eamag/protocols-with-steps huggingface dataset:
TITLE: DRAGEN COVID Lineage App SARS-CoV-2 Strain Characterization on the Illumina BaseSpace Platform
AUTHORS: Technical  Outreach and Assistance for States Team

[DESCRIPTION]
This protocol provides instructions on how to run the DRAGON COVID Lineage app on the Illumina BaseSpace Sequence Hub. The DRAGON COVID Lineage app reads in fastq sequence files and produces Lineage, Clade, and Kmer Detection reports for each run. The information provided in these reports include Pangolin lineage classification, variant calls, and the fraction of human and SARS-CoV-2 kmers detected. The DRAGON COVID Lineage app also assembles a consensus sequence fasta file for each sample. This document applies to all whole-genome sequencing runs on the Illumina platform and downstream bioinformatics for public health laboratories.

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

[STEPS]
SECTION: Create Basespace Project
1. Login to the Illumina BaseSpace Platform and create a new BaseSpace project
 

 

SECTION: Add Fastq files to BaseSpace Project
2. Add Fastq files to the new project directory. This can be done by either uploading fastq files from a local directory or by importing sequences using their Sequence Read Archive (SRA) accession numbers from NCBI using the ‘SRA Import’ app.   

 




SECTION: Run DRAGEN COVID Lineage App
3. 
Run the DRAGEN COVID Lineage App

 

 

 

4. Accessing the DRAGEN COVID Lineage app summary report

 

 

5. Downloading consensus sequences generated by the DRAGEN COVID Lineage app

 


 


 

 

SECTION: Alternative Lineage Assignment
6. The SARS-CoV-2 consensus sequence assembly generated by the CDRAGEN COVID Lineage app can also be uploaded to other lineage assignment software.
SECTION: Alternative Lineage Assignment
6.1. Upload the consensus sequence for each sample to the Pangolin COVID-19 Lineage Assigner at:

https://pangolin.cog-uk.io/


Click the 'Start analysis' button:

  

The Pangolin COVID-19 Lineage Assigner returns the lineage classification and assignment probability:

  

SECTION: Alternative Lineage Assignment
6.2. Or upload the consensus sequence for each sample to the Nextclade clade assignment web portal at: 

https://clades.nextstrain.org/

  

The Nextclade server provides clade classification as well as QC metrics and a list of amino acid substitutions. A summary output file can be downloaded with the 'Export to CSV' button.

  

SECTION: Run DRAGON COVID Lineage
3. Run the DRAGEN COVID Lineage App

 

 

 

SECTION: Access Summary Report
4. Accessing the DRAGEN COVID Lineage app summary report

 

 

SECTION: Downloading SARS-CoV-2 Consensus Sequences
5. Downloading consensus sequences generated by the DRAGEN COVID Lineage app
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>A very detailed four-day protocol for DNA extraction for yeast PacBio sequencing modified from Promega's protocol for yeast <a href="https://www.promega.co.uk/~/media/files/resources/protocols/technical%20manuals/0/wizard%20genomic%20dna%20purification%20kit%20protocol.pdf" target="_blank" rel="noopener noreferrer">p13-14</a>.</p>

[BEFORE_START]
<p>Future improvements: This is a mini-prep kit for DNA extractions from 1.5ml of yeast culture. Consider using a midi-prep kit for higher yield without needing 8 reactions per strain.</p>
<h2> </h2>

[GUIDELINES]
<h2>Promega's Wizard® Genomic DNA Purification Kit</h2>
<p><a href="https://www.promega.com/products/dna-purification-quantitation/genomic-dna-purification/wizard-genomic-dna-purification-kit/?catNum=A1120" target="_blank" rel="noopener noreferrer">Wizard® Genomic DNA Purification Kit</a> (Catalog number: A1125) Other reagents:</p>
<ul>
<li>0.5M EDTA (Life Technologies, Catalogue number: AM9260G). Dilute 1:10 for 50mM EDTA.</li>
<li>lyticase (Sigma, Catalogue number: L2524-50KU). For a 25 units/ul stock, suspend in 2ml UltraPure H2O and dispense into 2x 1ml aliquots, store at -20C</li>
</ul>
<p>Note: This is a very detailed protocol because it is actually just our standard lab protocol x 8 with a couple of extra steps to increase purity for PacBio.</p>
<p> </p>
<p>Modified from Promega's protocol for yeast <a href="https://www.promega.co.uk/~/media/files/resources/protocols/technical%20manuals/0/wizard%20genomic%20dna%20purification%20kit%20protocol.pdf" target="_blank" rel="noopener noreferrer">p13-14</a>:</p>
<p> </p>
<p>Some of the changes to our standard protocol might have been unnecessary e.g. We spun samples at 16,162g and for longer than suggested: for 10 minutes after the addition of Nuclei Lysis Solution (Promega) and Protein Precipitation Solution (Promega); for 10 minutes after DNA precipitation with isopropanol; and for 5 minutes after washing the DNA pellet with 70% ethanol. I am not sure the extra time on spins is really necessary if you know your centrifuge is good: we had just had problems with a lab centrifuge, which lowered DNA quality and yield.</p>

[STEPS]
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TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>As one of the most recognizable characteristics in birds, plumage colour has a high impact on understanding the evolution and mechanisms of colouration. Feather and skin are ideal tissues to explore the genomics and complexity of colour patterns in vertebrates. Two species of the genus Chrysolophus, golden pheasant (Chrysolophus pictus) and Lady Amherst’s pheasant (Chrysolophus amherstiae), exhibit brilliant colours in their plumage, but with extreme phenotypic differences, making these two species great models to investigate plumage colouration mechanisms in birds. Here we provide details of the protocols used for plumage pigments identification by High-performance liquid chromatography. The fat-soluble pigments (carotenoids) and oxidation products of melanins (TTCA and PTCA) can be qualitatively and quantificationally analyzed by HPLC with the corresponding standards, respectively.</p>
<p> </p>

[GUIDELINES]
<p>Carotenoids should be extracted from feathers by a thermochemical treatment. The melanins from feathers should be treated under alkaline H2O2 conditions to obtain oxidation products.</p>

[STEPS]
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TITLE: Preparing 10 L of M9 buffer for nematode culture
AUTHORS: Gurdon Institute media kitchen

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Prepare 10 litres of M9 solution for collecting and washing </span><span style = "font-style:italic;">C. elegans</span><span style = "font-style:italic;">.</span></div></div>

[STEPS]
?. AB11Dissolve ingredients in 8L double distilled H2O22Adjust volume to10L using double distilled H2O33Measure or use pump to dispense aliquots accurately.&nbsp;44Label, date and autoclave.&nbsp;55After autoclaving, add 100ul 1M MgSO4 per 100ml. (ie. 100ul to 100ml and 200ul to 200ml bottles).6 7NB1M&nbsp; MgSO4 at 1ul/1ml in
  the M9 buffer gives a final concentration of 1mM
AB11Dissolve ingredients in 8L double distilled H2O22Adjust volume to10L using double distilled H2O33Measure or use pump to dispense aliquots accurately.&nbsp;44Label, date and autoclave.&nbsp;55After autoclaving, add 100ul 1M MgSO4 per 100ml. (ie. 100ul to 100ml and 200ul to 200ml bottles).6 7NB1M&nbsp; MgSO4 at 1ul/1ml in
  the M9 buffer gives a final concentration of 1mM
?. The autoclave is SYCHEM VS Series. The media cycle is 15 minutes at 121 degrees centigrade. It is then cooled down in the machine for 3 hours.
?. After autoclaving, add 100 μl 1M MgSO4 per 100 ml. (ie. 100 μl to 100 ml and 200 μl to 200 ml bottles). NB: 1M  MgSO4 at 1 μl/1ml in the M9 buffer gives a final concentration of 1 mM
?. ABC1IngredientsQuantity2Na2HPO4 60g3KH2PO4 30g4NaCl 50g5Double
  distilled H2Oup to 10L6   7Add 1M MgSO4 after autoclaving @ 100ul/100ml&nbsp;
ABC1IngredientsQuantity2Na2HPO4 60g3KH2PO4 30g4NaCl 50g5Double
  distilled H2Oup to 10L6   7Add 1M MgSO4 after autoclaving @ 100ul/100ml&nbsp;
TITLE: Collecting Bark and Ambrosia Beetles
AUTHORS: Jiri Hulcr, Andrew J. Johnson, Demian F Gomez

[DESCRIPTION]
This protocol describes the different methods to collect and preserve bark ambrosia beetles. 

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 https://doi.org/10.1007/s13199-020-00686-9.


This new version of the protocol contains this link that takes you to a supplemental video with extra context and tips, as part of the protocols.io Spotlight series, featuring conversations with protocol authors

[STEPS]
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
Odontogenic lesions are divided into odontogenic cysts and tumors. They affect the osseous marrow and cortex of the jaw bones, and are uniquely derived from the tissues of developing teeth. Odontogenic cysts are cavities lined by odontogenic derived epithelium. They are the most common lesions of the jaw, specially radicular cysts (RC) and odontogenic keratocysts (OKC). While, RC shows an indolent behavior and rarely recurs after surgical removal, the KOT is invasive and destructive. On the other hand, odontogenic tumors are classified according to behavior into benign and malignant in addition, according to origin into epithelial and mesenchymal. The most common benign odontogenic tumor is ameloblastoma.

[STEPS]
TITLE: Predicting_MWM_with_ANN
AUTHORS: Akinori Higaki, Masaki Mogi, Jun Iwanami, Li-Juan Min, Hui-Yu Bai, Bao-Shuai Shan, Masayoshi Kukida, Harumi Kan-no, Shuntaro Ikeda, Jitsuo Higaki, Masatsugu Horiuchi

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">>> We would share the raw data and python scripts used in the study 'Predicting the outcome of Morris water maze test in vascular dementia mouse model with deep learning' published for PLoS One.</div><div class = "text-block">>> 'ann_pred_0114.py' is the main code of ANN constructed with Chainer framework. This code can read 'data_set_0114.xlsx' and run the deep learning program. This code also includes the cross validation method and calculation for correlation coefficient.</div><div class = "text-block">>> In 'data_set_0114.xlsx' file, you can see raw MWM data for WT-sham, WT-BCAS and WT-control mice.</div><div class = "text-block">>> "svr_pred_0114.py" is a script file for prediction with support vector regression (used in Supporting Information).</div><div class = "text-block">>> "morris_3day_1204.py" is a script file for predicting the outcome based on 3-day data (used in Supporting Information).</div></div>

[STEPS]
?. [Raw_Data]
TITLE: Protein Expression Using BL21(DE3), Large Scale (C2527)
AUTHORS: New  England   Biolabs

[DESCRIPTION]
This is the protocol for a large-scale Protein Expression Using BL21(DE3) Competent E. coli cells (C2527).

[BEFORE_START]
Determine the optimal time/temperature for the protein expression in a small scale trial.

[GUIDELINES]
BL21(DE3) Genotype:
fhuA2 [lon] ompT gal (λ DE3) [dcm] ∆hsdS
λ DE3 = λ sBamHIo ∆EcoRI-B int::(lacI::PlacUV5::T7 gene1) i21 ∆nin5

NOTES:
1. Caution: This product contains DMSO, a hazardous material. Review the MSDS before handling.

2. Storage and Handling: Competent cells should be stored at -80°C. Storage at -20°C will result in a significant decrease in transformation efficiency. Cells lose efficiency whenever they are warmed above -80°C, even if they do not thaw.

[STEPS]
1. Transform expression plasmid into BL21(DE3).
2. Plate on antibiotic selection plates.
3. Incubate   at 37 °C. 
4. Inoculate 1 L with a freshly grown colony or with 10 mL.
5. Incubate at 37 °C until OD600 reaches 0.4–0.8.
6. Induce with 4 µL or 40 µL of 100 Milimolar (mM) (final concentration of 40 Micromolar (µM) or 400 Micromolar (µM)).

7. Express protein using optimal time/temperature determined in a small scale trial (3 to 300 min at 37 °C).
8. Check for expression either by Coomassie stained protein gel, Western Blot or activity assay. Check expression in both the total cell extract (soluble + insoluble) and the soluble fraction only.
TITLE: Glucosylceramidase Beta (GBA) Genotyping
AUTHORS: Huw Morris, Nigel Williams 

[DESCRIPTION]
This protocol details the steps for GBA genotyping. This protocol has been adapted from the PRoBaND Clinical Consortium (incorporating methods described by Neuman et al., 2009 and Stone et al., 2000) and has been used for all publications for PRoBaND / Tracking Parkinson's describing clinical data and outcomes with respect to GBA status 

[BEFORE_START]
Check that you have the correct forward and reverse primers and required materials, supplies and equipment.


[GUIDELINES]
To avoid amplification of the pseudogene, design primer sequences to DNA regions exclusively found within the GBA gene. 

As an internal control, calculate the size of the PCR products resulting from amplification of the GBA pseudogene. 

Refer to Table 2 (Steps) for the PCR conditions for amplification of the GBA gene.

[STEPS]
SECTION: Primer Sequences
1. Use the following primer sequences:

  

SECTION: Amplification of the GBA gene
2. Three different PCR reactions are performed. Refer to Table 2 for a detailed description of the PCR conditions used for each fragment.

SECTION: Amplification of the GBA gene
2.1. In order to avoid amplification of the pseudogene, primer sequences are designed to bind to DNA regions exclusively found within the GBA gene. As an internal control, calculate the size of the PCR products resulting from amplification of the pseudogene for these three fragments. Confirm they are an alternative size to those amplified from GBA. 
SECTION: Amplification of the GBA gene
2.2. Amplify three distinct fragments spanning all exonic and most intronic sequences of GBA. 
SECTION: Amplification of the GBA gene
2.3. PCR conditions  

  

SECTION: PCR
3. Prepare the following reagents for the PCR in a total reaction volume of 15 µL : 
7.5 µL fast start PCR master mix (Roche)
1 µLof 10 µM Forward primer
4.5 µL Deionised water 
1 µL Genomic DNA template (50 ng/µl)
SECTION: PCR
4. Run all PCR products on a 1% agarose gel with ethidium bromide and size check to rule out amplification of the GBA pseudogene (GBAP). 
 

SECTION: PCR
6. Perform cycle sequencing for each exon and the flanking intronic sequences using the Dye Terminator Sequencing Kit (Applied Biosystems) and run on an ABI 3700xl genetic analyzer (Applied Biosystems). 

 
SECTION: PCR
5. If the initial primers failed or showed an incomplete read then and alternative set of primers can be used: 
Table 3. 

  
SECTION: PCR
7. Sequence all amplicons both in the forward and the reverse direction. 
SECTION: PCR
8. Analyse sequence chromatograms using Sequencher software (Genecodes). 

 

SECTION: PCR
9. Analyse all exons and the flanking intronic regions when clean, complete sequence reads are obtained.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>A protocol for routine flash freezing of fruit fly samples prior to use in downstream protocols (e.g. RNA extraction).</p>
<p> </p>
<p> </p>

[BEFORE_START]
<p>Make sure you have the following items:  LN<sub>2</sub>, dewar (~2L), a large rectangular Styrofoam tub, colored timex tape and permanent markers.</p>

[GUIDELINES]
<p>Freezing should be done for a standard age or age range and within a 2 hour standardized window. Many genes are regulated according to the circadian rhythms and we want to minimize expression variation that results from the time of day.</p>

[STEPS]
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TITLE: No Title
AUTHORS: 

[DESCRIPTION]
Clearing zones on lawns of host bacteria potentially contain all lytic phages against the given host that were present in the original water sample. Little is still known about the occurrence and diversity of phages infecting specific hosts, but generally isolation procedures as those described above may reveal multiple phages against specific target bacteria (e.g., Comeau et al. 2006; Holmfeldt et al. 2007; Stenholm et al. 2008). It is therefore necessary to further isolate the phages to obtain specific stocks of single phages.

[GUIDELINES]
If the relative abundance of individual phages in a phage assemblage obtained from a single clearing zone vary significantly (more than 10-100-fold), it will be very difficult to isolate the least abundant types as they would be diluted out in the attempt to obtain single plaques on the plates. Consequently, the method selects for isolation of the dominant fraction of lytic phages against a certain host bacterium at the time of sampling.

[STEPS]
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TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>Please contact Dr. Steven Wilhelm (wilhelm@utk.edu) for additional information regarding this protocol.</p>
<p> </p>
<p>Adapted from the original publication Morel, F. M. M., J. C. Westall, J. G. Reuter &amp; J. P. Chaplick, 1975. Description of the algal growth media ‘Aquil’ and ‘Fraquil’. Water Quality Laboratory, Ralph Parsons Laboratory for Water Resources and Hydrodynamics, Massachusetts Institute of Technology, Technical Report 16, 33 pp.</p>

[STEPS]
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TITLE: Neural differentiation of AAVS1-TRE3G-NGN2 pluripotent stem cells
AUTHORS: Jiuchun Zhang, Harper JW

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is about neural differentiation of AAVS1-TRE3G-NGN2 pluripotent stem cells.</div></div>

[STEPS]
?. [Day 0:]
Treat H9 AAVS1-TRE3G-NGN2 cells with Accutase and plate the dissociated cells in matrigel-coated 6-well plates (2x105 cells/well) in ND1 Medium supplemented with Y27632 ().
?. [Day 1:]
Replace the medium with ND1 Medium.
?. [Day 2:]
Replace the medium with ND2 Medium.
?. [Day 4:]
Exchange 50% of the medium from each well.
?. [Day 6:]
Treat the cells with Accutase and replate the dissociated cells in matrigel-coated 6-well plates (2-4x105 cells/well) in ND2 Medium.
?. [Day 8 and thereafter:]
Exchange 50% of the medium from each well every other day.
* Doxycycline can be withdrawn on Day 10 (or even earlier-not tested yet).* Cells can be split from Day 5 to Day 7 (or even earlier-not tested yet).
TITLE: SARS-CoV-2 Receptor Binding Domain Deoxy Fragment Sequencing 
AUTHORS: Noor Saber Jawad, Nuha Joseph Kandala

[DESCRIPTION]
Since first reporting of SARS-CoV-2 case in China, there were urgent need to report and monitor emerging variants and keep track circulating mutation, in this methodology, we used simple, cost-effective method to monitor the circulating mutations which could be used to predict the SARS-CoV-2 variants based on accumulating mutations in the receptor binding domain. 

[STEPS]
SECTION: RNA Extraction
1. The RNA of SARS-CoV-2 extracted using Automated Extraction System ExiPrep‱ 96 Lite from Bioneer (South Korea) using the Exiprep 96 Viral DNA/RNA kit using the standard recommended procedure by the manufacturer. 
SECTION: cDNA synthesis
2. The extracted RNA used as a template to construct complementary DNA, cDNA synthesis considered using the GoScript‱ Reverse Transcription Mix, Random Primers, Promega (USA) using manufacturer recommended procedure. this will ensure synthesis of the first DNA strand only. 
SECTION: cDNA synthesis
3. Concentration of synthesized DNA measured by Quantus Fluorometer (Promega, USA). 
SECTION: Amplicon Amplifications
4. RBD specific primers, amplification regions, and other details listed below: 

 

SECTION: Amplicon Amplifications
5. Reaction setups include: 
1- GoTag Green Master Mix (Promega, USA)
2- Ladder gel Marker (100-1500), (Promega, USA) 
the following program used for amplification: 

 

SECTION: Amplicon Sequencing
6. Amplicon Sequencing referred to Macrogen, South Korea to be sequenced using the ABI3730XL sequencing Machine.
TITLE: U Michigan - Intra-Epidermal Fiber Density
AUTHORS: Eva L. Feldman

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span><span style = "font-weight:bold;"> </span></div><div class = "text-block">Intra-epidermal nerve fiber density (IENFD) is used as a tool to assess small fiber neuropathy.</div></div>

[STEPS]
?. Reagents: Phosphate buffer (PB, 0.1 M, pH 7.2) SucroseEquipment: Razor blades, embedding molds, 24 well plateSolutions: 2% zamboni’s in phosphate buffer (PB, 0.1 M, pH 7.4)                    30% sucrose in PBSProcedure:Fresh mouse or rat:
1. Remove footpad and fix (4 hours) in 2% zamboni’s fixative for 4-6 hours.
2. Place skin in 30% sucrose in 1x PBS overnight.
3. Embed tissue in OCT using scheme below.
4. Cut 10-14 sections at 30um using scheme below and place into a single well of a 24 well plate. 5. Follow IHC protocol using Ptroteintech rabbit anti-PGP9.5(14730-1-ap), 1:2000 followed by AlexaFluor 488 highly cross absorbed, 1:1000 (Molecular Probes). Apply coverslips with ProLong gold or platinum antifade kit with dapi (Molecular Probes) 6. Block for 1-2 hours in blocking solution.
7, Primary at RT for 1 hour, then in to cold room overnight. 8. Rinse 3x1 hour in PBS
9. Secondaty at RT for 1 hour, then in to cold room overnight. 10. Rinse 3x1 hour in PBS.
11. Coverslip using dapi gold with prolong.Imaging:
1. Three images per sample are collected on an Olympus FluoView 500 confocal microscope using a 20 X air objective at a resolution of 1024 X 1024 pixels. The optical section thicknessis3.3um. 10images per stack are flattened using MetaMorph(version7.70) arithmetic max option. Data are presented as the fibers crossing the epidermal border of PGP9.5 positive fibers per area of epidermis.
TITLE: RNA Synthesis with Modified Nucleotides (E2050)
AUTHORS: New  England   Biolabs

[DESCRIPTION]
This is the synthesis protocol for modified nucleotides using the HiScribe™ T7 Quick High Yield RNA Synthesis Kit (E2050). The kit is capable of synthesizing biotin- or dye-modified RNA.

[BEFORE_START]
We strongly recommend wearing gloves and using nuclease-free tubes and reagents to avoid RNase contamination. Reactions are typically 20 µL but can be scaled up as needed. Reactions should be assembled in nuclease-free microfuge tubes or PCR strip tubes.

The kit is capable of synthesizing biotin- or dye-modified RNA with the following protocol. The recommended molar ratio of modified NTP (Biotin-, Fluorescein-, Digoxigenin-, or Aminoallyl-NTP) to standard NTP is 1:2. The following reaction set-up assumes modified UTP is used. Please note that Dye- or Biotin-NTPs are not supplied with the kit.

[GUIDELINES]
Figure 1 shows the time course of labeled RNA synthesis using 1 µg control template with Biotin-16-UTP and Fluorescein-12-UTP following the above reaction setup.

Modified ribonucleotides reduce transcription efficiency; therefore, lower transcription yields should be expected as compared to transcription using unmodified NTPs. In general, Biotin-NTP and Aminoallyl-NTP have an insignificant effect on yields, while lower yields can be expected for transcription reactions containing Fluorescein-NTP or Cy-NTP. In addition, transcripts containing modified ribonucleotides have reduced electrophoretic mobility due to higher molecular weight.
 

Figure 1. RNA synthesis with modified nucleotides
Reactions were incubated at 37°C in a thermocycler. Transcripts were purified by spin columns and quantified on a NanoDrop Spectrophotometer.

[STEPS]
1. Thaw the necessary kit components.
2. Mix and pulse-spin in microfuge to collect solutions to the bottoms of tubes.
3. Assemble the reaction at Room temperature in the following order (Total reaction volume is 20 µL):  
 

 

4. Mix thoroughly and pulse-spin.
5. Incubate at 37 °C for 120 min. 
 

 

 

6. Optional step: To remove template DNA, add 30 µL and 2 µL, mix and incubate at 37 °C for 15 min.
7. Proceed with purification synthesized RNA (we recommend the Monarch RNA Cleanup Kits, NEB #T2040 or #T2050) or analysis of transcription products by gel electrophoresis.