eamag/protocols-with-steps huggingface dataset:
TITLE: Conexão do actígrafo no computador - ActTrust 
AUTHORS: Daniel Vartanian

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Este protocolo faz parte do processo de coleta de dados actigráficos do Grupo Interdisciplinar de Pesquisa em Sono (GIPSO). Ele foi desenhado para os actígrafos provenientes da companhia </span><a href="https://www.condorinst.com.br/" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">Condor Instruments</span></a><span>. Algumas das configurações mencionadas podem ser específicas desses aparelhos.</span></div><br/><div class = "text-block">Se você não é membro ou parceiro do GIPSO, você pode utilizar este protocolo como referência para o processamento de seus equipamentos. Neste caso, por favor, não envie os formulários mencionados neste ou em outros protocolos relacionados ao processo.</div><br/><div class = "text-block"><span>Se você utilizar os protocolos do GIPSO em sua pesquisa, por favor considere citá-los na seção de materiais e métodos de seu estudo. Nós nos esforçamos bastante para elaborar e manter protocolos de acesso aberto à comunidade científica. Você pode encontrar a citação deste protocolo na aba</span><span style = "font-weight:bold;font-style:italic;"> </span><span style = "font-style:italic;">metadata</span><span>.</span></div><br/><div class = "text-block"><span>Consulte a aba </span><span style = "font-style:italic;">Guidelines</span><span> para visualizar o fluxograma do processo e os demais protocolos relacionados.</span></div><br/><div class = "text-block"><span>Para dúvidas ou sugestões, entre em contato pelo e-mail </span><a href="mailto:gipso@usp.br" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">gipso@usp.br</span></a><span>.</span></div></div>

[STEPS]
?. Abra o software ActStudio
Caso apareça algum pop-up solicitando a configuração da latitude e longitude, clique em Não. Para este procedimento essa configuração não é necessária.
?. Acesse a tela Controle
Na parte superior do ActStudio você verá um botão chamado Controle. Clique sobre ele e depois selecione a aba CONTROLE.
?. Conecte o ActDock (base de conexão) no computador
Conecte a ponta USB A-Type (a ponta com o conector maior) do cabo de conexão no computador e a outra ponta do mesmo cabo no ActDock.
?. Conecte o actígrafo no ActDock
Pegue o actígrafo e conecte-o no ActDock, cuidando para que os contatos dourados do aparelho estejam alinhados aos contatos dourados da base de conexão.Feche o ActDock até ouvir um "click" (sem pressionar demais o actígrafo contra a base). Após isso, o registro do actígrafo deve aparecer na aba CONTROLE do software ActStudio.ATENÇÃOApós concluir esta etapa pode ocorrer que o actígrafo não conste na aba CONTROLE. Isso normalmente se dá por uma falha de contato. Neste caso, tente adicionar um peso sobre o actígrafo com o ActDock aberto.Quando o actígrafo está com a bateria esgotada é possível que ocorra um erro ao conectar. Se esse for o caso, ignore o erro e aguarde alguns minutos com o aparelho conectado. Assim que o actígrafo receber alguma carga ele será identificado pelo sistema.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>Giardia is a protozoan parasite of public health relevance that causes gastroenteritis in a wide range of hosts. Two genetically distinct lineages (assemblages A and B) are responsible for the human disease. Although it is clear that differences in virulence occur, pathogenesis and virulence of Giardia remains poorly understood. The genome of Giardia is believed to contain ORFs which could encode as many as 6,000 proteins. By successfully applying quantitative proteomic analyses to the whole parasite and to the supernatants derived from parasite culture of assemblages A and B, we confirm expression of ~1,600 proteins from each assemblage, the vast majority of which being common to both lineages. To look for signature enrichment of secreted proteins, we considered the ratio of proteins in the supernatant compared with the pellet which defined a small group of enriched proteins, putatively secreted at a steady state by cultured growing trophozoites of both assemblages. This secretome is enriched with proteins annotated to have N-terminal signal peptide. The most abundant secreted proteins include known virulence factors such as cathepsin B cysteine proteases and members of a <em>Giardia</em> superfamily of cysteine rich proteins which comprises VSPs, HCMPs and a new class of virulence factors, the <em>Giardia</em> tenascins. We demonstrate that physiological function of human enteric epithelial cells is disrupted by such soluble factors even in the absence of the trophozoites. We are able to propose a straightforward model of Giardia pathogenesis incorporating key roles for the major Giardia derived soluble mediators.</p>

[STEPS]
TITLE: 城市微生物菌相調查計畫 — 採集土壤教學
AUTHORS: Hsin-Mao  Wu

[DESCRIPTION]
城市微生物菌相調查計畫 — 採集土壤教學

[STEPS]
SECTION: 如何加入專案
1. 開啟Line app，將頁面切換成「聊天」，並按下頂部的掃描圖示(紅框處)
  

SECTION: 如何加入專案
2. 掃描以下QR code或點選此連結微生物公民科學
  

SECTION: 如何加入專案
3. 加入成功後會顯示以下畫面
  

SECTION: 如何加入專案
4. 接著等待採集工具包寄送即可開始採集！
SECTION: 採土
5. 移除表土，取距離土表5~7公分之處的土，裝入塑膠夾鏈袋中
[示意圖片待補]
SECTION: 採土
6. 將塑膠袋中的土均勻混合，倒入採集罐之中
 

SECTION: 採土
7. 在採集紀錄紙上勾選採樣地點、採樣種類，以及填寫日期、城市、鄉鎮、地點、採集者等資訊
SECTION: 採土
8. 最後拍兩張照片
 

   
   

 

SECTION: 採土
9. 打開iNaturalist app，上傳剛剛拍攝的兩張照片
[上傳之螢幕截圖與步驟待補]
SECTION: 採土
10. 上傳完成後，在詮釋資料中找到ID(如下圖紅框處)  
 


SECTION: 採土
11. 在採集紀錄紙上填入ID，並將紀錄紙放入採集罐中
[示意圖片待補]
SECTION: 採土
12. 將採集罐保存於室溫，並於10天內以郵信寄回高雄醫學大學生物系
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>Test cropora for evaluation of drNER, together with the obtained results for each documment, separetly.</p>

[GUIDELINES]
<p>drNER is a rule-based Named-entity recognition method for knowledge extraction of evidence-based dietary recommendations.</p>
<p> </p>
<p>The files are available at: <a href="http://cs.ijs.si/eftimov/drNER." target="_blank">http://cs.ijs.si/eftimov/drNER</a>.</p>
<p> </p>
<p>The “Scientifically_validated_documents.xlsx” contains 50 documents extracted from scientifically validated web sites that are used for evaluation of drNER.</p>
<p> </p>
<p>The “PubMED_abstracts.xlsx” contains 50 documents that are PubMED abstracts and they are used for evaluation of drNER.</p>
<p> </p>
<p>In the “drNER results” folder, the obtained results by the drNER are presented. For each document the obtained results are presented into “csv” file, “DocNumber.csv”. Number that is presented in the name of the “csv” file is related to a document from the test sets. The documents from  “Scientifically_validated_documents.xlsx” have numbers form 1 to 50, while the documents from “PubMED_abstracts.xlsx” have numbers from 51 to 100.</p>
<p> </p>
<p>Each “csv” file consists of 6 parameters, “Entity”, “Label”, “SOP label”, “Sentence segment”, “Sentence”, and “Document”. “Entity” is the extracted phrase from the document. “Label” is the category to which the extracted entity belongs. “SOP label” gives indication about the location from where the entity is extracted (S- Subject, P - Predicate, O - Object ). “Sentence segment” is the number of sentence segment if the sentence is split into segments according to the preprocessing that is defined. “Sentence” corresponds to the number of sentence when the text is split on sentences. “Document” is the number of document from the test set.</p>
<p> </p>
<p>CONTACT</p>
<p> </p>
<p>tome.eftimov@ijs.si</p>

[STEPS]
?.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>This protocol is used to stain late larval <em>Drosophila</em> lipid droplets in fat bodies and intestines with Nile Red, which emits fluorescence in the 552/636 nm range. </p>

[BEFORE_START]
<p>1. Prepare Nile Red (Sigma-Aldrich) in acetone (1000 ug/mL).</p>
<p>2. Dissect tissues in ice cold PBS. </p>
<p>3. Fix tissues in 4% paraformaldehyde (formalin) diluted in PBS with 0.1% Triton X-100. </p>
<p>4. Wash tissues 3x in PBS. </p>
<p> </p>
<p> </p>

[GUIDELINES]
<p>In brief, dissect animals in ice cold phosphate-buffered saline (PBS). Keep tissues in PBS on ice while obtaining your desired sample size. Fix tissues in 4% PFA (diluted in PBS with 0.1% Triton X-100), for 20 minutes, wash 3x in PBS, and stain tissues light-protected at room temperature for 1 hour. </p>
<p> </p>
<p>* Do not use any serums for this protocol because Nile Red will instead be drawn away from your tissues and into serum. </p>

[STEPS]
?. 
?. 
?. 
?. 
?. 
?.
TITLE: Polymerase Chain Reaction (PCR)
AUTHORS: NUS iGEM

[DESCRIPTION]
This is the common Polymerase Chain Reaction (PCR) protocol followed by the 2023 NUS-Singapore iGEM team. 

[STEPS]
4. Vortex the PCR tubes to mix well.
3. For a 50μL PCR sample, add the following into a PCR tube (follow the sequence):

 

5. Place the PCR tube into the Thermal Cycler with the following conditions:

**Lid Temperature: 105°C; Volume: 50μL
 

6. Upon finishing, cancel the current protocol and take out the PCR sample from the Thermal Cycler. Keep the sample in the 4°C fridge for storage. Otherwise, gel electrophoresis may be carried out to isolate the DNA fragment of interest.
1. Prepare a PCR tube.
2. Thaw the KOD OneTM PCR Master Mix (Blue) from the -20°C fridge.
TITLE: Washington University SenNet Case Collection Protocol
AUTHORS: Daniel Rapp, Matthew Wyczalkowski

[DESCRIPTION]
This document outlines inclusion and exclusion criteria for healthy participants for the WUSTL Senescence Network (SenNet) by the Tissue Mapping Center (TMC) at Washington University. 

[STEPS]
1. Study coordinator will receive surgeon schedules at the beginning of each week. All surgeons should be IRB approved for the study.
4. Study coordinator will evaluate patient for eligibility using criteria detailed in following sections. 
2. Study coordinator will call potential study participants over phone using IRB approved phone script to see if participants are interested. Other option is to approach potential participants in Clinic when they are meeting with surgeon before the surgery date. Discuss with surgeon team which is best option as to not disrupt clinic flow.
3. Once patient is identified and interested, go over IRB approved consent form with patient. Answer all questions and allow for time if they need to think the process over. Must give patient a signed copy of consent form for their own personal records. Enter subjects into Oncore within 24 hours of consent process.
SECTION: Inclusion Criteria
5. Able to understand and willing to sign an IRB-approved written informed consent document
Undergoing routine surgery under general anesthesia for non-cancer diagnosis, including: 
Laparoscopic upper gastrointestinal surgery (for benign diagnosis, e.g. cholecystectomy, hernia repair) or Open abdominal surgery for similar indications. (need access to liver and omental fat)
Orthopedic knee and hip replacement surgeries
18 years of age or older
All races and ethnicities eligible
All BMIs eligible
Equal number of female and male donors will be accepted
Past history of cancer and chemo are eligible
SECTION: Exclusion Criteria
6. Undergoing a Cancer surgery
Currently receiving Chemo treatment
Positive for HIV
Under 18 years of age
Unable to fully understand/sign consent form. (e.g. language barrier, compromised mental status)
SECTION: Documents
7. Signed consent document saved and stored in secure location. Copy of signed consent also given to patient
Signed W9 tax form saved and uploaded for payment of participant.
Check request form signed by PI saved and uploaded for payment of participant.
TITLE: Git workflow
AUTHORS: Naeem.Muhammad

[DESCRIPTION]
Git workflow for research group Numa

[STEPS]
SECTION: Numa_Git_Workflow
1. Create  feature branch 
 

SECTION: Numa_Git_Workflow
2. Make required changes
SECTION: Numa_Git_Workflow
4. Push feature branch to remote
 

SECTION: Numa_Git_Workflow
5. Create a merge request
SECTION: Numa_Git_Workflow
3. Commit changes
TITLE: Generating pPB-CAG-mCherry-CAAX Plasmid
AUTHORS: Shiyi Wang

[DESCRIPTION]
Generating pPB-CAG-mCherry-CAAX Plasmid

[STEPS]
1. **Obtain Plasmids** - Obtain pPB-CAG-EGFP and pGLAST-PBase plasmids from Dr. Joseph Loturco.
2. **Insert mCherry-CAAX into pPB-CAG-EGFP** - Insert mCherry-CAAX between XmaI and NotI restriction sites in pPB-CAG-EGFP to replace EGFP.
3. **Insert hU6 Promoter and shRNA into pPB-CAG-mCherry-CAAX** - Amplify a DNA fragment containing hU6 promoter and shRNA from pLKO.1-shRNA using Phusion High-Fidelity DNA Polymerase with primers introducing SpeI restriction sites: - Forward Primer: GGACTAGTCAGGCCCGAAGGAATAGAAG - Reverse Primer: GGACTAGTGCCAAAGTGGATCTCTGCTG - Purify the PCR products and digest them with SpeI.
4. **Ligation into pPB-CAG-mCherry-CAAX** - Ligase the purified and SpeI-digested DNA fragment containing hU6 promoter and shRNA into pPB-CAG-mCherry-CAAX at the SpeI restriction site.
5. **Confirmation by Analytical Digest and Sequencing** - Perform an analytical digest with EcoRI to confirm the correct orientation of the inserted DNA fragment. - Sequence the plasmid to confirm the accurate insertion of hU6 promoter and shRNA sequences.
TITLE: No Title
AUTHORS: 

[GUIDELINES]
<table cellspacing="0" cellpadding="0" align="center">
<tbody>
<tr>
<td align="left" bgcolor="#FFFFFF" width="450">
<ul>
<li>Cell Staining Buffer (BioLegend Cat. No. <a href="https://www.biolegend.com/cell-staining-buffer-1494.html" target="_blank" rel="noopener noreferrer">420201</a>)</li>
<li>Red Cell Lysis Buffer (BioLegend Cat. No. <a href="https://www.biolegend.com/rbc-lysis-buffer-10x-1498.html" target="_blank" rel="noopener noreferrer">420301</a>)</li>
<li>7-AAD Viability Staining Solution (BioLegend Cat. No. <a href="https://www.biolegend.com/7-aad-viability-staining-solution-1649.html" target="_blank" rel="noopener noreferrer">420403</a>)</li>
</ul>
</td>
<td align="left" bgcolor="#FFFFFF" width="450">
<ul>
<li>TruStain FcX™ (anti-CD16/32, BioLegend Cat. No. <a href="https://www.biolegend.com/trustain-fcx-anti-mouse-cd16-32-antibody-5683.html" target="_blank" rel="noopener noreferrer">101319</a>)</li>
<li>Human TruStain FcX™ (Fc Receptor Blocking Solution, BioLegend Cat. No. <a href="https://www.biolegend.com/human-trustain-fcx-fc-receptor-blocking-solution-6462.html" target="_blank" rel="noopener noreferrer">422301</a>)</li>
</ul>
</td>
</tr>
</tbody>
</table>

[STEPS]
SECTION: Harvest Tissue or Cells
?. 
SECTION: Harvest Tissue or Cells
?. 
SECTION: Lyse Red Cells
?. 
SECTION: Lyse Red Cells
?. 
SECTION: Lyse Red Cells
?. 
SECTION: Lyse Red Cells
?. 
SECTION: Block Fc-Receptors
?. 
SECTION: Cell-Surface Staining with Antibody
?. 
SECTION: Cell-Surface Staining with Antibody
?. 
SECTION: Cell-Surface Staining with Antibody
?. 
SECTION: Cell-Surface Staining with Antibody
?. 
SECTION: Cell-Surface Staining with Antibody
?. 
SECTION: Cell-Surface Staining with Antibody
?. 
SECTION: Cell-Surface Staining with Antibody
?. 
SECTION: Block Fc-Receptors
?.
TITLE: Collecting Bark and Ambrosia Beetles
AUTHORS: Jiri Hulcr, Andrew J. Johnson, Demian F Gomez

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the different methods to collect and preserve bark ambrosia beetles. </div><div class = "text-block"><span>This protocol is part of the Bark Beetle Mycobiome (BBM) Research Coordination Network. For more information on the BBM international network: Hulcr J, Barnes I, De Beer ZW, Duong TA, Gazis R, Johnson AJ, Jusino MA, Kasson MT, Li Y, Lynch S, Mayers C, Musvuugwa T, Roets F, Seltmann KC, Six D, Vanderpool D, & Villari C. 2020. Bark beetle mycobiome: collaboratively defined research priorities on a widespread insect-fungus symbiosis. Symbiosis 81: 101–113 </span><a href="https://doi.org/10.1007/s13199-020-00686-9" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">https://doi.org/10.1007/s13199-020-00686-9</span></a><span>.</span></div></div>

[STEPS]
TITLE: Heptane preparation of Annonaceae pollen
AUTHORS: Couvreur LP Thomas, Tanawat Chaowasku, Raymond W. J. M. van der Ham

[DESCRIPTION]
The protocol used to study Annonaceae pollen taken from herbarium dried specimens or in field alcohol conserved material. The protocol deviates from previous versions by using Heptane instead of n-Hexane.

[GUIDELINES]
This protocol uses Heptane, which is a highly volatil solvent and all steps must be done under a fune cabinet.

[STEPS]
SECTION: Sample material
1. Use a stereo microscope to collect anthers at anthesis of flowers from herbarium specimen or conserved in alcohol (spirit material). Depending on the size of the anthers take 3-10. Place the anthers in a glass vial.

 

SECTION: Sample material
2. Crush the anthers with a glass rod. Make sure to clean the rod in between crushed to avoid contamination.

 

SECTION: Sample material
3. If you have alcohol preserved material continue; for herbarium dried material jump to Step 6.
SECTION: Alcohol preserved material
4. Wash anthers in alcohol 100% for 5 min. Remove excess alcohol if needed.

 


SECTION: Alcohol preserved material
5. Place vials in fume cabinet.
Wash again but this time with alcohol 100% + Hepatne in a 1/1 mix for 5 min.

SECTION: Herbarium preserved material
6. Start here with herbarium dried material, and continue here with alcohol preserved material. Place vials in fume cabinet.

Add 1 mL of Heptane to each vial, swirl the solution a bit and then leave for 1 min.

 


SECTION: Herbarium preserved material
7. Remove most of the Heptane carefully with a pipette. Try to keep the pollen material on the bottom of the vial; take a clean pipette for each sample to avoid contamination.
SECTION: Herbarium preserved material
8. Repeat steps 6 and 7 twice. The samples must go through three rounds of washing.
SECTION: Herbarium preserved material
9. After the third step of Heptane, try to pipette off as much of the solution as possible without removing pollen material. Let the remaining Heptane evaporate so the sample becomes dry. You can recheck to make sure your sample still has pollen under the stereo microscope.
SECTION: Herbarium preserved material
10. Transfer the material to labelled tubes for microscope viewing.
TITLE: Serapure Bead production 
AUTHORS: Eric Pederson

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Production of DNA size separation magnetic beads.</div></div>

[STEPS]
?. [Serapure bead production]
In a 50 mL conical using sterile stock solutions, prepare TE (10 mM Tris-­‐HCl and 1 mM EDTA);- 500 μL 1 M Tris pH8 - 100 μL 0.5 M EDTAFill conical to 50 mL mark with dH20.
?. [Serapure bead production]
To a  to a new 50 mL, sterile conical add;- 9 g PEG-­‐8000- 10 mL 5 M NaCL (or 2.92 g)- 500 μL1 M Tris-­‐HCL- 100 μL0.5 M EDTA- 0.250 ul 10% tween-20- Fill to ~ 49 mL using sterile dH20.Mix conical for about 3-­‐5 minutes until PEG goes into solution (solution, upon sitting, should be clear).-Fill to ~ 49 mL using sterile dH20. gently.
?. [Serapure bead production]
Mix Sera-­‐mag SpeedBeads and transfer 1 mL to a 1.5 mL microtube.
?. [Serapure bead production]
Place SpeedBeads on magnet stand until beads are drawn to magnet.Discard supernatant
?. [Serapure bead production]
Add 1 mL TE to beads, remove from magnet, mix, return to magnet.Discard supernatant
?. [Serapure bead production]
Add 1 mL TE to beads, remove from magnet, mix, return to magnet.Discard supernatant
?. [Serapure bead production]
Add 1 mL TE to beads and remove from magnet. Fully resuspend and set microtube in rack (i.e. not on magnet stand).
?. [Serapure bead production]
Mix 1 mL SpeedBead + TE solution and transfer to 50 mL conical.
?. [Serapure bead production]
Fill conical to 50 mL mark with dH20 (if not already there) and gently mix 50 mL conical until brown.
?. [Serapure bead production]
Wrap in tinfoil (or place in dark container) and store at 4°C.
?. [Serapure bead production]
Test against AMPure XP using aliquots of ladder (Fermentas GeneRuler).I recommend the 50 bp ladder in place of the ultra-­‐low rangeladder.
?. [Serapure bead production]
Mix 2 μLGeneRuler with 18 μL dH20.
?. [Serapure bead production]
Incubate mixture 5 min.at room temperature.
?. [Serapure bead production]
Add 20 μLGeneRuler mixture to a volume of Serapure and/or AMPure(the specific volume depends on whether you are trying exclude small fragments or not; see the figure on the next page).
?. [Serapure bead production]
Place on magnet stand.Discard supernatant.
?. [Serapure bead production]
Add 500 μL70 % EtOH.
?. [Serapure bead production]
Incubate on stand for 1 min.Discard supernatant.
?. [Serapure bead production]
Add 500 μL 70% EtOH.
?. [Serapure bead production]
Incubate on stand for 1 min.Remove supernatant.
?. [Serapure bead production]
Place beads on 37°C heat block for 3-­‐4 min.until dry.
?. [Serapure bead production]
Re-hydrate with 20 μLdH20 for 5 minutes.
?. [Serapure bead production]
Place on magnet stand.Transfer supernatant to new tube.
?. [Serapure bead production]
Mix supernatant with 3 μLloading dye.Use the same ladderElectrophorese in 1.5 % agarose for 60 minutes at 100 V (or as you please)
?. [Serapure bead production]
Use 20ul of the ladder/water mix and add to these amounts of the serapure beads and the ampure beads.0.9X sample - 18 ul1.2X sample- 24 ul1.5X sample -  30 ul1.8X sample- 36 ul2.1X sample -  42 ul2.5X sample - 50 ul2.7X sample - 54 ul
TITLE: Homogenate of A. cervicornis
AUTHORS: Stephanie Rosales, Ana M Palacio-Castro

[DESCRIPTION]
This protocol is to study disease in Acropora cervicornis by using a disease homogenate method. These methods are adapted from methods presented in Muller 2018 https://elifesciences.org/articles/35066.

[BEFORE_START]
Prepare sterilized and 0.2 micron filtered seawater (FSW).
Collect healthy coral fragments
Collect diseased coral fragments
Randomly assign tanks to treatments 
Label and UV Ziploc bags and Falcon tubes and other material taht cannot be autoclaved 


[STEPS]
4. Clean -up
4.1. Bleach tweezers, clippers, slates, airgun, surfaces

3. Dose experimental corals with the placebo and disease homogenates
1. Obtain healthy and diseased Acropora cervicornis fragments. These fragments are preferably collected from the same area and with similar disease progression.
 
 

2. Prepare placebo and disease homogenates
2.1. Grab healthy fragments from the holding tank.
 

2.4. Grab a fragment and hold it over a pre-labeled Ziploc bag (** this will require two people**). 

Airbrush the tissue with an airgun and FSW.

Approximately 5 min  
 

 


2.2.  Take a picture of every fragment with a size scale to estimate the amount of tissue blasted.
2.5. Pour homogenate in a pre-labeled 50mL falcon tube(s). Measure volume and store in the fridge. 
2.6. Grab diseased fragments from the holding tank. And repeat steps 2.2 - 2.5.
2.8. Bring placebo and diseased homogenates to the same volume by adding FSW
2.9. Add 20 beads to each falcon tube containing ~ 40mL of homogenate and vortex for 10 minutes

10 min 

3.1. Sterile razor with bleach and scratch a small area of each experimental coral
 

3.2. Apply 500 uL of placebo and disease homogenate above each coral fragments in their respective treatments.
2.10. Save and preserve ~ 500 ul of both homogenates for sequencing.

2.7. Change gloves
3.3. Add 16 L of seawater to each tank to completely cover the fragments 
4.2. Discard bags and falcon tubes
2.3. Rinse fragments with FSW, and place them in a sterile container with enough FSW to cover them. 
3.4. Maintained closed system for 3hours