eamag/protocols-with-steps huggingface dataset:
TITLE: How to make a cup of tea DOI Forked
AUTHORS: ines.boehm 

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is part of the </span><a href="https://carpentries-incubator.github.io/fair-bio-practice/06-record-keeping/index.html" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">Record Keeping</span></a><span> lesson within the </span><a href="https://carpentries-incubator.github.io/fair-bio-practice/" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">FAIR in (biological) practice</span></a><span> DataCarpentry course. Here we explore the perfect protocol to brew tea.</span></div></div>

[STEPS]
?. [Preparation of water and tea]
Fill the kettle with ~250mL of water, or until your min fill line and boil the water.
?. [Preparation of water and tea]
In the meantime prepare your tea bag, unpack it and place it in the cup/mug so that the tag is positioned outside of the mug.
?. [Preparation of water and tea]
Once the water is boiled, instantly pour the hot water into the mug. Ensure you fix the tag on the outside of the mug with your finger, to avoid falling in of the string + tag of the tea bag. Otherwise removal of the tea bag becomes more difficult.
?. [Brewing]
Brew the tea for 3 min
?. [Brewing]
Use the string/tag to remove the tea bag. Discard the tea bag in your compost for most appropriate recycling.
?. [Flavouring]
Add 5 mL = 1 teaspoon full fat milk to your tea
?. [Flavouring]
Enjoy!
TITLE: RNAseH-based ribodepletion
AUTHORS: Nicole Schonrock, Helaine Graziele Santos Vieira, Oguzhan Begik, Eva Maria Novoa

[DESCRIPTION]
Goal: Method to ribodeplete samples from rRNAs using RNAseH nuclease. 
Summary: DNA oligos are complementary to human rRNAs. They will anneal to the rRNA molecules. RNAseH will degrade RNA-DNA duplexes, leaving the RNA samples depleted from rRNAs
Tested on :Human, Mouse and Yeast (for 18s and 28s ribodepletion).
Cost: DNA oligonucleotides will be expensive the first time ordered, but will last for many rounds of ribodepletion. Once the DNA oligonucleotides have been purchased, the major cost comes from the RNAseH enzyme. In our hands, the cost is much lower than commercial kits, thus being scalable for high input samples where the ribodepleted material needs to be high. 
Recommended for: NGS-based approaches. Do not use for Nanopore-based approaches as nuclease-based methods degrade RNA molecules. 

[STEPS]
TITLE: Vegan  Latkes
AUTHORS: Lenny Teytelman, Hannah Gershik

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This recipe is a traditional Eastern-European Jewish latkes (potato pancakes). It is finely grated, unlike coarse in American latkes. Also, egg turns out to be completely unnecessary, so this is also vegan.</div><div class = "text-block">(Usually you eat them with sour cream though, and I'm not sure how widely available vegan sour cream is.)</div></div>

[STEPS]
?. Peel and wash 6 Russet potatoes.
?. Add 1 teaspoon of salt.
?. Add \frac{1}{4} cup of flour to the potatoes
?. Cut up the potatoes and grate in a food processor.
?. Cover bottom of a frying pan with oil and heat to medium-high.
?. Use a spoon to remove the water; keep doing this as you fry.Put the spoon onto the surface of the batter, pressing it down a little bit. Let the liquid seep in.
?. Fry for 3-5 minutes until crisp.
?. Flip, add more oil, and fry another 3-5 minutes.
?. Process quickly again to mix the salt and flour.
TITLE: No Title
AUTHORS: 

[BEFORE_START]
<p>Prepare Edwards buffer</p>
<table style="width: 50px;">
<tbody>
<tr>
<td style="width: 10.0167px;"> </td>
<td style="width: 33.9833px;">
<table style="height: 148px; width: 416px;">
<tbody>
<tr>
<td style="width: 76px;">Reagent</td>
<td style="width: 76px;">Final conc. </td>
<td style="width: 92px;">[g] for 100 ml</td>
<td style="width: 105px;">molar mass</td>
<td style="width: 30px;">comment</td>
</tr>
<tr>
<td style="width: 76px;">Tris</td>
<td style="width: 76px;">200 mM</td>
<td style="width: 92px;">3,15</td>
<td style="width: 105px;">157,6 g/mol</td>
<td style="width: 30px;"> </td>
</tr>
<tr>
<td style="width: 76px;">EDTA</td>
<td style="width: 76px;">25 mM</td>
<td style="width: 92px;">0,93</td>
<td style="width: 105px;">372,24 g/mol</td>
<td style="width: 30px;">EDTA-Disodium-Dihydrate</td>
</tr>
<tr>
<td style="width: 76px;">NaCl</td>
<td style="width: 76px;">250 mM</td>
<td style="width: 92px;">1,46</td>
<td style="width: 105px;">58,44 g/mol</td>
<td style="width: 30px;"> </td>
</tr>
<tr>
<td style="width: 76px;">SDS</td>
<td style="width: 76px;">0,5% (w/v)</td>
<td style="width: 92px;">0,5</td>
<td style="width: 105px;"> </td>
<td style="width: 30px;"> </td>
</tr>
</tbody>
</table>
</td>
</tr>
</tbody>
</table>
<p>Adjust to pH 8 (with HCl) before adding SDS, then fill up to 100 ml with ddH<sub>2</sub>O.</p>

[STEPS]
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?.
TITLE: Minipump Subcutaneous Implantation for Rats
AUTHORS: Lani Tieu, Lauren Smith, Olivier George

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines the step-by-step procedure for performing subcutaneous implantation of osmotic minipumps on rats. </div></div>

[STEPS]
?. [Procedure]
Anesthetize rat in induction chamber with isoflurane vaporizer dial on 5.
?. [Procedure]
Shave the rat’s back starting from above the hind legs to the shoulders.
?. [Procedure]
Weigh the rat and record weight on the surgery sheet.
?. [Procedure]
Place the rat on surgery table and put its nose in the nose cone. Put vaporizer dial on 3.
?. [Procedure]
Clean the rat’s back with alcohol prep pad and betadine swabstick.
?. [Procedure]
With sharp scissors or scalpel, make an incision on the lower back just above the hind legs. Make the cut wide enough for the minipump to be inserted.
?. [Procedure]
Use tooth/tissue forceps to hold the skin up and blunt-dissect with blunt scissors.
?. [Procedure]
Pick up the filled minipump by the top and insert it with the end going in first.
?. [Procedure]
Close the incision site with sutures and vetbond. Write down how surgery went in surgery sheet.
?. [Procedure]
Give point-body weight intramuscular cefazolin injection.
?. [Procedure]
Give point-body weight subcutaneous flunixin injection.
?. [Procedure]
Place the rat in recovery box. Wait for the rat to wake up and show some active behavior before returning to home cage. Write down recovery notes in surgery sheet.
?. [Procedure]
Put POST-OP sticker on cage card with date and type of surgery.
?. [Procedure]
Sterilize surgery tools before operating on the next rat.
?. [Procedure]
Insert closed blunt scissors into the incision, keeping them parallel to the rat's back.
?. [Procedure]
Open the scissors while they are inside to separate the skin from the muscle, and create a subcutaneous pocket.
?. [Procedure]
Pull scissors out while they are open and repeat steps 7.1 and 7.2 moving towards the shoulders. Make the pocket big enough for the minipump to sit inside.
The minipump should not rest against the incision when it is closed up.
Never close the scissors while they are inside the animal.
TITLE: Protocol Collection: Perfusing, Sectioning, IHC, Mounting and Coverslipping Mouse Brain Specimens
AUTHORS: Naveen Ouellette, daphne.toglia, Holly Myers

[DESCRIPTION]
This protocol collection details the steps for a whole mouse brain specimen to be perfused, sliced, stained with antibodies, DAPI, or both, and made into slides. The intracardiac perfusion fixation includes anesthesia, exsanguination, fixation, brain removal, and post-fixation storage. A sliding microtome is used to slice the whole brain into sections, and the sections are stained, mounted on glass slides, and coverslipped. The result is that anatomical structures in brain regions of interest may be labeled in a way that can be viewed by laser channels on a microscope and imaged for data collection. 


[STEPS]
SECTION: Sectioning Mouse Brain with Sliding Microtome
2. Reference the Sectioning Mouse Brain with Sliding Microtome protocol.
 

SECTION: Immunohistochemistry (IHC) Staining Mouse Brain Sections
3. If antibody staining or both antibody and DAPI staining is needed, reference the Immunohistochemistry (IHC) Staining Mouse Brain Sections protocol.
 

SECTION: DAPI Staining Mouse Brain Sections
4. If DAPI staining only is needed, reference to DAPI Staining Mouse Brain Sections protocol.
 

SECTION: Mounting and Coverslipping Mouse Brain Sections
5. Reference the Mounting and Coverslipping Mouse Brain Sections protocol.


 



SECTION: Mouse Cardiac Perfusion Fixation and Brain Collection V.5
1. Reference the Mouse Cardiac Perfusion Fixation and Brain Collection V.5 protocol.
TITLE: 0.01M Phosphate buffered saline (1L)
AUTHORS: Thomas R Clarke

[DESCRIPTION]
Guide for making 0.01M PBS.

Used as the solution for slicing brains in the vibratome, and for transcardial perfusionsTHIS IS A DRAFT PROTOCOL - PLEASE EXERCISE CAUTION

[STEPS]
1. Measure ~900mL distilled water
2. Add 5 phosphate buffered saline tablets (Sigma) and stir with magnetic flea
3. Fill up to 1000ml with distilled water
4. Measure pH and adjust to 7.4
TITLE: C1 - redesign
AUTHORS: Maria Gul

[DESCRIPTION]
Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Integer in sapien. Praesent id justo in neque elementum ultrices. Cras elementum. Sed ac dolor sit amet purus malesuada congue. Nunc auctor. Quis autem vel eum iure reprehenderit qui in ea voluptate velit esse quam nihil molestiae consequatur, vel illum qui dolorem eum fugiat quo voluptas nulla pariatur? In convallis. Etiam quis quam. Aliquam ornare wisi eu metus. Curabitur bibendum justo non orci. Pellentesque sapien. Nullam at arcu a est sollicitudin euismod. Phasellus rhoncus. Maecenas libero. Praesent vitae arcu tempor neque lacinia pretium. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Phasellus faucibus molestie nisl. Vivamus ac leo pretium faucibus.
Etiam neque. Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Nulla est. Etiam ligula pede, sagittis quis, interdum ultricies, scelerisque eu. Nulla quis diam. Curabitur ligula sapien, pulvinar a vestibulum quis, facilisis vel sapien. Sed convallis magna eu sem. Nulla accumsan, elit sit amet varius semper, nulla mauris mollis quam, tempor suscipit diam nulla vel leo. Etiam ligula pede, sagittis quis, interdum ultricies, scelerisque eu. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Vestibulum erat nulla, ullamcorper nec, rutrum non, nonummy ac, erat. Aenean vel massa quis mauris vehicula lacinia. Maecenas sollicitudin. Integer vulputate sem a nibh rutrum consequat. Etiam bibendum elit eget erat. Etiam neque. Aliquam erat volutpat. Aliquam erat volutpat.

[STEPS]
TITLE: DNA Gel Electrophoresis
AUTHORS: NUS iGEM

[DESCRIPTION]
<div class = "text-blocks"></div>

[STEPS]
?. Load of 6X loading dye into of P product
10 µl
50 µl
?. Mix and load entire volume into 1% agarose gel
?. Load  of 1kb or 100bp ladder
10 µl
?. Run gel at 120V for
?. Visualize band under blue light transilluminator
TITLE: READDI protocol: Crystallisation of CHIKV nsP3 macrodomain
AUTHORS: Jasmin Aschenbrenner, Peter Marples, Daren Fearon

[DESCRIPTION]
The crystallization protocol and buffer conditions used to obtain reproducible Chikungunya Virus NS3 macrodomain crystals suitable for XChem fragment screening.

[GUIDELINES]
N/A

[STEPS]
SECTION: Crystallisation experiment
3. Protein and buffer requirements:
21.6 µL11 mg/mL  
2.88 mL 
10.08 µL   Seeds, dilution 1:100

SECTION: Crystallisation experiment
5. Dispense 30 µL into SwissCI 3 lens plate reservoir wells using a 100 µl multi-channel pipette.
Dispense 75 278311 mg/mL    to each lens using the SPT mosquito.
Dispense  40 2783 to each lens using the SPT mosquito.
Dispense  35 2783 to each lens using the SPT mosquito.

Drop ratio: 15:8:7 ratio (75 nl   : 40 nl Crystallisation solution: 35 nl Seeds)
Final drop volume: 150 nl
SECTION: Crystallisation experiment
4. Crystallisation screen composition:
0.1 Molarity (M)  Tris-NaOH pH 7.8  
0.1 Molarity (M)  Potassium thiocyanate
0.1 Molarity (M) Sodium bromide
25 % v/v PEG Smear Broad

Stock solutions used:
1 Molarity (M) Tris adjusted to pH 7.8 with NaOH
1 Molarity (M)  Potassium thiocyanate
1 Molarity (M)  Sodium bromide
50% v/v PEG Smear Broad

 

SECTION: Crystallisation experiment
7. 
 


SECTION: Crystallisation experiment
6. Incubate at 20 °C for 1440 min in Formulatrix Rock Imager.

Imaging Schedule: The first images are taken after 12 h and the imaging schedule follows a Fibonacci sequence of days for further collections. 
SECTION: Equipment needed
1. Formulatrix Rock Imager (or incubator of choice)
SPT mosquito 
 
P100 8 multi-channel pipette
SwissCI 3 lens plate

SECTION: Crystallisation experiment
2. Prepare seed stock:
 
1: 100 dilution    seeds
SECTION: Data collection at Synchrotron
8. Diamond Light Source
Unattended Data Collection (UDC)
Data Collection Temperature: 100K
Detector: DECTRIS EIGER2 X 9M
Beamline: I04-1
Wavelength:  0.9212 Å
Resolution (Å): 1.64
Beam Size (μm): 60 X 50
Number of images: 3600
Oscillation: 0.10°
Exposure (s): 0.0020
Transmission (%): 100
Flux (ph/s): 3.80e+12
TITLE: Allicin as a Complementary Medicine of Triple/Quadruple Therapy for Helicobacter pylori: A Systemic review and Meta-analysis of Randomized Controlled Trials (protocol)
AUTHORS: Xiaobei Si

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Backgrounds: </span><span>Allicin (allyl 2-propene-1-thiosulfinate or diallyl thiosulfinate), a garlic compound, had been proved to be one of the active ingredients of anti-Hp effects. In recent years, a series of clinical trials further explored the anti-Hp effect of allicin as a complementary therapy were published with variable results. </span><span style = "font-weight:bold;">Aim: </span><span>This study aims to systemic review the allicin as a Complementary medicine of Triple/Quadruple Therapy for Hp infection and further assess such efficacy based on previous randomized controlled trials. We also aim to assess the quality of current evidences of allicin as complementary therapy of Hp infection. </span><span style = "font-weight:bold;">Methods: </span><span>Electronic databases, including Medline, Embase, Web of Science, Cochrane Central Register of Controlled Trial, Wanfang Database, and VIP Database, will be searched using the keywords of “allicin”, “Helicobacter pylori”, “randomized clinical trials” and their synonyms. A funnel plot may be adopted to evaluate the publication bias. The meta-analysis may be performed using fixed effect model for low heterogeneity and randomized effect model for high heterogeneity. Publication bias will be evaluated by Egger’s test, and funnel plot as well if enough (n>10) studies are included. What’s more, Trial Sequential Analysis (TSA) will be performed to evaluate whether the required information size has been met in order to make a determination of treatment benefit, harm or futility. The results of the meta-analysis will also be evaluated using the GRADE method and whether degradation is considered in terms of risk of bias, inconsistency, indirectness, accuracy, and publication bias, divided into “high quality”, “moderate quality”, “low quality”, and “very low quality”. </span><span style = "font-weight:bold;">Conclusions: </span><span>Our review will provide an evidence of moderate quality that allicin as a complementary medicine for Helicobacter pylori.</span></div><div class = "text-block"> </div></div>

[STEPS]
TITLE: f/2 medium
AUTHORS: Roscoff Culture Collection

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Medium to grow most phytoplankton species in particular diatoms.</div></div>

[STEPS]
?. [Prepare using Sigma Aldrich stock]
Filter 1L of old seawater of at least two months on prefilter and 0.2 µm filterHeat seawater during 10/20 min at 100°C (pasteurisation)Let the water cool downUnder laminar flow hood, , add 25 mL of Guillard’s (f/2) Marine Water Enrichment Solution (Sigma-Aldrich G9903)Filter the medium on 0,2 µm
?. [Prepare from base chemicals]
See: https://ncma.bigelow.org/media/wysiwyg/Algal_recipes/NCMA_algal_medium_f_2_1.pdf
TITLE: How to Play Minesweeper
AUTHORS: Cheng Zhang

[DESCRIPTION]
Minesweeper is a classic single-player puzzle game that is very fun to play. Let's begin!

[STEPS]
SECTION: Setup
2. Choose a difficulty level according to your experience and preference: Beginner, Intermediate, Expert, or Custom.
SECTION: Setup
1. Launch the Minesweeper application or online game on your computer or mobile device. My favorite website for playing Minesweeper is https://minesweeper.online/.
SECTION: Starting the Game
4. Left-click on any cell to start the game. You will not encounter a mine at the initial click.
SECTION: Starting the Game
6. On some versions, you can use hints when unsure of the next cell to open.
SECTION: Understanding the Interface
3. The board is divided into cells, with mines randomly distributed. To win, you need to open all the cells. Cells suspected of being mines can be marked with a flag using the right-click.
SECTION: Reflections and Starting a New Game
7. After a game, you can see many statistics such as time, clicks, efficiency and win streak. Try to beat yourself!
SECTION: Reflections and Starting a New Game
8. You can start a new game by clicking the smiley face (or the sad face if you just lost) on top of the board. Have fun!
SECTION: Starting the Game
5. Keep clicking to try to reveal more safe cells based on the clue you get from opened cells. After clicking a cell, you'll see one of three things:
A number: This number indicates the count of mines adjacent to that cell.
An empty cell: If the clicked cell has no adjacent mines, the game will automatically reveal adjacent empty cells until it reaches cells with numbers.
A mine: If you reveal a mine, the game is over, and you lose.
TITLE: Section 3: Libraries quality control (QC)
AUTHORS: Ester Kalef-Ezra, Ben Harvey, Katherine Roper, Christos Proukakis

[DESCRIPTION]
This protocol details quality control of libraries and should be performed after Section 2: NGS library preparation for sequencing.

[STEPS]
SECTION: Libraries quality control (QC)
1. Thaw the libraries on ice.
SECTION: Libraries quality control (QC)
2. Centrifuge briefly.
SECTION: Libraries quality control (QC)
3. Quantify the libraries using BR or HS Qubit (depending on the starting material and the amplification cycles).
SECTION: Libraries quality control (QC)
4. Analyse libraries using TapeStation with HS D1000 or D1000 Screen tapes and reagents (depending on the starting material and the amplification cycles), according to manufacturer guidelines. Examples of these are presented in Figure 8. Other methods can be used such as Agilent 2100 Bioanalyzer system with DNA 1000 kit. 
 
SECTION: Libraries quality control (QC)
5. Dilute the libraries to concentration needed and pool them together. The QC the pooled library using both HS Qubit and HS D1000 tapes.
TITLE: Evagreen Dye Fluorescence Verification
AUTHORS: Chia-Hsien  Shih

[DESCRIPTION]
This protocol is to establish the relationship between Evagreen Dye fluorescent intensity and DNA concentration.

[STEPS]
SECTION: Preparation
1. Take 30 µL of 10µM ssDNA (T4 ligation primer) into a new eppendorf

SECTION: Preparation
2. Dilute 10µM ssDNA into 1µM : 
Take 3 µL of 10µM ssDNA and 27 µL RNase-free water into a new eppendorf

SECTION: Preparation
3. Dilute 1µM ssDNA into 100nM : 
Take 3 µL of 1µM ssDNA and 27 µL RNase-free water into a new eppendorf

SECTION: Preparation
4. Dilute 100nM ssDNA into 10nM : 
Take 3 µLof 100nM ssDNA and 27 µL RNase-free water into a new eppendorf

SECTION: Preparation
5. Dilute 10nM ssDNA into 1nM : 
Take 3 µL of 10nM ssDNA and 27 µL RNase-free water into a new eppendorf

SECTION: Preparation
6. Dilute 1nM ssDNA into 100pM : 
Take 3 µL of 1nM ssDNA and 27 µL RNase-free water into a new eppendorf

SECTION: Preparation
7. Dilute 100pM ssDNA into 10pM : 
Take 3 µL of 100pM ssDNA and 27 µL RNase-free water into a new eppendorf

SECTION: Measure
9. Respectively load 20 µL of 10µM,1µM, 100nM, 10nM, 1nM, 100pM and 10pM ssDNA into each well

SECTION: Measure
10. Measure the fluorescence excitation and emission intensity
SECTION: Preparation
8. Add 1.5 µL of 20X evagree dye into each eppendorf.
TITLE: Cloning the Class Github Repository
AUTHORS: Bonnie Hurwitz, Ken Youens-Clark

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>We are going to use Github (http://github.com) to share code examples and assignments with you for the class. We set up a master repository that will get updated with assignments as the course progresses. You are going to use the "git clone" command to make your own copy of this repository. You can edit and add your own code to this cloned repository, and then "push" the code back to us so we can run the code and grade your assignments. See the </span><a style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">Setting up Github protocol</span></a><span> for how to get started with Github.  This protocol focuses on how to make a clone or copy of the class master repo in your own directory on the UA HPC (/rsgrps/bh_class/username). The master repository is available in Github (</span><a style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">https://github.com/hurwitzlab/biosys-analytics</span></a><span>) on remote server. The "git clone" command copies that existing Git repository to your own directory. This “working copy” is a full-fledged Git repository—has its own history, manages its own files, and is a completely isolated environment from the original repository.</span></div></div>

[STEPS]
?. Login to your Github account and choose the "Settings" under your menu.
?. Select the SSH Keys section on the left (1) and then click on "New SSH key" in the upper-right (2).
?. Paste the public key (~/.ssh/id_rsa.pub) from above into the "Key" on the Github site and give the key a title like "UA HPC," then click on the big green "Add SSH Key" button.
?. Clone your project via SSH. On the UA HPC web portal, go to the "/rsgrps/bh_class/username" directory and clone your version of the biosys-analytics repository.  Replace "username" with YOUR username in each of the Unix commands below.$ cd /rsgrps/bh_class/username$ git clone git@github.com:username/biosys-analytics.git
?. You should now be able to push/pull from your repo without having to type your Github password.
?. Login to the UA HPC web portal. See the protocol if needed.
?. Go to the .ssh directory in your home directory and copy the SSH key, using the commands below.$ cd$ cd .ssh$ cat id_rsa.pub