eamag/protocols-with-steps huggingface dataset:
TITLE: CAMbank: CPT Field Processing v1
AUTHORS: Eliah G Overbey, Krista A Ryon, jak, chm2042

[DESCRIPTION]
Field processing of CPT vacutainers for the Cornell Aerospace Medicine Biobank (CAMbank).

Instructions for preserving: Plasma, PBMCs, and RBC Pellets.

[STEPS]
SECTION: Perform Venipuncture
1. After venipuncture, invert the tubes 8 to 10 times to fully mix in the sodium heparin anticoagulant.

Store the tube upright at room temperature until centrifugation.

To ensure proper barrier formation, blood samples should be centrifuged within 2 hours of blood collection. Centrifugation more than 2 hours after specimen collection may cause incomplete barrier formation.
SECTION: Centrifuge Settings
2. Note: A swing bucket centrifuge is required. 

Set centrifuge:
acceleration: 9
deceleration: 0
temperature: RT
duration: 30 minutes
speed: 1800xg
SECTION: Centrifuge Settings
3. Place the CPTs in the centrifuge. 
Place a protective cover over the swing buckets in case of tube breakage. 
Start the centrifuge. 
Stand by the centrifuge until the centrifuge reaches max speed. Listen for signs of imbalance or compromised tube integrity. 
SECTION: Aliquot Plasma
4. Carefully remove CPTs from the centrifuge and inspect for separation of red blood vs PMBCs vs plasma layers. 

Transfer CPTs to a sanitized laminar flow hood. 
SECTION: Wash PBMCs
6. Prepare the wash buffer (PBS + 2% FBS)

In a 50mL conical tube, mix:
24.4mL of PBS
600µL of FBS

Create more wash buffer as needed (depending on the number of tubes drawn). 
SECTION: Wash PBMCs
7. Add 5mL PBS + 2% FBS to each CPT tube.

Gently resuspend the peripheral blood mononucleocyte cells (PBMC) layer into the PBS + 2% FBS using a serological pipet.
SECTION: Aliquot Plasma
5. Using a P1000, carefully aliquot plasma (yellow layer above buffy layer) into 2D barcoded tubes at 500µL each. 

Do not pipet close enough to disturb the buffy coat (the cloudy PBMC cell layer).

Return 2D tubes with plasma to the rack and place in the -80C freezer.
SECTION: Wash PBMCs
8. One CPT tube at a time, transfer the resuspended cells into a new 15mL conical tube.
SECTION: Wash PBMCs
9. Add fresh wash buffer to bring the conical tube volume to 15mL. 
SECTION: Wash PBMCs
10. Repeat steps  8-9 for all CPTs.
SECTION: Wash PBMCs
11. Pellet the PBMCs in the centrifuge. 

Set centrifuge:
acceleration: 9
deceleration: 9
temperature: RT
duration: 15 minutes
speed: 300xg


SECTION: Wash PBMCs
12. Return the 15mL conical tubes to the laminar flow hood. 
Gently aspirate the media away from the cell pellet. 
SECTION: Viably Freeze Cells
13. Prepare freezing media: 10% DMSO, 90% FBS. 
One CPT will require 6mL of freezing media.

SECTION: Viably Freeze Cells
14. Resuspend the cells of each 15mL conical tube in 6mL of freezing media. 
SECTION: Viably Freeze Cells
15. Transfer 1mL of PBMCs into each cryovial. 
SECTION: Viably Freeze Cells
16. Place the cryovials into Mr. Frosty containers.
SECTION: Viably Freeze Cells
17. Store the Mr. Frosty's at -80C overnight, then ship back to WCM for liquid nitrogen storage. 
18. Recap and freeze the CPT tubes to preserve DNA in the red blood cell pellet
TITLE: Bulk RNA sequencing (mRNA seq)
AUTHORS: Klaus H. Kaestner Lab, Suzanne Shapira

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Bulk RNA sequencing (RNA-seq) is a quantitative method used to interrogate the transcriptome of a biological sample at a given point in time. This protocol describes a method for generating bulk RNA-seq libraries from human islet material. This method also allows for isolation of genomic DNA, which can be used for additional assays such as whole genome bisulphite sequencing.</span></div><br/><br/><br/></div>

[STEPS]
?. [Steps in pre-processing]
1. 250,000 to 500,000 cells for use in Qiagen DNA/RNA AllPrep kit: for >500,000 cells, use DNA/RNA Universal AllPrep kit; for a. Centrifuge cells, then carefully remove all supernatant by aspiration.b. Loosen pellet by flicking and add RLT Plus buffer (prepared with   Beta-mercaptoethanol)6cells, 5 x 106– 1 x 107cells, 2. Pipet the lysate directly into a QIAshredder spin column and centrifuge for 2 min at maximum speed.3. Continue with AllPrep protocol, or snap freeze and store at   for future use.
350 µl
600 µl
-80 °C
?. [Links to kits used in post-processing]
1. All recent samples (using 750pg input) were processed using Takara Pico kit with Total RNA-Seq Kit v22. All samples prior to 2020 (used 100ng input) were processed using Illumina TruSeq Stranded Total RNA Library prep Gold
Note:The cells go through the All Prep kit to get RNA and then utilized for bulk RNA-seq processing. From this preparation, we also acquire DNA which is used for Whole Genome Bisulphide Sequencing (WGBS).
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>This protocol was standarized in our lab based on the publication of Ahn T et al (2001): <strong> Polyacrylamide Gel Electrophoresis without a stacking Gel: Use of Amino Acids as Electrolytes. DOI:<a href="https://dx.doi.org/10.1006/abio.2001.5038" target="_blank">10.1006/abio.2001.5038</a><br /></strong></p>
<p>These gels run similar to a gradient gel: In a 6% gel you will be able to separate proteins ranging from 270 kDa to 25 kD an dhave them in the same gel.</p>
<p>The adaptation to Stain-Free system was done based on the publication by Ladner CL et al (2004) :<strong> Visible fluorescent detection of proteins in polyacrylamide gels without staining. DOI:<a href="https://dx.doi.org/10.1016/j.ab.2003.10.047" target="_blank">10.1016/j.ab.2003.10.047</a></strong></p>
<p>We have applied this protocol in the following publications: <em>Zeitler AF, Gerrer KH, Haas R, Jiménez-Soto LF. Optimized semi-quantitative blot analysis in infection assays using the Stain-Free technology. J Microbiol Methods. 2016 Jul;126:38-41. doi: 10.1016/j.mimet.2016.04.016. PubMed PMID: 27150675.Jiménez-Soto LF, Haas R. The CagA toxin of Helicobacter pylori: abundant production but relatively low amount translocated. Sci Rep. 2016 Mar 17;6:23227. doi: 10.1038/srep23227. PubMed PMID: 26983895; PubMed Central PMCID: PMC4794710.Jiménez-Soto LF, Clausen S, Sprenger A, Ertl C, Haas R. Dynamics of the Cag-type IV secretion system of Helicobacter pylori as studied by bacterial co-infections. Cell Microbiol. 2013 Nov;15(11):1924-37. doi: 10.1111/cmi.12166. PubMed PMID: 23844976.</em></p>

[BEFORE_START]
<p>Pouring these gels is not much different than with other acrylamide gels:</p>
<ul>
<li>Read the safety information of ALL solutions before strating and take all measures necessary to protect yourself and those working around you.</li>
<li>Clean your glass and combs throughly with alcohol to remove any dirt that may cause bubbles in your gel. If bubbles appear while pouring, tap gently the glass. They will tend to float (if you have luck!)</li>
<li>If you add Trichlorethanol for the Stain-Free, make sure you solubilize the trichlorethanol properly BEFORE adding the TEMED solution (You will see how little white bubbles will disappear after throughly mixing the solution)</li>
<li>We use 20-well combs, but in order to have well define bands, we use 1 mm thickness plates for this combs. 0.75 mm do not work well.</li>
</ul>

[STEPS]
?. 
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TITLE: Isolation of Nuclei from Adult Mouse Brain Tissue Protocol
AUTHORS: Allen Institute for Brain Science

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for isolation of nuclei from microdissected mouse brain tissue sections for FPCR and/or RNA-seq analysis. </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: Photomap of the polythenic chromosomes of Drosophila and in situ mapping 
AUTHORS: Pierre Teodosio

[STEPS]
?. Making the photomap of polythenic chromosomes
?. 1 The slides of politenic chromosomes of D. malerkotliana of the population of Parque Dois Irmãos (Recife) were prepared by crushing the dissected salivary glands of zero-hour pre pupae, fixed with a solution of acetic acid, water and lactic acid, in a 3:2:1 ratio. The material was stained with aceto-lactic orcein (1g of orcein-MERCK, 45ml of acetic acid, 25ml of lactic acid 85%, and 30ml of distilled water), according to ASHBURNER (1967). The best slides were photographed under Leica Microscope in increase of 100 X 1.25 with Kodak TMAX Iso 100 film.
?. In situ hibridization
?. For in situ hybridization, the ENGELS et al. (1986) technique was used. After dissection of the larvae, the salivary glands were fixed in 45% acetic acid and crushed with cover slip in a lactic-acetic solution (lactic acid, water and acetic acid, 1:2:3). The slides were stored at 4°C for at least 18 hours. The slides were removed and the slides were submitted to several washes in 2X SSC and ethanol. The slides were air dried and stored at 4°C. After these steps, the best slides were selected and only those with intact chromosomes, spread properly, were stored for further hybridization.
?. For the marking and mapping of the Hsp83 locus in D. malerkoltiana, the clone lambda 6 of the Hsp83 gene of D. melanogaster (HOLMGREN et al., 1981), inserted in the plasmid pBR322, was used as probe. The plasmid was amplified by the transformation of the Xm1 strain of the bacterium Escherichia coli, cultivated in LB medium with ampicillin (100°g/ml) (SAMBROOK et al., 1989) and was extracted by non-phenolic method (PHILIPPSEN et al., 1991).
?. To prepare the probe, 1g of the plasmid containing the gene fragment, marked with biotin by nick-translation with gibco's Bionick kit, was used. The probe marking was tested in "dot blot" with revelation with Estreptavidin – Alkaline Phosphatase (SA-AP), Nitroblue tetrazolium chloride (NBT), 5-bromine-4-chloro-3-indolylphosphate p-Toluidine salt (BCIP). 500ng of probe per blade was used under high astringency conditions (temperature of 36º C and 50% of formamide) for 48 hours. The revelation was performed with SA-AP, NBT and BCIP, followed by the lacto-acetic orcein counter-dye at 0.2%. After drying the blades, the material was permanently assembled with Entellan.
TITLE:   Direct ELISA for investigating the binding of Protein-G  to immunoglobulins.
AUTHORS: Angel  Justiz-Vaillant, Monica F. Smikle

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Streptococcal protein G is an immunoglobulin-binding protein that interacts with the Fc region of many mammalian immunoglobulins [1].</div><div class = "text-block">References</div><div class = "text-block">1.Vaillant AJ, McFarlane-Andersonv N, Wisdom B, Mohammed W, Vuma S, et al. (2013) Immunoglobulin-binding Bacterial Proteins (IBP) Conjugates and their Reactivity with Immunoglobulin in Enzyme-Linked Immunosorbent Assays (ELISA). J Anal Bioanal Tech 4: 175. doi:10.4172/2155-9872.1000175 </div></div>

[STEPS]
?. This ELISA is used to study the interaction of Streptococcal protein-G (SpG) with diverse immunoglobulins.
?. The 96 well microtitre plate is coated overnight at 4°C with 1 µg/µl per well of purified immunoglobulins or 50 µl of any animal sera in carbonate-bicarbonate buffer pH 9.6.
?. Then plate is treated with bovine serum albumin solution and washed 4X with PBS-Tween.
?. Then 50 µl of peroxidase-labeled-protein-G conjugate diluted 1:5000 in PBS-non-fat milk is added to each well and  incubated for 1.30h at RT. After that the plate is washed 4X with PBS-Tween.
?. Pipette 50 μl of 3,3',5,5' - tetramethylbenzidine (TMB; Sigma-Aldrich) to each well.
?. The reaction is stopped with 50 µl of 3M H2SO4 solution.
?. The plate is visually assessed for the development of colour and read in a microplate reader at 450 nm.
?. A cut-off point should be calculated as the mean of the optical density of negative controls x 2 SD.
TITLE: COOMASSIE COLLOIDAL STAIN - CHEM 584
AUTHORS: Ken Christensen

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Staining polyacrylamide gels using a colloidal Coomassie Blue stain. Adapted from a JoVE article.</div></div>

[STEPS]
?. Wash gel with ~50 mL ddH2O 3x for ~ for each wash on a shaker NOTE: insufficient washing causes poor sensitivity because the remaining SDS on the gels disturbs the bounding of the dye to the protein
?. Shake the colloidal Coomassie solution before use to disperse particles evenly.
?. Incubate the gels with the Coomassie solution by agitation on a shaker up to . This staining generates marginal background so you can observe the staining progress.Note: after 10 minutes you should see some protein bands appearing, within 2 hours of incubation about 80% maximum staining is completed. For nearly maximum sensitivity, an overnight incubation is recommended. In some cases, when the amount of protein to be stained is large, the solution turns a bright blue color. If this happens, you should refresh the staining solution as necessary.
?. After staining, remove the Coomassie solution and rinse the gels twice with ddH2O.
Note: you can reuse the staining solution as long as particles still remain, otherwise discard it appropriately.
?. Remove any dye particles from the staining dish with a lint-free paper towel and destain for up to  in ddH2O or a Coomassie destain solution (10% (v/v) 96% ethanol, 2% (v/v) orthophosphoric acid 85% in ddH2O.)
?. Finally rinse the gels twice with ddH2O: the gels will reach their original thickness (the alcohol-acid media makes the gels shrink). Neutralization in water also enhances the Coomassie stain’s color intensity.
?. You can record your gel using the gel documentation system or scan it on the Licor using the 680/700 nm channel.
TITLE: In vivo Electrophysiology Protocol
AUTHORS: Sasha Burwell

[DESCRIPTION]
This protocol details the procedure used to collect extracellular single unit dopamine recordings for this paper.

[STEPS]
SECTION: In vivo Electrophysiology Protocol
1. Headfix mouse on a treadmill.
SECTION: In vivo Electrophysiology Protocol
2. Attach prepared internal cannula (see DART Infusion protocol for details on how to set this up) to the implanted guide cannula.
SECTION: In vivo Electrophysiology Protocol
3. Attach implanted electrode bundle to the Open Ephys Acquisition board using an Intan RHD 16-channel headstage (C3335) and an Intan ultra-thin SPI interface cable (C3211).
SECTION: In vivo Electrophysiology Protocol
4. Open the Open Ephys GUI.
SECTION: In vivo Electrophysiology Protocol
4.1. Open Ephys GUI must have 

(1) an Acquisition Board node followed immediately by 
(2) a Recording Node, saving the raw data in a binary format.

 

SECTION: In vivo Electrophysiology Protocol
4.2. Optional: downstream in the processors graph, you can include a bandpass filter, common average reference node, LFP viewer, spike sorter, and spike viewer to view channels with spikes online during the recording.

 

Begin recording (press “Play” then “Record”).
After 15 minutes of baseline recording, begin the infusion (1.5 µL at 0.1 µL/min, taking 15 minutes).
After the infusion is complete, continue recording for 90 min, then stop the recording.
Advance the electrodes by 26 1622.
Return the mouse to its home cage to recover, and wait 2 weeks before recording again.
TITLE: Immunocytochemical analysis
AUTHORS: Felix Kraus

[DESCRIPTION]
Protocol for the immunocytochemical analysis of cell culture cells. 

[STEPS]
SECTION: Seeding of HeLa
1. Wash HeLa cells with 1x PBS
SECTION: Seeding of HeLa
2. Add Trypsin to cells for 5 min and incubate at 37°C to dissociate cells from plastic well
SECTION: Seeding of HeLa
3. Resuspend cells in 1 mL DMEM media
SECTION: Seeding of HeLa
4. Count cells
SECTION: Seeding of HeLa
5. Seed appropriate number of cells into 6-/12-/24-well glass bottom dish
SECTION: Seeding of HeLa
6. Top up glass bottom dish with either 3-/1.5/1 mL DMEM and place cells back into incubator
SECTION: Seeding of HeLa
7. The next day exchange DMEM with DMEM + 2µg/ml doxycycline for 18h to induce Parkin expression.
SECTION: Seeding of HeLa
8. Induce mitophagy using Antimycin A / Oligomycin A for the desired time.
SECTION: Staining
9. Aspirate DMEM and fix cells in 1 ml pre-warmed 4% PFA for 30 min.
SECTION: Staining
10. Aspirate PFA solution and wash wells 3x with PBST (1x PBS, 0.02% Tween 20)
SECTION: Staining
11. Permeabilize the cells by adding 0.2% Triton X-100 in PBS.
SECTION: Staining
12. Remove the detergent solution by aspiration.  Wash wells 3x with PBST (1x PBS, 0.02% Tween 20). Drain well.
SECTION: Staining
13. Block cells for 10 min with 3% BSA – 1x PBS.
SECTION: Staining
14. Remove BSA solution by aspiration.  Wash wells 3x with PBST (1x PBS, 0.02% Tween 20). Drain well.
SECTION: Staining
15. Incubate with primary antibodies in 3% BSA - 1x PBS for 3h at RT or overnight at 4°C with gentle shaking.
SECTION: Staining
16. Wash wells 3x with PBST (1x PBS, 0.02% Tween 20). Drain well.
SECTION: Staining
17. Incubate with secondary antibodies in 3% BSA - 1x PBS for 45 min – 1h.
SECTION: Staining
18. Wash wells 3x with PBST (1x PBS, 0.02% Tween 20). Drain well.
SECTION: Staining
19. If required, add Hoechst33342 or DAPI 1:2000 to wells for 5 min with gentle shaking.
SECTION: Staining
20. Wash wells 3x with PBST (1x PBS, 0.02% Tween 20). Drain well.
SECTION: Staining
21. Exchange PBST with 1x PBS and keep cells at 4°C until imaging. Image within the next few days.
TITLE: The efficacy of albumin with diuretics in the mechanically ventilated patients                                          with hypoalbuminemia : systematic review and meta-analysis
AUTHORS: Yuki Itagaki, Naofumi Yoshida, Kohei Yamada, Masahiro Banno, Ryo Momosaki, Mineji Hayakawa, Yuki Kataoka

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Hypoproteinemia is significantly correlated with fluid overload, development of ARDS and mortality[1, 2]. According to a large European observational study, a positive fluid balance is one of the factors for death (OR 1.1, 95%CI 1.0-1.1, p-value 0.001)[3]. Thus, to achieve the improvement of systemic status and increase ventilator free days, reducing fluid volume is essential[4]. </span><span style = "font-weight:bold;"></span></div><div class = "text-block"><span style = "font-weight:bold;">So far, the effect of albumin with the diuresis in hypoalbuminemia has been investigated in several randomized controlled trials (RCTs)[5-9]. Furthermore, a systematic review and meta-analysis suggested that the effect of albumin was limited only to transient improvements of urine volume[10]. However, this analysis did not investigate the mechanically ventilated critically ill patients. Although a systematic review in 2014 was conducted to investigate that colloids could improve diuresis in patients mechanically ventilated, this review did not include recent RCTs[11]. Thus, we still don't have a clear answer for the improvement of the haemodynamic stability, mortality or ventilator free days. </span><span style = "font-weight:bold;"></span></div><div class = "text-block"><span style = "font-weight:bold;">Our aim is to clarify the benefit of albumin administration for the mechanically ventilated patients in combination with the diuresis in this systematic review and meta-analysis.</span></div></div>

[STEPS]
?. 
?.
TITLE: Linker Design and Optimization
AUTHORS: boc.protac  

[DESCRIPTION]
The linker is responsible for linking two key domains of PROTAC: the domain that specifically binds to the target protein that needs to be degraded, and the domain that binds to the E3 ubiquitin ligase. To date, several types of connectors have been reported and used in the formation of PROTAC ternary complexes, such as PEG liner, alkyl liner and "click chemical" liner. It plays an important role in the effective ubiquitination and final degradation of target proteins.

As a leading service provider in drug discovery and research, BOC Sciences is fully qualified and committed to providing one-stop PROTAC®development, which has become a promising strategy in the field of small molecular drug discovery. With a comprehensive and advanced platform, we provide Linker Design and Optimization Services to customers around the world to meet new drug discovery goals.

[STEPS]
TITLE: Clarification of cheese whey for microalgae cultivation
AUTHORS: Bruna Emerenciano, Maria Izabel P Batista, Adriano H N Rangel

[STEPS]
?. Collect the cheese whey from dairy industry as a by-product of cheese production and put it in clean and dry bottles.
?. If the cheese whey is not be clarified after collect, it should be frozen in a freezer at -20 °C.
?. For clarification, defrost the cheese whey in a refrigerator at 5 ° C.
?. Then sterilize the cheese whey by autoclaving at 121 °C for 15 minutes.
?. Filter the cheese whey using 20 μm sieve.
?. Then centrifuge the filtered material using a centrifuge at 1500 rpm for 15 minutes for the removal of the precipitated material.
?. Place the supernatant in a container and autoclave at 1500 rpm for 15 minutes again before use.
?. Add the clarified cheese whey in the culture medium of the microalga at room temperature.
TITLE: CRISPRa tiling screens
AUTHORS: Andrea R Daniel

[DESCRIPTION]
This protocols describes methods for characterizing the activity of dSaCas9 as a activator using promoter tiling guide RNA screens in Jurkat cells. 

[STEPS]
SECTION: Construction of CRISPRa Jurkat lines
1. Polyclonal dSaCas9VP64 and VP64dSaCas9VP64 Jurkat cell lines were generated by transducing Jurkat cells with lentivirus encoding for either dSaCas9VP64–2A–PuroR or VP64dSaCas9VP64–2A–PuroR. 
SECTION: Construction of CRISPRa Jurkat lines
2. Cells were selected for 5 days using 0.5 µg ml−1 of puromycin.
SECTION: IL2RA CRISPRa tiling screen
3. After selection, 1 × 106 dSaCas9VP64 and VP64dSaCas9VP64 Jurkat cells were plated and transduced in triplicate with the IL2RA gRNA library lentivirus at a low multiplicity of infection (MOI).
SECTION: IL2RA CRISPRa tiling screen
4. Cells were expanded for 10 days, selected for Thy1.1 using a CD90.1 Positive Selection Kit (StemCell Technologies), and stained for Thy1.1 and IL2RA.
SECTION: IL2RA CRISPRa tiling screen
5. Transduced cells in the lower and upper 10% tails of IL2RA expression were sorted for subsequent gRNA library construction and sequencing.
SECTION: IL2RA CRISPRa tiling screen
6. All replicates were maintained and sorted at a minimum of 500× coverage.
SECTION: gRNA sequencing
7. Genomic DNA was isolated using Qiagen’s DNeasy Blood and Tissue Kit. Genomic DNA was split across 100 μl PCR reactions (25 cycles at 98 °C for 10 s, 60 °C for 30 s, and 72 °C for 20 s) with Q5 2× Master Mix and up to 1 μg of genomic DNA per reaction.

SECTION: gRNA sequencing
8. PCRs were pooled together for each sample and purified using double-sided (SPRI)bead selection at 0.6× and 1.8×. 

SECTION: gRNA sequencing
9. Libraries were run on a High Sensitivity D1000 tape (Agilent) to confirm amplicon size and quantified using Qubit’s dsDNA High Sensitivity assay.

SECTION: gRNA sequencing
10. Libraries were diluted to 2 nM, pooled together at equal volumes, and sequenced using Illumina’s MiSeq Reagent Kit v2 (50 cycles).
SECTION: gRNA sequencing
11. Primers are available in Supplementary Table 5 of McCutcheon et al. Nature Genetics, 2023. https://doi.org/10.1038/s41588-023-01554-0
SECTION: Processing gRNA sequencing and gRNA analysis
12. FASTQ files were aligned to custom indexes for each gRNA library (generated from the bowtie2-build function) using Bowtie 2 (ref. 67). 
SECTION: Processing gRNA sequencing and gRNA analysis
13. Counts for each gRNA were extracted and used for further analysis in R.
SECTION: Processing gRNA sequencing and gRNA analysis
14. Individual gRNA enrichment was determined using the DESeq2 (ref. 68) package to compare gRNA abundance between groups for each screen.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
For use in <a href="https://www.protocols.io/view/CviRI-Purification-From-XZ-6E-Virus-Infected-NC64A-er4bd8w" target="_blank">CviRI Purification From XZ-6E Virus Infected NC64A Chlorella</a>.

[STEPS]
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