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Comprehensive RNA sequencing of healthy human endometrium at two time points of the menstrual cycle
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

Endometrium receptivity is crucial for implantation and establishment of a normal pregnancy. The process of receptivity and subsequent implantation is still far from understood. This paper present a comprehensive transcriptome of the human endometrium comparing endometrial biopsies from proliferative phase with consecutive biopsies during window of implantation. The result shows 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 lists 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 unresponsive to receptive endometrium.

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 20160404

Available from: 2016-03-29 Created: 2016-03-29 Last updated: 2016-04-04Bibliographically 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

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Sigurgeirsson, Benjamín
Endocrinology and Diabetes

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