eamag/protocols-with-steps huggingface dataset:
TITLE: HuBMAP - STANFORD RTI Multiplex Ion Beam Imaging (MIBI) MODALITY OVERVIEW
AUTHORS: Marc Bosse, Ferda Filiz, Noah Greenwald, Christine Camacho, Alex Kong, Adam  Kagel, Sean Bendall, Mike Angelo

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">We aim to provide high resolution, high dimensional images of human placenta in early pregnancy by using our multiplexed ion beam imaging methodology for building an atlas of human organs.</div></div>

[STEPS]
?. [Sample collection and preparation]
Formalin fixation and paraffin embedding of specimens dx.doi.org/10.17504/protocols.io.bqp6mvre
?. [Sample collection and preparation]
Sectioning of FFPE specimens https://dx.doi.org/10.17504/protocols.io.bfz4jp8w    MIBI slide specifications is detailed in MIBI staining dx.doi.org/10.17504/protocols.io.bt9tnr6n
?. [Antibody panel validation for MIBI]
Immunohistochemistry validation of antibodies for MIBI staining    IHC staining dx.doi.org/10.17504/protocols.io.bf6ajrae    MIBI and IHC solutions dx.doi.org/10.17504/protocols.io.bhmej43e
?. [Antibody panel validation for MIBI]
Antibody preparation for MIBI    Metal-antibody labelling dx.doi.org/10.17504/protocols.io.bhyej7te    Antibody lyophilization dx.doi.org/10.17504/protocols.io.bhmgj43w    Lyophilized antibody reconstitution dx.doi.org/10.17504/protocols.io.bjd6ki9e
?. [Antibody panel validation for MIBI]
MIBI antibody panel titration    MIBI staining dx.doi.org/10.17504/protocols.io.bt9tnr6n    MIBI and IHC solutions dx.doi.org/10.17504/protocols.io.bhmej43e
?. [MIBI data acquisition]
MIBI staining dx.doi.org/10.17504/protocols.io.bt9tnr6nInstrument Quality Control    Performed according to the manufacturer (IonPath) specifications Field of view selection    Performed according to the manufacturer (IonPath) specifications
?. [MIBI data analysis]
MIBI data extraction    Image processing Ionpath instrument internal document
?. [MIBI data analysis]
MIBI image segmentation     Greenwald et al. https://www.biorxiv.org/content/10.1101/2021.03.01.431313v2
?. [MIBI data analysis]
Cell type identification TBD
?. [MIBI data analysis]
High dimensional data analysisTBD
TITLE: Overviews on adverse events in pharmacological interventions
AUTHORS: Elena Dorando, Thilo Sachse, Tim Matthes, Simone Heß, Petra Thürmann, Sven Schmiedl, Salmaan Kanji, Carole Lunny, Pierre Thabet, Dawid Pieper

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Please find detailed information on our protocol in the attached PDF file.</div></div>

[STEPS]
TITLE:       ELISA for quantification of IL-36 in human serum.
AUTHORS: Angel  Justiz-Vaillant

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Interleukins (IL) are a type of cytokine first thought to be expressed by leukocytes alone but have later been found to be produced by many other body cells. They play essential roles in the activation and differentiation of immune cells, as well as proliferation, maturation, migration, and adhesion. They also have pro-inflammatory and anti-inflammatory properties. The primary function of interleukins is, therefore, to modulate growth, differentiation, and activation during inflammatory and immune responses. Interleukins consist of a large group of proteins that can elicit many reactions in cells and tissues by binding to high-affinity receptors in cell surfaces. </div><div class = "text-block"><span>Phagocytes mainly make IL-36. It acts on T lymphocytes and NK cells regulating the IFN-γ synthesis. It stimulates the hematopoiesis and expression of both MHC class I and II molecules as well as intracellular adhesion molecules (ICAM)-1. </span><a href="https://www.ncbi.nlm.nih.gov/books/NBK499840" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">[1]</span></a><span style = ":;"></span></div><div class = "text-block">Reference</div><div class = "text-block"><span>1. Justiz Vaillant AA, Qurie A. Interleukin. In:</span><span style = "font-style:italic;">StatPearls</span><span>. Treasure Island (FL): StatPearls Publishing; June 12, 2019.</span></div></div>

[STEPS]
?. An anti-human IL-36 coating antibody is adsorbed onto the microwells by incubation overnight at 4°C with carbonate-bicarbonate buffer.
?. Add 50 µl of human serum. Human IL-36 present in the serum sample binds to antibodies adsorbed into the microwells.
?. The microplate is blocked with 3% non-fat milk-PBS buffer and later wash to remove unbound proteins.
?. Fifty (50) µl of biotin-conjugated anti-human IL-36 antibody is added. The optimal dilution must be investigated.
?. The microplate is rewashed with PBS-Tween 20 buffer, pH 7.4.
?. One hundred µl of streptavidin-HRP conjugate is added and it binds to the biotin-conjugated anti-human IL-36 antibody. The optimal dilution of this conjugate must be investigated.
?. The plate is washed following incubation to remove the unbound Streptavidin-HRP.
?. Add 100 µl of 3',3',5',5'- tetramethylbenzidine (TMB; Sigma-Aldrich) into each well.
?. Incubate the microwells in the dark for 15 min.
?. A colored product is formed in proportion to the quantity of human IL-36 present in the sample or standard.
?. The reaction is terminated by addition of 100 µl 3M H2SO4  and the absorbance is measured at 450 nm.
?. A standard curve is made from 7 human IL-36 standard dilutions and the human IL-36 sample concentration is determined.
?. For better results place the microplate on a microplate shaker in every incubation.
TITLE: Preparo de meio de LB e LB ágar em placa 11/11/20
AUTHORS: Mariana Jacques

[STEPS]
?. [Preparo do LB]
Dissolver 25 g de LB  em  1 L de H2O filtrada
?. [Preparo do LB ágar]
Dissolver 12 g de LB ágar   300 mL de H2O filtrada
?. Depois de pronto autoclavar  os meios LB e LB em placa, em temperatura- controlada.
?. Ao retirar e o meio atingir uma temperatura ideal ( ) adicionar , Ampicilina.
?. Colocar os meios em placa e guardar.
TITLE: Seizures – like behavior assay for D. melanogaster
AUTHORS: Natalie Kaempf, Patrik Verstreken

[DESCRIPTION]
This protocol allows to assess the susceptibility of flies to seizure-like behavior based on mechanically
hyper-stimulating sensory inputs and assessing seizure-like activity.

[STEPS]
SECTION: Seizures – like behavior assay
1. prepare groups of 5 ± 1 flies and transfer them to transparent empty vials
SECTION: Seizures – like behavior assay
2. let them rest for at least 30 min after CO2 anesthesia

SECTION: Seizures – like behavior assay
3. mechanically stimulate the flies by vortexing the vial for 10 s at maximum intensity
SECTION: Seizures – like behavior assay
5. Numbers of resistant flies and flies with seizure-like behavior are counted within 10 s post
stimulation
SECTION: Seizures – like behavior assay
4. move the vial immediatly on an even surface before a white background and start recording the behavior
TITLE: U54 SCENT Pediatric Colonoscopy Tissue Collection Procedure
AUTHORS: Mary Jordan*

[DESCRIPTION]
This document outlines the required criteria for pediatric colonoscopy inclusion of colon specimens collected at Duke University Hospital through the Biorepository and Precision Pathology Center (BRPC) in the Department of Pathology. 

[STEPS]
SECTION: Inclusion and Exclusion Criteria
1. Inclusion Criteria:
    • Healthy patients age 5-18 years of age presenting for outpatient colonoscopy. 
    • Screening may wish to focus on the following indications: abdominal pain, constipation, diarrhea,         
       bloating/gas, patients with normal labs and/or imaging.

Exclusion Criteria:
    • Systemic Illness such as diabetes is a relative exclusion but may be hard to avoid
    • Autoimmune disease such as SLE (lupus) or rheumatoid arthritis 
    • Active infectious disease such as HIV, HBV, active COVID, active (not treated) HCV
    • Obesity (BMI > 35) is a relative exclusion 
    • BMI < 18.5
    • Any chemotherapy or radiation for any condition, including cancer treatment in any organ         
      (patients may be included with untreated or surgically only treated cancer in another organ)         
    • Metastatic malignancy
    • Whole blood transfusion in the past 48 hours
    • Inflammatory bowel disease, microscopic colitis, and infectious colitis
    • Known inherited conditions with increased risk of colon cancer such as Lynch Syndrome, FAP, 
       DNA repair defects etc 
    • Use of blood thinners other than a baby aspirin (due to increased bleeding risk)
    • Underlying liver disease with cirrhosis or coagulopathy (due to increased bleeding risk) 
       Note: while diverticulosis and colon polyps are not exclusions, we will not collect samples within
       10 cm of these lesions.
TITLE: KAPP-Sen TMC: Whole human kidney preparation
AUTHORS: Juliana Alcoforado Diniz, Ramalakshmi Ramasamy, Alejandro Peña, Qian Wu, Jillian L. Woodworth, Vladislav Bugay, Manpreet Semwal, Paul Robson

[DESCRIPTION]
This protocol describes removal, shipping, dissection, formalin preservation of a whole human kidney from a brain-dead donor.

[STEPS]
1. Remove the whole kidney from a brain-dead donor. Flush the kidney with UW solution and perfuse with 1 liter of Waters IGL Pulsatile Perfusion Solution (PPS) for shipping.
3. Once received, bring the sample still on ice to the pathology department at UConn Health for dissection. The whole process was performed at room temperature (RT) and non-sterile.
4. Cut the whole organ in half along the middle plane (coronal section) and remove tissue pieces with a scalpel. The samples are roughly 1 cm x 1 cm and 0.5 cm thick and placed directly in labelled containers with 10 ml of 10% Neutral buffered formalin (NBF).
5. The samples are kept in RT and shipped the same day to JAX Histology Services in Bar Harbor. The samples are submitted to paraffinization (embedding of tissue blocks in paraffin) the same day they are received.
2. Use overnight (ON) shipping, cold with ice.
TITLE: Archived Human Tissue Collection Sept 2015 - 2019 -- University of Minnesota TMCs
AUTHORS: Laura J Niedernhofer, David A Bernlohr

[DESCRIPTION]
Tissue collection and processing protocols for liver and adipose tissue samples obtained and archived by the UMN Biospecimen Repository from Sept 2015 to 2019. 

[STEPS]
SECTION: BioNet Gross Room SOP for tissue acquisition
1. The following document the correct procedure for tissue acquisition in the
University of Minnesota Medical Center, Fairview/ East Bank Gross Room.
  

SECTION: BioNet Tissue Processing SOP
2. The purpose of this document is to describe BioNet’s current tissue processing procedure for
Formalin Fixed Paraffin Embedded (FFPE) blocks.
  

SECTION: Specimen Procural Procedures
3.
TITLE: SYSB 3036 W06: Annotating a Complete Genome with HMMs
AUTHORS: Frank Aylward

[STEPS]
?. First let's download some files from GitHub:git clone https://github.com/faylward/hmm_tutorialAnd move inside the new folder and see what is there:cd hmm_tutorialls
?. In the new file you should see a gzipped file that contains proteins from a mystery genome. We can gunzip it now:gunzip mystery_genome_proteins.faa.gzFor this analysis we want to annotate all of the proteins in this genome using a suite of HMMs. We will use the TIGRfam database today. I have uploaded this database onto a Virginia Tech library link, so we can download it with the followingn command. wget -O tigrfams.tar.gz https://data.lib.vt.edu/downloads/pc289j19bThis should download a .tar.gz file, which is essentially a gzipped folder, also called a "tarball". This is a bit different then just a gzipped file, and we need a special command to unzip it. tar xvfz tigrfams.tar.gzIf you look inside of the tigrfams file you should see two files- one HMM file and one .txt file.The HMM file contains thousands of HMMs all merged together. This is the full TIGRfam database. Note that the file is quite large. The .txt file contains descriptions of each HMM. When we want to annotate a protein we don't just want to know that the best hit was TIGR20034. We also want to know what the function of TIGR20034 is. That's what this file is for.
?. To run the initial HMM annotation we can use the hmmsearch command in HMMER3:hmmsearch --tblout mystery_genome.hmmout --cut_tc tigrfams/all_tigrfam.hmm mystery_genome_proteins.faa > full_hmmout.txtNote that in the command above we are using the --cut_tc option, which specifies that we want to use pre-specified bit score cutoffs to classify these proteins. All hits that have bit scores below the specifications for each HMM will be disregarded, regardless of their e-value.
?. After we run the hmmsearch we can parse the results with a Python script that I wrote. This script goes through the tabular hmmsearch output and finds only the best hits for each protein. It also removes the weird space-delimited format that HMMER3 insists on using and converts it into a nice tab-delimited format. We can run it with:python parse_hmmout.py tigrfams/profile_annotations.tigr.txt mystery_genome.hmmout > mystery_genome.parsed.hmmout.txtNote that we need to specify the profile annotations file, since we want the final annotation file to contain the TIGRfam descriptions.
?. Another way to annotate genomes, and get some visualizations of pathway-level annotations, is to use the Kyoto Encyclopedia of Genes and Genomes (KEGG). They host an annotation server here:https://www.genome.jp/kaas-bin/kaas_mainUpload the protein file, add in your email, and make sure to use the "For Prokaryotes" option at the bottom of the page so that the correct reference database is used.  A link will be mailed to you, and you need to click the "submit" option in that email for the annotation to begin. After that you will need to wait ~10-45 minutes for the annotation to finish, and the link will be mailed to you again.
TITLE: Isolation and Fixation of Nuclei from the Mouse Brain for Dip-C
AUTHORS: Longzhi Tan

[STEPS]
?. [Reagents]
Prepare 1.5 M sucrose (): (final:  ,  ) waterHeat and vortex to mix.Filter to sterilize.Store at .
40 mL
20.538 g
40 mL
4 °C
?. [Reagents]
Prepare Nuclei Isolation Medium 1 (; note that Tris is replaced with HEPES): 1.5 M sucrose (final: , ) (final: ) (final: ) (final: ) waterStore at .
45 mL
7.5 mL
562.5 µl
450 µl
225 µl
36.2625 mL
4 °C
?. [Nuclei Isolation]
Chill a  (or larger sizes: , , , or ) .
on ice
?. [Nuclei Isolation]
Prepare 1 mM DTT: water(aliquoted and stored at )
1 mL
1 µl
-20 °C
?. [Nuclei Isolation]
Prepare Nuclei Isolation Buffer without Triton ( per sample): Nuclei Isolation Medium 1 1 mM DTT (final: )Chill .
6 mL
6 mL
6 µl
on ice
?. [Nuclei Isolation]
Add  ice-cold Nuclei Isolation Buffer with Triton to the homogenizer.
2 mL
?. [Nuclei Isolation]
Dounce the tissue with 5 strokes of the loose pestle (A), and 15 strokes of the tight pestle (B).
?. [Nuclei Isolation]
Transfer the homogenate to a tube.
?. [Reagents]
Prepare 1% BSA in PBS ( per sample; recipe below for ):Vortex to mix.Rotate until fully dissolved.Chill .Store at  if needed.
1.2 mL
10 mL
0.1 g
10 mL
on ice
-20 °C
?. [Nuclei Isolation]
Centrifuge at .
Centrifuge: 100 34, 8 min, 4 10
?. [Nuclei Isolation]
Carefully remove supernatant without disrupting the soft pellet.
?. [Nuclei Isolation]
Resuspend in  Nuclei Isolation Buffer without Triton.
2 mL
?. [Nuclei Isolation]
Centrifuge at .
Centrifuge: 100 34, 8 min, 4 10
?. [Nuclei Isolation]
Carefully remove supernatant without disrupting the soft pellet.
?. [Nuclei Isolation]
Resuspend in  Nuclei Isolation Buffer without Triton.
2 mL
?. [Nuclei Isolation]
Filter with  or .
?. [Fixation]
To every  of cells, add  (final: ).
1 mL
66.7 µl
?. [Fixation]
Rotate at  for .
-20 Room temperature
?. [Fixation]
Add  1% BSA in PBS.
200 µl
?. [Fixation]
Centrifuge at .
Centrifuge: 1000 34, 5 min, 4 10
?. [Fixation]
Remove supernatant.
?. [Fixation]
Count with  , and aliquot to up to 0.5 million cells per tube.
?. [Fixation]
Centrifuge at .
Centrifuge: 1000 34, 5 min, 4 10
?. [Fixation]
Invert to mix.
?. [Fixation]
Resuspend in  ice-cold 1% BSA in PBS.
1 mL
?. [Fixation]
Remove supernatant.
?. [Fixation]
Store at .
-80 °C
?. [Nuclei Isolation]
Prepare Nuclei Isolation Buffer with Triton ( per sample): Nuclei Isolation Buffer without Triton (final: )Chill .
2 mL
2 mL
20 µl
on ice
TITLE: 10x Protocols: Visium v1 FFPE Deparaffinization, H&amp;E staining, and Imaging-- University of Minnesota  TMCs (CG000409 Rev C)
AUTHORS: IOx Genomics, Laura J Niedernhofer, David A Bernlohr

[DESCRIPTION]
Protocols from 10x Genomics for Visium Spatial Gene Expression v1 chemistry on FPPE samples without the CytAssist component. 2nd version used by UMN TMC.

Protocol ID# (CG) and Revision letter provided here: 
    10x protocol CG000409, Revision C -- Deparaffinization, H&E staining, coverslipping, and imaging

Additional protocols added for guidance:
    10x protocol for imaging guidelines 
    10x protocol for tissue preparation guidelines 

Note: These protocols may not be the current version offered by 10x Genomics but were used to produce the specific datasets connected to them. Please review the 10x Genomics support website for the most recent versions of the protocols prior to starting your experiment. 

[STEPS]
2. Additional Protocols/Resources
  
  
https://www.10xgenomics.com/support/spatial-gene-expression-ffpe

1. 10x protocol CG000409, Rev C (Deparaffinization, H&E, etc)
TITLE:        ELISA for quantification of RANTES (Regulated on Activation, Normal T cell Expressed and Secreted) in human serum or plasma.
AUTHORS: Angel  Justiz-Vaillant

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">RANTES (Regulated on Activation, Normal T cell Expressed and Secreted) also known as CCL5 is a chemotactic cytokine for T cells, basophils, and eosinophils. RANTES also acts as a recruitment signal for immune cells into inflammatory sites.</div></div>

[STEPS]
?. An anti-human RANTES coating antibody is adsorbed onto the microwells by incubation overnight at 4°C with carbonate-bicarbonate buffer.
?. Add 50 µl of human serum or plasma. Human RANTES (CCL5) present in the serum or plasma binds to antibodies adsorbed into the microwells.
?. The microplate is blocked with 3% non-fat milk-PBS buffer and later wash to remove unbound proteins.
?. Fifty (50) µl of biotin-conjugated anti-RANTES antibody is added. The optimal dilution must be investigated.
?. The microplate is rewashed with PBS-Tween 20 buffer, pH 7.4.
?. One hundred µl of streptavidin-HRP conjugate is added and it binds to the biotin-conjugated anti-RANTES antibody. The optimal dilution of this conjugate must be investigated.
?. The plate is washed following incubation to remove the unbound Streptavidin-HRP.
?. Add 100 µl of 3',3',5',5'- tetramethylbenzidine (TMB; Sigma-Aldrich) into each well.
?. Incubate the microwells in the dark for 20 min.
?. A colored product is formed in proportion to the quantity of RANTES (CCL5) present in the sample or standard.
?. The reaction is terminated by addition of 100 µl 3M H2SO4  and the absorbance is measured at 450 nm.
?. A standard curve is made from 7 human RANTES standard dilutions and the human RANTES sample concentration is determined.
?. For better results place the microplate on a microplate shaker in every incubation.
TITLE: Bat Measurements - ISL Peru
AUTHORS: Cristian Tirapelle, Gideon Erkenswick, Jorge Luis Mendoza-Silva, Pamela Sánchez-Vendizú, Mrinalini Watsa

[DESCRIPTION]
This protocol describes the external morphological measurements taken on bats prior to release and is actively used by Field Projects International at the Estación Biológico Los Amigos, Madre de Dios, Peru.

All measurements are taken with a digital caliper.



[GUIDELINES]
This protocol accompanies the "Bat Capture and Processing - ISL Peru" protocol.





[STEPS]
SECTION: Bat Anatomical References
1. Noseleaf length: The noseleaf is a membranous fold of skin of variable size located on or around the nostrils. This length is measured from the base of the horseshoe until the tip of the spear. 

 
SECTION: Bat Anatomical References
4. Tragus length: The tragus is a small flap of skin in front of the external opening of the ear. The measurement corresponds to the greatest length from its base to its tip.
   
SECTION: Bat Anatomical References
3. Ear length: Distance from the notch to the fleshy tip of the pinna.   

SECTION: Bat Anatomical References
5. Forearm length: Distance between the elbow and the wrist when the wing is folded. this measurement is taken 3 times for each bat, then averaged.

  
  

SECTION: Bat Anatomical References
6. Tibia length: Distance from the proximal end of the tibia to the posterior base of the calcar.

  
  
SECTION: Bat Anatomical References
7.  Thumb length: From the metacarpal-phalangeal joint to the tip of the claw

 
SECTION: Bat Anatomical References
8. Calcar length: The calcar is a cartilage that extends from the tarsus and it is connected to the uropatagium. The length is taken from its base in the tarsus to the tip.
   
  

SECTION: Bat Anatomical References
2. Noseleaf width: The greatest distance of the noseleaf at the level of the horseshoe.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
This protocol details the use of various unix commands commonly used in bioinformatics.

[GUIDELINES]
<p><strong>Unix Commands<br /></strong></p>
<table>
<tbody>
<tr>
<td>pwd</td>
<td>rm</td>
<td>grep</td>
<td>tail</td>
<td>install</td>
</tr>
<tr>
<td>ls</td>
<td>'&gt;'</td>
<td>sed</td>
<td>cut</td>
<td> </td>
</tr>
<tr>
<td>cd</td>
<td>cat</td>
<td>nano</td>
<td>top</td>
<td> </td>
</tr>
<tr>
<td>mkdir</td>
<td>'&lt;'</td>
<td>history</td>
<td>screen</td>
<td> </td>
</tr>
<tr>
<td>touch</td>
<td>'|'</td>
<td>$PATH</td>
<td>ssh</td>
<td> </td>
</tr>
<tr>
<td>cp</td>
<td>sort</td>
<td>less</td>
<td>df</td>
<td> </td>
</tr>
<tr>
<td>mv</td>
<td>uniq</td>
<td>head</td>
<td>rsync/scp</td>
<td> </td>
</tr>
</tbody>
</table>
<p> </p>
<p><img id="s-mce-img" class="s-mce-img" src="https://s3.amazonaws.com/pr-journal/ej6c2w6.png" width="500" data-src="https://s3.amazonaws.com/pr-journal/ej5c2w6.png" data-ofn="ulay.png" /></p>

[STEPS]
?. 
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?. 
?. 
?. 
?. 
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?. 
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?. 
?. 
?. 
?. 
?. 
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?. 
?. 
?. 
?. 
?. 
?. 
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?. 
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?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
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?. 
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TITLE: Hornwort sporophyte induction -OXF
AUTHORS: Eftychis Frangedakis

[STEPS]
?. To induce sporophytes, plants were grown for one month in petri dishes on Lorbeer’s medium.
?. Afterwards, plants were transferred to Magenta pots on 1/10 Knop medium (2.5 g/L K2HPO4, 2.5 g/L KH2PO4, 2.5 g/L KCL, 2.5 g/L MgSO4.7H2O, 10 g/L Ca(NO3)2.4H2O, 37 mg/L FeSO4.7H2O) at pH 6.2 and containing 0.7% (w/v) agar.
?. Pots were then placed in a Panasonic MLR-352 Versatile Environmental Test Chamber (16oC, 16 h of light and 8 h of dark, 1500 lux light intensity).
?. After approximately one month, antheridia started to appear and after one more month sporophytes emerged.
TITLE: Open field test in rats
AUTHORS: eduard.bentea, María Sanchiz Calvo, Veerle Baekelandt

[DESCRIPTION]
Protocol for performing the open field test in rats. The open field test measures spontaneous locomotion during 5-min free exploration of an open field arena (1m x 1m), and can be used to measure hypolocomotion in animal models of Parkinson's disease. Rats with decreased nigrostriatal dopaminergic neurotransmission show decreased mobility during the open field test.

[STEPS]
SECTION: Test
1. Bring cages to the behavioral room for at least 60 min prior to the test for habituation
SECTION: Test
2. Place rat individually in a clean open field arena (1m x 1m)
SECTION: Test
3. Video tape from above for 5 min and record parameters of spontaneous activity (distance traveled, movement time, immobility) using an activity tracking software.

SECTION: Test
4. Clean arena with mild soap solution