eamag/protocols-with-steps huggingface dataset:
TITLE: Decontamination of tooth roots/petrous bone cores for ancient DNA extraction
AUTHORS: Marcel Keller, Christiana L Scheib

[DESCRIPTION]
Protocol for decontamination of tooth roots and petrous bone cores from archaeological human remains for reduction of surface contaminations and increase of endogenous DNA prior to DNA extraction.

[BEFORE_START]
Previous step:
This protocol follows the sampling protocol (tooth roots and petrous bones).

Following step:
Proceed with the extraction protocol (chunk samples/high volume).

Equipment and consumables:
 


[GUIDELINES]
Please read the general guidelines for working in the Ancient DNA protocol collection – University of Tartu, Institute of Genomics.

[STEPS]
SECTION: Preparation
1. Clean drill hood and table bench surfaces with DNA Exitus and rinse with water
SECTION: Preparation
2. Set up 100 ml beaker decontamination station:
1x NaOCl (bleach, 6% v/v)
1x MilliQ water
1x Ethanol
SECTION: Preparation
3. Place toothbrush and tweezers in bleach.
SECTION: Preparation
4. Prepare two 50 ml tubes per sample, label with sample ID and B for bleach and E for ethanol.
SECTION: Preparation
5. Add around 5 mL NaOCl (bleach, 6% v/v) to each B tube (sample needs to be submerged).

SECTION: Preparation
6. Add around 5 mL ethanol (70%) to each E tube (sample needs to be submerged).

SECTION: Preparation
7. Place paper towels on a drying rack (e.g. upside-down multi-rack lid) and tape in place. Label with sample IDs. Place in the hood on a piece of aluminum foil and UV the rack in the drill hood while decontaminating samples.
SECTION: Decontamination
9. 
 

SECTION: Decontamination
10. Place samples in NaOCl (B tube) for 5 min and shake while incubating.

SECTION: Decontamination
11. Pour excess NaOCl down the sink with normal faucet running to dilute the bleach, careful not to drop the samples.
SECTION: Decontamination
12. Rinse with MilliQ water 3 times.


SECTION: Decontamination
13. Shake, pour out excess water, and place sample in ethanol for 2 min.

SECTION: Decontamination
14. Wash down sink with normal facet to dilute/remove remaining bleach in the drain.
SECTION: Decontamination
15. Pour out excess ethanol from tubes into the sink and place back into the rack. Rinse with normal faucet water when finished.
SECTION: Drying
16. In the hood, place paper towels in front of the rack for catching excess ethanol. One at a time, remove as much ethanol as possible before placing samples onto the square with the corresponding sample ID on drying rack.
SECTION: Drying
17. Leave UV on while allowing the samples to dry at least for 120 min or   .

SECTION: Drying
18. 
 

SECTION: Decontamination
9.1. Put out one medium weighing boat for each sample and label it in the corner.
SECTION: Decontamination
9.2. Take sample to be used for extraction and place in weighing boat labeled with sample ID.
SECTION: Decontamination
9.3. Remove surface dirt gently from the sample using the toothbrush soaked in NaOCl. Be careful with scrubbing to not spray bleach/dirt onto yourself or other samples.
SECTION: Decontamination
8.
TITLE: Vivarium Population Spenser: Mortality protocol
AUTHORS: Camila Rangel Smith, Kasra Hosseini

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

[STEPS]
?. Divide the annual mortality rates for a given local authority by the number of time steps existing in a year.
?. For each time step:
?. Select all individuals in the sample that appear as "alive" and have an associated gender.
?. For these individuals, get the mortality rate given their age, gender, ethnicity and location and turn it into a probability.
?. Using random sampling and the mortality probability of the individuals, choose which individuals die in that time step. Change their status from "alive" to "dead".
TITLE: Shipping Paraffin Blocks to the Bodenmiller Lab for IMC Analysis
AUTHORS: Marda Jorgensen

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This SOP describes the methods used to ship paraffin-embedded blocks to the University of Zurich. </div></div>

[STEPS]
?. Create a shipping label through the FedEx website. Select Priority Overnight Shipping. Enter the address in the document box below. Print out label.
Stefanie EnglerWinterthurestrasse 190Bodenmiller Lab, Y11-J80Zurich, CH805741446356630
?. In addition to the shipping label, a customs invoice must be created to ship internationally (template attached).
?. Obtain a small box, large enough to accomodatea FedEx shipping label.  Wrap each paraffin block seperately with protective wrapping. Include paperwork identifying theblock numbers for the blocks being shippedStuff the empty space in the box to secure the blocks in place. Seal the box with shipping tape.
?. Place the customs invoice underneath the shipping label and have the shipping label barcode facing out. Deposit sealed box into a FedEx station.
TITLE: Co-production scoping review: protocol 
AUTHORS: Helen J  J. Smith, Luke Budworth, Chloe Grindey, Isabel Hague, Natalie Hamer, Roman Kislov, Peter van der Graaf, Joe Langley

[DESCRIPTION]
Background
Interest in and use of co-production in healthcare services and research is growing. Previous reviews have summarised co-production approaches in use, collated outcomes and effects of co-production and focused on replicability and reporting, but none have critically reflected on how co-production in applied health research might be evolving and the implications of this for future research. We aim to conduct a scoping review to systematically map recent literature on co-production in applied health research in the UK to inform co-production practice and guide future methodological research.

Methods
Scoping review using established methods. We will created an evidence map to show the extent and nature of the literature on co-production and applied health research, based on this we described the characteristics of the articles and scope of the literature and summarised conceptualisations of co-production and how it was implemented. We will extract implications for co-production practice or future research and conduct a content analysis of this information to identify lessons for the practice of co-production and themes for future methodological research.

Results
We will report on lessons for the practice of co-production and themes for future research on co-production.

[STEPS]
TITLE: Patch-Seq Internal Solution with Biocytin
AUTHORS: Allen Institute for Brain Science

[DESCRIPTION]
This SOP provides instruction to prepare Internal Solution which is used for patch clamp electrophysiology, modified for cleanliness and mRNA capture and sustainability.

Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number U19MH114830. 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: No Title
AUTHORS: 

[DESCRIPTION]
<p>Introduction to functional annotation and Integrated Microbial Genomes (IMG) at the Joint Genome Institute (JGI).</p>
<p> </p>
<p>Open this protocol inside the virtual machine (details in 'Start Instructions') for easy copy, paste of commands into the command line terminal window. </p>

[BEFORE_START]
<p>Before starting, please visit the ECOGEO website for more information on this "Introduction to Environmental 'Omics" training series. The site contains a pre-packaged virtual machine that can be downloaded and used to run all of the protocols in this protocols.io collection. In addition to the VM, the website contains video and presentations from our initial "Intro to Env 'Omics" workshop held at the Univ. of Hawai'i at Manoa on 25-26 Jul 2016.<br /><br />Please email ‘ecogeo-join@earthcube.org’ to join the ECOGEO listserv for future updates.</p>

[GUIDELINES]
<p>BLAST has multiple output options:</p>
<table>
<tbody>
<tr>
<td>-outfmt</td>
<td> </td>
</tr>
<tr>
<td>&lt;String&gt;</td>
<td>5 = XML Blast output,</td>
</tr>
<tr>
<td>alignment view options:</td>
<td>6 = tabular,</td>
</tr>
<tr>
<td>0 = pairwise,</td>
<td>7 = tabular with comment lines,</td>
</tr>
<tr>
<td>1 = query-anchored showing identities,</td>
<td>8 = Text ASN.1,</td>
</tr>
<tr>
<td>2 = query-anchored no identities,</td>
<td>9 = Binary ASN.1,</td>
</tr>
<tr>
<td>3 = flat query-anchored, show identities,</td>
<td>10 = Comma-seperated values,</td>
</tr>
<tr>
<td>4 = flat query-anchored, no identities,</td>
<td>11 = BLAST archive format (ASN.1)</td>
</tr>
</tbody>
</table>
<p> </p>
<p>BLAST - tabular output (fmt = 6)</p>
<p>Lots of custom format options for formats 6, 7, 10</p>
<table style="width: 394px;">
<tbody>
<tr>
<td style="width: 201px;">
<p>qseqid means Query Seq-id</p>
</td>
<td style="width: 181px;">
<p>sallgi means All subject GIs</p>
</td>
</tr>
<tr>
<td style="width: 201px;">
<p>qgi means Query GI</p>
</td>
<td style="width: 181px;">
<p>sacc means Subject accession</p>
</td>
</tr>
<tr>
<td style="width: 201px;">
<p>qacc means Query accesion</p>
</td>
<td style="width: 181px;">
<p>saccver means Subject accession.version</p>
</td>
</tr>
<tr>
<td style="width: 201px;">
<p>qaccver means Query accesion.version</p>
</td>
<td style="width: 181px;">
<p>sallacc means All subject accessions</p>
</td>
</tr>
<tr>
<td style="width: 201px;">
<p>qlen means Query sequence length</p>
</td>
<td style="width: 181px;">
<p>slen means Subject sequence length</p>
</td>
</tr>
<tr>
<td style="width: 201px;">
<p>sseqid means Subject Seq-id</p>
</td>
<td style="width: 181px;">
<p>qstart means Start of alignment in query</p>
</td>
</tr>
<tr>
<td style="width: 201px;">sallseqid means All subject Seq-id(s), separated by a ';'</td>
<td style="width: 181px;">
<p>qend means End of alignment in query</p>
</td>
</tr>
<tr>
<td style="width: 201px;">
<p>sgi means Subject GI</p>
</td>
<td style="width: 181px;">
<p>sstart means Start of alignment in subject</p>
</td>
</tr>
<tr>
<td style="width: 201px;"> </td>
<td style="width: 181px;">
<p>send means End of alignment in subject</p>
</td>
</tr>
</tbody>
</table>
<p> </p>

[STEPS]
?. 
?. 
?. 
?. 
?. 
?. 
?.
TITLE: Untargeted IMS Tentative Identification Lipidomics
AUTHORS: Lukasz Migas, Madeline E. Colley, Katerina V Djambazova, Martin Dufresne, Angela R.S.  Kruse, David       Anderson, Olof  Isberg, Jamie Allen, ali.zahraei, Melissa Farrow, Jeff Spraggins, Raf Van De Plas

[DESCRIPTION]
The purpose of this protocol is to generate tentative annotations for lipids detected using IMS. 

[STEPS]
1. Following pre-processing, tentative identification is performed using an in-house developed annotation software - annotine.
2. Generate an average mass spectrum of the dataset (in profile mode).
3. Scale the mass spectrum between 0 and 1, and peak-pick its profile to retrieve a list of m/z features (commonly 100s to 1000s).
4. Filter the peak list to retain only peaks that have a relative intensity above 0.001 (sensitive mode) or 0.01 (standard mode). Peaks whose intensity value falls below this threshold are removed.
5. (optional) De-isotope the peak list to remove M+1, M+2, … and other potential isotopes from further consideration.
6. Generate an internal database on the basis of a user-supplied list of molecular species databases and a set of user-supplied expected adduct types:

Databases:
    a. coreMetabolome, LMSD, SHexCer, HMDB5
    b. (optional) a local LC-MS database
Adducts:
    a. Positive mode:  [M+H]+, [M+Na]+, [M+K]+
    b. Negative mode: [M-H]-, [M-CH3]-

 

7. Perform tentative identification by comparing the peak list with the built database of species and adduct combinations. If a peak is within a ±5 ppm window of an annotation in the database, that annotation is assigned to that peak. This process is repeated until each peak has been compared to the database.
8. Evaluate each tentative annotation using metrics.
9. (optional) To reduce the number of unlikely annotations, calculate a false discovery rate (FDR) for every tentative identification. Annotations can be filtered based on the FDR (or any other) score.
10. (optional) If LC-MS results are available (see LC-MS/MS lipidomics protocol below), associate these directly with the annotine results. This allows immediate highlighting of which tentative identifications have also been observed by LC-MS/MS, increasing the confidence of the identification.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p><strong>Background</strong></p>
<p>Recently, neoadjuvant chemotherapy with docetaxel/cisplatin/5-fluorouracil (NAC-DCF) was identified as a novel strong regimen with a high rate of pathological complete response (pCR) in advanced esophageal cancer in Japan. Predicting pCR will contribute to the therapeutic strategy and the prevention of surgical invasion. However, a predictor of pCR after NAC-DCF has not yet been developed. The aim of this study was to identify a novel predictor of pCR in locally advanced esophageal cancer treated with NAC-DCF.</p>
<p><strong>Patients and Methods</strong></p>
<p>A total of 32 patients who received NAC-DCF followed by esophagectomy between June 2013 and March 2016 were enrolled in this study. We divided the patients into the following 2 groups: pCR group (9 cases) and non-pCR group (23 cases), and compared gene expressions between these groups using DNA microarray data and KeyMolnet. Subsequently, a validation study of candidate molecular expression was performed in 7 additional cases.</p>
<p><strong>Results</strong></p>
<p>Seventeen molecules, including transcription factor E2F, T-cell-specific transcription factor, Src (known as “proto-oncogene tyrosine-protein kinase of sarcoma”), interferon regulatory factor 1, thymidylate synthase, cyclin B, cyclin-dependent kinase (CDK) 4, CDK, caspase-1, vitamin D receptor, histone deacetylase, MAPK/ERK kinase, bcl-2-associated X protein, runt-related transcription factor 1, PR domain zinc finger protein 1, platelet-derived growth factor receptor, and interleukin 1, were identified as candidate molecules. The molecules were mainly associated with pathways, such as transcriptional regulation by SMAD, RB/E2F, and STAT. The validation study indicated that 12 of the 17 molecules (71%) matched the trends of molecular expression.</p>
<p><strong>Conclusions</strong></p>
<p>A 17-molecule set that predicts pCR after NAC-DCF for locally advanced esophageal cancer was identified.</p>

[STEPS]
?.
TITLE: Culturing C. elegans worms in liquid culture
AUTHORS: Cristian Riccio, Asia Kosalka, WormBook

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Growing C. elegans worms in liquid culture</div></div>

[STEPS]
?. Reagents
?. S Basal [5.85 g NaCl, 1 g K2 HPO4, 6 g KH2PO4, 1 ml cholesterol (5 mg/ml in ethanol), H2O to 1 litre. Sterilize by autoclaving.]
?. 1 M Potassium citrate pH 6.0 [20 g citric acid monohydrate, 293.5 g tri-potassium citrate monohydrate, H2O to 1 litre. Sterilize by autoclaving.]
?. Trace metals solution [1.86 g disodium EDTA, 0.69 g FeSO4•7 H2O, 0.2 g MnCl2•4 H2O, 0.29 g ZnSO4•7 H2O, 0.025 g CuSO4•5 H2O, H2O to 1 litre. Sterilize by autoclaving. Store in the dark.]
?. 1 M CaCl2 [55.5 g CaCl2 in 1 litre H2O. Sterilize by autoclaving.]
?. S Medium [1 litre S Basal, 10 ml 1 M potassium citrate pH 6, 10 ml trace metals solution, 3 ml 1 M CaCl2, 3 ml 1 M MgSO4. Add components using sterile technique; do not autoclave.]
?. 4 large plates of C. elegans, just cleared of bacteria
?. concentrated E. coli OP50
?. Methods
?. Add 250 ml S Medium to a sterilized 1-2 litre flask.
?. Inoculate the S Medium with a concentrated E. coli OP50 pellet made from 2-3 litres of an overnight culture.
?. Wash each of 4 large plates of C. elegans (just cleared of bacteria) with 5 ml S Medium and add to the 250 ml flask.
?. Put the flask on a shaker at 20°C. Use fairly vigorous shaking so that the culture is well oxygenated.
?. Cultures should be monitored bychecking a drop of the culture under the microscope. If the food supplyis depleted (the solutionis no longer visibly cloudy) add moreconcentrated E. coli OP50 suspended in S Medium. When there are many adult animals in each drop, the culture is ready to be harvested. This isusually on the 4th or 5th day.
?. Put the flask on ice for 15 minutes to allow the worms to settle.
?. Aspirate most of the liquid from the flask.
?. Transfer the remaining liquid to a 50 ml sterile conical centrifuge tube and spin for at least 2 min at 1150 × g to pelletthe worms. Young larvae may take longer than 2 min to pellet.
?. Aspirate the remaining liquid.The worms harvested from growth in liquid culture areusually longer and thinner than those grown on petri plates, and tendto hold their eggs. The number of adults, larvae and eggsobtained depends on the strain of worms used, the amount of bacteriaprovided and the length of time the culture is grown.Freshly cleared cultures will yield worms equal to half the weight ofthe bacteria used (Lewis and Fleming, 1995).
?. Copy-pasted protocol from the Wormbook. Got a protocol from Asia Kosalka.  Added my notes below.
?. [Notes]
Add arrested L1 worms to the liquid culture. This has several benefits:- minimises contamination- synchronised growth which means that the bacterial depletion will occur at a more predictable rate
TITLE: KAPP-Sen TMC: Xenium Pancreas FFPE Tissue Preparation 
AUTHORS: Emily Soja, Shruti Bhargava, Santhosh Sivajothi, William F Flynn, Elise T Courtois

[DESCRIPTION]
Xenium protocol for sectioning FFPE tissue blocks.

[STEPS]
1. Xenium In Situ for FFPE - Tissue Preparation Guide CG000578 Rev C: 

The optimal water bath temperature for pancreas tissue was determined to be 38 C (see page 22 of CG000578 Rev C).
TITLE: 13 Gel filtration
AUTHORS: TJUSLS China

[STEPS]
?. [Choice of Gel]
According to the size of the target protein, firstly select the appropriate gel to adapt to the size of protein.
?. [Column equilibrium]
Connect the proper column which adapts to target protein to AKTA high pressure tomographic system, use buffer of gel filtration chromatography (buffer: 25mMTris， 150mMNaCl，pH8.0) to prebalance the column of gel filtration chromatography of about 1.5 columns.
?. [Sample concentration]
Concentrate the protein to less than 1mL by centrifuging at 4℃, 3400rpm for 10 minutes in a high-speed centrifuge to remove insoluble substances and bubbles.
4 °C
1 ml
?. [Add Sample]
Add the protein to the column of gel filtration chromatography through a 1mL sample collecting loop. The protein is eluted at a flow rate of 0.5mL/min. The eluent was collected according to the peak position.
1 ml
?. Use SDS-PAGE to check the result.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p><em>The MELD Project is an international collaboration aiming to create open-access, robust and generalisable tools for FCD detection. To this end, we will train a neural network classifier on MRI features from FCD patients from multiple centres worldwide.</em></p>
<p><strong> </strong></p>
<p><strong>Protocol 3 provides instructions on how to quality control the FreeSurfer reconstructions.</strong></p>
<p> </p>
<p>These instructions are based on the freely available protocols on the ENIGMA-epilepsy website http://enigma.ini.usc.edu</p>
<p> </p>
<p>We are very grateful to Derrek Hibar, Neda Jahanshad, Roberto Toro, Jerod Rasmussen, Theo van Erp, Esther Walton and Stefan Ehrlich who wrote the orginal ENIGMA protocols and offered them with an unlimited license without warranty! </p>
<p> </p>
<p>The main change is correct co-registration of FLAIR to T1 is now checked. </p>
<p> </p>
<p> </p>

[BEFORE_START]
<p>Ensure that you have logged onto the MELD github (https://github.com/MELDProject/meld) and cloned the repository.</p>
<p> </p>
<p>This will contain the essential MELD_QC folder.</p>
<p> </p>
<p>You also need to have MATLAB installed. </p>
<p> </p>
<p><strong>If you have any questions or run into problems, please feel free to contact the MELD project: (meld.study@gmail.com)</strong></p>

[GUIDELINES]
<p>These instructions are based on the freely available protocols on the ENIGMA-epilepsy website http://enigma.ini.usc.edu/ongoing/enigma-epilepsy/enigma-epilepsy-protocols/</p>
<p> </p>
<p>We are very grateful to Derrek Hibar, Neda Jahanshad, Roberto Toro, Jerod Rasmussen, Theo van Erp, Esther Walton and Stefan Ehrlich who wrote the orginal ENIGMA protocol.</p>

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

[DESCRIPTION]
<p>This protocol (like its companion protocol for liposome suspension and extrusion) was original created by <a href="&quot;http://www.whoi.edu/sbl/liteSite.do?litesite" target="_blank">Krista Longnecker</a> and <a href="http://jamesrco.github.io/" target="_blank">Jamie Collins</a> for creating lipsomes to be used in lipid photo-oxidation experiments. The results of these experiments are detailed in Chapter 4 of:</p>
<p> </p>
<p>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:<a href="http://dx.doi.org/10.1575/1912/8721" target="_blank">10.1575/1912/8721</a></p>
<p> </p>
<p>A manuscript of the chapter is forthcoming.</p>

[STEPS]
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?.
TITLE: In Vitro FSCV Testing of Carbon Fiber Electrodes to Characterize Functional Operation in Dopamine Detection
AUTHORS: Helen N Schwerdt, Ann M Graybiel, Michael J Cima

[DESCRIPTION]
Methods to measure performance characteristics of carbon fiber electrodes for neurochemical recording are described.

[GUIDELINES]
An integrated system of hardware and software capable of recording dopamine signals up to 16 channels simultaneously using fast scan cyclic voltammetry (FSCV) was built with off-the-shelf electronics and a PC based data acquisition system. Guidance on constructing this system, including the circuit board layout as well as the MATLAB software for visualizing dopamine recording in real-time can be found on the GitHub Repository (https://github.com/hschwerdt/multifscv). 

[STEPS]
1. Each carbon fiber (CF) electrode was tested in vitro in a beaker containing 0.9% sodium chloride saline to determine its functional properties (i.e., background current and noise) before soldering to another circuit board. 
2. In vitro testing was performed in a Faraday cage to minimize electromagnetic interference (EMI) during test recording. A custom designed printed circuit board adapter was used to temporarily attach and connect up to 16 electrodes for testing in parallel, in some tests.
4. Electrodes were determined to be suitable for in vivo recording if they met both of the following 2 criteria: (1) current noise < 0.05 nA, and (2) magnitude of background current was in the range of 500 – 800 nA, which corresponds, respectively, to the limit of detection and the sensitivity to dopamine, as established previously.
5. In instances in which the magnitude of background current was above 800 nA, a steel razor blade was used to trim the tip of the exposed CF slightly and then the electrode was retested.
6. The trimming and test process was repeated until the final background current was in the target range of 500 – 800 nA.
7. Electrodes were determined to be nonfunctional and would not be trimmed if they met any of the following 2 criteria: (1) a mechanical break of the electrode along its shaft or etched tip that resulted in a measurement of background current less than 100 nA, or (2) a perforation of the electrode that resulted in current noise ≥ 0.05 nA or background current saturation (magnitude of background current at any potential ≥ 2000 nA).
3. Electrodes were inserted into the beaker and connected to the FSCV headstage for recording current. An Ag/AgCl reference electrode was also inserted in the beaker to serve as a current return and voltage reference.