eamag/protocols-with-steps huggingface dataset:
TITLE: Apparent Diffusion Coefficient Measurement of Myelofibrosis in Mouse Tibia
AUTHORS: Thomas L Chenevert

[DESCRIPTION]
The goal of this Co-Clinical Imaging Research Program (CIRP) pre-clinical imaging protocol (PIP) is to provide detailed description of key steps used to achieve a stated level of technical repeatability (precision) embodied in “Claims”, for MRI measurement of apparent diffusion coefficient (ADC) in tibia bone marrow of myelofibrosis mouse models. This pre-clinical imaging procedure document will be referred to as a “profile” and adheres to a PIP MRI template provided in: https://www.protocols.io/workspaces/pre-clinical-imaging-protocols. This profile details procedures for ADC measurement from diffusion weighted imaging (DWI) acquisition and image processing in MF mouse tibia to achieve stated performance claims. Tibia bone marrow composition in MF mouse models has gradation going from proximal to distil ends of the tibia, therefore separate claims are made for volume of interest (VOI) analysis of ADC maps for each of three distinct sections along the length of the tibia (see Figure 1):
Section 1 (proximal)º VOI (~4-5mm3) within 9mm of proximal end of tibia
Section 2 (transition)º VOI (~0.4-0.5mm3) from 10 to 12mm of proximal end of tibia
Section 3 (distil)º VOI (~0.1-0.2mm3) from 13 to 14mm of proximal end of tibia

Claim 1:A measured change in the mean ADC in Section 1 VOI of MF mouse model tibia that exceeds ±0.037µm2/ms indicates a true biological change has occurred in the tibia bone marrow with 95% confidence.
Claim 2:A measured change in the mean ADC in Section 2 VOI of MF mouse model tibia that exceeds ±0.087µm2/ms indicates a true biological change has occurred in the tibia bone marrow with 95% confidence
Claim 3:A measured change in the mean ADC in Section 3 VOI of MF mouse model tibia that exceeds ±0.030µm2/ms indicates a true biological change has occurred in the tibia bone marrow with 95% confidence

[STEPS]
TITLE: HuBMAP: Embedding Fresh Frozen OCT Samples
AUTHORS: Marda Jorgensen, Jerelyn Nick

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The purpose of this Standard Operating Procedure (SOP) is to outline procedures for the OCT embedding of HuBMAP fresh frozen specimens.</div></div>

[STEPS]
?. Collect tissue specimen from the designated common coordinate framework sites. (See case processing SOP diagrams)
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{"blocks":[{"data":[],"depth":0,"entityRanges":[],"inlineStyleRanges":[],"key":"4itmc","text":"This is an appendix for spleen SOP. ","type":"unstyled"}],"entityMap":[]}
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?. Prepare a pre-labeled Cryomold  and fill it half way with OCT compound.
?. Place the tissue into the OCT-containing Cryomold, maintaining tissue orientation.
?. Using forceps, push the tissue lightly to the bottom of the Cryomold to secure it.
?. Prepare dry ice/methylbutane slurry for freezing OCT blocks.
?. Fill the mold with OCT, covering tissue completely. Avoid bubbles.
?. Place 1-2 inches of dry ice pellets into the bolltom of an ice bucket or styrofoam box.
?. Add enough 2-methylbutane solution to cover the dry ice by roughly 5mm.
?. Place lid on freezing chamber and allow methylbutane to chill. Chamber is ready when fog dissipates and bottom of bucket becomes visible.
?. When the OCT Cryomold is thoroughly frozen and opaque, wrap the mold containing the tissue in a pre-labeled aluminum foil square and store at -80° C in a freezer rack box.
Enter block location if Freezer Log for future retrieval.
?. Gently blot tissue piece on dry gauze to remove any excess moisture.
?. Freeze the tissue in the Cryomold by resting it on the surface of the methylbutane slurry. Use long handled forceps to transfer the mold onto the slurry.As the OCT inside the Cryomold begins to freeze, lightly push the tissue into the bottom of the mold one last time.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>BioLegend MojoSort™ nanobeads work in commonly used separation columns, based on our internal research as well as validation by external testing by academic labs. This simple protocol consists of following the MojoSort™ protocol to label the cells with pre-diluted MojoSort™ reagents and using the columns as indicated by the manufacturer</p>
<p> </p>
<p>Note: Due to the properties of our beads, it may be possible to use far fewer beads and less antibody cocktail that with other commercial suppliers. We recommend a titration to find the best dilution factor. However, as a general rule, dilutions ranging from 1:2 to 1:10 for the antibody cocktail can be used. Dilutions ranging from 1:5 to 1:20 for the Streptavidin Nanobeads can be used.</p>

[GUIDELINES]
<p><strong>Commercially available columns:</strong></p>
<p> </p>
<p><strong><img id="s-mce-img" class="s-mce-img" src="https://s3.amazonaws.com/pr-journal/dsnecje.jpg" data-src="https://s3.amazonaws.com/pr-journal/dsmecje.jpg" data-ofn="mojosort negative selection.JPG" /></strong></p>
<p><strong>Example of magnetic separation with medium capacity columns:</strong></p>
<p><strong><br /></strong>a) Place the column in a magnetic separator that fits the column.<br />b) Wash the column with 3 mL of buffer.<br />c) Add the labeled cell suspension to the column through a 30 μm filter and collect the fraction containingthe unlabeled cells. These are the cells of interest; do not discard.<br />d) Wash the column 3 times with 3 mL of buffer and collect the fraction containing the untouched cells.Combine with the collected fraction from step c.<br />e) If desired, the labeled cells can be collected by taking away the column from the magnet and place it ona tube. Then add 5 mL of buffer and flush out the magnetically labeled fraction with a plunger orsupplied device. The labeled cells may be useful as staining controls, to monitor purity/yield, or otherpurposes.</p>
<p> </p>
<p><strong>See Biolegend.com for <a href="http://www.biolegend.com/media_assets/support_protocol/MojoSort_Negative_Selection_Columns_01052015.pdf" target="_blank">Data</a></strong></p>

[STEPS]
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TITLE: Quick staining procedure of nuclei in Euplotes using DAPI
AUTHORS: Rachele Cesaroni

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

[STEPS]
?. Mix concentrated Euplotes cells together with Ethanol 70% in a ratio of 1:1.
Better to have a completely starved Euplotes culture to avoid autofuorescence from bacteria/algae.
?. Add DAPI (0.01 mg/ml) to the mix in a ratio of 1:10, and stain for 15 minutes at room temperature.
?. Observe cells by fluorescence microscopy.
TITLE: Barcoding PCR for MiSeq sequencing
AUTHORS: Eva Petrova, Roey Angel

[DESCRIPTION]
Barcoding PCR for MiSeq sequencing
 
Barcode head 8mer-GCT ATG CGC GAG CTG C   Modified  from Rudi et al. (2003)
 

[STEPS]
SECTION: PCR mixture
1.  
 
* Buffer already contains MgCl2 at a final conc. of 2.0 mM.
SECTION: PCR program
2. 1.  94◦C – 4′
2.  x 4 – 9 {
       a.  52◦C – 30′′
       b.  72◦C – 45′′
       c.  94◦C – 30′′
      }
3.  52◦C – 30′′
4.  72◦C – 10'
TITLE: Digitalization of home-based records for maternal, newborn and child health (MNCH): a scoping review protocol
AUTHORS: Marije Geldof, Anayda Gerarda Portela, Nina  Gerlach, Caroline  Sauvé

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Background: </span></div><div class = "text-block">A home-based record (HBR) is a document used to record the history of health services and key health information of an individual and through which health education messages can be shared. The record is kept by the individual or their parent/caregiver at home, and is intended to compliment the records kept at the health facility. The great majority of these HBRs are paper-based, although many countries have future plans for digitalizing them for improved access and use, as well as higher rates of recording. In some middle- and high income countries, electronic HBRs are already being used in order to promote information sharing between providers to improve the integration in care, as well as reduce the risk of data loss. There is a need to better understand what efforts have already been undertaken in terms of the digitalization of HBRs and what lessons can be learned moving forward.</div><br/><div class = "text-block"><span style = "font-weight:bold;">Objective:</span></div><div class = "text-block"><span>The main objective of this scoping review is to map the peer-reviewed and grey literature available on the digitalization of HBRs for MNCH. The following review question is guiding the exercise towards this objective: </span><span style = "font-style:italic;">What efforts have already been undertaken for the digitalization of home-based records for maternal, newborn and child health (MNCH)? </span></div><br/><div class = "text-block"><span style = "font-weight:bold;">Methods:</span></div><div class = "text-block">The scoping review will include the following steps: 1) a search strategy to identify relevant materials, 2) inclusion and exclusion criteria for the selection of relevant materials, 3) data extraction from the relevant materials, 4) synthesizing the results</div><br/></div>

[STEPS]
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>The Microbial mutagenicty Ames bioassay is a short term microbial assay performed in<em> vitro.</em> It consisting of several <em>Salmonella typhimurium/E.coli </em>different strains, which are used to evaluate the mutagenicity of different environmental carcinogens and mutagen.  Ames assay is used to detect the revert mutations (revertants) which are present in these strains. While, these bacterial strains synthesize the essential amino acid by restoring their functional capacity, it is also used to detect the mutagenicity of different environmental samples such as drugs, dyes, reagent, cosmetics, waste water, pesticides and other substances which are easily solubilized in water and form micro-suspension with strain. This recipe is best applicable for researchers who wish to perform Ames assay in their research.</p>

[GUIDELINES]
<p>Before starting our experiment:</p>
<p> </p>
<ol>
<li>Immediately after receiving the cultures, strain are genetically studied for their genotypes (R-factor, histidine necessity, <em>rfa</em> and <em>uvr </em>B mutation).</li>
<li>Before performing experiment, always a new set of frozen strains are to be prepared.</li>
<li><em>Salmonella</em> is a pathogenic bacterium and so one needs to be careful while  performing the experiments.</li>
</ol>

[STEPS]
?.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
This is a protocol from: <br /><br />Stedman, K. M., K. Porter, and M. L. Dyall-Smith. 2010. Chapter 6: The isolation of viruses infecting Archaea. Manual of Aquatic Viral Ecology. Waco, TX:American Society of Limnology and Oceanography. doi:10.4319/mave.2010.978-0-9845591-0-7<br /><br />Please see the <a href="http://www.aslo.org/books/mave/MAVE_057.pdf" target="_blank">published manuscript</a> for additional information.

[GUIDELINES]
<strong>Authors: </strong>Kenneth M. Stedman<sup>1</sup>, Kate Porter<sup>2</sup>, and Mike L. Dyall-Smith<sup>3</sup> <br /><sup>1</sup>Department of Biology, Center for Life in Extreme Environments, Portland State University, P.O. Box 751, Portland, OR 97207, USA <br /><sup>2</sup>Biota Holdings Limited, 10/585 Blackburn Road, Notting Hill Victoria 3168, Australia <br /><sup>3</sup>Max Planck Institute of Biochemistry, Department of Membrane Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany<strong><br /><br />Artificial salt water and medium MGM:</strong> <br />Artificial salt water solutions are designed to mimic the natural concentrated brines where haloarchaea are found. The formulation used by M. Dyall-Smith (described in the online handbook, the <em>Halohandbook</em>, <a href="http://www.haloarchaea.com/resources/halohandbook/" target="_blank">http://www.haloarchaea.com/resources/halohandbook/</a>) is based on that described by Rodriguez-Valera et al. (Rodriguez-Valera et al. 1980; Torreblanca et al. 1986). <br />Per liter, it contains:  <br />
<table>
<tbody>
<tr>
<td>4 M NaCl</td>
</tr>
<tr>
<td>150 mM MgCl<sub>2</sub></td>
</tr>
<tr>
<td>150 mM MgSO<sub>4</sub></td>
</tr>
<tr>
<td>90 mM KCl</td>
</tr>
<tr>
<td>3.5 mM CaCl<sub>2</sub></td>
</tr>
</tbody>
</table>
adjusted to pH 7.5 using ca. 2 mL 1 M Tris-HCl (pH 7.5). At 30% w/v, the total salts are present in a much higher concentration than in seawater, but in approximately the same proportions. Adjustments of Mg<sup>2+</sup>, pH, or other conditions may be necessary for specific haloarchaeal groups. Modified growth medium (MGM) contains 5 g peptone and 1 g yeast extract per liter of salt water. The salt concentration is varied according to the host strain, and is detailed in the <a href="http://www.haloarchaea.com/resources/halohandbook/" target="_blank">Halohandbook</a><em>.<br /><br /></em><em><br /></em>

[STEPS]
TITLE: Yale - Alanine Aminotransferase
AUTHORS: Gary Cline, John Stack

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Procedure used to measure the Alanine Amino activity in blood, plasma, and serum. Alanine Amino (ALT) activity is measured by the enzymatically coupled reactions of ALT (to form pyruvate from alanine and α-ketoglutarate) and Lactate dehydrogenase (conversion of pyruvate to lactate with oxdiation of NADH to NAD). The rate of NAD formation is monitored by the change in absorbance at 340 nm. </div></div>

[STEPS]
?. Calibrate Cobas for Alanine Transaminase Activity analysis by running two assayed control serum.
?. Sample handling as performed by the Cobas Mira Plus.    a) Pipette 16 µL of sample into a cuvette slot.     b) Add 145 µL of Alanine Transaminase Reagent.     c) Mixture is incubated at 37˚C and spun for 10 minutes.     d) Absorbance is measured at 340 nm.
TITLE: Ampure bead clean up for high molecular weight DNA 
AUTHORS: Natalie Solonenko

[STEPS]
?. [Add beads ]
Make sure beads are completely resuspended before use by vortexing vigorously.
?. [Add beads ]
Add ratio of resuspended beads specified in your main protocol.
This ratio is dependent on the length of DNA you want to recover.
?. [Add beads ]
Flick tube gently to mix beads and sample.
?. [Incubate ]
Incubate at room temperature for 5 minutes.
0 Room temperature
Flick gently periodically throughout the incubation to prevent beads from settling to the bottom of the tube.
?. [Separation]
Place tubes on a magnetic rack.
?. [Separation]
Wait 2 min for the beads and buffer to seaparate.  Beads will stick to magnetic side of the tube and the solution should be clear.
?. [Wash ]
Add 500ul 80% EtOH to each sample.
Volume of 80% EtOH can be adjusted. Just so long as the amount added is enough to cover beads.
?. [Wash ]
Incubate at room temperature for 30 seconds.
0 Room temperature
?. [Wash ]
Remove 80% EtOH, being careful not to disturb the beads.
?. [Wash ]
Repeat the step 4.
?. [Wash ]
Spin down breifly and place back on the magnetic stand. Remove residual EtOH.
?. [Dry Beads and Resuspend DNA]
Leaving the caps open, remove tubes from magnet, and dry until surface of the beads has a matte finish.
Caution: If the surface of beads appear cracked, they are overdrying! Resuspend immediately. Over-dried beads will not resuspend well.
?. [Dry Beads and Resuspend DNA]
Resuspend DNA by adding a minimun of 15ul water or low EDTA TE and gently mix by flicking. The exact resuspension volume should be specified in your main protocol.
?. [Dry Beads and Resuspend DNA]
Incubate for 2 minutes at 55 C.
55 °C
?. [Collect]
Place tubes back on magnetic rack
?. [Collect]
Wait 2 min for the beads to seaparate.  Beads will stick to magnetic side of the tube and the solution should be clear.
?. [Collect]
Pipette out your specified volume of eluate and keep as your sample.
Do not carry over any beads! They are a significant inhibitor of various downstream aplications. Carefully check to your pipette tip for bead carryover. If there are beads, replace the sample into the tube and wait another 2 min. You may need to decrease the volume removed from the tube by 1-2 ul.
?. [Separation]
Remove and discard the clear solution. DNA will remain in the tube bound to the beads.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>Functional SMN protein of peripheral blood-derived mononuclear cells was detected with an anti-SMN antibody labeled with a fluorescent dye and analyzed semiquantitatively using intracellular expression intensity and SMN spot formed in cell nucleus as an index, Consider the relationship with the clinical condition and motor function.</p>
<p> </p>
<p>Briefly,</p>
<p>1) In order to identify the cell fraction, the fluorescently labeled cell surface antigen-specific antibody is added to the whole blood sample and stained.</p>
<p>2) Hemolyze peripheral blood and fix mononuclear cells.</p>
<p>3) Intracellular staining is performed with SMN protein and nuclear-specific fluorescently labeled antibody.</p>
<p>4) SMN protein expression analysis was performed on a strongly CD33 cell population detected as a cell surface marker, SMN spot detection algorithm was used to analyze the proportion of cells in which intracellular SMN expression and SMN protein aggregated in the nucleus.</p>
<p> </p>
<p> </p>
<p> </p>

[STEPS]
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TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>The NEBNext rRNA Depletion Kit (Human/Mouse/Rat) depletes both cytoplasmic (5S rRNA, 5.8S rRNA, 18S rRNA and 28S rRNA) and mitochodrial ribosomal RNA (12S rRNA and 16S rRNA) from human, mouse and rat total RNA preparations. This product is suitable for both intact and degraded RNA (e.g. FFPE RNA). The resulting rRNA-depleted RNA is suitable for RNA-Seq, random-primed cDNA synthesis, or other downstream RNA analysis applications.</p>

[BEFORE_START]
<p><strong>Starting Material: </strong>5 ng–1 μg total RNA (DNA free) in a 12 μl total volume. If the total RNA may contain gDNA contamination, treat the RNA sample with DNase I to remove all traces of DNA, then purify the treated RNA to remove DNase I.</p>
<p>------------------------------------------------------------------------------------------------------------------------------------------ </p>
<p><strong>RNA Sample Requirements</strong></p>
<p>The RNA sample should be free of salts (e.g., Mg2+, or guanidinium salts) or organics (e.g., phenol and ethanol). RNA must be free of DNA. gDNA is a common contaminant from RNA preps. It may be carried over from the interphase of organic extractions or when the silica matrix of solid phase RNA purification methods is overloaded. If the total RNA sample may contain gDNA contamination, treat the sample with DNase I to remove all traces of DNA (not provided in this kit). After treatment with DNase I the enzyme should be removed from the sample. Any residual activity of DNase I will degrade the single stranded DNA probes necessary for the ribosomal depletion. DNase I can be removed from the extraction using phenol/chloroform extraction and ethanol precipitation.</p>
<p>  </p>
<p><strong>Typical Yield of rRNA-depleted RNA from a Reaction </strong></p>
<p>The actual yield is dependent on the quality of the input RNA, the rRNA content of the sample, and the method used to purify the rRNA-depleted RNA. Recoveries of 3%–10% of the input RNA are typical.</p>
<p>  </p>
<p><strong>RNA Input </strong></p>
<p>5 ng to 1 μg DNA free total RNA in up to 12 μl total volume.</p>
<p>Note: for RNAseq samples we recommend using total RNA inputs higher than 5 ng to increase library complexity and reduce sequencing duplication rates.</p>
<p>When using NEBNext rRNA Depletion Kit (Human/Mouse/Rat; NEB #E6310 or #E6350) with the below NEBNext kits please follow the appropriate chapter in the corresponding kit manual and start with the appropriate input amount of RNA.</p>
<p>NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760)</p>
<p>NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB #E7770)</p>
<p>NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB #E7420)</p>
<p>NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #E7530)</p>

[STEPS]
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TITLE: Arctos Portable AC Reviews- Scam or Legit? REad Canada Price Before Buy
AUTHORS: health  

[DESCRIPTION]
Arctos Portable Air Cooler runs very successfully, including humidity to the air the usage of evaporation generation. Simply plug it in to start using your private cooler as a humidifier.

[STEPS]
1. Arctos Portable AC Fresh water filters are absolutely to be had on the reputable Arctos website and may be changed right now.  Adjustable vents: The vents on the Arctos Portable Air Cooler are conveniently adjustable. The chilly air emitted from the air cooler spreads for your environment via these vents, which create tiny areas. Because the vents may be effectively adjusted, you could direct cool, refreshing air anyplace you need it. The Arctos Portable Air Cooler is a small air cooler for personal use. Its features exhibit that it changed into created with the person's consolation and delight in thoughts. Do not pass up the chance to enjoy the non-public cooling and luxury furnished by this powerful air cooler.  3 Fan Speeds: The Arctos Air Cooler has 3 fan settings, maintaining with the tool's better non-public comfort layout. 
Official Web : https://www.outlookindia.com/business-spotlight/arctos-portable-ac-reviews-arctos-ac-work-or-scam-arctos-air-cooler-canada-price-or-where-to-buy--news-209617
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<strong>Viral Bioinformatic Resource Centre</strong>
<ul>
<li><strong>Provide databases of viral genomic information.</strong>
<ul>
<li>Please check the <strong><em>Organisms</em></strong> menu to see which viruses we support: we’re now focusing on large DNA viruses</li>
<li>The VOCs (Virus Orthologous Clusters) database is at the heart of our system.</li>
<li>The database links directly to integrated tools for comparative analyses.</li>
<li>VOCs sorts genes into ortholog clusters (e.g. RNA polymerase) to simplify data retrieval.</li>
</ul>
</li>
<li><strong>Provide easy access to the genes, gene families, and genomes of the different virus families.</strong>
<ul>
<li>via a unique series of powerful Java tools that support multiple computer platforms (see <strong><em>VBRC Tools</em> </strong>menu).</li>
<li>design and build software to tackle specific bioinformatics/virology problems, often in collaboration with virologists.</li>
</ul>
</li>
<li><strong>Rally the research community to provide expert curation of these viral genomes by:</strong>
<ul>
<li>Adding value to GenBank sequences through enhancing and updating genome annotations</li>
<li>Linking to research reviews/papers for the research community.</li>
</ul>
</li>
<li><strong>Collaborate with researchers to help on specific bioinformatics problems, e.g.</strong>
<ul>
<li>Custom searches of the databases</li>
<li>Building new features into our tools</li>
<li>Help with genome annotation</li>
</ul>
</li>
</ul>

[STEPS]
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