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Comprehensive RNA sequencing of healthy human endometrium at two time points of the menstrual cycle
KTH, School of Biotechnology (BIO), Gene Technology.ORCID iD: 0000-0002-2219-0197
Show others and affiliations
2016 (English)Manuscript (preprint) (Other academic)
Abstract [en]

Endometrial receptivity is crucial for implantation and establishment of a normal pregnancy. The shift from proliferative to receptive endometrium is still far from understood. In this paper we comprehensively present the transcriptome of the human endometrium by comparing endometrial biopsies from proliferative phase with consecutive biopsies 7-9 days after ovulation. The results show a clear difference in expression between the two time points using both total and small RNA sequencing.  3297 mRNAs, 516 long non-coding RNAs and 102 small non-coding RNAs were identified as statistically differentially expressed between the two time points. We show a thorough description of the change in mRNA between the two time points and display lncRNAs, snoRNAs and snRNAs not previously reported in the healthy human endometrium. In conclusion this paper reports in detail the shift in RNA expression from the proliferative to receptive endometrium.

Place, publisher, year, edition, pages
2016.
Keyword [en]
RNA-seq, endometrium, menstruation cycle, differential expression, small RNA, total RNA
National Category
Endocrinology and Diabetes
Identifiers
URN: urn:nbn:se:kth:diva-184156OAI: oai:DiVA.org:kth-184156DiVA: diva2:915144
Funder
Swedish Research Council
Note

QC 20161124

Available from: 2016-03-29 Created: 2016-03-29 Last updated: 2016-11-24Bibliographically approved
In thesis
1. Analysis of RNA and DNA sequencing data: Improved bioinformatics applications
Open this publication in new window or tab >>Analysis of RNA and DNA sequencing data: Improved bioinformatics applications
2016 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Massively parallel sequencing has rapidly revolutionized DNA and RNA research. Sample preparations are steadfastly advancing, sequencing costs have plummeted and throughput is ever growing. This progress has resulted in exponential growth in data generation with a corresponding demand for bioinformatic solutions. This thesis addresses methodological aspects of this sequencing revolution and applies it to selected biological topics.

Papers I and II are technical in nature and concern sample preparation and data anal- ysis of RNA sequencing data. Paper I is focused on RNA degradation and paper II on generating strand specific RNA-seq libraries.

Paper III and IV deal with current biological issues. In paper III, whole exomes of cancer patients undergoing chemotherapy are sequenced and their genetic variants associ- ated to their toxicity induced adverse drug reactions. In paper IV a comprehensive view of the gene expression of the endometrium is assessed from two time points of the menstrual cycle.

Together these papers show relevant aspects of contemporary sequencing technologies and how it can be applied to diverse biological topics. 

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2016. 135 p.
Series
TRITA-BIO-Report, ISSN 1654-2312 ; 2016:2
Keyword
RNA sequencing, exome sequencing, bioinformatics, gene expression, differential expression, variant calling
National Category
Bioinformatics and Systems Biology
Research subject
Biotechnology
Identifiers
urn:nbn:se:kth:diva-184158 (URN)978-91-7595-894-1 (ISBN)
Public defence
2016-04-22, Inghesalen, Tomtebodavägen 18A, Solna, Stockholm, 10:00 (English)
Opponent
Supervisors
Funder
Swedish Research CouncilKnut and Alice Wallenberg Foundation
Note

QC 20160329

Available from: 2016-03-29 Created: 2016-03-29 Last updated: 2016-03-29Bibliographically approved
2. Library Preparation for High Throughput DNA Sequencing
Open this publication in new window or tab >>Library Preparation for High Throughput DNA Sequencing
2017 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Order 3 billion base pairs of DNA in the correct order and you get the blueprint of a human, the genome. Before the introduction of massively parallel sequencing a little more than a decade ago it would cost around $10 million to get this blueprint. Since then, sequencing throughput and cost have plummeted and now that figure is around $1000, and large sequencing centres such as the National Genomics Infrastructure in Stockholm is sequencing the equivalent of 25 human genomes per hour. The papers that form the basis of this thesis cover different aspects of the rapidly expanding DNA sequencing field.

 

Paper I describes a model system that employ massively parallel sequencing to characterize the behaviour of type IIS restriction enzymes. Enzymes are biological macromolecules that catalyse chemical reactions in the cell. All commercially available sequencing systems use enzymes to prepare the nucleic acids before they are loaded on the machine. Thus, intimate knowledge of enzymes is vital not only when designing new sequencing protocols, but also for understanding the limitations of current protocols. Paper II covers the automation of a library preparation protocol for spatially resolved transcriptome sequencing. Automation increases the sample throughput and also minimises the risk of human errors that can introduce technical noise in the data. In paper III, the power of massively parallel sequencing is employed to describe the RNA content of the endometrium at two different time points during the menstrual cycle. Finally, paper IV covers the sequencing of highly degraded nucleic acids from formalin fixed, paraffin embedded samples. These samples often have a rich clinical background, making them extremely valuable for researchers. However, it is challenging to sequence these samples and this study looks at the impact that different preparation kits have on the quality of the sequencing data. 

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2017. 56 p.
Series
TRITA-BIO-Report, ISSN 1654-2312 ; 2017:1
Keyword
DNA, RNA, sequencing, massively parallel sequencing, library preparation, automation, genome, transcriptome
National Category
Biological Sciences
Research subject
Biotechnology
Identifiers
urn:nbn:se:kth:diva-196560 (URN)978-91-7729-212-8 (ISBN)
Public defence
2017-01-13, Air & Fire, Science for Life Laboratory, Tomtebodavägen 23, Solna, 13:00 (English)
Opponent
Supervisors
Note

QC 20161124

Available from: 2016-11-24 Created: 2016-11-16 Last updated: 2016-11-24Bibliographically approved

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