eamag/protocols-with-steps huggingface dataset:
TITLE: Radiographic evaluation
AUTHORS: geoffrey.pages  

[DESCRIPTION]
This radiographic evaluation protocol was used perioperatively to manage dogs treated by TPLO for cranial cruciate ligament disease.

[BEFORE_START]
Two experienced observers (1 Dipl. ECVS and 1 ECVS resident, with more than 3 years in TPA measurement) assessed the radiographs.
Radiographs were anonymized.


[STEPS]
SECTION: Tibial Plateau Angle measurement
1. Tibial Plateau Angle was measured following previously described landmarks (Dismukes 2008).

Mechanical axis:
The landmarks used to determine the mechanical axis were the midpoint between the apices of the 2 tibial intercondylar eminences and the center of the circle created by the talus for proximal and distal tibia, respectively. 

Joint surface landmarks:
- landmarks established for the proximal tibial joint orientation line were the cranial and caudal aspects of the medial tibial condyle,
- landmarks established for the distal tibial joint orientation line were the distal aspect of the distal intermediate ridge of the tibia, cranially, and the caudodistal aspect of the cochlea tibia, caudally.

SECTION: Bone healing
2. Bone healing was subjectively graded using a previously developed scale (Oxley 2012), modified to allow numerical grading:


    Score   Healing grade   Description     0   None   No biological activity     1   Poor   Some evidence of bone healing but unbridged cortices and/or osteotomy gap     2   Good   Active bridging callus and/or osteotomy mostly blurred or filled with callus     3   Complete   Remodeled callus at all cortices and/or osteotomy indistinct    
 
SECTION: Postoperative follow-up
3. Owners of dogs presenting insufficient bone healing (grades 0 and 1) at follow-up were asked for a recheck after 4 to 6 weeks to ensure sufficient bone healing (grades 2 or 3).
TITLE: CPTAC FFPE Sample Processing 
AUTHORS: Jingxian Liu

[DESCRIPTION]
This is a description of the steps that Clinical Proteomic Tumor Analysis Consortium (CPTAC) has developed to collect surgical resection biospecimens. There are multiple protocols with various preservation methods and targeted assays. Here only the Formalin-Fixed Paraffin-Embedded (FFPE) related information is provided. 

Excerpted protocol from: 
Li Y, Lih TM, Dhanasekaran SM, Mannan R, Chen L, Cieslik M, Wu Y, Lu RJ, Clark DJ, Kołodziejczak I, Hong R, Chen S, Zhao Y, Chugh S, Caravan W, Naser Al Deen N, Hosseini N, Newton CJ, Krug K, Xu Y, Cho KC, Hu Y, Zhang Y, Kumar-Sinha C, Ma W, Calinawan A, Wyczalkowski MA, Wendl MC, Wang Y, Guo S, Zhang C, Le A, Dagar A, Hopkins A, Cho H, Leprevost FDV, Jing X, Teo GC, Liu W, Reimers MA, Pachynski R, Lazar AJ, Chinnaiyan AM, Van Tine BA, Zhang B, Rodland KD, Getz G, Mani DR, Wang P, Chen F, Hostetter G, Thiagarajan M, Linehan WM, Fenyö D, Jewell SD, Omenn GS, Mehra R, Wiznerowicz M, Robles AI, Mesri M, Hiltke T, An E, Rodriguez H, Chan DW, Ricketts CJ, Nesvizhskii AI, Zhang H, Ding L; Clinical Proteomic Tumor Analysis Consortium. Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness. Cancer Cell. 2023 Jan 9;41(1):139-163.e17. doi: 10.1016/j.ccell.2022.12.001. Epub 2022 Dec 22. PMID: 36563681; PMCID: PMC9839644.

[STEPS]
SECTION: Sample Processing for CPTAC Renal Cell Carcinoma
1. The CPTAC Biospecimen Core Resource (BCR) at the Pathology and Biorepository Core of the Van Andel Research Institute in Grand Rapids, Michigan manufactured and distributed biospecimen kits to the Tissue Source Sites (TSS) located in the US, Europe, and Asia. Each kit contains a set of pre-manufactured labels for unique tracking of every specimen respective to TSS location, disease, and sample type, used to track the specimens through the BCR to the CPTAC proteomic and genomic characterization centers.
SECTION: Sample Processing for CPTAC Renal Cell Carcinoma
2. Tissue specimens averaging 200 mg were snap-frozen by the TSS within a 30 min cold ischemic time (CIT) (CIT average = 13 min) and an adjacent segment was formalin-fixed paraffin-embedded (FFPE) and H&E stained by the TSS for quality assessment to meet the CPTAC ccRCC requirements. Routinely, several tissue segments for each case were collected.
TITLE: Simple Panzanella Salad
AUTHORS: Lenny  Teytelman

[DESCRIPTION]
(This recipe is based on the "Panzanella With Mozzarella and Herbs" by Melissa Clark in the New York Times.)

This Tuscan salad is like an Italian version of Gazpacho. Perfect when tomatoes are in season and you have some stale white bread.

This version is simplified; please see the NYT recipe for a fancier meal.

[STEPS]
1. Cut up the bread in 1-inch cubes and toast at 425 degrees for ~10 minutes. Let them cool.
2. Place cut up tomatoes in a large salad bowl.
3. Add cut/torn mozzarella, sliced red onion, minced garlic.
4. Add:
 2 tablespoon red wine vinegar
 oregano or thyme
1/2 teaspoon of salt
6 tablespoons of extra virgin olive oil
black pepper to taste
Mix and let sit for a few minutes so that the tomatoes release the juice.
5. Chop or slice cucumbers and cut up basil and parsley. Add them to the bowl.
7. Enjoy!

  

6. Add the bread cubes and let the salad sit at room temperature for 30min to couple of hours.
TITLE: Imaging- Confocal
AUTHORS: daniel.dautan daniel, Per Svenningsson

[DESCRIPTION]
Protocol for imaging using confocal microscope. Sections for analysis should be mounted on slides, stained for appropriate markers, and coverslipped. This protocol is using a Carl Zeiss LSM 880 confocal microcope.

[STEPS]
1. Using the confocal microscope, capture images at 10x magnification using a resolution of either 1024x1024 or 2048x2048.
2. If needed for larger area of the brain, use tile-scanning with a 0.6 zoom factor and 10% overlap for automated reconstruction.
3. If acquiring z-stack images use 1-4um spacing. Use stack projection in ImageJ and exclude approximately 10% of the section's surface.
4. Making sure to use the same settings across all images for the same experiment, use ImageJ to process the images.
TITLE: Handwriting Test for Preschool Children (HT-PRE): a new tool to assess the handwriting ability of preschool children aged 5–6 years old in Mainland China
AUTHORS: Qin Hong

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The Handwriting Test for Preschool Children (HT-PRE), which is a newly developed handwriting screening tool for preschool children aged 5–6 years old in Mainland China, has displayed a very good internal consistency, acceptable test-retest reproducibility, and good criterion-based validity, and has also shown good application prospects for handwriting difficulty screening in a clinical setting.</div></div>

[STEPS]
?. Before the test, parents completed the "Children's Basic Situation Questionnaire" so that necessary information about the participants could be gathered, including the child's age, gender, medical history, and trauma history.
?. The HT-PRE was then conducted one-on-one.
?. Write the most familiar contents, including name, age, class, Arabic number (1-9) in sequence by memory.
?. “The Individual Record Form” was used to record all special behavior observed during testing.
?. Write 10 two-digit numbers the numbers, which is randomly selected in the random number table by listening.
?. 24 alphabet letters (except O and I which are easily to be confused with the numbers), which are randomly arranged into two lines, are required to be copied sequentially.
?. 12 Chinese characters contained all the basic strokes and structures were selected from the 1st to the 4th volume of the primary school textbooks, and were requested to be copied in the same blank standard character grid.
TITLE: Reagent prep - Stanford TMC
AUTHORS: John Hickey

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>See our detailed protocol published with the following title: </span><span style = "font-weight:bold;">CODEX multiplexed tissue imaging with DNA-conjugated antibodies.</span></div></div>

[STEPS]
?. See our detailed protocol published with the following title: CODEX multiplexed tissue imaging with DNA-conjugated antibodies.
TITLE: ADP assay (Colorimetric)
AUTHORS: Kiichi Hirota, Yoshiyuki Matsuo

[STEPS]
?. [Standard preparation]
Reconstitute the ADP standard (1 µmol) in 100 µl of water to generate a 10 mM ADP stock solution.
?. [Standard preparation]
Dilute 10 µl of the 10 mM ADP stock solution with 90 µl of ADP Assay Buffer to prepare a 1 mM ADP standard solution.
?. [Standard preparation]
Prepare dilutions of a ADP standard using ADP Assay Buffer (0, 0.04, 0.08, 0.12, 0.16, 0.2 mM). 100 µl of each dilution is required to set up duplicate reading (2 x 50 µl).
?. [Sample preparation]
Remove media and wash cells with cold PBS.
?. [Sample preparation]
Lyse cells in 100 µl of ADP Assay Buffer.
?. [Sample preparation]
Prepare cells in a 12-well plate.
?. [Sample preparation]
Incubate the lysate for 10 min on ice.
?. [Sample preparation]
Centrifuge at 18,000 x g for 5 minutes at 4°C.
?. [Sample preparation]
Collect the supernatant in a new microcentrifuge tube and keep on ice.
?. [Assay procedure (for the colorimetric assay)]
Prepare 50 µl of Reaction Mix for each reaction. Prepare an amount of Reaction Mix sufficient for all samples including ADP standards.  AB1ComponentVolume (µl)2ADP Assay Buffer443ADP Probe24ADP Converter25ADP Developer2
AB1ComponentVolume (µl)2ADP Assay Buffer443ADP Probe24ADP Converter25ADP Developer2
?. [Assay procedure (for the colorimetric assay)]
Add 50 µl of ADP standards or samples per well to a clear 96-well plate.
?. [Assay procedure (for the colorimetric assay)]
Add 50 µl of Reaction Mix to each well.
?. [Assay procedure (for the colorimetric assay)]
Incubate for 30 min at room temperature.
?. [Assay procedure (for the colorimetric assay)]
Measure the absorbance at 750 nm using iMark™ Microplate Absorbance Reader.
?. [Assay procedure (for the colorimetric assay)]
Test all samples with a minimum of two replicates.
?. [Assay procedure (for the colorimetric assay)]
Dilute the lysate 3-fold in ADP Assay Buffer.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
This protocol describes how to build up a freezer stock of a given bacterial strain. 

Following this protocol will result in individual, glycercol-suspended aliquots of genetically similar bacteria originating from a clone of cells forming an isolated colony, derived from a single precursor cell. 

Using an isolated colony to build up a freezer stock of a bacterial strain ensures the individual aliquots are genetically similar and not contaminated with another bacterial strain. For full instructions, users must follow the steps in 'How to isolate a single bacterial colony' by the same author before commensing with the current protocol.

[BEFORE_START]
Before starting this protocol users should follow the instructions in the protocol 'Plating bacteria to isolate a single colony' in order to obtain a single colony isolate of a bacterial strain.



[GUIDELINES]
It is important to ensure that all  frozen aliquots of a bacterial strain originated from the same isolated colony. This ensures that the bacteria is genetically similar for the duration of an experiment where several aliquots must be grown up on different days or similarly between different experiments.

[STEPS]
?. 
?. 
?. 
?.
TITLE: Protocol in dev - Seq Analysis pipeline
AUTHORS: Emma  Ganley

[DESCRIPTION]
test

[STEPS]
SECTION: Section 1
1. 
 

 
    


=sum(a1,b1,c1)

SECTION: Section 1
2. Add 50 mL A
Add 100 mL B

Leave for 10 min



Add 50 µL 

50 µL 

 

SECTION: Section 2
3. 
 

SECTION: Section 2
4.  

Download latest version of 
 



SECTION: Section 2
6. 

SECTION: Section 2
5. Download latest dataset from 
 
 
SECTION: Section 2
7.
TITLE: FCMPASS - Fluorescence calibration
AUTHORS: Joshua Welsh, Jennifer Jones

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines the steps required to input fluorescence calibration parameters 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]
?. If fluorescence calibration is being performed click the '+' button to add a calibration parameter to the table. If fluorescence calibration is not required, click 'Next'.
?. If you have not yet added the MESF reference bead information that will be used for calibration into the Catalogue', click 'Catalogue' in the top menu bar and complete as per the protocol..
?. Once a parameter is added double click the ‘Reference Fluorophore’ item and select the bead set used for calibration. The displayed sets are those that have previously been added to the Catalogue.
?. Double click the parameter to select the associated parameter with the correct fluorophore.
?. Double click the relevant cell in the 'New Parameter Name' column to adjust how the calibrated parameter’s name will appear once written to the fcs file.
?. The reference bead values for the selected parameter should appear in the 'Regression Values' table.
?. Click in the 'Acquired Value' box next to each bead reference value and input the acquired statistic
?. Repeat steps 1 to 5 for any further parameters that need to be calibrated. To change the 'Ref Value' table to other fluorophores select them in the reference 'Fluorescence Calibration Parameters' table.
?. Once completed click ‘Next’.
The regression plots for the inputted fluorescence calibration parameters can be checked at any time using the ‘Check Regression(s)’ button. The ‘Advanced Settings’ button can be used to specify an fluorophore:protein ratio or alter the regression method between linear, log, weighted linear, weighted log.
TITLE: Proteome analysis
AUTHORS: Leonardo A Parra-Rivas

[DESCRIPTION]
Proteome analysis

[STEPS]
1. Mass spectrometry data was
analyzed according to a published protocol 
 






2. Spectra were searched using  Proteome Discoverer (RRID:SCR_014477) (https://www.thermofisher.com/order/catalog/product/IQLAAEGABSFAKJMAUH) software version 2.1 against 2020 mouse UniProtKB/Swiss-Prot
(RRID:SCR_021164)( https://www.expasy.org/resources/uniprotkb-swiss-prot) (17,042 target sequences) along with the human α-synuclein protein sequence. 

3. Searching parameters included full tryptic or Asp-N restriction, precursor mass tolerance
(± 20 ppm), and fragment mass tolerance (± 0.05 Da). Serine, threonine, and tyrosine
phosphorylation (+79.9663 Da), methionine oxidation (+15.99492 Da),
asparagine and glutamine deamidation (+0.98402 Da), and protein N-terminal
acetylation (+42.03670 Da) were variable modifications (up to 3 allowed per
peptide); cysteine was assigned a fixed carbamidomethyl modification (+57.021465
Da).
4.  Percolator was used to filter the peptide spectrum matches to a false
discovery rate of 1%. 
5. Gene ontology was analyzed using The Database for Annotation, Visualization and
Integrated Discovery DAVID (RRID:SCR_001881)(https://david.ncifcrf.gov/tools.jsp-DAVID97. 
6. Biological processes involving synaptic function were selected for grouping analysis. Functional grouping was based on Fisher’s exact test (p<0.05). 
Protein-protein interaction networks were then identified using the STRING (RRID:SCR_005223 ) (https://string-db.org/) version 11.5 , and the protein class was determined using PANTHER
(RRID:SCR_004869)( http://www.pantherdb.org/).
TITLE: Effect of Therapeutic Exercise, Educational booklet and Vitamin D3 Supplement for the Management of Chronic Mechanical Low Back Pain
AUTHORS: Muhammad  Shahidul Islam, Dr.  Md. Ashrafuzzaman Zahid, Professor  Dr. Md. Sohrab Hossain, K M Amran  Hossain

[DESCRIPTION]
The protocol titled "Effect of Therapeutic Exercise, Educational booklet and Vitamin D3 Supplement for the Management of Chronic Mechanical Low Back Pain" is authored by Muhammad Shahidul Islam, Ph. D. student at the Department of Nutrition and Food Technology, Jashore University of Science and Technology, Jashore-7408, Bangladesh. This is a part of his Ph. D. thesis titled “Therapeutic Exercise, Educational booklet and Vitamin D3 Supplement for the Management of Chronic Mechanical Low Back Pain” under the supervision of Dr. Md. Ashrafuzzaman Zahid, Ph. D., Associate Professor, Department of Nutrition and Food Technology, Jashore University of Science and Technology, Jashore-7408, Bangladesh. He is co-supervised by Professor Dr. Md. Sohrab Hossain, Ph. D., Professor, Department of Physiotherapy, Bangladesh Health Professions Institute (BHPI), CRP, Savar, Dhaka-1343, Bangladesh.

[BEFORE_START]
Medical screening is necessary 

[GUIDELINES]
The protocol consists of three phases
1) Cross-sectional study on Vitamin D deficiency in Chronic Mechanical Low Back pain   
2) Randomized control trial on Booklet and Therapeutic Exercise 
3) Randomized control trial on Booklet, Therapeutic exercise, and Vitamin d supplement 

[STEPS]
SECTION: Protocol Description
1. Introduction

SECTION: Protocol Description
1.1. Background
SECTION: Protocol Description
1.2. Justification 
SECTION: Protocol Description
1.3. Objectives 
SECTION: Protocol Description
2. Literature Review 
SECTION: Protocol Description
3. Conceptual Framework
SECTION: Protocol Description
4. Methodology 
SECTION: Protocol Description
4.1. Study Design 
SECTION: Protocol Description
4.2. Research Outline 
SECTION: Protocol Description
4.3. Study Population and area 
SECTION: Protocol Description
4.4. Study Period 
SECTION: Protocol Description
4.5. Sample size
SECTION: Protocol Description
4.6. Sampling Criteria 
SECTION: Protocol Description
4.7. Outcome tools
SECTION: Protocol Description
4.8. Interventions 
SECTION: Protocol Description
4.9. Data Analysis 
SECTION: Protocol Description
5. Expected Outcome
SECTION: Protocol Description
6. Ethical Considerations 
SECTION: Protocol Description
7. Funding
SECTION: Timeline
8. Gantt chart
SECTION: References
9.
TITLE: Electrocompetent E. coli 
AUTHORS: Alba Balletbó

[STEPS]
?. Grow 5 mL culture of LB w/o salts overnight
?. Pre-cool centrifuge to 4ºC.
?. Inoculate 400 mL LB w/o salts with 5 ml pre-culture and incubate for 3 hours to OD600 0.5-1.0.
?. Transfer culture volume to 8 Greiner tubes of 50 mL and leave on ice for 15 minutes.
?. Centrifuge for 10 minutes at 2000g and 4ºC.
?. Remove supernatant and add 5 mL + 45 mL of 10% glycerol.
?. Centrifuge for 10 minutes at 2000g and 4ºC.
?. Remove supernatant and add 5mL + 45mL of 10% glycerol.
?. Hold on ice for 10 minutes.
?. Centrifuge for 10 minutes at 2000g and 4ºC.
?. Remove supernatant and resuspend in 1 mL ice-cold 10% glycerol, pool fractions.
?. Centrifuge for 5 minutes at 1500g and 4ºC.
?. Remove supernatant and add 400 μL 10% glycerol (=800 μL suspension).
?. Aliquot 40μL in pre-cooled eppendorfs and flash freeze with N2(l). Store -80ºC.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
 amino acid analysis service, It is widely known that protein/peptide quantities is highly needed for further applications, quantitative amino acid analysis, qAAA, is a suitable assay. It can  precisely determine protein quantities and provide detailed information regarding the relative amino acid composition and free amino acids. The method of  amino acid analysis service is very different from Very long Chain Fatty Acids and Bile Acids Analysis

[STEPS]
TITLE: Total RNA extraction
AUTHORS: Izabela Rezende, Lívia Sacchetto

[DESCRIPTION]
<p>For purification of viral RNA from serum and cell-culture supernatants.</p>

[STEPS]
?. Centrifuge the samples at 8000 x g for 8 min to clarify.
?. Transfer 140 µl of the supernatant into a 1.5 ml microcentrifuge tube.
?. Use this amount to RNA extraction with QIAamp® Viral RNA Mini (Qiagen, USA), according to the manufacturer's instructions. Available at: https://www.qiagen. com/br/resources/re sourcedetail?id=14e7cf6e-521a-4cf7-8cbc-bf9f6fa33e24&lang=en.
?. Introduction of a negative control (Nuclease Free Water) into the purification procedure.
?. Pipet the samples in the same order and before the negative control.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>The origin of animals, which occurred over 600 million years ago, left no evidence in the fossil record. To trace the earliest events in animal prehistory, we compare extant animals to their closest living relatives, the choanoflagellates, in order to reconstruct the gene content of their last common ancestor and how it evolved on the stem lineage leading to animals. In this project, we increase the accuracy of ancestral animal and choanoflagellate gene content reconstructions by sequencing the transcriptomes of 19 species of choanoflagellates selected for their phylogenetic diversity.</p>

[STEPS]
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
An alternative epifluorescence microscopy (EFM) technique for virus enumeration has been developed using polycarbonate Track Etch (PCTE) filter membranes in place of aluminum oxide Anodisc membranes. The established EFM technique, first developed by Hennes and Suttle in 1995 and later expanded upon by Noble and Fuhrman in 1998, uses supported 20 nm pore-size Anodisc filter membranes to determine virus abundance in natural environments. Increased price and sporadic availability of Anodisc filters stimulated the evaluation of alternative filters for use in the procedure. The feasibility of using 30 nm pore-size PCTE filters for virus enumeration was assessed using the Anodisc filter procedure as a control. Although virion particle counts are slightly less precise using PCTE filters, they offer a substitute for Anodiscs while requiring only minor adjustments to the established protocol. Per slide, the PCTE costs approximately ten times less to prepare than the Anodisc-based method.

[STEPS]
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?.