eamag/protocols-with-steps huggingface dataset:
TITLE: U Mass - Glucose
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 measures blood or plasma glucose concentration using Analox GM9 Glucose Analyzer or GM7 Micro-Stat Rapid Multi-assay Analyzer.  The measurement is based on the rate of oxygen uptake in the reaction between sample glucose and glucose oxidase.  Plasma glucose levels are elevated (i.e., hyperglycemia) in obesity, insulin resistance, and type 2 diabetes.</div></div>

[STEPS]
?. Check waste and fill glucose reagent reservoir.
?. Prepare  ~0.1ml of standard solution (~144 mg/dl).
?. Press “Enter”, and then “No” to cycle the Analox Analyzer.
?. When cycling is finished, wait for reading to return to ~0 mg/dl (±1mg/dl).
?. Enter calibration mode.
?. Using precision pipet, inject 10 µl of standard solution.
?. Rinse pipet with dH2O.
?. When value is reached, accept calibration.
?. When reading has returned to ~0 mg/dl, inject 10 µl of standard solution, and ensure that the value is ~144 mg/dl.
?. Repeat steps #5~#9 until calibration value is stable.
?. Check calibration by injecting 5 µl of standard and multiplying reported value by 2.
?. The final calculated value should be ~144 mg/dl.
?. Instrument is now ready for sample measurement.  Use 5 or 10 µl of plasma sample for glucose concentration measurement.
TITLE: BSCI:414--Lab 11:Confirming Cloning of spike(RBD)-SUMO/pET28     
AUTHORS: Harley King

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">We've amplified our target genes (SARS-CoV-2 spike and spike (RBD) and SUMO) with primers. Then we purified and performed Gibson Assembly. After transformation we tested a few colonies and found that they were positive. We sent the purified plasmid away for sequencing and now we wish to confirm if we correctly cloned. </div></div>

[STEPS]
?. [Create Alignment with Chromatograms]
Open the "F20_spike(RBD)-SUMO/pET28" plasmid from our BSCI:414 plasmids folder. Make a copy into a new folder under "BSCI:414 Lab 11".
?. [Create Alignment with Chromatograms]
Download the 4 sequence chromatograms from our class folder onto your computer.BSCI414>Files>Lab Results>Lab 11 spike cloning>RBD_pET28 chromatogramsThese chromatograms represent sequence using single primers: T7_promoter and T7_terminator.  AB1PrimerPrimer Sequence2T7_promoterTAATACGACTCACTATAGGG3T7_terminatorgctagttattgctcagcgg
AB1PrimerPrimer Sequence2T7_promoterTAATACGACTCACTATAGGG3T7_terminatorgctagttattgctcagcgg
?. [Create Alignment with Chromatograms]
Select the "Alignments" icon on the right side.
?. [Create Alignment with Chromatograms]
Add the chromatograms and select "Align". Are there differences?What kind of differences?
?. [Watch Cloning Video]
Review the Benchling notebook regarding Gibson Assembly for cloning the spike-SUMO and RBD genes into pET28.https://benchling.com/s/etr-kXqsFUhKxGCbyUGyCx9V
?. [Which Cell Line Should Be Transformed?]
Next steps: transformation but into which cell lines?
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>This protocol describes how to use a short-term cold shock to render Aiptasia aposymbiotic.</p>
<p>After the cold shock it includes two possibilities to proceed one faster one with usage of DCMU and a slower and more gentle one with only keeping the animals in the dark.</p>

[BEFORE_START]
<p>Fluorescence filters:</p>
<p>Every wavelength between 400 and 550 nm efficiently axcites the algal chlorophyll.</p>
<p>The chlorophyll fluorescence emission peaks between 650 and 720 nm.</p>
<p>This means that most RFP filter sets with a wide bandpass or longpass emission filter at above 600 nm will work well.</p>
<p>GFP longpass filter sets will work as well but only in combination with an RGB camera to distinguish red algal fluorescence and green autofluorescence of the anemones themselves.</p>
<p>These numbers are only rough estimations based on a few algal strains. For purchasing new filter sets it will be still best to test them before buying.</p>

[GUIDELINES]
<p><strong>Preparing DCMU (3-(3,4-dichlorophenyl)-1,1-dimethylurea) stock solution:</strong></p>
<p>0.0313 M DCMU in 95-100% ethanol.</p>
<p>For 50 ml, dissolve 7.3 mg in 50 ml ethanol.</p>
<p> </p>
<p>For an end concentration of 50 µM add 32 µl of the stock to 200 ml of artificial seawater. </p>

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

[DESCRIPTION]
<p><strong>Background: </strong>The field of cancer cure is flooded with various newer technologies ranging from advanced form of surgeries to new drugs to novel forms of radiotherapy techniques. While the newer forms of radiotherapy i.e., Intensity modulated radiotherapy (IMRT) or 3-dimensional conformal radiotherapy (3D-CRT) may have the potential of providing improved health outcomes, but they require an additional cost. Thus, it becomes necessary to compare the costs and benefits of a new technology, before considering its inclusion in the current health system. The present study will be done to assess the cost effectiveness of IMRT as compared to the conventional 2 dimensional radiotherapy (2DRT) for the treatment of head and neck cancers (HNCs) in India.</p>
<p><strong> </strong></p>
<p><strong>Methods: </strong>The present study will be a model based effectiveness evaluation. The study will include collecting data on health system cost and out of pocket expenditure incurred on the treatment of HNC, followed by assessment of health outcomes in the form of survival rates and quality of life subsequent treatment with IMRT and 2DRT and finally the development of Markov Model for estimating the incremental cost effectiveness ratio. The present study will be undertaken in the Departments of Radiotherapy and Otolaryngology of a large tertiary care hospital in North India. Health system costs will be assessed using bottom up methodology. Cost of illness approach would be followed for interviewing patients for assessing out of pocket (OOP) expenditure. Patients will be recruited from the Radiotherapy Department, and will be followed up till one year for assessing quality of life weights. Systematic review cum meta-analysis of the existing randomised controlled trials comparing IMRT and 2DRT would be undertaken for assessing pooled survival rates. A Markov model based on the natural history of the progression of HNC will be developed, following societal perspective and lifetime study horizon.</p>

[STEPS]
TITLE: Scanning electron microscopy protocol 
AUTHORS: Rene Flores Clavo, Francisco Breno S. Teófilo

[DESCRIPTION]
This protocol briefly summarizes the basic steps of a scanning electron microscopy processing. The methods adopted for fixation, post-fixation, dehydration, drying in a critical point chamber, sputter coating, and the visualization and acquisition of images are described here.

[STEPS]
SECTION: MATERIAL SELECTION
1. 1 mm2 samples were selected in the colony.


SECTION: FIXATION
2. Samples were fixed in a solution of 2.5 % volume   and 0.1 Molarity (M)   buffer pH 7.3) , at Room temperature, for 240 min.


SECTION: POST-FIXATION
4. Samples was then post-fixed with 1 % volume osmium tetroxide in 0.1 Molarity (M)   buffer, pH 7.3, at Room temperature, for 60 min, protected from ambient light.

SECTION: WASHING AFTER FIXATION
3. Samples was then rinsed three times in 0.1 Molarity (M)    (pH 7.3), at Room temperature , for 20 min for each rinse.

SECTION: WASHING AFTER POST-FIXATION
5. Samples was then rinsed three times in sodium 0.1 Molarity (M)    buffer pH 7.3, at Room temperature, for 20 min for each rinse.

SECTION: DEHYDRATION
6. Samples were dehydrated with ascending acetone series, for 20 min  minutes each step - 30 % volume; 50 % volume, 70 % volume, 90 % volume, 100 % volume (last one step, for three times). 

SECTION: CRITICAL POINT DRYING
7. Samples was then dried using the critical point method with CO2.
SECTION: MOUTING ON THE STUBS
8. Samples was then placed on aluminum stubs.
SECTION: SPUTTER-COATER
9. Samples was then coated with a layer of 30−40 nm gold using a Balzers SCD 050 sputter-coater.
SECTION: OBSERVATIONS AND IMAGE ACQUISITION
10. Observations and photomicrograph aquisitions were obtained using a JEOL JSM 5800LV at 10 kV with SemAfore 5.21 software.
TITLE: World&#39;s Best Cup of Coffee
AUTHORS: timothy.propst  

[DESCRIPTION]
Basic instructions on how to create a cup of coffee.

[BEFORE_START]
Make sure to utilize filtered water for best flavor results.

[GUIDELINES]
Follow instructions carefully.

[STEPS]
1. Measure your coffee. The standard ratio is approximately 2 tablespoons of coffee per 6 ounces of water. Don’t be afraid to add a few extra beans to be on the safe side – you can more approximately measure out your coffee using a scale after it’s ground.
 
1600 mg   
177 mL  water

2. Prepare the water. 

 


 




3. Pour. Saturate the grounds evenly with a smooth, steady pour that will agitate the coffee grounds. Do not put the lid on top of the brewer just yet.
4. Soak and stir. Let the grounds absorb the water for approximately 30 seconds before stirring – a few gentle motions using the back of a spoon around the top layer of the mixture and along the sides, to immerse any grounds that are stuck.
5. Brew. Let the water extract from the grounds for 2 minutes and 30 seconds. Less than that, and you’ll find your coffee may be too sweet or even sour. Any longer, and your coffee will be over-extracted and unappetizingly bitter – so, set a timer.
6. Plunge. There really is no wrong way to push here – just a simple, even push-through of the filter down to the bottom. However, it’s not a clogged toilet – don’t exert too much force or, of course, your coffee will splash. Or you may break the machine, if it’s glass.
7. Pour. Word to the wise: The flavor notes of your coffee will change as the cup cools. If at first you’re not tasting what was intended, let it continue to setup. What you taste when it’s piping hot is not what you’ll taste when it’s cooled to a lukewarm temperature.
8. Flavor to taste.
TITLE: SPARC Cat - Sham Control Chronic Cat 3, Day 14
AUTHORS: Brett        Hanzlicek, Anna Rietsch, Margot Damaser

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a procedure for a sham control chronic cat experiment (Day 14) for cystotomy (bladder surgery).  The cystotomy is performed without UroMOCA implantation.  The cat is observed daily and imaged on day 0, 14 and 30 to track changes to the bladder and overall cat health in response to the cystotomy.  This protocol includes urodynamics and imaging for Day 14 in the chronic experiments.</div></div>

[STEPS]
?. [Transport Cat]
Transport cat from housing site to surgery site.
?. [Animal Prep and catheter placement]
Animal is anesthetized and abdomen is shaved by the vet team.  The cat is then moved into the surgery room and attached to monitors by the vet team.
?. [Animal Prep and catheter placement]
Drape animal and perform betadine scrub on abdomen and genitals.
?. [Animal Prep and catheter placement]
Put surgilube on 3.5Fr catheter and insert into bladder through the urethra.  Advance the catheter until resistance is met, then pull back 2-3cm.
?. [Animal Prep and catheter placement]
Use gentle suction with syringe to withdraw urine from bladder through the catheter.  Measure the volume and save the urine for urinalysis.  urine removed
20 mL
?. [Cystogram - DYNA CT]
Use 1:5 dilution of contrast to saline to visualize bladder.Fill the bladder with   contrast and take a single CT image.Add   more to bladder (total of 20 ml) and take single CT imageTake a 3D CT image with 20ml contrast:saline in the bladder
10 mL
10 mL
?. [Cystogram - DYNA CT]
Empty Bladder
?. [Urodynamics/Cystometry 1]
Performed after cat is transferred from Isoflurane to propofol anesthetic.
Fill rate is 2ml saline/minute using syringe pump.
Data is recorded using Labview software.
Pressure is recorded using an external pressure transducer connected to syringe pump on one end and tubing that leads to the catheter on the other end.
?. [Urodynamics/Cystometry 1]
Fill bladder with saline and record pressure using pressure transducer connected to  LabViewFill to  ;End round 1 urodynamicsTug on catheter after filling to visualize contraction in Labview software
15 mL
?. [Urodynamics/Cystometry 1]
Empty Bladder
?. [Urodynamics/cystometry 2]
Fill bladder with saline at 2ml/min
?. [Urodynamics/cystometry 2]
Fill to  ; End round 2 urodynamics
20 mL
?. [Wake and return cat]
Wait for cat to wake up and return to housing site.
TITLE: No Title
AUTHORS: 

[GUIDELINES]
<p>Reagent List:</p>
<p><br />- Sterile PBS<br />- Cell culture medium (IMDM supplemented with 10% FBS)<br />- Sterile plastic petri dishes<br />- RBC Lysis Buffer (Cat. No. 420301)<br />- Anti-mouse CD3ε, clone 145-2C11 (LEAF™ format, Cat. No. 100314)<br />- Anti-mouse CD28, clone 37.51, (LEAF™ format, Cat. No. 102112)<br />- Anti-mouse IFN-γ, clone XMG1.2, (LEAF™ format, Cat. No. 505812)<br />- Recombinant mouse IL-2 (carrier-free) (Cat. No. 575402)<br />- Recombinant mouse IL-4 (carrier-free) (Cat. No. 574302)<br />- Recombinant human TGF-β1 (carrier-free) (Cat. No. 580702)<br />- Monensin Solution (Cat. No. 420701)<br />- PMA (Phorbol 12-myristate 13-acetate) (Cat. No. P8139 from Sigma)<br />- Ionomycin (Cat. No. I0634 from Sigma)</p>

[STEPS]
?. 
?. 
?. 
?. 
?. 
?. 
?.
TITLE: U Mass - Albumin
AUTHORS: Jason Kim

[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">
This experiment involves a spectrophotometric measurement using Roche Cobas Clinical Chemistry Analyzer. Albumin is a major circulating protein in body.</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 Albumin test on display and run the analysis.
?. Collect and analyze the data.
TITLE: PCR
AUTHORS: Ana Belem García González, Jair Alexis Gardea Sáenz, Irán Alessandra Chaparro Rodríguez, Georgina Diego

[DESCRIPTION]
50 µL volume PCR protocol

[STEPS]
SECTION: RECOVERY IDT SEQUENCES
1. Centrifuge the tubes with the sequences for one minute at 3,000 g x m in the centrifuge
SECTION: RECOVERY IDT SEQUENCES
2. Centrifuge for 5 seconds in the microcentrifuge 
SECTION: RECOVERY IDT SEQUENCES
3. Add nuclease-free water needed to have a final concentration of 10 ng/uL.
SECTION: RECOVERY IDT SEQUENCES
4. Vortex, followed by incubating for 20 minutes at 50°C.
SECTION: RECOVERY IDT SEQUENCES
5. Mix briefly by vortex and centrifuge for 8 seconds in mini centrifuge. 
SECTION: PCR
6. Add nuclease-free water to the first forward and reverse until a concentration of 100 uM is reached, centrifuged quickly in microcentrifuge.
SECTION: PCR
7. Make dilutions with 10 uL of primers and 90 uL of nuclease-free water to reach a concentration of 10 uM
SECTION: PCR
8. In 0.2 mL Eppendorf tubes make the following mixture.
SECTION: PCR
9. 
 

SECTION: PCR
10. Perform the next cycle in thermocycler
TITLE: Welcome &amp; Onboarding
AUTHORS: Andy Alexander, Emma Cimino

[DESCRIPTION]
Must knows for onboarding at UCSB and in the Alexander laboratory.

[STEPS]
SECTION: Welcome to the Alexander lab!🙂 Please complete the following steps to get started:
1. IACUC researcher training checklist:

Email IACUC
PI: Andy Alexander, Protocol: 986
Skim through our protocol: you will NOT be quizzed on the it by us or IACUC, but just read the beginning to get a gist of our research and everything involved.

OHS form: 
Boxes: 
Husbandry: never
Anesthesia: weekly
Surgery: weekly
Behavioral testing: daily
blood/tissue collection: never
Injections: monthly
Trapping wildlife: never
Tagging wildlife: never
Euthanasia: monthly
Hazard administration: never
Animal transport: never
Noninvasive sampling: never
Species we work with: mice and rats

LSF training: login to UCLC netID (if you have done training through this website before)
If unable to login, contact Emma to make an account for you
Skip animal husbandry step

Citiprogram training: follow attached PDF for the following instructions
Complete all boxes besides wildlife research and wild rodents/birds sections
For “working with… in research settings” and “aseptic surgery” courses, complete those for both mice and rats



SECTION: Welcome to the Alexander lab!🙂 Please complete the following steps to get started:
1.1. After completing the checklist, have Dr. Alexander sign and send it to IACUC
After meeting with IACUC on zoom and receiving a tour of ARC, you will have access to our animal holding rooms and will be authorized to work with animals
SECTION: Welcome to the Alexander lab!🙂 Please complete the following steps to get started:
2. Lab access (5175)
Fill out the 6 documents you were sent and send them to Christy Xu (christyxu@ucsb.edu) along with a picture of your UCSB access card
TITLE: Prediction of pneumoconiosis by serum and urinary biomarkers in workers exposed to asbestos-contaminated minerals
AUTHORS: Hsiao-Yu Yang

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Prediction of pneumoconiosis by serum and urinary biomarkers in workers exposed to asbestos-contaminated minerals</span></div><div class = "text-block">PLOS One</div></div>

[STEPS]
?. [Dataset preparation]
Download the dataset and store at "C:\r".
?. [Required software]
This protocol requires R-3.5.2 for Windows (32/64 bit) (https://cran.r-project.org/bin/windows/base/)
?. [Dataset preparation]
?. [Dataset preparation]
Download the file of “PLoS One Excel Main Raw Datafile.csv”. Store at “C:\r”
?. [Copy the R script of six machine learning algorhithms and pastes onthe R console.]
?. [Cpoy the R script of six machine learning algorithms on R consol.]
TITLE: Cluster Counting
AUTHORS: daniel.dautan daniel, Per Svenningsson

[DESCRIPTION]
Used for counting clusters labeled for pSer129 alpha-synuclein in mouse upper gastrointestinal tract (intestine). Sections should be stained, mounted, and imaged with high resolution (2048 x 2048 scanning).

[STEPS]
1. Stain structures for pSer129 and scan with high-resolution (pixel size of 6.25µm). 
2. Import the images into ImageJ.
4. Adjust signal intensity to a standardized threshold of 95%. (All thresholds, exposure settings, and laser intensities were applied consistently across all scans). 
3. Convert to grayscale.
5. Employ the "Process - Binary - Convert to Mask" function.
The mask function can be determined using the default method against a black background.
6. Apply a watershed filter to select clusters with similar distribution.
7. Execute the "Analyze Particles" function.
Size range: 0 to infinity
Display and summarize results.
This will extract all clusters including their coordinates and areas.
8. To extract clusters with a size equal to or smaller than 1 pixel (6.25µm²) and clusters identified as artifacts (>15000 µm²), use the Excel COUNTIF function, count the number of small clusters (6.25 to 50 pixels), medium-sized clusters (50 to 200 pixels), and large clusters (>200 pixels).
9. Determine relative density of clusters for the amount of tissue area analyzed.
TITLE: Ultra-freeze media
AUTHORS: David Shis, L. F. Gibson, J. T. Khoury

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This is a recipe for an "ultra-freeze" meda recipe. Taken stock from Gibson </span><span style = "font-style:italic;">et al. </span><span>This recipe enables the quicker recovery of cells stored as a glycerol stock at -80. Cells revived when frozen in this medium seem to revive quicker, especially when inoculated into minimal media. </span></div><div class = "text-block">A bit onerous to prepare when compared to the standard 15%v/V glyceorl stock approach but can cut up to 24hrs in revival time, very valuable when dealing with slow growing undomesticated microorganisms. </div></div>

[STEPS]
?. [100mL recipe]
Mix Together the following reagentsTryptone Soya brothGlucose Skim milk powder Glycerol
3 g
0 g
2 g
4 g
?. [100mL recipe]
Autoclave for 30 minutes
?. [100mL recipe]
Solution should be turbid, heterogeneous. Store at RT
?. [Using Ultra-freeze media]
The paper suggests growing up a lawn but I have found 5mL of liquid culture at stationary phase of chosen microbe works just as well. Just need lots of stationary phase cell material to resuspend in ultra-freeze media for storage. Inoculate overnight culture in media volume that will yield about similar wet cell mass of 5mL of Escherichia coli.
?. [Using Ultra-freeze media]
If using a lawn of microbes... scrape clean plate of solid media containing lawn of microbe monoculture. Resuspend goop in 1mL of ultrafreeze media, preferabbly in a labeled cryovial.If using stationary phaes culture. Pellet cells, spin down at 5000rcf for 10 minutes. Pipette off supernatant and resuspend pellett in 1mL of ultrafreeze media, preferrably in a  labeled cryovial.
?. [Using Ultra-freeze media]
Freeze!Store cryovial with ultra-freeze resuspension in -80.
?. [Recovery]
Scrape a little bit of ice from cryobial. Inoculate onto solid or liquid media and wait for growth. In my experience the pellett is pretty hard. It may be worthwhile to modify the recipe to 18.75g for more vitrious ice. However, 4g glyceorl in a 100mL solution, does not seem to be particularly pernicious to the microbes.