Title:
Uniquely quantifying highly similar RNA transcripts at the single molecule level

dc.contributor.advisor Kim, Harold D.
dc.contributor.author Wadsworth, Gable Marsh
dc.contributor.committeeMember Ratcliff, Will
dc.contributor.committeeMember Gumbart, James C.
dc.contributor.committeeMember Yunker, Peter
dc.contributor.committeeMember Wartell, Roger
dc.contributor.department Physics
dc.date.accessioned 2020-01-14T14:42:54Z
dc.date.available 2020-01-14T14:42:54Z
dc.date.created 2018-12
dc.date.issued 2018-11-09
dc.date.submitted December 2018
dc.date.updated 2020-01-14T14:42:54Z
dc.description.abstract Understanding RNA expression is critical to understand the connection between phenotype and genotype in living cells. To further complicate things, RNA splicing leads to the generation of multiple distinct isoforms which are developmentally regulated and highly homologous. Current methods for identifying transcripts in situ are unable to uniquely identify most isoforms due to the fact that the sequence is shared. While these splicing variations can be identified using ensemble methods such as RNA-seq, this does not preserve spatial information. We demonstrate new Fluorescence In Situ Hybridization (FISH) techniques based on a short probe and hybridization chain reaction, which can uniquely identify RNA isoforms in both budding yeast and C. Elegans. We establish that with a singly labeled FISH probe ~60% of transcripts can be quantified. We demonstrate this technique on the SUS1 gene in single yeast cells and on the NURF1 gene in the C. Elegans germline. This technique enables cost effective interrogation of all of the isoforms of an RNA transcript.
dc.description.degree Ph.D.
dc.format.mimetype application/pdf
dc.identifier.uri http://hdl.handle.net/1853/62219
dc.language.iso en_US
dc.publisher Georgia Institute of Technology
dc.subject RNA
dc.subject FISH
dc.subject Fluorescenct in situ hybridization
dc.subject Single molecule
dc.subject Single cell
dc.subject Yeast
dc.subject C.elegans
dc.subject Strand displacement
dc.title Uniquely quantifying highly similar RNA transcripts at the single molecule level
dc.type Text
dc.type.genre Dissertation
dspace.entity.type Publication
local.contributor.advisor Kim, Harold D.
local.contributor.corporatename College of Sciences
local.contributor.corporatename School of Physics
relation.isAdvisorOfPublication 5f237b00-63ae-49ad-a092-205e4b0318b3
relation.isOrgUnitOfPublication 85042be6-2d68-4e07-b384-e1f908fae48a
relation.isOrgUnitOfPublication 2ba39017-11f1-40f4-9bc5-66f17b8f1539
thesis.degree.level Doctoral
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