eamag/protocols-with-steps huggingface dataset:
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>We attempt to link laboratory-based measures of preferences with measures of school performance. We measured in an incentivized way risk, time, social and competitive preferences and also cognitive abilities of university students and look for associations between these measures and two important academic outcome measures: exam results and GPA.</p>
<p>We find consistently that cognitive abilities (proxied by the Cognitive Reflection Test (Frederick 2005)) are very well correlated with school performance. Regarding non-cognitive skills, we find suggestive evidence for many of our measured preferences. We used two alternative measures of time preference: patience and present bias. Present bias explains exam grades relatively better, while patience is better explaining GPA. Both measures of time preferences have a non-linear relation to school performance. Competitiveness matters, as students, who opt for a more competitive payment scheme in our experiments have a higher average GPA and better exam grades. We observe also that risk-averse students perform a little better than risk-loving students. That makes sense in case of multiple choice exams, because risk-loving students may want to try to pass the exam less prepared, as the possibility of passing as exam just by chance is not zero. Finally, we have also detected that cooperative preferences – the amount of money offered in a public good game – associates strongly with GPA, but in a non-linear way. Students who offered around half of their possible amounts had significantly higher GPAs than those, who offered none or all their money.</p>
<p>Keywords: <em>competititive preferences,</em> <em>experiment, non-cognitive skills, risk preferences, school performance, social preferences, time preferences.</em></p>
<p>JEL codes: C91; D91; I20</p>

[STEPS]
?.
TITLE: UC Davis - LDL Protocol
AUTHORS: Peter Havel

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:  </span></div><div class = "text-block">LDL and VLDL are separated from HDL using a precipitation reagent. Then the HDL fraction is measured for either TC or TG using the same reagents for total cholesterol or triglyceride.</div></div>

[STEPS]
?. Add 25µl 2X precipitation buffer to 25µl of sample using a positive displacement pipet.
?. Vortex and let sit at RT for 10 minutes.
?. Centrifuge at 2000×g for 10 minutes at 4°C.
?. Pipet supernatant into new tube, this is the HDL fraction.
?. Add 5 µl of calibrator and sample to each well.IMPORTANT: Make sure not to add any bubbles to the wells when dispensing reagents, this will interfere with reading in the platereader.
?. Add 300 µl of  TC or TG reagent to each well. Incubate at 37°C for 5 minutes. Read at 540 nm. IMPORTANT: If samples are hemolyzed, pipet a blank well with 5µl sample and 300µl PBS
?. Subtract blank readings from final readings. The assay will be linear so the unknown samples can be calculated as (Sample Absorbance ÷ Calibrator Absorbance) × Calibrator Concentration.
?. HDL samples are diluted ½ so multiply these by 2 to get the final value. Subtract this from the total triglyceride or cholesterol value to get the LDL/VLDL value.
TITLE: Calibrating Vaisala HMP45
AUTHORS: USDA

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Calibrating Vaisala HMP45</div></div>

[STEPS]
?. Clean the sensorRemove the cap and filter. The filter is like Teflon tape, very fragile. Use DI water and a Q-tip to remove dirt/dust. The filter can usually be unscrewed from inside the cap, if it will not turn while using your finger, then a screwdriver to push it out from the top is a last resort. There is a possibility of damaging the filter and filter frame.This is a good time to re-tin the connecting wires. Makes install much easier.After the cap and filter have dried, re-assemble the HMP. Remove the rubber covering for the “W, D, T” potentiometer screws.Have a close look at the screw orientation. Use the smallest CSI flat screwdriver or the special Vaisala tool (if you can find one). These screws are sometimes tough to engage. They are also very sensitive, just slightly pushing on the screw will change the output values. I’ve sometimes had to observe how much change was imparted by my screwdriver pressure and then set to slightly off of 60%, then release the potentiometer and see if it sets on 60% or just off and repeat.
?. Setup your chamber, LI610, logger, HMP and thermistors. Connect everything, start prog and Li610. Check the logger to verify the chamber temp and thermistors are working. Insert the HMP into the chamber so that you can access the calibration potentiometers easily. You will be changing the “Dry” and “Temp.”Fill top of radiator with DI water. Fill the condenser following the instructions in the manual (use DI water only).Connect the LI610 to the chamber “Output 1”. Use the shortest amount of tubing you can. A longer length will allow the air to change by the time it reaches the chamber.
?. Calibration time. Using the following table (Li610_Cal on the s:drive and hard copy in the black book), set the LI-610 to output 60% RH based on the chamber temp reported by the thermistors. If chamber temp is 21, then Li-610 set temp for 60% RH would be 12.94.When the sensor RH levels out and the chamber reaches equilibrium, record the values on the calibration worksheet:DateSN (factory Vaisala SN)NSTL SN (sometimes written in marker, “NSTL 01” or “2010-01”)Chamber Temp (Thermistor avg temp)Li-610 Set Temp 60% RH21X 60% RH (what is the sensor reading before changing potentiometer)Now go ahead and change the “Temp” potentiometer to match the average of the thermistors.Record the new value under “Vaisala Temp”Next change the “Dry” potentiometer to match the 60% RH in the chamber.Record the value you were able to set to under the “Adjusted to 60% RH” column. Most of the time it is 59.99 to 60.01. Now we want to test what it will read at 90% RH. Find the LI-610 setpoint for 90% RH and adjust the Dewpoint Generator. It will take a few minutes to equilibrate. When the sensor reaches a plateau, record the value under “21X 90% RH” Finish by adding your initials.
TITLE: SuperSoil - Soil DNA Extraction
AUTHORS: Jie Hao Ou, Yin-Tse   Huang

[DESCRIPTION]
SuperSoil - Soil DNA Extraction

[GUIDELINES]
Keep all solutions at room temperature

[STEPS]
SECTION: Lysis
1. Add  following materials to 1.8 ml centrifuge tube
250 mg soil
1.5 g Bead
800 µl SD1
SECTION: Lysis
2. Vortex for 10 min at max speed

 

SECTION: Lysis
3. 14000 rpm, 1 min

SECTION: Lysis
4. Transfer the supernatant  to a clean 1.5 ml or 2 ml tube

 

SECTION: Remove inhibitor
5. Add 200 ul SD2
 

SECTION: Remove inhibitor
6. Vortex for 5 s at max speed

SECTION: Remove inhibitor
7. 14000 rpm, 1 min 

 

SECTION: Remove inhibitor
8. Transfer the supernatant to a clean 1.5 ml or 2 ml tube
 

SECTION: Bind DNA to silica membrane
9. Add 600 µl SD3
SECTION: Bind DNA to silica membrane
10. Vortex for 5 s at max speed

SECTION: Bind DNA to silica membrane
11. Transfer 650 ul lysate to spin column
SECTION: Bind DNA to silica membrane
12. 14000 rpm, 1 min, discard flow-through

SECTION: Bind DNA to silica membrane
13. Transfer remaining lysate to spin column
SECTION: Wash silica membrane
14. Add 500 ul SEA to spin column
SECTION: Wash silica membrane
18. 14000 rpm, 1 min, discard flow-through
SECTION: Wash silica membrane
15. 14000 rpm, 1 min, discard flow-through
SECTION: Wash silica membrane
16. Add 500 ul S5 to spin column
SECTION: Wash silica membrane
17. 14000 rpm, 1 min, discard flow-through
SECTION: Elution
19. Add 50–100 ul S6
TITLE: Air Compressor Use and Maintenance
AUTHORS: Ksenija Sabic

[DESCRIPTION]
This manual includes instructions for regular use and maintenance of ACGP Series Air Compressor by Newport. 

Instructions are taken directly from manufacturer website: https://www.newport.com/p/ACGP (also attached).

Please use the printed Air Compressor Maintenance Checklist in Alcove D to record maintenance activity. 

[GUIDELINES]
Observe these general warnings when operating or servicing this equipment:
• Read the operating instructions and recommendations before using the compressor.
• Make sure the compressor is kept upright at all times.
• Heed all warnings on the unit and in the operating instructions.
• Do not use the compressor if the switch does not turn it on and off. Any compressor that cannot be controlled with the switch is dangerous and must be repaired.
• Disconnect power before cleaning and servicing the equipment. Do not use liquid or aerosol cleaners; use only a damp lint-free cloth.
• Lockout all electrical power sources before servicing the equipment.
• To avoid explosion, do not operate this equipment in an explosive atmosphere.

[STEPS]
SECTION: Weekly Maintenance
3. Check for oil leaks, abnormal noise or vibration.
SECTION: Monthly Maintenance
4. Check oil level.

Drain the condensate that has collected in the air tank. It may be necessary to do more often when operated in high humidity.

Drain the water collected in the air outlet filter.

Clean the compressor using a soft cloth. Wipe off any oil or dirt.

Check compressor efficiency (make sure all nuts and bolts are tight, check for air leaks, pressure hose wear, pipe fittings and electrical connections).
SECTION: Quarterly Maintenance
5. Check the air intake filter. Replace if necessary.
SECTION: Annual Maintenance
6. Replace oil.

Check pressure relief valve function.
SECTION: Weekly Maintenance
3.1. Check oil level through the sight glass weekly to make sure the oil level is aligned with the red marker line next to the sight glass. Add or remove oil as needed.
SECTION: Operation (before and after use of Xenium instrument)
1. Turn on (if not already)

Make sure that the power supply voltage is the same with what’s indicated on the data label: 230V/50 Hz or 115V/60 Hz. Use only 3-pole receptacles that accept the compressor’s plug.
The on/off switch is located on the top of the pressure switch. To switch the unit on, turn the switch to position “1”. When switched on, the compressor starts to build up pressure until the tank reaches the maximum allowed pressure (8 bar/120 psi). The unit will then be automatically
switched off until air is used and the pressure in the tank drops to the minimum operating pressure (6 bar/90 psi), at which point the compressor automatically switches on.
SECTION: Operation (before and after use of Xenium instrument)
2. Check the outlet pressure
 
The outlet pressure can be adjusted using the knob on the filter/regulator so that the air output is enough for the application, but the output will not exceed the maximum air pressure specified by the application. Turn the knob clockwise to increase the pressure and counter-clockwise to decrease pressure.
TITLE: KAPP-Sen TMC: Dissociation of Pancreatic Acinar and Ducts (non-recovered)
AUTHORS: Juliana Alcoforado Diniz, Jessica Garofalo, Dylan Baker, Paul Robson

[DESCRIPTION]
The dispersed samples were shipped cold from PRODOLABS. Prior to scRNA-seq, dispersed samples from brain dead donor’s pancreatic acinar and ducts were dissociated as follows.

[STEPS]
SECTION: Cell Dissociation with TrypLE
1. 
 

SECTION: Fixation of Cells &amp; Nuclei for Chromium Fixed RNA Profiling
2. Cells were fixated prior to scRNAseq according to https://dx.doi.org/10.17504/protocols.io.x54v9py5zg3e/v1
SECTION: Cell Dissociation with TrypLE
1.1. Distribute specimens into 50 ml conical tubes, try to make similar cell concentrations across all tubes. *** Receive acinar in ~300 ml, should distribute into 12 tubes with 25 ml each***
SECTION: Cell Dissociation with TrypLE
1.2. Centrifuge acinar samples for 2 min at 230 g and 4°C. Leave duct samples to settle without disturbance.
SECTION: Cell Dissociation with TrypLE
1.3. Wash samples 3X with 25 ml PBS.
SECTION: Cell Dissociation with TrypLE
1.4. Add 10 ml TrypLE E and incubate at 37°C, mixing with a pipette approximately every 5 min.
Acinar: in TrypLE E at 37°C for approximately 30 mins.
Ducts: in TrypLE E at 37°C for approximately 15 mins.
SECTION: Cell Dissociation with TrypLE
1.5. To stop reaction, add 30 ml per tube of stopping media.
SECTION: Cell Dissociation with TrypLE
1.6. Centrifuge acinar and ducts at 1300 rpm, 4°C, 2 mins.
SECTION: Cell Dissociation with TrypLE
1.7. To stop: add 30 ml per tube of stopping media.
SECTION: Cell Dissociation with TrypLE
1.8. Centrifuge acinar and ducts at 1300 rpm, 4C, 2 mins.
SECTION: Cell Dissociation with TrypLE
1.9. Aspirate TrypLE E and wash 1X with stop media. Aspirate then resuspend in stop media to (Acinar) 5 ml or (Ducts) 2 ml.
SECTION: Cell Dissociation with TrypLE
1.10. Transfer cell suspension through 70 µm filter then combine to 2 ml (Acinar) and 1ml (Ducts). Filter again through a 40 µm Flowmi.
SECTION: Cell Dissociation with TrypLE
1.11. Count cells using AO/PI (acridine orage/propidium iodide) Cell Viability Kit for Luna-FL automated cell counter.
SECTION: Cell Dissociation with TrypLE
1.12. Proceed to cell fixation.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>This protocol decribes how to make 1 L of Luria-Bertani liquid medium (also known as LB broth) for the culturing of bacteria.</p>

[GUIDELINES]
<p>LB broth can be stored at room temperature once autoclaved and kept for up to 6 months.</p>
<p>If your broth becomes cloudy it has become contaminated and is no longer viable. Contaminated LB broth must be disinfected (i.e. by adding Virkon at 2% final concentration) and then autoclaved before disposal.</p>

[STEPS]
?. 
?. 
?. 
?.
TITLE: Streptococcal protein G and Protein-AG sandwich ELISA
AUTHORS: Angel  Justiz-Vaillant

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This ELISA was used to study the interactions between Staphylococcal protein-G (SpG) and protein-AG (SpAG) with different immunoglobulin preparations from mammalian and avian species. </div></div>

[STEPS]
?. This ELISA was used to study the interactions between Staphylococcal protein-G (SpG) and protein-AG (SpAG) with different immunoglobulin preparations from mammalian and avian species. The 96 well microtiter plate was coated overnight at 4°C with 2 µg/µl per well of SpG in carbonate-bicarbonate buffer pH 9.6.
?. The plate was then treated with bovine serum albumin solution and washed 4X with PBS-Tween. 50 µl of immunoglobulins (1 mg/ml) is added and incubated for 1h at room temperature, and the microplate is rewashed 4X with PBS-Tween.
?. Then, 50 µL of peroxidase-labeled SpAG conjugate diluted 1:5000 in PBS-non-fat milk was added to each well and incubated for 1h at RT. The plate was washed 4X with PBS-Tween.
?. Then, 50 µL of o-phenylenediamine solution (4 mg/mL) was added, and the plate was incubated for 15 min at RT in the dark. The reaction was stopped with 50 µL of a 3M H2SO4 solution.
?. The plate was visually assessed for color development and read on a microplate reader at 492 nm. A cut-off point was calculated as the mean of the optical density of the negative controls multiplied by two. The cut-off value was set to 0.32.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>Denville LE Agarose is an all purpose agarose for routine nucleic acid electrophoresis of fragments between 500bp-23,000 bp.</p>
<p>Denville LE Agarose has no detectable DNase or RNase activity.</p>
<p> </p>
<p>Please refer to the appropriate protocol below, depending on whether you are using a hot plate or a microwave.</p>

[STEPS]
TITLE: FCMPASS - Cataloguing fluorescence reference materials
AUTHORS: Joshua Welsh, Sean Cook, Jennifer Jones

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines the steps required to catalogue fluorescence reference materials using the FCMPASS software. This is one of a number of protocols in the pipeline for performing small particle calibration using the fcmpass software package.</div></div>

[STEPS]
?. [Opening the Bead Catalogue]
Open FCMPASS
?. [Opening the Bead Catalogue]
Click ‘Catalogue’ in the top menu bar
?. [Bead Catalogue Fluorescence Overview]
Under the ‘Fluorescence’ tab entry fields exist for each of the pertinent metadata for reporting with fluorescence calibration.
?. [Bead Catalogue Fluorescence Overview]
Enter the name of the fluorophore on the fluorescence reference beads.
?. [Bead Catalogue Fluorescence Overview]
Enter the manufacturer, catalogue number, and lot number fields appropriately.
?. [Bead Catalogue Fluorescence Overview]
In the ‘Bead Ref Values’ field enter each fluorescence beads reference values. This may be in molecules of equivalent soluble fluorophore, equivalent reference fluorophore, or antibody binding capacity.
?. [Bead Catalogue Fluorescence Overview]
After each reference value click the ‘+’ button. To remove a reference value, select the reference value from the listbox below and press the '-' button.
?. [Bead Catalogue Fluorescence Overview]
Once all fields and reference values have been added, press the ‘Create Set’ button. The beads will then appear in the table below as a new row and will be available for selection when performing fluorescence calibration.
?. [Bead Catalogue Fluorescence Overview]
The 'Delete Set' button is also available to delete any unwanted entries. Simply select the rows that are unwanted and press the 'Delete Set; button.
?. [Bead Catalogue Fluorescence Overview]
The 'Append Set' button allows for the editing of already existing entries. By selecting the desired row, the information is written into the entry fields above. This information can be modified as needed, and then the 'Append Set' button can be pressed to append the selected table entry. Note: You can only append a single table entry at a time.
TITLE: Ex vivo electrophysiology
AUTHORS: Katerina Rademacher, Ken Nakamura

[DESCRIPTION]
This protocol describes steps for ex vivo electrophysiology in mouse brain slices. This protocol also includes instructions for clozapine N-oxide (CNO) testing in DREADD-expressing neurons.

[STEPS]
SECTION: Tissue Preparation
1. Deeply anesthetize the mouse with isofluorane, decapitate, and remove the brain.
SECTION: Tissue Preparation
2. Using a vibratome, cut 150mm horizontal slices containing the region of interest in ice-cold aCSF solution and allow to recover at 33˚ C in aCSF for at least one hour.
SECTION: Recording
3. For fluorescent imaging, visualize slices under an Axio Examiner A1 equipped with Dodt and IR optics using a Zeiss Axiocam 506 mono and Neruolucida 2023 software.
SECTION: Recording
4. Whole-cell patch-clamp recordings are made at 33˚ C using 3 – 5 MOhm pipettes. Recordings are made using Sutter IPA and SutterPatch v2.3.1 software (Sutter Instruments), filtered at 5 kHz and collected at 10 kHz.
SECTION: Recording
4.1. For Ih: voltage clamp cells at -60mV and step to -40, -50, -70, -80, -90, -100, -110, and -120 mV. Ih magnitude is quantified as the difference between the initial steady-state response to the -120mV step and the asymptote of the slow current sag.
SECTION: Recording
4.2. For spontaneous firing rates: record in current-clamp mode (I= 0 pA). Spontaneous firing rate is measured as the mean firing rate during the first 2 min of whole-cell recording. 
SECTION: Recording
4.3. Action potential (AP) waveform measurements are made from averages across at least 8 APs from the first 2 min of recording.
SECTION: Recording
4.4. For input resistance: Apply a brief hyperpolarizing pulse once every 10 sec and average across the measurements made during the first 2 min of recording.
SECTION: Recording
4.5. For CNO testing in DREADD-expressing neurons: spontaneous firing rate or resting membrane potential are monitored until a stable baseline is observed for at least 5 min. Then switch the perfusion solution to 1mM CNO for 5 min.
SECTION: Recording
5. When recordings are complete, drop fix slices in 4% formaldehyde in PBS for at least 2 hr.
SECTION: Recording
6. Complete statistical analyses in R, first testing whether data meet the criteria for parametric statistical evaluation.
TITLE: Isolation of Nuclei from Human or NHP Brain Tissue
AUTHORS: Allen Institute for Brain Science

[DESCRIPTION]
Isolation of nuclei from frozen adult human brain tissue or thawed and microdissected brain tissue sections for FPCR and/or RNA-seq analysis. 
 
Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number U01MH114812. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

[STEPS]
TITLE: Making worm picks
AUTHORS: Bonnie  Evans

[DESCRIPTION]
Making platinum wire picks for transferring C.elegans onto plates

[STEPS]
3. Light the ethanol burner. Take care that there is nothing directly above it, eg. papers attached to shelf.
1. Put on safety glasses.
4. Hold a disposable glass Pasteur pipette in one hand and the platinum wire with forceps in the other hand. 
5. Place the platinum wire inside the pipette and move it above the flame for a short while to seal the glass around the wire. If preferred, use flat-ended pliers to flatten the end of the platinum wire.
6. Remove the pick from the flame and wait for it to cool down before touching.
7. Use the cap to extinguish the flame and check to see that it is gone out. 
2. Use pliers to cut an appropriate length of platinum wire.
TITLE: Neuromelanin staining (Fontana-Masson staining)-DAB staining on midbrain organoids
AUTHORS: michela.deleidi, María José Pérez J., Hariam Raji, Pascale Baden, Federico   Bertoli

[DESCRIPTION]
Fontana-Masson staining is a silver staining technique that is commonly used to identify melanin-containing cells. That was combined with DAB-TH staining that works by using an antibody to detect the presence of TH, followed by a reaction with a substrate (DAB) that results in the formation of a brown-colored product at the site of the antigen-antibody interaction.

[STEPS]
SECTION: Neuromelanin staining
1. Incubate human midbrain organoid sections in a fresh solution of 3:1 methanol (MeOH)/3% hydrogen peroxide at Room temperature for 20 min.

SECTION: Neuromelanin staining
2. Wash the slides and block it.
SECTION: Neuromelanin staining
3. Apply primary antibodies in NGS 5% in PBS+ Triton-X 0.2% solution 60 min at 4 °C. 

SECTION: Neuromelanin staining
4. Next, wash slides. 
SECTION: Neuromelanin staining
5. Prepare ABC solution from Vectastain according to the manufacturer’s instructions (VECTASTAIN® Elite® ABC-HRP Kit, Peroxidase (Standard) PK-6100) and apply to sections for 60 min at Room temperature. 
SECTION: Neuromelanin staining
6. Wash the slides. 
SECTION: Neuromelanin staining
8. Apply DAB solution to the sections at Room temperature for 30 seconds to 12 min depending on when the visible reaction occurred. 

SECTION: Neuromelanin staining
9. For the visualization of neuromelanin, use the Fontana-Masson stain kit, according to the manufacturer’s instructions.  (Fontana-Masson Stain Kit; Sigma‒Aldrich-HT200). 
SECTION: Neuromelanin staining
10. Eventually mount slides with synthetic resin.
SECTION: Neuromelanin staining
2.1. Wash the slides in PBS for 5 min. (1/3)

SECTION: Neuromelanin staining
2.2. Wash the slides in PBS for 5 min. (2/3)
SECTION: Neuromelanin staining
2.3. Wash the slides in PBS for 5 min. (3/3)
SECTION: Neuromelanin staining
2.4. Then, block with NGS 10% in PBS+ Triton-X 0.2% for 60 min at Room temperature.

SECTION: Neuromelanin staining
4.1. Wash the slides in PBS for 5 min. (1/3)
SECTION: Neuromelanin staining
4.2. Wash the slides in PBS for 5 min. (2/3)
SECTION: Neuromelanin staining
4.3. Wash the slides in PBS for 5 min. (3/3)
SECTION: Neuromelanin staining
4.4. Apply secondary antibodies to NGS 5% in PBS+ Triton-X 0.2% solution for 60 min at Room temperature.
SECTION: Neuromelanin staining
7. Prepare DAB solution according to the manufacturer’s instructions by diluting in 50 mL of 1x PBS with 50 µL of 3% H2O2. 

SECTION: Neuromelanin staining
6.1. Wash the slides in PBS for 5 min. (1/3)
SECTION: Neuromelanin staining
6.2. Wash the slides in PBS for 5 min. (2/3)
SECTION: Neuromelanin staining
6.3. Wash the slides in PBS for 5 min. (3/3)