RNA Isolation from Environmental Samples of a Harmful Algal Bloom for Metatranscriptome Next-Generation Sequencing Article Swipe
Diana Lorons
,
Kenneth Francis Rodrigues
,
Madihah Jafar Sidik
,
Grace Joy Wei Lie Chin
·
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.47836/pjst.30.4.23
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.47836/pjst.30.4.23
During a harmful algal bloom (HAB), the seawater contains a high abundance of microorganisms and elemental ions. Such components can interfere with RNA isolation, leading to RNA degradation. The complex HAB seawater property makes isolating high-quality RNA for metatranscriptomic sequencing difficult, which is required for effective RNA sequencing and transcriptome profiling. This study used three isolation techniques to find the optimal strategy for isolating total RNA from bloom samples. One of the isolation techniques was the phenol-chloroform extraction method, which uses organic solvents to isolate RNA. The remaining two isolation techniques used the same commercial RNA extraction kit, TransZol Up Plus RNA kit (TransGen Biotech, China). One followed the extraction kit’s protocol, while the other modified the protocol. Total RNA was extracted from three seawater samples of three occasions of HAB in Sepanggar Bay. The most effective approach used to extract high-quality RNA from the environmental samples of the HABs was the TransZol Up Plus RNA kit, with modified protocol. Results of the modified protocol generated a high-purity total RNA, ranging from 2.081 to 2.474 for both the absorbance ratios A260/280 and A260/230. The RNA integrity number value ranged from 6.2 to 7.6. All of the samples resulted in concentrations up to 91 ng/µl. We concluded that the modified protocol of TransZol Up Plus RNA kit yielded the highest quality total RNA for metatranscriptome next-generation sequencing (NGS). Apart from NGS, the high-quality RNA can also be used for various downstream applications, including real-time PCR, RNA cloning, and RNA microarray analysis.
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Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.47836/pjst.30.4.23
- http://www.pertanika.upm.edu.my/resources/files/Pertanika PAPERS/JST Vol. 30 (4) Oct. 2022/23 JST-3270-2021.pdf
- OA Status
- hybrid
- Cited By
- 1
- References
- 47
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4298037128
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4298037128Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.47836/pjst.30.4.23Digital Object Identifier
- Title
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RNA Isolation from Environmental Samples of a Harmful Algal Bloom for Metatranscriptome Next-Generation SequencingWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2022Year of publication
- Publication date
-
2022-09-21Full publication date if available
- Authors
-
Diana Lorons, Kenneth Francis Rodrigues, Madihah Jafar Sidik, Grace Joy Wei Lie ChinList of authors in order
- Landing page
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https://doi.org/10.47836/pjst.30.4.23Publisher landing page
- PDF URL
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https://www.pertanika.upm.edu.my/resources/files/Pertanika PAPERS/JST Vol. 30 (4) Oct. 2022/23 JST-3270-2021.pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
hybridOpen access status per OpenAlex
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https://www.pertanika.upm.edu.my/resources/files/Pertanika PAPERS/JST Vol. 30 (4) Oct. 2022/23 JST-3270-2021.pdfDirect OA link when available
- Concepts
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RNA, RNA extraction, Biology, Gene, BiochemistryTop concepts (fields/topics) attached by OpenAlex
- Cited by
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1Total citation count in OpenAlex
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2024: 1Per-year citation counts (last 5 years)
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47Number of works referenced by this work
- Related works (count)
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.total | 64, 168, 220 |
| abstract_inverted_index.value | 187 |
| abstract_inverted_index.which | 41, 79 |
| abstract_inverted_index.while | 112 |
| abstract_inverted_index.(HAB), | 5 |
| abstract_inverted_index.(NGS). | 226 |
| abstract_inverted_index.During | 0 |
| abstract_inverted_index.number | 186 |
| abstract_inverted_index.ranged | 188 |
| abstract_inverted_index.ratios | 179 |
| abstract_inverted_index.China). | 105 |
| abstract_inverted_index.Results | 160 |
| abstract_inverted_index.complex | 29 |
| abstract_inverted_index.extract | 140 |
| abstract_inverted_index.harmful | 2 |
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| abstract_inverted_index.isolate | 84 |
| abstract_inverted_index.kit’s | 110 |
| abstract_inverted_index.leading | 24 |
| abstract_inverted_index.method, | 78 |
| abstract_inverted_index.ng/µl. | 203 |
| abstract_inverted_index.optimal | 60 |
| abstract_inverted_index.organic | 81 |
| abstract_inverted_index.quality | 219 |
| abstract_inverted_index.ranging | 170 |
| abstract_inverted_index.samples | 125, 146, 196 |
| abstract_inverted_index.various | 238 |
| abstract_inverted_index.yielded | 216 |
| abstract_inverted_index.A260/280 | 180 |
| abstract_inverted_index.Biotech, | 104 |
| abstract_inverted_index.TransZol | 98, 152, 211 |
| abstract_inverted_index.approach | 137 |
| abstract_inverted_index.cloning, | 245 |
| abstract_inverted_index.contains | 8 |
| abstract_inverted_index.followed | 107 |
| abstract_inverted_index.modified | 115, 158, 163, 208 |
| abstract_inverted_index.property | 32 |
| abstract_inverted_index.protocol | 164, 209 |
| abstract_inverted_index.required | 43 |
| abstract_inverted_index.resulted | 197 |
| abstract_inverted_index.samples. | 68 |
| abstract_inverted_index.seawater | 7, 31, 124 |
| abstract_inverted_index.solvents | 82 |
| abstract_inverted_index.strategy | 61 |
| abstract_inverted_index.(TransGen | 103 |
| abstract_inverted_index.A260/230. | 182 |
| abstract_inverted_index.Sepanggar | 132 |
| abstract_inverted_index.abundance | 11 |
| abstract_inverted_index.analysis. | 249 |
| abstract_inverted_index.concluded | 205 |
| abstract_inverted_index.effective | 45, 136 |
| abstract_inverted_index.elemental | 15 |
| abstract_inverted_index.extracted | 121 |
| abstract_inverted_index.generated | 165 |
| abstract_inverted_index.including | 241 |
| abstract_inverted_index.integrity | 185 |
| abstract_inverted_index.interfere | 20 |
| abstract_inverted_index.isolating | 34, 63 |
| abstract_inverted_index.isolation | 55, 72, 89 |
| abstract_inverted_index.occasions | 128 |
| abstract_inverted_index.protocol, | 111 |
| abstract_inverted_index.protocol. | 117, 159 |
| abstract_inverted_index.real-time | 242 |
| abstract_inverted_index.remaining | 87 |
| abstract_inverted_index.absorbance | 178 |
| abstract_inverted_index.commercial | 94 |
| abstract_inverted_index.components | 18 |
| abstract_inverted_index.difficult, | 40 |
| abstract_inverted_index.downstream | 239 |
| abstract_inverted_index.extraction | 77, 96, 109 |
| abstract_inverted_index.isolation, | 23 |
| abstract_inverted_index.microarray | 248 |
| abstract_inverted_index.profiling. | 50 |
| abstract_inverted_index.sequencing | 39, 47, 225 |
| abstract_inverted_index.techniques | 56, 73, 90 |
| abstract_inverted_index.high-purity | 167 |
| abstract_inverted_index.degradation. | 27 |
| abstract_inverted_index.high-quality | 35, 141, 231 |
| abstract_inverted_index.applications, | 240 |
| abstract_inverted_index.environmental | 145 |
| abstract_inverted_index.transcriptome | 49 |
| abstract_inverted_index.concentrations | 199 |
| abstract_inverted_index.microorganisms | 13 |
| abstract_inverted_index.next-generation | 224 |
| abstract_inverted_index.metatranscriptome | 223 |
| abstract_inverted_index.phenol-chloroform | 76 |
| abstract_inverted_index.metatranscriptomic | 38 |
| cited_by_percentile_year.max | 94 |
| cited_by_percentile_year.min | 90 |
| countries_distinct_count | 1 |
| institutions_distinct_count | 4 |
| sustainable_development_goals[0].id | https://metadata.un.org/sdg/14 |
| sustainable_development_goals[0].score | 0.8700000047683716 |
| sustainable_development_goals[0].display_name | Life below water |
| citation_normalized_percentile.value | 0.58240849 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |