eamag/protocols-with-steps huggingface dataset:
TITLE: JM SW modified medium
AUTHORS: Roscoff Culture Collection

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Medium used for Cryptophytes</div><div class = "text-block">Adapted from CCAP web site:   http://www.ife.ac.uk/ccap/MediaRecipes2.html#jm </div></div>

[STEPS]
?. Change from standard JM medium  ABCDE1Volume for 1 litre
Component
Concentration Stock Solutions
21 ml
KH2PO4
KH2PO4
2.48 gr
200 ml
31 ml
CaCl2
CaCl2.2H2O
0.5 gr
200 ml
42 ml
NaNO3
NaNO3
16 gr
200 ml
51 ml
MgSO4
MgSO4.7H2O
10 gr
200 ml
61 ml
NaHCO3
NaHCO3
3.18 gr
200 ml
71 ml
Na2EDTA.FeCl3
From K media
&nbsp;
&nbsp;
80.66 ml
H3B03
H3B03
0.496 gr
200ml
90.66 ml
MnCl2
MnCl2.4H2O
0.278 gr
200 ml
100.66 ml
NH46Mo7024
NH46Mo7024.4H2O
0.20 gr
200 ml
111 ml
Na2HPO4
Na2HPO4.12H2O
7.2 gr
200 ml
12100 µl
Vitamines
&nbsp;
&nbsp;
&nbsp;
13990 ml
SW sterile
&nbsp;
&nbsp;
&nbsp;
ABCDE1Volume for 1 litre
Component
Concentration Stock Solutions
21 ml
KH2PO4
KH2PO4
2.48 gr
200 ml
31 ml
CaCl2
CaCl2.2H2O
0.5 gr
200 ml
42 ml
NaNO3
NaNO3
16 gr
200 ml
51 ml
MgSO4
MgSO4.7H2O
10 gr
200 ml
61 ml
NaHCO3
NaHCO3
3.18 gr
200 ml
71 ml
Na2EDTA.FeCl3
From K media
&nbsp;
&nbsp;
80.66 ml
H3B03
H3B03
0.496 gr
200ml
90.66 ml
MnCl2
MnCl2.4H2O
0.278 gr
200 ml
100.66 ml
NH46Mo7024
NH46Mo7024.4H2O
0.20 gr
200 ml
111 ml
Na2HPO4
Na2HPO4.12H2O
7.2 gr
200 ml
12100 µl
Vitamines
&nbsp;
&nbsp;
&nbsp;
13990 ml
SW sterile
&nbsp;
&nbsp;
&nbsp;
TITLE: 2-step PCR mixture and conditions (Barcoded-head primers for seqs pooling)
AUTHORS: Yin-Tse   Huang, Tsu-Chun Hung

[DESCRIPTION]
PCR mixture and condition (2X SUPERGREEN PCR MASTER MIX)

[STEPS]
1. Wear glove, clean up the working bench w. 1% bleach
SECTION: For 1&#x27; PCR head-primers
2. Prepare 1' PCR master mixutre for head-primers (prepare 1.2X of solutions for pipetting error if needed)
 
PCR mixture for head-primers for each reaction
 

 

SECTION: For 1&#x27; PCR head-primers
3. Mix the 1' PCR master mixture gently by pippeting. Quick spin the tube.
SECTION: For 1&#x27; PCR head-primers
4. Transfer  23.75 µL 1' PCR master mixutre in 8-strip PCR tubes.

SECTION: For 1&#x27; PCR head-primers
5. Add 1.25 µLDNA template in 8-strip PCR tubes, resulting in a 25 µL reaction mixture for 1' PCR.


 

SECTION: For 1&#x27; PCR head-primers
6. Mix the reaction mixture gently by tapping the tubes. Quick spin the tubes.
SECTION: For 1&#x27; PCR head-primers
7. Carry out PCR using the following condition:  

1' PCR condition for head-primers
 

SECTION: For 1&#x27; PCR head-primers
7.1. 1' hear-primers used in Huang lab
 

SECTION: For 1&#x27; PCR head-primers
8. Carry out electrophoresis for inspection of DNA products

   

SECTION: For 1&#x27; PCR head-primers
9. Markdown wells and upload the pictures to the Lab Google drive

  

SECTION: For 2&#x27; PCR barcoded-head primers
10. Prepare 2' PCR master mixutre for barcoded-primers (prepare 1.2X of solutions for pipetting error if needed)
 
PCR mixture for barcoded-primers for each reaction (NO PRIMERs at this point!!)
 

 

SECTION: For 2&#x27; PCR barcoded-head primers
11. Mix the 2' PCR master mixture gently by pippeting. Quick spin the tube.
SECTION: For 2&#x27; PCR barcoded-head primers
12. Transfer 13.05 µL of the 2' PCR master mixture to 8-strip PCR tubes.

SECTION: For 2&#x27; PCR barcoded-head primers
13. Add 1.2 µL pre-mixed barcoded-head primers (Forward + Reverse) to each PCR tubes.

SECTION: For 2&#x27; PCR barcoded-head primers
14. Add 0.75 µL of 1' PCR product as template, resulting in 15 µL reaction mixture for 2' PCR.

Negative control contains only 14.25 µL master mixture and premixed barcoded-head primers but not DNA template
SECTION: For 2&#x27; PCR barcoded-head primers
15. Mix gently by tapping the tubes. Quick spin the tubes.
SECTION: For 2&#x27; PCR barcoded-head primers
16. Carry out 2' PCR using the following condition:  

2' PCR condition for barcoded-head primers
 

SECTION: For 2&#x27; PCR barcoded-head primers
17. Carry out electrophoresis for inspection of DNA products

  

SECTION: For 2&#x27; PCR barcoded-head primers
18. Markdown wells and upload the pictures to the Lab Google drive
TITLE: Patch-Seq Internal Solution with Biocytin
AUTHORS: Allen Institute for Brain Science

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This SOP provides instruction to prepare Internal Solution which is used for patch clamp electrophysiology, modified for cleanliness and mRNA capture and sustainability.</div><div class = "text-block"><span style = "font-weight:bold;">Note</span><span>: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number U19MH114830. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.</span></div></div>

[STEPS]
TITLE: 20% Paraformaldehyde in 5X PBS
AUTHORS: Allen Institute for Brain Science

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used to prepare 20% Paraformaldehyde (PFA) in 5X Phosphate-buffered saline (PBS). 20% PFA in 5X PBS is utilized to make the 4% PFA in 1X PBS reagent.</div><div class = "text-block"><span style = "font-weight:bold;">Note</span><span>: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number U19MH114830. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.</span></div></div>

[STEPS]
TITLE: Participants’ recruitment and samples collection
AUTHORS: Barbara Rizzacasa, Elena Morini, Ruggiero Mango, Chiara Vancheri, Simone Budassi, Gianluca Massaro, Sara Maletta, Massimiliano Macrini, Silvio D’Annibale, Francesco Romeo, Giuseppe Novelli, Francesca Amati

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A total of 99 patients has been enrolled to study circulating microRNAs, as diagnostic biomarkers, in patients with chronic stable coronary artery disease (CAD) and with acute myocardial infarction (AMI). For each patient, we have collected 10 mL of whole blood. All the samples have been processed maintaining the same conditions and timing. The samples with hemolysis and clots have been excluded from the study.</div></div>

[STEPS]
?. [Partecipant's recruitment]
A total of 99 patients has been enrolled for our study: 61 patients with chronic stable coronary artery disease (CAD) and 38 patients after a myocardial infarction event (AMI). For each patient, we took a blood sample.
?. [Sample collection]
•	10mL of whole blood have been collected in tube with K2 EDTA anticoagulant at the time of hospitalization from the 61 patients of CAD group;
?. [Sample collection]
•	10mL of whole blood have been collected in tube with K2 EDTA anticoagulant from the 38 patients of AMI group within 24 hours from the onset of myocardial event (AMI_T0 group);
?. [Sample collection]
•	10 ml of whole blood have been collected  in tube with K2 EDTA anticoagulant at 6 months post-AMI from 11 patients, previous recruited after a myocardial infarction event, who accepted to participate (AMI_T1 group).
?. [Partecipant's recruitment]
All the samples, maintained at room temperature, have been processed within 4h from the blood’s withdrawal.Before the processing, all the sample have been controlled to exclude the presence of hemolysis and clots.
TITLE: E. coli transformation
AUTHORS: iGEM Dusseldorf

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><ul style = "list-style-type:disc;"><li style = "counter-reset:ol0;list-style-type:disc;">Take tubes with 50 µL of TOP10F’ competent cells from -80°C freezer and place on ice.</li><li style = "counter-reset:ol0;list-style-type:disc;"><span>Add 5 µL of each ligation reaction directly to competent cells and mix by tapping gently. </span><span style = "font-weight:bold;">Do not mix cells by pipetting up and down</span><span>. Store any remaining ligation at -20°C.</span></li><li style = "counter-reset:ol0;list-style-type:disc;">Incubate cells on ice for 30 min. [while waiting, turn on 42°C water bath]</li><li style = "counter-reset:ol0;list-style-type:disc;">Incubate for exactly 30 sec in 42°C water bath. Do not mix or shake.</li><li style = "counter-reset:ol0;list-style-type:disc;">Remove vials and place quickly on ice. Store for 2 min on ice.</li><li style = "counter-reset:ol0;list-style-type:disc;">Add 500 µL of LB medium (pH. 7.5) to each tube.</li><li style = "counter-reset:ol0;list-style-type:disc;">Incubate tubes (taped horizontally to platform) for 60 min at 37°C and 225 rpm.</li><li style = "counter-reset:ol0;list-style-type:disc;">Plate 550 µL (variable) of each transformation on LB + AB plates.</li><li style = "counter-reset:ol0;list-style-type:disc;">Incubate overnight at 37°C, in the dark.</li></ul></div></div>

[STEPS]
TITLE: Troubleshooting guide for DDNS V2 
AUTHORS: Joyce Akello, Alex Shaw, Catherine Troman, Erika Bujaki, Manasi Majumdar, Aine.OToole, c.ansley, Zoe Vance, rachel.colquhoun, Andrew Rambaut, Javier Martin, Nick Grassly

[DESCRIPTION]
This document provides general guidance for troubleshooting problems encountered in the DDNS method. It outlines the factors that might influence the outcome of the DDNS PCR assay run, the common problems encountered, possible causes of the problems, and provides recommendations on corrective action and preventative action. 
This document is primarily developed for DDNS performed on stool samples, but included are other factors to consider for other sample types.

[STEPS]
TITLE: Simplified protocol for Agrobacterium-mediated transformation of the liverwort Marchantia polymorpha, includes protocols for spore sterilisation
AUTHORS: Suvi Honkanen, Victor A. S. Jones

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Simplified protocol for Agrobacterium-mediated transformation of haploid liverwort Marchantia polymorpha spores. See the attached file for all steps, notes and information on reagents. Includes protocols for spore collection, storage and sterilisation. </div><div class = "text-block">By Suvi Honkanen and Victor A. S. Jones. Modified from Ishizaki et al. Plant Cell Physiol. 2008 Jul;49(7):1084-91. doi: 10.1093/pcp/pcn085. Developed at the Dolan lab (The University of Oxford) and at the Small lab (The University of Western Australia).</div><div class = "text-block"><span>Working on a high-throughput T-DNA mutant screen published in </span><a href="https://doi.org/10.1016/j.cub.2016.09.062" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">https://doi.org/10.1016/j.cub.2016.09.062</span></a><span> , </span><a href="https://doi.org/10.1016/j.cub.2015.11.042" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">https://doi.org/10.1016/j.cub.2015.11.042</span></a><span> , </span><a href="https://doi.org/10.1016/j.cub.2016.09.062" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">https://doi.org/</span></a><a href="https://doi.org/10.7554/eLife.38529" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">10.7554/eLife.38529</span></a><span> , </span><a href="https://dev.biologists.org/content/144/8/1472" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">https://doi.org/10.1242/dev.144287</span></a><span>   , </span><a href="https://doi.org/10.1016/j.cub.2016.09.062" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">https://doi.org/</span></a><a href="https://dx.doi.org/10.1371%2Fjournal.pbio.3000560" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">10.1371/journal.pbio.3000560</span></a><span> taught us a thing or two about Marchantia transformation. I have further refined the protocol during my current semi high-throughput project. I hope you find some of this useful.</span></div></div>

[STEPS]
TITLE: Marchantia chloroplast isolation
AUTHORS: Eftychis Frangedakis

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is a modifiction of the </span><span style = "font-weight:bold;">ISOLATION OF MAIZE CHLOROPLASTS FOR PROTEIN IMPORT STUDIES  </span><span>
 protocl from Mark Settles (modified from Ken Cline). 
 
 
 </span></div></div>

[STEPS]
?. Prepare 20 ml 30% Percoll solution by mixing 6ml Percoll, 14ml Buffer GR.
?. Prepare 10 ml 70% Percoll solution by mixing 7ml Percoll and 3ml Buffer GR.
?. Add 15ml of 30% Percoil soution in a 50ml Falcon tube. Very carefully underlay 6ml of 70% (denser) Percoll solution using a 5ml Gilson pipette (A in Figure).
?. Keep the gradient on ice until further use.
?. Weigh 10g of thallus (grown in 12h light : 12h dark cycle – harvest the tissue 2-3 hours at the start of the light cycle - to reduce starch accumulation) (B in Figure).
?. Homogenize the tissue using a mortar and pestle into 100ml buffer GR (C and D in Figure).
?. Filter homogenate through two layers of Miracloth into two 50ml falcon tubes (E and F in Figure)
?. Remove supernatant and resuspend the pellet carefully in 2ml of buffer GR.
?. Spin at 7000g for 17 min at 4ºC. USE A SLOW ACCELERATION AND TURN DECELERATION OFF. Broken chloroplasts will reside in the top fraction, intact chloroplasts will reside in the interface of the two Percoll layers (I in Figure).
?. Carefully transfer intact chloroplasts from the interface, to a new 50 mL Falcon tube.
?. Wash intact chloroplasts with 25ml of Buffer GR (without BSA). This step removes residual Percoll. Centrifuge at 1500g for 5min at 4oC (J in Figure).
?. Flash freeze pellet if not used immediatly and store at -80oC
?. 
?. 
?. Centrifuge at 1200 g for 7 min (G in Figure)
?. Transfer the resuspended pellet to the top of the Percoll Gradient using a cut-off pipette tip (H in Figure).
TITLE: Methodology for TFP Bioeconomy Impact post Covid-19 on the agricultural economy
AUTHORS: C A Zuniga-Gonzalez

[DESCRIPTION]
Methods: The panel data was organized with FAO Statistic data. Linear programming with an enveloping data analysis (DEA) approach was used to measure the Malmquist TFP indices to determine the inter-annual changes by region in productivity and technical efficiency.

[BEFORE_START]
The model of Georgescu-Roegen (1976)was considered to define the structure of Panel Data and the DEAP software. 

[STEPS]
SECTION: Methodology for TFP Bioeconomy Impact post Covid-19 on the agricultural economy
1. Panel Data. The data was organized from the statistic FAO in panel data.  These variables are Value Agriculture (VAit), Land use (LUit), Unit Capital Stock (UCSit), Annual population (APit), Trade Indices (TIit), Consumer Prices, and Food Indices (2015 = 100) (CPFIit).  All variables were affected by Covid-19. 
SECTION: Methodology for TFP Bioeconomy Impact post Covid-19 on the agricultural economy
2. DEAP 2.1, Data Envelopment Analysis (Computer) Program (RRID:SCR_023002) was used, Coelli [17]. Three text files were used for running computing. The text file refers to panel data containing 60 observations of six regions over the 2012-2021 years period. The second file is Instructions, where the procedure is indicated, and the third is the results (output) that are shown in the results sections. One output is considered with five inputs listed in the next section. 
SECTION: Methodology for TFP Bioeconomy Impact post Covid-19 on the agricultural economy
3. Processing data was the last phase for the built chart and table that explain the effect of Covid-19 on the agricultural economy.  The Bioeconomy was and is an alternative to change a mitigate the  effects.
TITLE:  Immunoblot analyses for investigating SpLG-binding to purified mammalian and avian immunoglobulins.
AUTHORS: Angel  Justiz-Vaillant

[STEPS]
?. Aliquots of egg yolks, sera or 2 µg/µl of purified immunoglobulins from birds, laboratory, wild, farm animals and pets are applied to the gels of SDS-PAGE as described elsewhere.
?. Gels are transferred to nitrocellulose membranes (Immobilon-Nc, pore size 0.45 µm, Sigma-Aldrich Co, St Louis, Missouri) during 75 minutes at 40 mAmps using a semi-dry electroblotter, HEP-1 Model, Owl Scientific Inc.
?. The running buffer contains 25 mM Tris, 192 mM glycine pH 8.3 and 20% methanol.
?. The nitrocellulose membranes are blocked overnight in 10% non-fat skim milk in PBS with 0.05% Tween-20 pH 7.4 and then washed 4x, 10 minutes with PBS-Tween 20.
?. Recombinant protein LG or a mixture of SpL and SpG at a concentration of 5 µg/ml is added to the membranes.
?. After that there is an incubation period at 4°C overnight.
?. The nitrocellulose membranes were washed as above.
?. A secondary antibody (rabbit anti-chicken IgY horseradish peroxidase, Sigma Aldrich) is added at a 1:15 000 dilution.
?. It is incubated for one hour at room temperature and washed as above.
?. Tetramethyl-benzidine (TMB) solution is added to the nitrocellulose membranes, which are then incubated in the dark for seven minutes.  Then, the membranes are shaken gently and rinsed thoroughly in de-ionized water to stop the blotting process and are left to dry.
?. Alternatively, Ig samples are transferred to nitrocellulose membranes and directly probed using SpLG-HRP (diluted 1:5000) and TMB (this system was mainly used for detecting avian Igs).
TITLE: Plasmid-reprogramming of human fibroblasts
AUTHORS: Pascale Baden, michela.deleidi

[DESCRIPTION]
This protocol details about plasmid-reprogramming of human fibroblasts.

[GUIDELINES]
Adapted from Okita et al PMID: 21460823.

[STEPS]
SECTION: Nucleofection (Day 0)- with Amaxa Nucleofector I/II
1. Prepare nucleofection solution: 
      Human Dermal   Fibroblast Nucleofector solution  82 µL     Supplement  18 µl     Plasmid  10 µg   
 
SECTION: Nucleofection (Day 0)- with Amaxa Nucleofector I/II
2. Nucleofect 700.000 fibroblasts (resuspended in the nucleofection solution) with the P-022 program.
SECTION: Nucleofection (Day 0)- with Amaxa Nucleofector I/II
3. Distribute nucleofected fibroblasts on a 6-Well plate, coated with Matrigel.
SECTION: Nucleofection (Day 0)- with Amaxa Nucleofector I/II
4. Culture cells in DMEM + GlutaMAX supplement (Gibco) + 10 % FBS (Gibco) without P/S.
SECTION: Day 1
5. Change medium to DMEM + GlutaMAX supplement + 10% FBS + 2 ng/mL FGF2 (Peprotech) with 1% P/S (Millipore).

SECTION: Day 3/4
6. Change medium to E8 medium + 100 micromolar (µM) Sodium Butyrate (Sigma Aldrich 303410-100G) + 0.1 % P/S and change medium every other day.

SECTION: Day 21-28
7. Pick iPS cell colonies.
TITLE: Colony PCR for screening transgenic Ostreococcus tauri
AUTHORS: Shikha  Adhikari, Faith  Losbanes, Anbarasu  Karthikaichamy

[DESCRIPTION]
Colony PCR protocol for screening transgenic Ostreococcus tauri

[STEPS]
1. Measure cell concentration using a hemocytometer. Ideally, the cell concentration should be around 1-2x10^5 cells/ml

2. Mix 50 µL of cells and 50 µL sterile water in a PCR tube.

3. Boil the PCR tube at 95 °C for 5 min in a thermocycler.

4. After boiling, briefly centrifuge the PCR tube. Use 1 µL from the boiled sample as PCR template.

5. Mix the PCR components in a sterile laminar hood.


 

6. Perform PCR using the following protocol,


 

7. Resolve and visualize the PCR product on an agarose gel.
TITLE: Quick Protocol for Monarch® DNA Gel Extraction Kit (NEB #T1020)
AUTHORS: New England Biolabs

[DESCRIPTION]
This is the quick version of the Monarch® DNA Gel Extraction Kit Protocol (NEB #T1020). For the full protocol, please click here.

[BEFORE_START]
Add 4 volumes of ethanol (≥ 95%) to one volume of DNA Wash Buffer. 
          –  For 50-prep kit, add 20 ml of ethanol to 5 ml of Monarch DNA Wash Buffer
          –  For 250-prep kit, add 100 ml of ethanol to 25 ml of Monarch DNA Wash Buffer
All centrifugation steps should be carried out at 16.000 x g (~13.000 rpm).
Please note: column holds 800 μl

[GUIDELINES]
For detailed protocol and more information, visit www.neb.com/T1020

The full protocol is available here. 

A video protocol is available here.

[STEPS]
1. Excise the DNA fragment from the agarose gel, taking care to trim excess agarose. Transfer to a 1.5 ml microfuge tube and weigh the gel slice. Minimize exposure to UV light.
2. Add 4 volumes of Gel Dissolving Buffer to the gel slice (e.g., 400 μl buffer per 100 μl or 100 mg agarose).
3. Incubate the sample between 37–55°C (typically 50 °C), vortexing periodically until the gel slice is completely dissolved (generally 5-10 minutes).
 

 

4. Insert column into collection tube and load sample onto the column. Spin for 16000 x g, 1 min, then discard flow-through.
5. Re-insert column into collection tube. Add 200 µL and spin for 16000 x g, 1 min. Discarding flow-through is optional.
6. Repeat Step 5: Re-insert column into collection tube. Add 200 µL and spin for 16000 x g, 1 min. Discarding flow-through is optional.
7. Transfer column to a clean 1.5 ml microfuge tube. Use care to ensure that the tip of the column does not come into contact with the flow-through. If in doubt, re-spin for 1 min.
8. Add ≥ 6 µL to the center of the matrix. Wait for 1 min, and spin for 16000 x g, 1 min to elute the DNA.
TITLE: Measuring Turbidity and Fish Populations around Mo&#39;orea
AUTHORS: Ellis Gelt

[DESCRIPTION]
The ocean is often viewed as a fridge or pantry for many island communities, especially that of Mo’orea, French Polynesia.  But, it's known that sedimentation can cause coral death, and corals are vital places for reef fish around the island, including species consumed daily such as parrot fish. With the rapidly increasing population and amount of agriculture on the island, there's a possibility that levels of sediment in the water are increasing. If turbidity affects fish populations, there could be a problem. For this reason, I will be conducting an experiment designed to answer the question: Does turbidity affect fish populations?


[BEFORE_START]
- Construct buoy (see steps) and gather materials
- Determine 6 locations each 10 km apart the team will be visiting and mark with GPS

[GUIDELINES]
- wear protection on feet while conducting experiment
- avoid stepping on or interfering with sea life
- to accurately count fish populations and measure turbidity, the researchers must be cautious and minimize noise and movement

[STEPS]
SECTION: GRID CONSTRUCTION
1. lay out buoys in a 6x6 grid each a meter apart (5 meters squared)
SECTION: GRID CONSTRUCTION
2. cut rope into 12 pieces of equal length
SECTION: GRID CONSTRUCTION
3. tie rope to each buoy in every row of buoys vertically
SECTION: GRID CONSTRUCTION
4. repeat for each row of buoy horizontally
SECTION: FIELD
5. arrive to sample site 1 and identify shoreline (defined as the point where the sea water meets bare sand)
SECTION: FIELD
6. use measuring tape to measure 25 meters straight out
SECTION: FIELD
7. place 5x5 meter grid on top of ocean (centered around 25m point)

SECTION: FIELD
8. wait 5 minutes (to allow fish to return)
SECTION: FIELD
9. one researcher holds grid in place 
SECTION: FIELD
10. another researcher conducts a visual count of fish and notes species observed
SECTION: FIELD
11. researcher takes video where fish and grid are visible
SECTION: FIELD
12. researcher goes about 1 meter below surface and fills 1 L bottle
SECTION: POST-FIELD
14. for each site, observe video to count the number of fish visible and separate into species if possible
SECTION: POST-FIELD
15. for each site, measure turbidity of 1L bottle with a nephelometer
SECTION: FIELD
13. repeat steps for sites 2-6