eamag/protocols-with-steps huggingface dataset:
TITLE: XP nutrition keto gummies reviews - how does it works for you?
AUTHORS: nutritionketoiesreviews  

[DESCRIPTION]
XP nutrition keto gummies reviews - how does it works for you?


[STEPS]
1. XP nutrition keto gummies reviews - how does it works for you?
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TITLE: Thioflavin T Assay
AUTHORS: Michael X. Henderon

[DESCRIPTION]
This protocol details Thioflavin T assay.

[GUIDELINES]
Adapted from Alex Crowe, Jing Guo, Dustin Covell 032012 protocol, Mian Horvath Updates

[STEPS]
SECTION: Thioflavin T Assay
1. Resuspend fibril reaction. Fibrils will settle over time. Dilute 1.5 µL of 5 mg/mL fibrillization reaction 1:50 with PBS (total 75 µL).

 

SECTION: Thioflavin T Assay
2. Assay each fibrillization in triplicate on the 96 well black assay plate. Dispense 20 µL of diluted α- synuclein fibrils per well.

SECTION: Thioflavin T Assay
3. Dilute 1 millimolar (mM) Thioflavin T stock into PBS 1:1000 to obtain the required volume of Thioflavine T solution at a concentration of 1 micromolar (µM).

SECTION: Thioflavin T Assay
4. Dispense 180 µL of 1 micromolar (µM) Thioflvain T per well.

SECTION: Thioflavin T Assay
5. Maintain plate at Room temperature for 60 min in the dark.

SECTION: Thioflavin T Assay
6. Read plate on a Spectrophotometer excitation 450 nm, emission 510 nm, cutoff 475 nm.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>It is presumed that early detection and treatment of the chronic lung diseases cystic fibrosis (CF) and primary ciliary dyskinesia (PCD) are crucial for improving the prognosis. Mucus stagnation and secondary infections and inflammation in the airways causes progressive lung damage from infancy in CF and PCD, which again causes early death in CF and reduced pulmonary function in PCD. Early detection of ongoing lung damage will facilitate early intervention with intensive treatment, enhance disease surveillance and further improve preventive treatment. This will improve quality of life for patients with both CF and PCD and likely improve survival in CF.</p>
<p> </p>
<p>Pulmonary function is an important marker of prognosis and effect of treatment, but current pulmonary function tests do not register the earliest damages in the lungs in school children – and are inappliccable for infants and toddlers due to requirements for good coorporation. For this reason there is a demand for more sensitive methods that can be used in all age groups. Gas washout – multiple breath inert gas washout (MBW) – is a method that meets these criteria and seems promising for detection of minimal lung damage prior to debut of clinical symptoms and detection by other methods.</p>
<p> </p>
<p>MBW is for the first time in Denmark established in the Pediatric Pulmonary Service at Copenhagen University Hospital, where a recently established ”Respiratory Physiology Lab for Children” offers a wide range of methods to detect lung disease in children.</p>
<p> </p>
<p><strong>Aim:</strong></p>
<p>The aim of the Ph.D.-project is to investigate:</p>
<ul>
<li>Reliability of results conducted from MBW measurements under different standardized conditions (reproducibility), including establishment of a Danish reference material for children.</li>
<li>Whether MBW can be used as a marker of early lung disease compared to conventional lung function methods in the chronic lung diseases CF and PCD.</li>
<li>Whether MBW can be used as a relevant outcome to detect interventions in basic CF treatment.</li>
</ul>
<p> </p>
<p>The Ph.D.-project will generate a new and more aggressive approach to surveillance and treatment of patients with CF and PCD with an overall aim to reduce morbidity and mortality and improve quality of life. Furthermore, it is expected that this project will generate new knowledge that can be used in the more common lung diseases asthma and COPD, which affects 10% and 15% of children and adults, respectively.</p>

[STEPS]
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TITLE: Total Peptide Library Construction Technology
AUTHORS: Cathy  Miller

[DESCRIPTION]
The total peptide libraryis a collection of a large number of small peptide of specific length and different sequences, which includes the permutation and combination of various amino acid sequences in the short peptide of this length. The general synthetic peptide library uses 20 kinds of natural amino acids as building units, and the size of the library capacity is determined by the number of amino acids (n) that constitute a peptide of a specific length, which can be simply calculated as 20n. For example, to construct a dipeptide library, there are 202(400=4×102) combinations, the tripeptide library has 203(8,000=8×103) combinations, and so on. Therefore, the larger library capacity complicates the synthesis of peptide drugs and becomes a bottleneck in the development of peptide drugs.

Creative Peptides Design PlatformTM(CPDP) has developed peptide information compression technology, which uses bioinformatics methods to compress peptide information, which can integrate the information of multiple peptide into one peptide, so as to contain a large amount of peptide information in a relatively small storage volume. It opens up a new way to research and develop peptide drugs. Based on this technology, we have constructed a total peptide library, containing nearly 500 million different peptide sequence information in a library of approximately 80,000 peptides, which will increase the screening efficiency by approximately 6,000 times.

[STEPS]
TITLE: Kanamycin 50 mg/mL Stock Solution 
AUTHORS: Bailey  Clark

[DESCRIPTION]
The abstract will be added later.

[GUIDELINES]
Reference: Concentration for bacterial selection



[STEPS]
SECTION: Preparation of Stock Solution
1. Weigh 50 mg (0.05 g ) of Kanamycin. 


SECTION: Preparation of Stock Solution
2. Add the Kanamycin to a 1.5 mL tube. 

SECTION: Preparation of Stock Solution
3. Add deionized water to the 1 mL level on the tube. 
SECTION: Preparation of Stock Solution
4. Vortex the tube for 5 s , repeat 3 times. 

SECTION: Preparation of Stock Solution
5. Store the tube in the -20°C freezer.
TITLE: Parse Evercode WT  v2.0.1 Protocol  -- University of Minnesota TMCs
AUTHORS: Parse Biosciences, Laura J Niedernhofer, David A Bernlohr

[DESCRIPTION]
https://www.parsebiosciences.com/products/evercode-whole-transcriptome

Protocol for Parse Evercode, WT - for up to 48 samples and 100K cells.

Version 2.0.1 




[STEPS]
2. 
  

1. Complete dissociation of tissue and fixation of cells or nuclei
TITLE: Iodine-starch sweating assay
AUTHORS: Fanglin Lu

[DESCRIPTION]
This protocol outlines the procedure for assessing the sudomotor function in mice under restraint stress and under systemic pilocarpine stimulation. Both two kinds of sweating assays were based on the iodine-starch reaction. 

[BEFORE_START]
Check if the restraint tube is intact.
Prepare 100% starch–castor oil (1 g starch per 1 mL castor oil)
Prepare pilocarpine (diluted in 150 µL 0.9% saline).

[GUIDELINES]
Please follow the Animal Research: Reporting of In Vivo Experiments (ARRIVE) guideline.
It is favorable to not perform these two different kinds of sweating assays on the same day.

[STEPS]
SECTION: Restraint stress-induced sweating
1. The mouse is immobilized in a self-made restraint tube. 
SECTION: Restraint stress-induced sweating
2. Apply 10% povidone–iodine solution to the plantar surface of bilateral hind paws with a cotton bud. Once dry, coat the skin surface with a suspension of 100% starch–castor oil.
SECTION: Restraint stress-induced sweating
3. Sweat droplets are visualized as dark-colored spots because of iodine–starch reactions. Changes on footpads are video-recorded for 3 min. The number of dark spots was counted for each paw.
SECTION: Pilocarpine-induced sweating
4. The mouse is placed in the supine position under sevoflurane anesthesia (4 volume% in 1 L/min oxygen) . 
SECTION: Pilocarpine-induced sweating
5. Apply 10% povidone–iodine solution to the plantar surface of bilateral hind paws with a cotton bud. Once dry, coat the skin surface with a suspension of 100% starch–castor oil.
SECTION: Pilocarpine-induced sweating
6. Inject 100 µg pilocarpine hydrochloride (diluted in 150 µL 0.9% saline) intraperitoneally.
SECTION: Pilocarpine-induced sweating
7. Sweat droplets are visualized as dark-colored spots because of iodine–starch reactions. Changes on footpads are video-recorded for 5 min. The number of dark spots was counted for each paw.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>Method to filter Illumina sequence data by removing low quality reads and reads mapping to artifact and contamination databases using BBTools.</p>
<p>DNA sequencing produces low quality reads, reads that contain sequencing artifacts and contamination from lab processes.  Removing the bad data from the fastq produces more accurate results for mapping to references and assembly.</p>
<p> </p>
<p>BBTools is a bioinformatics software package developed at the DOE Joint Genome Institute and used worldwide.</p>
<p>http://bbtools.jgi.doe.gov</p>
<p> </p>
<p> </p>
<p> </p>

[STEPS]
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TITLE: Post-IMS Autofluorescence Microscopy
AUTHORS: Elizabeth Neumann, Jamie Allen, Heath Patterson, Danielle Gutierrez, Jeff Spraggins

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Scope: </div><div class = "text-block">Obtain autofluorescence microscopy images of tissues after IMS analysis</div><div class = "text-block">Expected Outcome: </div><div class = "text-block">A brightfield and green autofluorescence microscopy image of the tissue section that enables registration and correlation of different imaging modalities on a pixel by pixel basis.</div></div>

[STEPS]
?. Place microscope slide within adapter and insert into the Zeiss AxioScan Slide Scanner.
?. Perform Coarse focusing of the tissue using:GFP filter set (ex. 450–490 nm; em. 500–550, green)  High lamp power (~90%) and moderate exposure times (~ 150 ms).
?. Perform Fine focusing of the tissue using:GFP filter set (ex. 450–490 nm; em. 500–550, green) Brightfield lamp at similar power and exposure time used in step 2 to build a focus map.
?. Define the imaging region that includes the tissue.
?. Acquire brightfield and autofluorescence image.
?. Export autofluorescence image as an OME-TIF File with the following options: “BigTIFF”, “Use Tiles”, “Compress”, and “Convert to 8 Bit”. Alternatively, other image file types, such as “BigTIFF” and “pngs” can also be useful, depending on the application.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>Target cells are depleted by incubating your sample with the biotin antibody cocktail followed by incubation with magnetic Streptavidin Nanobeads (Cat. No. 480015/480016). The magnetically labeled fraction is retained by the use of a magnetic separator. The untouched cells are collected. These are your cells of interest; do not discard the liquid. Some of the downstream applications include functional assays, gene expression, phenotypic characterization, etc.</p>
<p> </p>

[GUIDELINES]
<p> <strong>Reagents and instruments required:</strong></p>
<p>-MojoSort™ Buffer (5X) (Cat. No. 480017)<br />-MojoSort™ Magnet (Cat. No. 480019) or compatible magnetic separation system<br />-Adjustable pipettes<br />-70 μm filters (one per sample)<br />-5 mL (12 x 75 mm) polystyrene tubes<br />-Reagents for sample preparation<br />-Reagents and instruments (Flow cytometer) to determine yield and purity</p>
<p> </p>
<p><strong>Protocol:</strong></p>
<p>This protocol has been optimized to remove washing steps after antibody cocktail and nanobeads incubations, resulting in a shorter and more convenient protocol. This procedure is optimized for the isolation of 10<sup>7</sup> to 2 x 10<sup>8</sup> cells per tube. If working with fewer than 10<sup>7</sup> cells, keep volumes as indicated for 10<sup>7</sup> cells. For best results, optimize the conditions to your specific cell number and tissue. Prepare fresh MojoSort™ Buffer solution by diluting the 5X concentrate with sterile distilled water.</p>
<p> </p>
<p> </p>
<p><img id="s-mce-img" class="s-mce-img" src="https://s3.amazonaws.com/pr-journal/dn8ecje.jpg" data-src="https://s3.amazonaws.com/pr-journal/dn7ecje.jpg" data-ofn="MojoSort_isolationnowash.JPG" /></p>

[STEPS]
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TITLE: Hot Chocolate Chip Cookies
AUTHORS: Ming-Dao Chia

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Adapted from https://www.the-girl-who-ate-everything.com/hot-chocolate-cookies/</div><div class = "text-block">Amounts for making 30 cookies, adapt as needed.</div></div>

[STEPS]
?. [Ingredient prep]
Acquire the following:2 tablespoons coconut butter0.25 cup coconut oil12 tablespoons olive oil1 cup white sugar1 egg1 teaspoon vanillaA dash of nutmegA dash of cinnamonA dash of allspice1.5 cups all-purpose flour0.5 cups hot chocolate mix (incl. sugar)1 teaspoon table salt1 teaspoon baking soda200g milk chocolate chips
?. [Ingredient prep]
Add the coconut butter, coconut oil, olive oil, vanilla, egg, nutmeg, cinnamon, and allspice to one bowl and mix well.
?. [Ingredient prep]
Add the flour, hot chocolate mix, salt, and baking soda to another bowl, and mix well.
?. [Ingredient prep]
Add the dry ingredients to the first bowl while mixing until evenly mixed.
The resulting dough may be quite crumbly. This is normal, but if there is still unmixed powder add more coconut oil.
?. [Ingredient prep]
Melt the coconut oil and coconut butter.
Soaking the original containers in hot water for a minute or two works well for this step.
?. [Ingredient prep]
Add sugar to the same bowl while stirring until evenly mixed.
?. [Ingredient prep]
Add chocolate chips to mix and stir in.
?. [Baking]
Preheat oven to 175ºC (350ºF)
?. [Baking]
Prepare baking paper on a tray.
?. [Baking]
Shape 1.5-2 tablespoons each of batter into balls and place on tray, with at least 2cm of separation between cookies.
?. [Baking]
Bake for 12 minutes.
?. [Baking]
Allow cookies to cool on tray for 2-5 minutes before serving.
Cookies may still be quite soft at this stage and will harden as they cool. Remove carefully if not serving in tray.
TITLE: Immunofluorescent staining of LN
AUTHORS: Guido Krähenbühl

[DESCRIPTION]
Generic Staining Protocol

[STEPS]
1. Thaw Tissuesections at RT
2. wash in PBS for 10 minutes
 10 min 

3. Circle samples with PAP-Pen
4. Block in 10% Serum for 30 minutes
30 min 

5. Add primary Antibody for 90 minutes at RT or o/n at 4C

6. wash 3x with PBS?
7. incubate with secondary AB for 60 minutes
8. wash 3x with PBS?
9. Add DABCO-Mowiol on samples to increase IF
10. Mikroskopie!
TITLE: Liquid Chromatography with Tandem Mass Spectrometry (LC-MS/MS)
AUTHORS: Leonardo A Parra-Rivas

[DESCRIPTION]
Liquid Chromatography with Tandem Mass Spectrometry (LC-MS/MS)

[STEPS]
1. The data acquisition by LC-MS/MS was adapted from a published procedure 
 








2. Derived peptides were resuspended in a loading buffer
(0.1% trifluoroacetic acid, TFA) and separated on a Water's Charged Surface
Hybrid (CSH) column (150 µm internal diameter x 15 cm; particle size: 1.7 µm).


3. The samples were run on an EVOSEP liquid chromatography system using the 15
samples per day preset gradient (88 min) and were monitored on a Q-Exactive
Plus Hybrid Quadrupole-Orbitrap Mass Spectrometer (Thermo Scientific). 
4. The mass spectrometer cycle was programmed to collect one full MS scan followed by 20
data-dependent MS/MS scans. The MS scans (400-1600 m/z range, 3 x 106
AGC target, 100 ms maximum ion time) were collected at a resolution of 70,000
at m/z 200 in profile mode. 
5. The HCD MS/MS spectra (1.6 m/z isolation width, 28%
collision energy, 1 x 105 AGC target, 100 ms maximum ion time) were
acquired at a resolution of 17,500 at m/z 200. Dynamic exclusion was set to
exclude previously sequenced precursor ions for 30 seconds. Precursor ions with
+1, and +7, +8, or higher charge states were excluded from sequencing.
TITLE: High-Performance Liquid Chromatography (HPLC)
AUTHORS: Yingchao Xue, Xiping Zhan, Shisheng Sun, Senthilkumar S. Karuppagounder, Shuli Xia, Valina L Dawson, Ted M Dawson, John Laterra, Jianmin Zhang, Mingyao Ying

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes High-Performance Liquid Chromatography (HPLC) for lines ND1014, N1, and ND27760 from </span><span style = "font-style:italic;">Synthetic mRNAs Drive Highly Efficient iPS Cell Differentiation to Dopaminergic Neurons</span><span>. </span></div></div>

[STEPS]
?. [HPLC Preparation]
Replace neuron culture medium with Hanks’ balanced saline solution buffer with the addition of .
[KCl]
?. [HPLC Preparation]
Incubate for  at .
37 °C
?. [HPLC Preparation]
Collect media and centrifuge to clear cell debris. Collect neuron pellet.
?. [HPLC Preparation]
Freeze immediately and store at .
-80 °C
?. [HPLC Analysis]
Thaw samples.
?. [HPLC Analysis]
Concentrate using a vacuum (Savant SPD 121P) connected with a refrigerated vapor trap (Savant RVT 5105).
?. [HPLC Analysis]
Resuspend freeze-dried samples in .
[perchloric acid]
?. [HPLC Analysis]
Analyze monoamines using HPLC electrochemical detection by dual channel Coulochem III electrochemical detector (model 5300).
?. [HPLC Analysis]
Separate monoamines using a reverse phase C18 column (3-mm 3 150-mm C-18 RP-column) with a flow rate of 0.600 ml/minute.
?. [HPLC Analysis]
Quantify monoamine concentrations by comparison of the area under the curve to known standard dilutions.
TITLE: One Part CPEC and quick change
AUTHORS: N.J. Hillson

[STEPS]
?. Setup 2 PCR-like reactions, each with only one of the two full-length primers:Sterile water 13.5 µLGC buffer 5 µLDMSO (30% stock) 2.5 µLdNTPs (10 mM stock) 0.5 µLPrimer (10 µM stock) 2.5 µLMini-prepped template DNA 0.5 µLPolymerase (Pfu) 0.5 µLTotal 25 µL
?. Combine both reactions and add 1 µL more of polymerase.
?. DpnI digest for 1 hour at 37 C.
?. Gel extract (optional).
?. Transform 10 µL into chemically competent cells.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p><span class="TextRun SCX27213965" lang="EN-US" style="font-size: 14pt; font-family: Cambria,serif; line-height: 24px;" xml:lang="EN-US"><span class="NormalTextRun SCX27213965" style="background-color: inherit;">Procedure</span></span><span class="TextRun SCX27213965" lang="EN-US" style="font-size: 14pt; font-family: Cambria,serif; line-height: 24px;" xml:lang="EN-US"><span class="NormalTextRun SCX27213965" style="background-color: inherit;"> in order to prepare EDTA media (</span></span><span class="TextRun SCX27213965" lang="EN-US" style="font-size: 14pt; font-family: Cambria,serif; line-height: 24px;" xml:lang="EN-US"><span class="NormalTextRun SCX27213965" style="background-color: inherit;">a</span></span><span class="TextRun SCX27213965" lang="EN-US" style="font-size: 14pt; font-family: Cambria,serif; line-height: 24px;" xml:lang="EN-US"><span class="NormalTextRun SCX27213965" style="background-color: inherit;">lso known as </span></span><span class="TextRun SCX27213965" lang="EN-US" style="font-size: 14pt; font-family: Cambria,serif; line-height: 24px;" xml:lang="EN-US"><span class="SpellingError SCX27213965" style="background-color: inherit;">Aquil</span><span class="NormalTextRun SCX27213965" style="background-color: inherit;">).</span></span></p>
<p> </p>
<p> </p>

[GUIDELINES]
<p><strong>Reagents</strong></p>
<ul>
<li>Sodium Silicate</li>
<li>Sodium Nitrate:</li>
<li>Sodium dihydrogen Phosphate:</li>
<li>Vitamin B12</li>
<li>Biotin</li>
<li>Thiamine</li>
<li>FeCl<sub>3</sub>6H<sub>2</sub>O</li>
<li>ZnSO<sub>4</sub>7H<sub>2</sub>O</li>
<li>MnCl<sub>2</sub>4H<sub>2</sub>O</li>
<li>CoCl<sub>2</sub>6H<sub>2</sub>O</li>
<li>CuSO<sub>4</sub>5H<sub>2</sub>O</li>
<li>Na<sub>2</sub>MoO42H<sub>2</sub>O</li>
<li>Na<sub>2</sub>SeO<sub>3</sub></li>
</ul>
<p> </p>

[STEPS]
?. 
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TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>Protocol for Northern Blot using radioactive RNA probes.</p>

[BEFORE_START]
<p>Generate a PCR product with a T7 promoter for generating riboprobes. Make sure the riboprobe is antisense to the RNA of interest.</p>

[STEPS]
?. 
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