</strong><br />
<ul>
<li>Electric juicer, juice press, or <strong>eager rotation students</strong></li>
<li>4 liter beaker</li>
<li>1 liter graduated cylinder</li>
<li>Sterile pipette, 5 or 10 ml</li>
<li>2 plates</li>
<li>Glass or plastic cups</li>
</ul>

[STEPS]
?. 
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?.
TITLE: How to Cook Ramen
AUTHORS: wenchaoh

[DESCRIPTION]
The complete guide to making delicious ramen. 

[STEPS]
SECTION: Supplies You Will Need
1. Cooking Pot
One Package of Instant Ramen
Chopsticks/Fork
Egg
Any Frozen Veggies (Corn, Peas, etc)

 

SECTION: The Noodles
2. Pour 2.5 cups of water into a cooking pot and put on a high-heat stove. Wait until the water boils.
  

SECTION: The Noodles
3. After the water starts boiling, add the Ramen and Sauce packet from the Instant Ramen package and cook for two minutes. To make the final product more tasty, add any frozen vegetables such as corn, peas, lettuce to the mix.  212 °F 

SECTION: The Noodles
3.1. While cooking, occasionally stir the noodles and submerge the noodles  in water to make sure it cooks properly. 
SECTION: Optional Toppings
4. While plating the ramen, there are some optional toppings to consider putting in your ramen such as:
Soft-boiled eggs (Boil eggs on high heat for 7 minutes, give it an ice bath, and peel)
Fried eggs (Fry egg with a little cooking oil)
Fresh scallions
Pan-fried spam 
Shiitake Mushrooms
Cooked Sesame Seeds / Sesame Oil