On the optimal design of metabolic RNA labeling experiments
Massively parallel RNA sequencing (RNA-seq) in combination with metabolic labeling has become the de facto standard approach to study alterations in RNA transcription, processing or decay. Regardless of advances in the experimental protocols and techniques, every experimentalist needs to specify the...
Gespeichert in:
| Hauptverfasser: | , , |
|---|---|
| Dokumenttyp: | Article (Journal) |
| Sprache: | Englisch |
| Veröffentlicht: |
August 7, 2019
|
| In: |
PLoS Computational Biology
Year: 2019, Jahrgang: 15, Heft: 8 |
| ISSN: | 1553-7358 |
| DOI: | 10.1371/journal.pcbi.1007252 |
| Online-Zugang: | Verlag, Volltext: https://doi.org/10.1371/journal.pcbi.1007252 Verlag: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007252 
|
| Verfasserangaben: | Alexey Uvarovskii, Isabel S. Naarmann-de Vries, Christoph Dieterich |
MARC
| LEADER | 00000caa a2200000 c 4500 | ||
|---|---|---|---|
| 001 | 1685415946 | ||
| 003 | DE-627 | ||
| 005 | 20220817183924.0 | ||
| 007 | cr uuu---uuuuu | ||
| 008 | 191212s2019 xx |||||o 00| ||eng c | ||
| 024 | 7 | |a 10.1371/journal.pcbi.1007252 |2 doi | |
| 035 | |a (DE-627)1685415946 | ||
| 035 | |a (DE-599)KXP1685415946 | ||
| 035 | |a (OCoLC)1341282099 | ||
| 040 | |a DE-627 |b ger |c DE-627 |e rda | ||
| 041 | |a eng | ||
| 084 | |a 33 |2 sdnb | ||
| 100 | 1 | |a Uvarovskii, Alexey |e VerfasserIn |0 (DE-588)1165607603 |0 (DE-627)1029676380 |0 (DE-576)51046260X |4 aut | |
| 245 | 1 | 0 | |a On the optimal design of metabolic RNA labeling experiments |c Alexey Uvarovskii, Isabel S. Naarmann-de Vries, Christoph Dieterich |
| 264 | 1 | |c August 7, 2019 | |
| 300 | |a 22 | ||
| 336 | |a Text |b txt |2 rdacontent | ||
| 337 | |a Computermedien |b c |2 rdamedia | ||
| 338 | |a Online-Ressource |b cr |2 rdacarrier | ||
| 500 | |a Gesehen am 10.12.2019 | ||
| 520 | |a Massively parallel RNA sequencing (RNA-seq) in combination with metabolic labeling has become the de facto standard approach to study alterations in RNA transcription, processing or decay. Regardless of advances in the experimental protocols and techniques, every experimentalist needs to specify the key aspects of experimental design: For example, which protocol should be used (biochemical separation vs. nucleotide conversion) and what is the optimal labeling time? In this work, we provide approximate answers to these questions using the asymptotic theory of optimal design. Specifically, we investigate, how the variance of degradation rate estimates depends on the time and derive the optimal time for any given degradation rate. Subsequently, we show that an increase in sample numbers should be preferred over an increase in sequencing depth. Lastly, we provide some guidance on use cases when laborious biochemical separation outcompetes recent nucleotide conversion based methods (such as SLAMseq) and show, how inefficient conversion influences the precision of estimates. Code and documentation can be found at https://github.com/dieterich-lab/DesignMetabolicRNAlabeling. | ||
| 650 | 4 | |a Biotinylation | |
| 650 | 4 | |a Experimental design | |
| 650 | 4 | |a Metabolic labeling | |
| 650 | 4 | |a Nucleotides | |
| 650 | 4 | |a RNA extraction | |
| 650 | 4 | |a RNA sequencing | |
| 650 | 4 | |a RNA synthesis | |
| 650 | 4 | |a RNA transcription labeling | |
| 700 | 1 | |a Naarmann-de Vries, Isabel S. |e VerfasserIn |0 (DE-588)1201521998 |0 (DE-627)1685418813 |4 aut | |
| 700 | 1 | |a Dieterich, Christoph |d 1975- |e VerfasserIn |0 (DE-588)130054844 |0 (DE-627)494359269 |0 (DE-576)297972448 |4 aut | |
| 773 | 0 | 8 | |i Enthalten in |a Public Library of Science |t PLoS Computational Biology |d San Francisco, Calif. : Public Library of Science, 2005 |g 15(2019,8) Artikel-Nummer e1007252, 22 Seiten |h Online-Ressource |w (DE-627)491436017 |w (DE-600)2193340-6 |w (DE-576)273890492 |x 1553-7358 |7 nnas |
| 773 | 1 | 8 | |g volume:15 |g year:2019 |g number:8 |g extent:22 |a On the optimal design of metabolic RNA labeling experiments |
| 856 | 4 | 0 | |u https://doi.org/10.1371/journal.pcbi.1007252 |x Verlag |x Resolving-System |3 Volltext |
| 856 | 4 | 0 | |u https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007252 |x Verlag |
| 951 | |a AR | ||
| 992 | |a 20191212 | ||
| 993 | |a Article | ||
| 994 | |a 2019 | ||
| 998 | |g 130054844 |a Dieterich, Christoph |m 130054844:Dieterich, Christoph |d 910000 |d 910100 |e 910000PD130054844 |e 910100PD130054844 |k 0/910000/ |k 1/910000/910100/ |p 3 |y j | ||
| 998 | |g 1165607603 |a Uvarovskii, Alexey |m 1165607603:Uvarovskii, Alexey |p 1 |x j | ||
| 999 | |a KXP-PPN1685415946 |e 3564195955 | ||
| BIB | |a Y | ||
| SER | |a journal | ||
| JSO | |a {"name":{"displayForm":["Alexey Uvarovskii, Isabel S. Naarmann-de Vries, Christoph Dieterich"]},"id":{"doi":["10.1371/journal.pcbi.1007252"],"eki":["1685415946"]},"person":[{"display":"Uvarovskii, Alexey","family":"Uvarovskii","role":"aut","given":"Alexey"},{"given":"Isabel S.","role":"aut","family":"Naarmann-de Vries","display":"Naarmann-de Vries, Isabel S."},{"role":"aut","given":"Christoph","family":"Dieterich","display":"Dieterich, Christoph"}],"relHost":[{"origin":[{"publisher":"Public Library of Science","dateIssuedDisp":"2005-","dateIssuedKey":"2005","publisherPlace":"San Francisco, Calif."}],"title":[{"subtitle":"a new community journal","title_sort":"PLoS Computational Biology","title":"PLoS Computational Biology"}],"note":["Gesehen am 23. November 2020"],"type":{"media":"Online-Ressource","bibl":"periodical"},"language":["eng"],"recId":"491436017","physDesc":[{"extent":"Online-Ressource"}],"disp":"Public Library of SciencePLoS Computational Biology","pubHistory":["1.2005 -"],"name":{"displayForm":["publ. by the Public Library of Science (PLoS) in association with the International Society for Computational Biology (ISCB)"]},"corporate":[{"display":"Public Library of Science","role":"aut"}],"part":{"year":"2019","extent":"22","text":"15(2019,8) Artikel-Nummer e1007252, 22 Seiten","volume":"15","issue":"8"},"id":{"zdb":["2193340-6"],"issn":["1553-7358"],"eki":["491436017"]}}],"origin":[{"dateIssuedKey":"2019","dateIssuedDisp":"August 7, 2019"}],"title":[{"title_sort":"On the optimal design of metabolic RNA labeling experiments","title":"On the optimal design of metabolic RNA labeling experiments"}],"note":["Gesehen am 10.12.2019"],"type":{"bibl":"article-journal","media":"Online-Ressource"},"language":["eng"],"recId":"1685415946","physDesc":[{"extent":"22 S."}]} | ||
| SRT | |a UVAROVSKIIONTHEOPTIM7201 | ||