{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/115939"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/115939","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Improving an rRNA depletion protocol with statistical design of experiments","abstract":"Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2024-08-01","abstract_html":"Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2024-08-01","abstract_has_math":false,"creators":["David, Benjamin"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"M.S.","degree_level":"Thesis","degree_discipline":"Bioengineering","degree_department":null,"school":null,"contributors":["Jensen, Paul A"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2022,"date_issued":"2022-08","date_published":"2022-08","updated_at":"2026-07-22T22:24:55Z","subjects":["DOE","Molecular Biology","NGS"],"languages":["en","eng"],"rights":["© 2022 Benjamin David"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/2142/115939","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Jensen, Paul A"]},{"key":"dc:creator","label":"Author","values":["David, Benjamin"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2022-08","2022-07-18"]},{"key":"dc:type","label":"Dc Type","values":["text","Thesis"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Bioengineering"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Thesis"]},{"key":"thesis:degree_name","label":"Degree Name","values":["M.S."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["DOE","Molecular Biology","NGS"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en","eng"]},{"key":"dc:rights","label":"Dc Rights","values":["© 2022 Benjamin David"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://hdl.handle.net/2142/115939"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2024-08-01","The student, Benjamin David, accepted the attached license on 2022-07-14 at 16:15.","The student, Benjamin David, submitted this Thesis for approval on 2022-07-14 at 16:21.","This Thesis was approved for publication on 2022-07-18 at 13:26.","DSpace SAF Submission Ingestion Package generated from Vireo submission #18318 on 2022-11-16 at 10:56:12","rRNA depletion is the most expensive step in prokaryotic RNA-seq library preparation. rRNA is so abundant that small increases in depletion efficiency lead to large changes in mRNA sequencing coverage. A variety of commercial and home-made methods exist to lower the cost or increase the efficiency of rRNA removal. Many of these techniques are suboptimal when applied to new species of bacteria or when the protocol or reagents need to be changed. Re-optimizing a protocol by trial-and-error is an expensive and laborious process. Systematic frameworks like the statistical design of experiments (DOE) can improve processes by exploring the quantitative relationship between multiple factors. DOE allows experimenters to find factor interactions that may not be apparent when factors are studied in isolation. We used DOE to optimize an rRNA depletion protocol by updating reagents and identifying factors that maximize rRNA removal and minimize cost. The optimized protocol more efficiently removes rRNA, uses fewer reagents, and is less expensive than the original protocol. Our optimization required only 17 experiments and identified two significant interactions among three factors. Overall, our approach demonstrates the utility of a rational, DOE framework for improving complex protocols."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Improving an rRNA depletion protocol with statistical design of experiments"]}]}],"canonical_facts":{"dc:contributor":["Jensen, Paul A"],"dc:creator":["David, Benjamin"],"dc:date":["2022-08","2022-07-18"],"dc:description":["Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2024-08-01","The student, Benjamin David, accepted the attached license on 2022-07-14 at 16:15.","The student, Benjamin David, submitted this Thesis for approval on 2022-07-14 at 16:21.","This Thesis was approved for publication on 2022-07-18 at 13:26.","DSpace SAF Submission Ingestion Package generated from Vireo submission #18318 on 2022-11-16 at 10:56:12","rRNA depletion is the most expensive step in prokaryotic RNA-seq library preparation. rRNA is so abundant that small increases in depletion efficiency lead to large changes in mRNA sequencing coverage. A variety of commercial and home-made methods exist to lower the cost or increase the efficiency of rRNA removal. Many of these techniques are suboptimal when applied to new species of bacteria or when the protocol or reagents need to be changed. Re-optimizing a protocol by trial-and-error is an expensive and laborious process. Systematic frameworks like the statistical design of experiments (DOE) can improve processes by exploring the quantitative relationship between multiple factors. DOE allows experimenters to find factor interactions that may not be apparent when factors are studied in isolation. We used DOE to optimize an rRNA depletion protocol by updating reagents and identifying factors that maximize rRNA removal and minimize cost. The optimized protocol more efficiently removes rRNA, uses fewer reagents, and is less expensive than the original protocol. Our optimization required only 17 experiments and identified two significant interactions among three factors. Overall, our approach demonstrates the utility of a rational, DOE framework for improving complex protocols."],"dc:format":["application/pdf"],"dc:identifier":["https://hdl.handle.net/2142/115939"],"dc:language":["en","eng"],"dc:rights":["© 2022 Benjamin David"],"dc:subject":["DOE","Molecular Biology","NGS"],"dc:title":["Improving an rRNA depletion protocol with statistical design of experiments"],"dc:type":["text","Thesis"],"thesis:degree_discipline":["Bioengineering"],"thesis:degree_level":["Thesis"],"thesis:degree_name":["M.S."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:24:55Z"}