On Transcriptome Sequencing

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MARC

Klevebring, Daniel,1981-KTH,Genteknologi,Division of Gene Technology (author)

On Transcriptome Sequencing

BookEnglish2009

Publisher, publication year, extent ...

Stockholm :KTH,2009
52 s.
electronicrdacarrier

Numbers

LIBRIS-ID:oai:DiVA.org:kth-11446
ISBN:9789174154900
https://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-11446URI

Supplementary language notes

Language:English
Summary in:English

Part of subdatabase

SwePubSwePub

Classification

Subject category:vet swepub-contenttype
Subject category:dok swepub-publicationtype

Series

Trita-BIO-Report,1654-2312 ;2009:26

Notes

QC 20100723
This thesis is about the use of massive DNA sequencing to investigate the transcriptome. During recent decades, several studies have made it clear that the transcriptome comprises a more complex set of biochemical machinery than was previously believed. The majority of the genome can be expressed as transcripts; and overlapping and antisense transcription is widespread. New technologies for the interroga- tion of nucleic acids have made it possible to investigate such cellular phenomena in much greater detail than ever before. For each application, special requirements need to be met. The work presented in this thesis focuses on the transcrip- tome and the development of technology for its analysis. In paper I, we report our development of an automated approach for sample preparation. The procedure was benchmarked against a publicly available reference data set, and we note that our approach outperformed similar manual procedures in terms of reproducibility. In the work reported in papers II-IV, we used different massive sequencing technologies to investigate the transcriptome. In paper II we describe a concatemerization approach that increased throughput by 65% using 454 sequencing,and we identify classes of transcripts not previously described in Populus. Papers III and IV both report studies based on SOLiD sequencing. In the former, we investigated transcripts and proteins for 13% of the human gene and detected a massive overlap for the upper 50% transcriptional levels. In the work described in paper IV, we investigated transcription in non-genic regions of the genome and detected expression from a high number of previ- ously unknown loci.

Subject headings and genre

NATURVETENSKAP Biologi Annan biologi hsv//swe
NATURAL SCIENCES Biological Sciences Other Biological Topics hsv//eng
NATURVETENSKAP Biologi Bioinformatik och systembiologi hsv//swe
NATURAL SCIENCES Biological Sciences Bioinformatics and Systems Biology hsv//eng
NATURVETENSKAP Biologi Genetik hsv//swe
NATURAL SCIENCES Biological Sciences Genetics hsv//eng
NATURVETENSKAP Biologi Biokemi och molekylärbiologi hsv//swe
NATURAL SCIENCES Biological Sciences Biochemistry and Molecular Biology hsv//eng
MEDICIN OCH HÄLSOVETENSKAP Medicinska och farmaceutiska grundvetenskaper Cell- och molekylärbiologi hsv//swe
MEDICAL AND HEALTH SCIENCES Basic Medicine Cell and Molecular Biology hsv//eng
Transcriptome
RNA-seq
DNA sequencing
gene expression profiling
non-coding RNA
small RNA
Functional genomics
Funktionsgenomik
Bioinformatics
Bioinformatik
Genetics
Genetik
Molecular biology
Molekylärbiologi
Cell biology
Cellbiologi

Added entries (persons, corporate bodies, meetings, titles ...)

Lundeberg, Joakim,ProfessorKTH,Genteknologi(Swepub:kth)u1qkn9kw (thesis advisor)
Gyllensten, Ulf,ProfessorUppsala Universitet, Institutionen för genetik och patologi (opponent)
KTHGenteknologi (creator_code:org_t)

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NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Other Biological ...

NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Bioinformatics a ...

NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Genetics

NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Biochemistry and ...

MEDICAL AND HEALTH SCIENCES: MEDICAL AND HEAL ...; and Basic Medicine; and Cell and Molecul ...

Parts in the series: Trita-BIO-Report ...

By the university: Royal Institute of Technology

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