eamag/protocols-with-steps huggingface dataset:
TITLE: Spectral photogrammetry protocol
AUTHORS: Aurore Mathys

[DESCRIPTION]
<div class = "text-blocks"></div>

[STEPS]
?. [Acquisition]
Place de specimen at the center of the turntable with scales, photogrammetry marker and MSI calibration card (CHSOS).
?. [Acquisition]
Setup the correct exposure for each wavelenght and verify that the exposure is correct in spectrashoot using the MSI calibration card. Adjust exposure until the specimen is correctly lit.
?. [Acquisition]
Setup lamp and camera distance. Place the camera at approximately 30°.
?. [Acquisition]
Start capturing: for one specimen position capture at all the 15 wavelengths + white light. Then add the UV-pass filter and capture pictures in the UV wavelengths (UVR). Next place the UV-cut off filter and capture picture for each UV wavelengths (UVF). Pictures should be capturated in raw format.
?. [Acquisition]
Rotate the turntable of 10° and repeat step 4. Do this for the complete rotation.
?. [Acquisition]
Move the camera at an angle of 60° at the approximately the same distance than previously and repeat the operation for the complete rotation.
?. [Acquisition]
If necessary turn the specimen and repeat the process for as many rotation/views as necessary.
?. [Pre-processing]
Separate the wavelengths in different folders.
?. [Processing]
Open Agisoft Photoscan and create a chunk for each wavelengths (rename the chunks accordingly). Import the pictures.
?. [Processing]
Go to workflow > batch process and add the following step: align pictures (highest), build dense cloud (high), build mesh (high).
?. [Processing]
Repeat the processing 3 times to make sure the results are reliable.
?. [Processing]
If the results are reliable, export the models as .stl for surface analysis.
TITLE: Influenza A Virus Infection
AUTHORS: Timothy S C Hinks, Bonnie van Wilgenburg, Huimeng Wang, Liyen Loh, Marios Koutsakos, Katherine Kedzierska, Alexandra J. Corbett, Zhenjun Chen

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is part 3.3 of the "Study of MAIT Cell Activation in Viral Infections In Vivo" collection of protocols.</div><br/><div class = "text-block"><span style = "font-weight:bold;">Collection Abstract: </span><span>MAIT cells are abundant, highly evolutionarily conserved innate-like lymphocytes expressing a semi-invariant T cell receptor (TCR), which recognizes microbially derived small intermediate molecules from the riboflavin biosynthetic pathway. However, in addition to their TCR-mediated functions they can also be activated in a TCR-independent manner via cytokines including IL-12, -15, -18, and type I interferon. Emerging data suggest that they are expanded and activated by a range of viral infections, and significantly that they can contribute to a protective anti-viral response. Here we describe methods used to investigate these anti-viral functions in vivo in murine models. To overcome the technical challenge that MAIT cells are rare in specific pathogen-free laboratory mice, we describe how pulmonary MAIT cells can be expanded using intranasal bacterial infection or a combination of synthetic MAIT cell antigen and TLR agonists. We also describe protocols for adoptive transfer of MAIT cells, methods for lung homogenization for plaque assays, and surface and intracellular cytokine staining to determine MAIT cell activation.</span></div></div>

[STEPS]
?. Thaw virus vial rapidly in a  water bath until all ice crystals have melted.
37 °C
?. Decontaminate the outer surface of the vial with .
[ethanol]
?. Perform serial dilutions in sterile PBS to achieve the desired inoculum. For example:(a) If titer of PR8 stock = 1.0 × 109 plaque-forming units (PFU)/mL, require 25 PFU/inoculum (see Note 14).(b) Volume of inoculum required for intranasal infection = 50 μL/inoculum.(c) 25 PFU/50 μL = 500 PFU/mL, dilution required from virus stock DF = 2,000,000.Dilution 1: 1/100:  + .Dilution 2: 1/100:  + .Dilution 3: 1/100:  + .Dilution 4: ½: (depends on volume required, e.g., 20 inoculations = 1000 μL)  and .
[virus stock]
[PBS]
[dilution 1]
[PBS]
[dilution 2]
[PBS]
[dilution 3]
[PBS]
?. Mix virus with vortex before administering the inoculum.
?. Infect mice i.n. with  under isoflurane anesthesia (see Note 7).
50 µl
?. Allow mice to recover and monitor mice for until recovery (typically 10 days) (see Note 15).
TITLE: Preparation of soluble and insoluble mitochondrial protein fractions for immunoblotting
AUTHORS: Louise Uoselis

[DESCRIPTION]
Preparation of soluble and insoluble mitochondrial protein fractions from HeLa cells for immunoblotting.

[STEPS]
1. 
 
Thaw mitochondrial stocks on ice, and take two aliquots of 15 ug of mitochondria each for each sample (one aliquot will be the ‘total’ sample fraction, and one aliquot will represent the ‘fractionation’ sample).  
2. Centrifuge samples at 10,000x rcf for 10 min at 4 deg C, and carefully aspirate the supernatant 

3. Add 15 µL of ice cold 0.5% TX-100 in PBS, vortex each sample for ~5 seconds, and leave samples to incubate on ice for 15 min. At the conclusion of the 15 min lysis incubation, vortex each sample for ~5 sec again. 

4. Set aside one fraction from each sample for processing downstream (referred to as the ‘total’ fraction). 
5. Centrifuge the remaining tube of each sample at 12,000x rcf for 10 min at 4 deg C

6. Using a pipette, carefully remove 14.24 µL of the supernatant (representing 95% of the lysis volume) and place this sample into a clean microfuge tube on ice, being sure not to disturb any pellets that have formed on the bottom of the tube. The volume removed represents the ‘soluble’ protein fraction. The tube containing the pellet represents the ‘insoluble’ protein fraction. 

7. Add 14.24 µL of 0.5% TX-100 in PBS to each insoluble protein fraction by pipetting on the side of the tube. Gently flick each tube to rinse the sides of the tube. 

8. Centrifuge the insoluble protein fractions at 12,000x rcf for 10 min at 4 deg C.

9. Using a pipette, carefully remove 14.24 µL of the supernatant from the insoluble protein fraction, and place into a clean microfuge tube (which will function as the waste collection tube for all samples).

10. Repeat steps 7 – 9, which will total 2 washes
11. Repeat step 7. You should now have three tubes for each sample (representing the total, soluble and insoluble protein fractions), and one waste tube. 
12. Bring all samples to room temperature. To the total and insoluble samples, add 5 µL of 4x SDS loading dye (4x: 20% w/v SDS, 400 mM DTT, 40% v/v glycerol, 200 mM Tris-Cl pH 6.8). To the soluble fraction, add 4.75 µL of 4x SDS loading dye. 
 


13. Vortex each sample for ~3 seconds
14. Boil all samples at 99 deg C for 10 min shaking at max speed 

15. Let samples cool to room temperature, and centrifuge quickly to bring all liquid to the bottom of the tubes. Vortex the samples again for ~3 sec to ensure homogeneity. 
16. Sonicate all samples in a waterbath sonicator set to ~21 deg C water temperature for 2 min. 

17. Remove all samples from the sonicator, vortex samples for ~3 sec to mix. 
18. Load 19 µL from each sample on an SDS-PAGE gel and proceed to run/transfer the gel as standard.
TITLE: Creating a Frankenstein&#39;s Genome
AUTHORS: Helena  Pound, Eric Gann, Steven Wilhelm

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This short, command-line protocol is used to combine coding sequences (nucleic acids) from reference genomes into a single file with all coding sequences, with customizable clustering levels.</div></div>

[STEPS]
?. Download the nucleic acid coding sequences from all reference genomes you wish to include in your Frankenstein's genome in a .fasta format.
?. 
?. X1 is the concatenated reference .fasta file, X2 is the output folder name, X3 is the clustering threshold, and X4 is the word size.
?. Fu, L., Niu, B., Zhu, Z., Wu, S., and Li, W. (2012). CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28, 3150-3152.
?. Combine all downloaded fasta files.
?. The linux cat command concatenates all files, in this case all files ending with .fasta in the working directory you are in. The output.fasta file will be the concatenated file to be used in the next step.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>This protocol describes the preparation of cryogenic cultures from liquid cultures of <em>Synechocystis</em> sp. PCC 6803 for a further storage under -80 °C.</p>
<p>The protocol was handed over by Anna Behle MSc.</p>
<p>You can also check the recipe for cyanobacteria in general in '<a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=Synthetic+Biology+in+Cyanobacteria+Engineering+and+Analyzing+Novel+Functions" target="_blank">Synthetic Biology in Cyanobacteria Engineering and Analyzing Novel Functions</a>' by Heidorn <em>et al. </em>They use a DMSO concentration of 5% in the final culture and cells that are in late log to early stationary phase. They also use glycerol as a cryptoprotectant.</p>

[BEFORE_START]
<p>Prepare 0.5 x BG-11 with 8% dimethyl sulfoxide (DMSO).</p>
<p> </p>
<p><strong>Inoculate </strong>your media with colonies from agar plates, fresh cultures or cryo cultures.</p>
<p>Incubate your liquid cultures for <strong>at least seven days.</strong></p>
<p>If your cultures contain plasmid with antibiotic restistances, apply appropriate antibiotics in your media.</p>

[STEPS]
?. 
?. 
?. 
?. 
?.
TITLE: Creare  baseurl per harvesting di repository OAI con OpenRefine
AUTHORS: Andrea Marchitelli

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Il protocollo descrive il metodo per creare le baseurl per l'harvesting di un repository OAI-PMH a partire da una lista di identificatori.</div></div>

[STEPS]
?. Aprire il progetto OpeRefine contenente la lista degli identificatori OAI predisposta per l'harvesting.La lista può essere predisposta seguendo le indicazioni del protocollo collegato Come importare identificatori OAI-PMH in OpenRefine.
{"blocks":[{"data":[],"depth":0,"entityRanges":[],"inlineStyleRanges":[],"key":"52lge","text":"Protocollo per importare in OpenRefine una lista di identificatori OAI-PMH per successive elaborazioni.","type":"unstyled"}],"entityMap":[]}
?. [Creare le URL per l'harvesting]
Cliccare sulla colonna identifier presente nel progetto e scegliere l'opzione Modifica colonna > Aggiungi colonna basata su questa.
?. [Test del risultato]
A questo punto confermando l'operazione si otterrà una nuova colonna denominata baseurl_oai contenente le URL per il GetRecord di ogni articolo.
?. [Creare le URL per l'harvesting]
Nella finestra di dialogo con le impostazioni della nuova colonna inserire baseurl_oai come nome della colonna e un'espressione GREL che concateni la baseurl_oai della rivista, il verb GetRecord e l'identificatore OAI già presente nei file.Es. 'http://www.bibliotecheoggi.it/trends/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier='+valueAttenzione a mantenere gli apici (') all'inizio e alla fine della stringa URL
?. [Test del risultato]
Testare il risultato ottenuto cliccando su un paio di link e verificando che la pagina corrispondente si apra correttamente
TITLE: Visium CytAssist FFPE v2 -- University of Minnesota TMCs
AUTHORS: Laura J Niedernhofer, David A Bernlohr

[DESCRIPTION]
The Visium CytAssist Spatial Gene Expression for FFPE assay is designed to analyze mRNA in
tissue sections derived from formalin fixed & paraffin embedded (FFPE) tissue samples. The Visium
CytAssist instrument requires a glass slide with intact tissue sections as input. 

Tissue sections are processed with Visium Spatial Gene Expression assay performed by the University of Minnesota Imaging Center and sequenced by the University of Minnesota Genomics Center.



[STEPS]
SECTION: Deparaffinization, H&amp;E Staining, Imaging &amp; Decrosslinking
1.   

SECTION: Library Preparation &amp; Sequencing
2.   

 


SECTION: FASTQ Generation
3. BCL data from Illumina sequencer is demultiplexed and converted into FASTQ format using bcl2fastq software version 2.20.0
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>This protocol was adapted from Chiyoda et al., 2007 and Boehm et al., 2015 </p>
<p> </p>
<p> </p>
<p> </p>
<p> </p>

[BEFORE_START]
<p>-filter sterilise the CaCl<sub>2</sub> solution and store aliquots in -20 °C</p>
<p>-store spermidine aliquots at -80 °C</p>
<p>-wash stopping screens with dH<sub>2</sub>O and sterilise by autoclaving</p>
<p>-sterilise the cellophane discs by autoclaving</p>
<p> </p>

[GUIDELINES]
<p>-use desiccated ethanol for steps 10.-14. of microprojectile preparation</p>
<p>-the chloroplast transformation vector used here is pCS Cl0*b. Linearising the vector using NotI increases transformation efficiency (Boehm et al., 2015). The linearised vector is ethanol precipitated and resuspended in TE buffer to obtain the concentration of approximately 1 ug/ul (quantification using NanoDrop is sufficient)</p>

[STEPS]
?. 
?. 
?.
TITLE: SPARC Serotonin 7 Receptor (5-HT7) Immunohistochemistry Protocol in Rat Tissues Labeled with Cholera Toxin B-fragment
AUTHORS: Elisa Gonzalez-Rothi, Yasin Seven, Latoya Allen, Marissa Ciesla, Gordon Mitchell

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the immunofluorescent labeling technique used to identify serotonin 7 receptor expression in CtB-labelled phrenic motor neurons and within a defined region of interest surrounding phrenic motor neurons.</div></div>

[STEPS]
?. Day 1: primary antibodies required:5-HT7 Receptor: Rabbit anti-5-HT7R (Immunostar #244430)Cholera toxin B-fragment: Goat anti-CT-B (Millipore #227040)
?. Place 40um transverse spinal cord sections into 1xPBS in 12 well cell culture plates
?. 3x washes in  1xPBS for 5 minutes each at room temperature
?. Antigen retrieval: place tissues into Heat-Induced Epitope Retrieval (TissuePro, Cat#: HIER01-32R) for 30 minutes at 85 degrees C
?. 3x washes in  1xPBS for 5 minutes each at room temperature
?. Blocking: place tissues in 10% Normal Donkey Serum (NDS) in 1xPBS-Triton (0.1%) for 60 minutes at room temperature
?. Primary Antibody Incubation: Incubate tissues in: 5%NDS in 1xPBS-Triton (0.1%), Rabbit anti-5HT7R (1:2000), and Goat anti-Ct-B (1:2500) overnight at 4 degrees C
?. Day 2: secondary antibodies required:AlexaFluor 488: donkey anti-goat (Invitrogen, Ref#A11055)AlexaFluor 594: donkey anti-rabbit (Invitrogen, Ref#A21207)
?. 3x washes in  1xPBS for 5 minutes each at room temperature
?. Secondary Antibody Incubation: Incubate tissues in: 5%NDS in 1xPBS-Triton (0.1%), donkey anti-goat (1:1000), and donkey anti-rabbit (1:1000) for 2 hours at room temperature
?. 3x washes in  1xPBS for 5 minutes each at room temperature
?. Mount tissues on Superfrost Plus microscope slides
?. Allow slides to dry overnight
?. Coverslip with VectaShield Antifade Hard Set Mounting Medium (Cat#:H-1400)
TITLE: Measurement of XylE (Catechol 2,3-Dioxygenase) enzyme activity by microplate reader
AUTHORS: Ji Gao

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Simple measurement of XylE (Catechol 2,3-Dioxygenase) enzyme activity by microplate reader. Catechol 2,3-Dioxygenase can catalyze catechol (1,2-Dihydroxybenzene) to 2-HMS, which has a high absorbance at 377 nm, so we may use photometric mode of microplate reader to measure the concentration of 2-HMS, product of the enzyme.</div><div style = "text-align :; float : ;"><img style = "" src = "https://s3.amazonaws.com/protocols-files/public/feff27b656ae40ef44442ad86e3606ebd1b18385231b66d3c64b4fe0c5f83229/bsja9exe.png" /></div></div>

[STEPS]
?. [Protocol for the instrument]
Shake the plate for   at  .
Centrifuge: 600 33
?. [Protocol for the instrument]
Measure the absorbance of cell culture at 600 nm as the estimation of cell amounts.
?. [Protocol for the instrument]
Plate out and add  catechol () to every well, then plate in immediately.
2.5 µl
The working concentration of substrate is    here. Other working concentration could also work.
?. [Protocol for the instrument]
Shake the plate for   at  .
Centrifuge: 600 33
?. [Protocol for the instrument]
Measure the absorbance of cell culture at 377 nm, continuously (like  per reading) or after a certain period of time (like  ).
?. [Manual steps]
Add    cell culture per well.
100 µl
It is recommanded to use replicates and controls to avoid mistakes or deviation.
?. [Protocol for the instrument]
Measure the absorbance of cell culture at 377 nm as the baseline of A377 before the reaction.
?. [Manual steps]
Normalize the A337 value by optical density at 600 nm.Make a Time-A377 plot like this:Or simply substract the absorbance before the reaction from the value after a specifc period of time:
?. [Manual steps]
Turn on the microplate reader and computer. Run the software to set the protocol and plate layout.
?. [Manual steps]
Export the data from the software.
Properly dispose of the contaminated cell culture and microplates!
TITLE: Mikro SARS-CoV-2 Multiplex Protocol
AUTHORS: Toby Overmaat

[DESCRIPTION]
<div class = "text-blocks"></div>

[STEPS]
?. [Sample Collection]
Remove the lid of sample collector. Direct the sample provider to expel saliva into the collector until 0.5 mL has been collected. Replace lid.
Teeth brushing, mouthwash, drinks, food, and nasal sprays should be avoided for half an hour before sample collection.
?. [Heat Pre-Treatment]
Load sample for RNA extraction.
?. [RNA Extraction]
Immediately proceed with RNA extraction. Do not store sample.
?. [RNA Extraction]
Prepare  of
500 µl
?. [RNA Extraction]
Add  of heat-treated sample to buffer.Mix for
100 µl
?. [RNA Extraction]
Incubate at room temperature for
?. [Heat Pre-Treatment]
Apply heat-treatment to sample  ABCD1StepActionSpecificationTime21Heat95°C2 min32CoolRoom temperature2 min43Centrifuge500 x g2 min5
ABCD1StepActionSpecificationTime21Heat95°C2 min32CoolRoom temperature2 min43Centrifuge500 x g2 min5
?. [Heat Pre-Treatment]
Collect cellular debris.Add  ofMix for
100 µl
?. [RT-qPCR]
Prepare  multiplex primer-probe-water mix in advance, containing the following:  ABCD1ComponentSpecConcentrationVolume (1 reaction)22019-nCoV_N1-FUS CDC200nM0.6 µL32019-nCoV_N1-RUS CDC400nM1.2 µL42019-nCoV_N1-PUS CDC200nM0.6 µL52019-nCoV_N2-FUS CDC200nM0.6 µL62019-nCoV_N2-RUS CDC400nM1.2 µL72019-nCoV_N2-P*Custom probe (JUN-QSY)200nM0.6 µL8RP-FUS CDC200nM0.6 µL9RP-RUS CDC400nM1.2 µL10RP-P*Custom probe (VIC-MGB)200nM0.6 µL11Nuclease-free water0.8 µL
8 µl
ABCD1ComponentSpecConcentrationVolume (1 reaction)22019-nCoV_N1-FUS CDC200nM0.6 µL32019-nCoV_N1-RUS CDC400nM1.2 µL42019-nCoV_N1-PUS CDC200nM0.6 µL52019-nCoV_N2-FUS CDC200nM0.6 µL62019-nCoV_N2-RUS CDC400nM1.2 µL72019-nCoV_N2-P*Custom probe (JUN-QSY)200nM0.6 µL8RP-FUS CDC200nM0.6 µL9RP-RUS CDC400nM1.2 µL10RP-P*Custom probe (VIC-MGB)200nM0.6 µL11Nuclease-free water0.8 µL
?. [RNA Extraction]
Centrifuge at 500 x g for Then remove buffer.
?. [RNA Extraction]
Proceed with RNA elution.
?. [RNA Extraction]
Add  of
60 µl
?. [RNA Extraction]
Centrifuge at 1000 x g for
?. [RT-qPCR]
Prepare  of master mix in advance, usingwith the following quantities:  AB1ComponentVolume (1 reaction)2UltraPlex 1-Step ToughMix15 µL3Primer-probe-water mix8 µL4Nuclease-free water117 µL
140 µl
AB1ComponentVolume (1 reaction)2UltraPlex 1-Step ToughMix15 µL3Primer-probe-water mix8 µL4Nuclease-free water117 µL
?. [RT-qPCR]
Add  of previously purified RNA sample to  of master mix. Load onto qPCR device.
60 µl
140 µl
?. [RT-qPCR]
Proceed with thermocycling, under the following conditions:  ABC1StepTemperatureTime2150°C10 min3295°C 1 min4395°C 3 sec5460°C30 sec6Repeat 40 Cycles for Step 3-4
ABC1StepTemperatureTime2150°C10 min3295°C 1 min4395°C 3 sec5460°C30 sec6Repeat 40 Cycles for Step 3-4
TITLE: RDH
AUTHORS: Irfan Uddin, Taeeb Ahmad, Furqan Aziz

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This algorithm implements Reversible Data Hiding (RDH) technique by rearranging the columns (or rows) of the image in a way that enhances the smooth regions of an image. Any difference based technique to embed data can then be used in the transformed image.</div></div>

[STEPS]
TITLE: Isolation of nuclei from paraffin-embedded tissue with subsequent immunostaining
AUTHORS: Dorothe Moellmann

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how individual nuclei are isolated from paraffin tissue and then stained immunhistochemically</div></div>

[STEPS]
?. cut 60µm sections from paraffin material and add to an 1,5ml tube
?. dewaxing by addition of xylene; 99%; 96%: 70% Ethanol each forremove and replace after incubation
0 Room temperature
?. after removing  the last rehydration step add Target Retrieval Solution
400 µl
?. add 0,2mm diameter stainless steel beadsplace the tube in a homogenizer such ashomogenize for   max. speed.check the result, repeat if necessary
There should be no more large pieces of tissue to be seen.
?. The heat induced epitope retrieval (HIER) in the water bath follows.Place the tube in a preheated water bathallow the tube to cool at room temperature for
98 °C
?. remove the buffer by centrifugationdiscard supernatant
Centrifuge: 5000 33
?. add 1x IHC- washing bufferresuspend pellet by vortexingrepeat step 7
?. prepare the antibody diluent compositeDako Real Antibody Diluent0,5% Saponin2% BSA
?. after centifugationdiscard supernatant start equilibrationadd antibody diluent composite resuspend the pelletincubate
400 µl
0 Room temperature
?. Addition of the primary Antibody The concentration must be determined for each antibody. Incubation   by agitation
[over Night]
4 °C
?. centrifugation, discard the supernatantadd IHC Waschpuffer repeat once
Centrifuge: 5000 33
?. preparation of the secondary antibody in the antibody diluent compositein a predetermined concentrationmix wellincubation
0 Room temperature
?. repeat step 7
?. store in Aqua dest   if necessary
4 °C
?. centrifugation discard the supernatantadd Target Retrieval Solution once.
Centrifuge: 5000 33
400 µl
?. We performed  fluorescence immonostaining for 3D reconstruction with laser-scanning microscope(Leica TCS SP8) afterwards.If a dapi staining is necessary, it can be connected at the end.
Dapi staining should be performed immediately before microscopy.
TITLE: Tissue Quality Evaluation for Brain Perfusion/Dissection Specimens
AUTHORS: Allen Institute for Brain Science

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol provides guidance in the assessment of quality of tissues post perfusion and dissection and applies to all such procedures. Perfusion and dissection quality will be categorized on the following scale: perfect, good, fair, and poor.  This SOP also presents written descriptions, and images, of specific category attributes. </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: (ILLUMINA MENU) Protocols for SARS-CoV-2 Library Prep with ARTIC Primers, Bioinformatic Analysis, and Database Submission 
AUTHORS: Technical  Outreach and Assistance for States Team

[DESCRIPTION]
This collection of protocols covers library preparation and sequencing on Illumina platforms as well as bioinformatic analysis and submission of SARS-CoV-2 data. These frequently used protocols have been assembled by the Technical Outreach and Assistance for States Team (TOAST) and the Office of Advanced Molecular Detection (OAMD) at the Centers for Disease Control and Prevention for use by participating State, Tribal, Local, and Territorial labs for sequencing of SARS-CoV-2. Individual protocols were developed by the protocol authors, and individual protocols should be credited accordingly. 

These documents are intended for laboratories designated by TOAST and should not be widely or openly disseminated.

  

For technical assistance, please contact: TOAST@cdc.gov

[STEPS]