eamag/protocols-with-steps huggingface dataset:
TITLE: Protocol-  Romantic relationships and family in Spaniards emerging adults
AUTHORS: Marta Díez

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The exploration of and search for romantic relationships is one of the developmental tasks that characterize emerging adulthood, a new developmental phase half way between adolescence and full adulthood. The present study aims to explore the relationships which exist between the subjective perception of some parental behaviour and the anxiety and avoidance dimensions of attachment during emerging adulthood. The results revealed that perceived family support and perceived parental warmth were negatively associated with the avoidance and anxiety dimensions. In contrast, perceived parental control (both behavioral and psychological) was found to be positively associated with both attachment dimensions. Perceived behavioral control was also found to play a moderator role between perceived parental warmth and romantic attachment anxiety. This research therefore adds to our knowledge of how to help young people establish healthy romantic relationships, one of the principal developmental tasks of emerging adulthood, and does so by analyzing the role played by the family in this undertaking. Indeed, the family continues to be a key development context for young people and influence them on the romantic partner choice. Young people who, in both Spain and many other Western countries, continue to live in the family home until well into their third decade of life. This is a new phenomenon which previous generations did not experience, and further study is required to enable a more thorough understanding of this period.</div></div>

[STEPS]
?.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>Please contact Dr. Steven Wilhelm (wilhelm@utk.edu) for additional information regarding this protocol.</p>
<p> </p>
<p>Adapted from Wetzel and Likens 2000. Limnological Analyses, Springer NY</p>

[STEPS]
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?.
TITLE: MDL-LDA Agile Method
AUTHORS: Freddie Prianes

[DESCRIPTION]
As a guide in modeling the document labels using Latent Dirichlet allocation for archived documents in an Integrated Quality Assurance System (IQAS), the researchers used the agile method as it promotes flexibility, speed, and, most importantly, continuous improvement in developing, testing, documenting, and even after delivery of the software. Since the phases of this model are light, the teams are not bound by a rigid systematic-based process on pre-set constraints and restrictions as some other models, like the waterfall model, and can adjust changes whenever they are needed. This flexibility on every stage propagates creativity and freedom within processes. Furthermore, development teams can modify and re-prioritize the backlog, allowing for speedy implementation.

[STEPS]
SECTION: MDL-LDA Methodology
1. Plan: the researchers collected previous documents involved in the accreditation process, such as compliance reports under the areas of student, faculty, facility, library, and administration. Also, understanding of the existing problems in tracking, tagging, and duplication of these documents during the accreditation process.
SECTION: MDL-LDA Methodology
2. Design: the requirement specifications in this stage were identified in relation to the existing problem of the HEI in tracking, tagging, and duplication of the documents for accreditation and quality assurance. Along with this, the researchers also created the process of the intelligent model, which will be the basis of document labelling.
SECTION: MDL-LDA Methodology
3. Develop: this stage is intended on the creation of the prototype, which involves the processing of the documents in order to identify the proper label for each document.
SECTION: MDL-LDA Methodology
4. Deploy: the prototype undergoes a test run during this stage.
SECTION: MDL-LDA Methodology
5. Review: the researchers conduct a checklist function review to check if each component is running properly.
SECTION: MDL-LDA Methodology
6. Launch: wherein the prototype is embedded to the local system of the HEI.
TITLE: Collecting needle and branch samples for terpenoid and expression analysis
AUTHORS: Vidya S Vuruputoor, Victoria Burton, Jill Wegrzyn

[DESCRIPTION]
This protocol is used by the PCG group for sampling needle and branch tissue from hemlock conifers for terpenoid analysis, as well as RNA expression analysis.

[STEPS]
1. Open Treesnap (https://treesnap.org/), record the accession number on the tree and fill in notes for hemlock woolly adelgid infestation (HWA) levels (scale provided by the app).

  

1.1. Use the comment field to enter: EHS present OR EHS absent to record the hemlock scale.

  

1.2. Take at least 3 photos with TreeSnap. This includes at least one of the trees itself, one photo of the tree tag if that is present, and one photo of the collection vial with the label as well.
1.3. Geolocation will be recorded automatically but TreeSnap can also connect with a more precise external GPS device.
1.4. Note DBH in appropriate column
1.5. Note any other observation you may have- including plant condition (Excellent/Good/Poor), and placement of individual (lower canopy, full sun, etc.)
2. If gathering samples for pooled data, choose four random areas around the tree to collect needle and branch samples
3. Look for the second branch from the shoot tip (stick to the right first) and snip off 5 cm to place in 10 ml cryovial
4. Repeat for the other 3 directions (check appropriate column in the sheet provided).  Place about 3-4 stems in each 10 ml cryovial.
5. Close cryovial, and using the appropriate gloves to handle liquid nitrogen (LN), place cryovial in LN dewar.


 

5.1. Cap vial tightly to prevent opening in the LN.
5.2. Depending on dewer configuration, you can tie tubes with string to a ‘halo’ to help keep vials from falling to the bottom. Fully submerged tubes can open.  

 


6. Clean trimmers between trees with ethanol (spray bottle).
7. Use clipboard to manually record notes on a pre-printed spreadsheet with sample names.
8. After returning from the field, ensure that notes are consistent with TreeSnap entries.  These entries can be amended after collection as needed.
TITLE: Propionylation and tryptic digestion
AUTHORS: Laura Corveleyn, Sigrid Verhelst

[DESCRIPTION]
Protocol to derivatize (propionylation) and digest histone proteins into peptides with the purpose of bottom-up label free LC-MS/MS analysis. In this method, aspecific overpropionylation at serine (S), threonine (T) and tyrosine (Y) is reversed by adding hydroxylamine (HA).

[STEPS]
SECTION: First propionylation
1. Start with vacuum dried sample (20 µg/sample)
SECTION: First propionylation
2. Add 20 µL 1M triethylammonium bicarbonate (TEAB)
SECTION: First propionylation
3. Add 20 µL prop-reagent (Isopropylalcohol:propionic anhydride (79:1))
SECTION: First propionylation
4. Spin down & Incubate at room temperature for 30 minutes
SECTION: First propionylation
5. Add 20 µL H2O
SECTION: First propionylation
6. Spin down & Incubate at 37°C for 30 minutes
SECTION: First propionylation
7. Vacuum dry sample
SECTION: Trypsin digest
9. Add correct volume of 500 mM TEAB, CaCl2 and ACN
SECTION: Trypsin digest
10. Resuspend trypsin in 500 mM TEAB
SECTION: Trypsin digest
11. Add trypsin at a 1:20 ratio (w/w) => 1 µg trypsin/20 µg histones
SECTION: Trypsin digest
12. Spin down & incubate overnight at 37°C
SECTION: Trypsin digest
13. Vacuum dry sample
SECTION: Trypsin digest
8. Calculate the amount of 500 mM TEAB, Calciumchloride (CaCl2), acetonitrile (ACN) and trypsin necessary to result in a 1:20 ratio (w/w) (1 µg trypsin/20 µg histones) in a final volume of 50µL.
 

SECTION: Second propionylation
14. Vacuum dried sample (20 µg/sample)
SECTION: Second propionylation
15. Add 20 µL 1M TEAB
SECTION: Second propionylation
16. Add 20 µL Prop-reagent (Isopropylalcohol:propionic anhydride (79:1))
SECTION: Second propionylation
17. Spin down & Incubate at room temperature for 30 minutes
SECTION: Second propionylation
18. Add 20 µL H2O
SECTION: Second propionylation
19. Spin down & Incubate at 37°C for 30 minutes
SECTION: Second propionylation
20. Vacuum dry sample
SECTION: Reversing overpropionylation hydroxylamine mediated
21. Vacuum dried sample (20 µg/sample)
SECTION: Reversing overpropionylation hydroxylamine mediated
22. Add 50 µL 0.5 M hydroxylamine (NH2OH)
SECTION: Reversing overpropionylation hydroxylamine mediated
23. Add 15 µL ammonium hydroxide (NH4OH) at pH 12
SECTION: Reversing overpropionylation hydroxylamine mediated
24. Spin down & Incubate at room temperature for 20 minutes
SECTION: Reversing overpropionylation hydroxylamine mediated
25. Adjust pH with formic acid (FA): 30 µl 100% FA
SECTION: Reversing overpropionylation hydroxylamine mediated
26. Vacuum dry sample
TITLE: OMS Atlas FFPE Spatial Mapping
AUTHORS: Brett Johnson, Danielle Galipeau, Todd Camp, George Thomas

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the procedure by which the OMS Atlas serially sections a FFPE block, prepares the resulting slides, and then distributes the specimens for downstream analysis.</div></div>

[STEPS]
?. [Preparation]
Verify the identity of the FFPE block to be cut against written request for sectioning.
?. [Preparation]
Label each Tanner slide with a unique BEMS ID and slide number, corresponding to the written request and FFPE spatial map (below).Note: Slides #1-4 compose the official OMS Atlas Dataset.  ABC1Slide#AssayRecipient21H&EOHSU, HSR32Cyclic Immunofluorescence (Tumor Panel)HMS, Alyce Chen43Cyclic Immunofluorescence (Immune Panel)HMS, Alyce Chen54Multiplex IHC (Discovery Panel)OHSU, Courtney Betts65Cyclic Immunofluorescence (Panel A)OHSU, Koei Chin76Cyclic Immunofluorescence (Panel B)OHSU, Koei Chin87Nanostring GeoMx Digital Spatial ProfilerOHSU, KDL98H&EOHSU, HSR
ABC1Slide#AssayRecipient21H&EOHSU, HSR32Cyclic Immunofluorescence (Tumor Panel)HMS, Alyce Chen43Cyclic Immunofluorescence (Immune Panel)HMS, Alyce Chen54Multiplex IHC (Discovery Panel)OHSU, Courtney Betts65Cyclic Immunofluorescence (Panel A)OHSU, Koei Chin76Cyclic Immunofluorescence (Panel B)OHSU, Koei Chin87Nanostring GeoMx Digital Spatial ProfilerOHSU, KDL98H&EOHSU, HSR
?. [Sectioning]
Align block on microtome to minimize tissue loss.
?. [Sectioning]
Face into block at 5μm until full section of tissue is achieved.
?. [Sectioning]
Cut adequate ribbon at 5μm to cover all 8 serial sections.
?. [Sectioning]
Mount tissue sections onto Tanner slides to maintain serial order and orientation of sections.
?. [Processing]
Perform hematoxylin and eosin (H&E) staining on slides #1 and #8.
?. Bake slides #2 through #6.Note: Slide #7 should NOT be baked.
?. Place slides #2 through #6 in  oven overnight.
55 °C
?. The next morning, raise the oven temperature to  for up to .Note: Slides should be baked at  for at least 30 minutes.
65 °C
65 °C
?. Remove slides from oven and deliver to Biolibrary for distribution.
?. Remove slides from oven. Place slides in slide boxes and store at room temperature.
?. Deliver slides #2 through #7 to BioLibrary for distribution.
TITLE: Protocol for &#34;Development and characterization of a non-human primate model of diseeminated synucleinopathy&#34;
AUTHORS: jlanciego, Alberto J. Rico, Julia Chocarro, Goiaz Ariznabarreta, Elvira Roda, Adriana Honrubia, Patricia Arnaiz, Almudena Corcho

[DESCRIPTION]
Here we took advantage of a retrogradely-spreading adeno-associated viral vector
serotype 9 coding for the alpha-synuclein A53T mutated gene to induce a
widespread synucleinopathy of cortical and subcortical territories innervating
the putamen. Four weeks post-AAV deliveries animals were sacrificed and a
comprehensive biodistribution study was conducted, comprising the
quantification of neurons expressing alpha-synuclein, rostrocaudal distribution
and their specific location.

This collection is made of (1) study design, (2) experimental animals, (3) viral vector production, (4) stereotaxic surgery for AAV deliveries, (5) necropsy, tissue processing and data analysis, (6) quantification of neurons expressing alpha-synuclein, (7) quantification of the nigrostriatal system

4 literature references included

3 figures included, as follows:
- Figure 1: Viral vector (synapsin)AAV9-SynA53T
- Figure 2: Ventriculography-assisted stereotaxic surgery
- Figure 3: Quantification of alpha-synuclein positive neurons

[STEPS]
TITLE: Infant formula sample preparation for element analysis using PIXE/RBS
AUTHORS: Seth H. Frisbie, Erika J. Mitchell, Stéphane Roudeau, Florelle Domart, Asuncion Carmona, Richard Orterga

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol was developed to quantify chemical elements from infant formula samples by PIXE/RBS (Particle Induced X-ray Emission / Rutherford Backscattering Spectrometry). This protocol aims to analyze powdered samples. Liquid samples can also be prepared begining from step 6.</div><div class = "text-block"><span class = "embed-element"></span></div></div>

[STEPS]
?. Work under a clean atmosphere to avoid dust contamination.
?. Use a disposable plastic spatula to deliver between 1.0000 grams (g) and 1.0099 g of powdered product to a laboratory-grade plastic centrifuge tube.
?. Add 10.00 milliliters (mL) of ultra-trace elemental analysis grade water (Water OptimaTM).
?. Vortex until the complete dissolution or uniform suspension of powder.
?. Store the solution or suspension at 4°C for a maximum of 24 hours.
?. Immediately before using, vortex the solution again.
?. Deliver 1.0 microliter (µL) of the solution or suspension with an air displacement pipet onto a labeled PIXE/RBS sample holder.
?. Repeat step 7 until a total of three different drops from the same sample are placed in three different locations of the same sample holder.
Use a different pipette tip to deliver each drop. Always vortex immediately before filling the pipette tip.
?. DDry the drops at room temperature in a laminar flow hood for 24h.
?. Superimpose onto each dried drop another 1.0 µL of solution or suspension to increase the quantity of matter in order to be more sensitive for analysis by PIXE/RBS.
Use a different pipette tip to deliver each drop. Always vortex immediately before filling the pipette tip.
?. Dry samples at room temperature in a laminar flow hood for 24h and store the solution or suspension at 4°C.
?. Repeat steps 11, 12 and 13 until each spot on the sample holder is comprised of three superimposed drops of 1.0 µL.
?. Store the sample holders with the dried spots in a desiccator and protect from dust until PIXE/RBS analyses.
?. After delivering the three 1.0 µL drops onto the three different locations on the sample holder, store the sample solution or suspension at 4 °C.
?. Vortex the solution.
TITLE: A new metabarcoding approach to survey diversity at the species level of Arcellinida (Amoebozoa: Tubulinea)
AUTHORS: R. González-Miguéns

[DESCRIPTION]
PCR protocol for the paper:" A needle in a haystack: a new metabarcoding approach to survey diversity at the species level of Arcellinida (Amoebozoa: Tubulinea)" 

[STEPS]
SECTION: Polymerase Chain Reaction protocol
1. First PCR

Primers:
Primer forward: LCO 1490 (5´ GGTCAACAAATCATAAAGATATTGG 3´)
Primer reverse: HCO 2198 (5´ TAAACTTCAGGGTGACCAAAAAATCA 3´)

Reagents for the PCR:
 
Total reaction mix per sample= 10 μL


Thermocycler program:
 

Denaturation temperatures and times may vary depending on the polymerase used. This protocol was tested with the MyTaq™ Red Mix™ polymerase.

Gel electrophoresis:
Analyze the results of your PCR reaction via gel electrophoresis. The resultant fragment was 692 bp long:
  

SECTION: Polymerase Chain Reaction protocol
2. Second PCR

Primers:
Primer forward: LCO 1490 (5´ GGTCAACAAATCATAAAGATATTGG 3´)
Primer reverse:  ArCOIR (5´ CCACYNGAATGWGCTARAATACC 3´)

Reagents for the PCR:
 
Total reaction mix per sample= 20 μL

Thermocycler program:
 
Denaturation temperatures and times may vary depending on the polymerase used. This protocol was tested with the MyTaq™ Red Mix™ polymerase.

Gel electrophoresis:
Analyze the results of your PCR reaction via gel electrophoresis. The resultant fragment was 407 bp long
TITLE: Virus production
AUTHORS: michela.deleidi

[DESCRIPTION]
Lentiviral production protocol

[STEPS]
SECTION: Virus production
2. HEK 293 T cells were seeded in a 10-cm dish to reach 80% confluency the day after
transfection.The next day, the medium was changed.
SECTION: Virus production
3. On days 4 and 5 after transfection, the medium was collected and filtered through a0.45-
μm PVDF membrane.
SECTION: Virus production
1. For lentiviral production, HEK cells were transfected with the plasmids expressing the shRNAs together with the lentiviral packaging plasmid psPAX2(RRID:Addgene_12260) and the envelope plasmid pMD2.G (RRID:Addgene_12259) using TransIT-X2 (Mirus).
SECTION: Virus production
4. To concentrate the virus, the filtered supernatant was centrifuged in a Vivaspin column (Sartorius Stedim Biotech) at 3000 RCF at 4 °C until the volume reached 500
–1000μl.
SECTION: Virus production
5. The virus-containing supernatant was collected, and the concentration
of p24 particles was determined with Lenti-X GoStix Plus (Takara).
SECTION: Virus production
6. Cells were infected with equal concentrations of p24 particles for the
scramble and respective shRNA.
TITLE: DNA and RNA stabilization
AUTHORS: Neilier Junior

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">DNA and RNA stabilization solution is an aqueous and non-toxic tissue storage reagent that rapidly permeates tissues to stabilize and protect nucleic acids in fresh specimens. Tissue pieces are harvested and immediately submerged in stabilization solution for storage. It can be used for DNA and RNA preservation with most tissues, cultured cells and is compatible with most DNA/RNA isolation methods. Proteins are precipitated, but can still be used for analyzes that do not require their native structure, such as western blotting or gel electrophoresis. Samples in DNA and RNA stabilization solution can be stored indefinitely in RNAlater Solution at –20 °C or below.</div></div>

[STEPS]
?. [Stabilization solution preparation (1.5 L)]
935 mL of autoclaved MilliQ water700 g ammonium sulfateStir until dissolved Add 25 mL of 1 M sodium citrateAdd 40 mL of 0.5 M EDTAAdjust to pH 5.2 using concentrated H2SO4Complete the volume to 1.5 L with autoclaved MilliQ water700 g ammonium sulfateStir until dissolved Add 25 mL of 1 M sodium citrateAdd 40 mL of 0.5 M EDTAAdjust to pH 5.2 using concentrated H2SO4Complete the volume to 1.5 L with autoclaved MilliQ waterStir until dissolved Add 25 mL of 1 M sodium citrateAdd 40 mL of 0.5 M EDTAAdjust to pH 5.2 using concentrated H2SO4Complete the volume to 1.5 L with autoclaved MilliQ waterAdd 25 mL of 1 M sodium citrateAdd 40 mL of 0.5 M EDTAAdjust to pH 5.2 using concentrated H2SO4Complete the volume to 1.5 L with autoclaved MilliQ waterAdd 40 mL of 0.5 M EDTAAdjust to pH 5.2 using concentrated H2SO4Complete the volume to 1.5 L with autoclaved MilliQ waterAdjust to pH 5.2 using concentrated H2SO4Complete the volume to 1.5 L with autoclaved MilliQ water
Store at room temperature.If any precipitation of stabilization solution is seen: heat to 37 °C and agitate to redissolve it.
?. [Procedure]
Do not freeze tissues before immersion in DNA and RNA stabilization solution.Use stabilization solution with fresh tissue only.
?. [Procedure]
Add the stabilization solution in an appropriate 1.5 mL microtube.
Use the minimum volume ratio 1:5 (tissue : solution).
?. [Procedure]
Cut large tissue samples to approx. 3 mm in any single dimension and transfer to microtube containing the solution.
?. [Procedure]
Do not freeze samples in stabilization solution immediately.
?. [Procedure]
Store at 4 °C overnight to allow the solution to thoroughly penetrate the tissue.
?. [Important notes]
The DNase and RNase inactivation is reversible. So, do not rinse stabilization solution from samples before DNA and/or RNA extraction.
?. [Important notes]
Tissue homogenization should be rapid once the tissue is in lysis/denaturation solution to nucleic acids extraction.
?. [Important notes]
Remove the stabilization solution from the cells prior to extraction for isolating DNA and RNA from cells.With the aid of a pipette, remove excess ofstabilization solution from the tube and then use an absorbent lab wipe or paper towel to help remove as much of the stabilization solution as possible.
TITLE: Parzenie herbaty
AUTHORS: tomasz.zielinski 

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is part of the 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> Carpentry course. Here we explore the perfect protocol to brew tea the polish way.</span></div><div class = "text-block">It is a polish translation of the english protocol.</div><div class = "text-block">Jak parzyć herbatę po polsku</div></div>

[STEPS]
?. [Preparation of water and tea]
Napełnij czajnik wodą, co najmniej 300ml wody.
?. [Preparation of water and tea]
W międzyczasie przygotuj herbatę, rozpakuj ją i umieść jedna torebkę w szklance. Pamiętaj wyłożyć etykietkę na zewnątrz szklanki.
?. [Preparation of water and tea]
Jak tylko woda się zagotuje wlej szybko wodę do szklanki. Wskazówka, przytrzymaj etykietę palcem żeby nie wpadła do środka szklanki.
?. [Brewing]
Parz herbate przez minutę albo dwie. Obserwuj kolor, powinine byc on lekko brązowy, przerwij zanim zrobi sie ciemno bązowy żeby nie mieć za mocnej herbaty.
?. [Brewing]
Wyciągnij herbatę pociągając za etykietke na sznurku albo łyżeczką
?. [Flavouring]
Dodaj dwie łyżki cukru
?. [Flavouring]
Odczekaj pięc minut (lub zrób to tuz przed piciem) i wyciśnij kilka kropel cytryny, lub wrzuc cięnki plasterek cytryny do środka. Zobacz jak herbata zmienia pięknie kolor na pomarańczowo żółty
?. [Flavouring]
Delektuj się
TITLE: LB Medium (1 Liter)
AUTHORS: Alba Balletbó

[STEPS]
?. Add LB medium components in a 1 L autoclavable. LB medium components (1 L):  AB1NaCl10 gram2Tryptone10 gram3Yeast Extract5 gram
AB1NaCl10 gram2Tryptone10 gram3Yeast Extract5 gram
?. Add 1 L of distilled water into the bottle.
?. Vigorously shake the bottle.
?. Place the bottle into the autoclave and sterilize.