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Improved CTAB method for RNA extraction of thick waxy leaf tissues from sago palm (Metroxylon sagu Rottb.)
Background There is a growing interest in transcriptomics studies parallel to the advancement of transcriptome databases and bioinformatics, which provided the opportunity to study responses to growths, stimuli and stresses. There is an increase in demand for excellent RNA extraction techniques. Gen...
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Published in: | Chemical and biological technologies in agriculture 2022-09, Vol.9 (1), p.1-14, Article 63 |
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description | Background
There is a growing interest in transcriptomics studies parallel to the advancement of transcriptome databases and bioinformatics, which provided the opportunity to study responses to growths, stimuli and stresses. There is an increase in demand for excellent RNA extraction techniques. General RNA extraction protocols can be used in RNA extraction, but the quality and quantity vary in different types of tissues from different organisms. Hence, a specific RNA extraction method for each organism’s tissue type is required to obtain the desired RNA quality and quantity.
Results
The improved CTAB RNA extraction method is superior to the PCI method and MRIP method for thick waxy leaves that were applied for mature sago palm (
Metroxylon sagu
Rottb.) leaf tissue and produce total RNA extract with good purity (OD 260/280 ≥ 1.8, OD 260/230 ≥ 2.0) and integrity (RIN ~ 7). RNA sequencing was conducted with the extracted samples and showed good assembly results (Q20 ≥ 97, Q30 ≥ 91%, assembly mean length ≥ 700 bp).
Conclusion
The improved CTAB RNA extraction method enables rapid, cost-effective, and relatively simple RNA extraction from waxy, fibrous and high-in-polyphenol sago palm (
M. sagu
Rottb.) leaf tissue with next-generation RNA sequencing recommended quality.
Graphical Abstract |
doi_str_mv | 10.1186/s40538-022-00329-9 |
format | article |
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There is a growing interest in transcriptomics studies parallel to the advancement of transcriptome databases and bioinformatics, which provided the opportunity to study responses to growths, stimuli and stresses. There is an increase in demand for excellent RNA extraction techniques. General RNA extraction protocols can be used in RNA extraction, but the quality and quantity vary in different types of tissues from different organisms. Hence, a specific RNA extraction method for each organism’s tissue type is required to obtain the desired RNA quality and quantity.
Results
The improved CTAB RNA extraction method is superior to the PCI method and MRIP method for thick waxy leaves that were applied for mature sago palm (
Metroxylon sagu
Rottb.) leaf tissue and produce total RNA extract with good purity (OD 260/280 ≥ 1.8, OD 260/230 ≥ 2.0) and integrity (RIN ~ 7). RNA sequencing was conducted with the extracted samples and showed good assembly results (Q20 ≥ 97, Q30 ≥ 91%, assembly mean length ≥ 700 bp).
Conclusion
The improved CTAB RNA extraction method enables rapid, cost-effective, and relatively simple RNA extraction from waxy, fibrous and high-in-polyphenol sago palm (
M. sagu
Rottb.) leaf tissue with next-generation RNA sequencing recommended quality.
Graphical Abstract</description><identifier>ISSN: 2196-5641</identifier><identifier>EISSN: 2196-5641</identifier><identifier>DOI: 10.1186/s40538-022-00329-9</identifier><language>eng</language><publisher>Cham: Springer International Publishing</publisher><subject>Agricultural production ; Agriculture ; Assembly ; Bioinformatics ; Biomedical and Life Sciences ; Dogs ; Gene sequencing ; Improved CTAB method ; Leaves ; Life Sciences ; Methodology ; Methods ; Metroxylon sagu ; Organic Chemistry ; Plant Biochemistry ; Plant Physiology ; Plant tissues ; Ribonucleic acid ; RNA ; RNA extraction ; Sago ; Soil Science & Conservation ; Transcriptomes ; Transcriptomics</subject><ispartof>Chemical and biological technologies in agriculture, 2022-09, Vol.9 (1), p.1-14, Article 63</ispartof><rights>The Author(s) 2022</rights><rights>The Author(s) 2022. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c359t-a4de7d13514f121ea251d229166b8bcb5dac29a6e31f374ae1ea95535ed773763</citedby><cites>FETCH-LOGICAL-c359t-a4de7d13514f121ea251d229166b8bcb5dac29a6e31f374ae1ea95535ed773763</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.proquest.com/docview/2713860510/fulltextPDF?pq-origsite=primo$$EPDF$$P50$$Gproquest$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/2713860510?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>314,780,784,25753,27924,27925,37012,44590,75126</link.rule.ids></links><search><creatorcontrib>Yan, Wei-Jie</creatorcontrib><creatorcontrib>Pendi, Fifi Hafizzah</creatorcontrib><creatorcontrib>Hussain, Hasnain</creatorcontrib><title>Improved CTAB method for RNA extraction of thick waxy leaf tissues from sago palm (Metroxylon sagu Rottb.)</title><title>Chemical and biological technologies in agriculture</title><addtitle>Chem. Biol. Technol. Agric</addtitle><description>Background
There is a growing interest in transcriptomics studies parallel to the advancement of transcriptome databases and bioinformatics, which provided the opportunity to study responses to growths, stimuli and stresses. There is an increase in demand for excellent RNA extraction techniques. General RNA extraction protocols can be used in RNA extraction, but the quality and quantity vary in different types of tissues from different organisms. Hence, a specific RNA extraction method for each organism’s tissue type is required to obtain the desired RNA quality and quantity.
Results
The improved CTAB RNA extraction method is superior to the PCI method and MRIP method for thick waxy leaves that were applied for mature sago palm (
Metroxylon sagu
Rottb.) leaf tissue and produce total RNA extract with good purity (OD 260/280 ≥ 1.8, OD 260/230 ≥ 2.0) and integrity (RIN ~ 7). RNA sequencing was conducted with the extracted samples and showed good assembly results (Q20 ≥ 97, Q30 ≥ 91%, assembly mean length ≥ 700 bp).
Conclusion
The improved CTAB RNA extraction method enables rapid, cost-effective, and relatively simple RNA extraction from waxy, fibrous and high-in-polyphenol sago palm (
M. sagu
Rottb.) leaf tissue with next-generation RNA sequencing recommended quality.
Graphical Abstract</description><subject>Agricultural production</subject><subject>Agriculture</subject><subject>Assembly</subject><subject>Bioinformatics</subject><subject>Biomedical and Life Sciences</subject><subject>Dogs</subject><subject>Gene sequencing</subject><subject>Improved CTAB method</subject><subject>Leaves</subject><subject>Life Sciences</subject><subject>Methodology</subject><subject>Methods</subject><subject>Metroxylon sagu</subject><subject>Organic Chemistry</subject><subject>Plant Biochemistry</subject><subject>Plant Physiology</subject><subject>Plant tissues</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA extraction</subject><subject>Sago</subject><subject>Soil Science & Conservation</subject><subject>Transcriptomes</subject><subject>Transcriptomics</subject><issn>2196-5641</issn><issn>2196-5641</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><sourceid>PIMPY</sourceid><sourceid>DOA</sourceid><recordid>eNp9kctOwzAQRSMEElXpD7CyxAYWKX7ETrwsFY9KBSQEa2sSOyUlqYvtQvv3GIKAFSvbo3PvzPgmyTHBY0IKce4zzFmRYkpTjBmVqdxLBpRIkXKRkf0_98Nk5P0SY0woKWTOBsly1q2dfTMaTR8nF6gz4dlqVFuHHu4myGyDgyo0doVsjcJzU72gd9juUGsgvhvvN8aj2tkOeVhYtIa2Q6e3Jji73bVRFasb9GBDKMdnR8lBDa03o-9zmDxdXT5Ob9L5_fVsOpmnFeMypJBpk2vCOMnqOKYByommVBIhyqKsSq6hohKEYaRmeQYmIpJzxo3Oc5YLNkxmva-2sFRr13TgdspCo74K1i0UuNBUrVESJGVG1BkrdaaphqIoBC5KjQUTlPHoddJ7xU96jbsGtbQbt4rjK5oTFmFOcKRoT1XOeu9M_dOVYPUZkeojUjEi9RWRklHEepGP8Gph3K_1P6oPxgCSRw</recordid><startdate>20220913</startdate><enddate>20220913</enddate><creator>Yan, Wei-Jie</creator><creator>Pendi, Fifi Hafizzah</creator><creator>Hussain, Hasnain</creator><general>Springer International Publishing</general><general>Springer Nature B.V</general><general>SpringerOpen</general><scope>C6C</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7X2</scope><scope>8FE</scope><scope>8FH</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>LK8</scope><scope>M0K</scope><scope>M7P</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>DOA</scope></search><sort><creationdate>20220913</creationdate><title>Improved CTAB method for RNA extraction of thick waxy leaf tissues from sago palm (Metroxylon sagu Rottb.)</title><author>Yan, Wei-Jie ; Pendi, Fifi Hafizzah ; Hussain, Hasnain</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c359t-a4de7d13514f121ea251d229166b8bcb5dac29a6e31f374ae1ea95535ed773763</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Agricultural production</topic><topic>Agriculture</topic><topic>Assembly</topic><topic>Bioinformatics</topic><topic>Biomedical and Life Sciences</topic><topic>Dogs</topic><topic>Gene sequencing</topic><topic>Improved CTAB method</topic><topic>Leaves</topic><topic>Life Sciences</topic><topic>Methodology</topic><topic>Methods</topic><topic>Metroxylon sagu</topic><topic>Organic Chemistry</topic><topic>Plant Biochemistry</topic><topic>Plant Physiology</topic><topic>Plant tissues</topic><topic>Ribonucleic acid</topic><topic>RNA</topic><topic>RNA extraction</topic><topic>Sago</topic><topic>Soil Science & Conservation</topic><topic>Transcriptomes</topic><topic>Transcriptomics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Yan, Wei-Jie</creatorcontrib><creatorcontrib>Pendi, Fifi Hafizzah</creatorcontrib><creatorcontrib>Hussain, Hasnain</creatorcontrib><collection>Springer Open Access</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Agricultural Science Collection</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest Central</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>AUTh Library subscriptions: ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Agriculture Science Database</collection><collection>Biological Science Database</collection><collection>Publicly Available Content (ProQuest)</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>Chemical and biological technologies in agriculture</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Yan, Wei-Jie</au><au>Pendi, Fifi Hafizzah</au><au>Hussain, Hasnain</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Improved CTAB method for RNA extraction of thick waxy leaf tissues from sago palm (Metroxylon sagu Rottb.)</atitle><jtitle>Chemical and biological technologies in agriculture</jtitle><stitle>Chem. Biol. Technol. Agric</stitle><date>2022-09-13</date><risdate>2022</risdate><volume>9</volume><issue>1</issue><spage>1</spage><epage>14</epage><pages>1-14</pages><artnum>63</artnum><issn>2196-5641</issn><eissn>2196-5641</eissn><abstract>Background
There is a growing interest in transcriptomics studies parallel to the advancement of transcriptome databases and bioinformatics, which provided the opportunity to study responses to growths, stimuli and stresses. There is an increase in demand for excellent RNA extraction techniques. General RNA extraction protocols can be used in RNA extraction, but the quality and quantity vary in different types of tissues from different organisms. Hence, a specific RNA extraction method for each organism’s tissue type is required to obtain the desired RNA quality and quantity.
Results
The improved CTAB RNA extraction method is superior to the PCI method and MRIP method for thick waxy leaves that were applied for mature sago palm (
Metroxylon sagu
Rottb.) leaf tissue and produce total RNA extract with good purity (OD 260/280 ≥ 1.8, OD 260/230 ≥ 2.0) and integrity (RIN ~ 7). RNA sequencing was conducted with the extracted samples and showed good assembly results (Q20 ≥ 97, Q30 ≥ 91%, assembly mean length ≥ 700 bp).
Conclusion
The improved CTAB RNA extraction method enables rapid, cost-effective, and relatively simple RNA extraction from waxy, fibrous and high-in-polyphenol sago palm (
M. sagu
Rottb.) leaf tissue with next-generation RNA sequencing recommended quality.
Graphical Abstract</abstract><cop>Cham</cop><pub>Springer International Publishing</pub><doi>10.1186/s40538-022-00329-9</doi><tpages>14</tpages><oa>free_for_read</oa></addata></record> |
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subjects | Agricultural production Agriculture Assembly Bioinformatics Biomedical and Life Sciences Dogs Gene sequencing Improved CTAB method Leaves Life Sciences Methodology Methods Metroxylon sagu Organic Chemistry Plant Biochemistry Plant Physiology Plant tissues Ribonucleic acid RNA RNA extraction Sago Soil Science & Conservation Transcriptomes Transcriptomics |
title | Improved CTAB method for RNA extraction of thick waxy leaf tissues from sago palm (Metroxylon sagu Rottb.) |
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