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Series GSE69825 Query DataSets for GSE69825
Status Public on Jul 20, 2015
Title Biomarker discovery: Quantification of microRNAs and other small non-coding RNAs using next generation sequencing
Organism Homo sapiens
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary Background: Small ncRNAs (sncRNAs) offer great hope as biomarkers of disease and response to treatment. This has been highlighted in the context of several medical conditions such as cancer, liver disease, cardiovascular disease, and central nervous system disorders, among many others. Here we assessed several steps involved in the development of an ncRNA biomarker discovery pipeline, ranging from sample preparation to bioinformatic processing. At each stage, we evaluated the pros and cons of different techniques that may be suitable for different experimental designs. Evaluation methods included quality of data output in relation to hands-on laboratory time, cost, and efficiency of processing.
Results: Our results show that good quality sequencing libraries can be prepared from small amounts of total RNA and that varying degradation levels in the samples do not have a significant effect on the overall quantification of sncRNAs via NGS. In addition, we describe the strengths and limitations of three commercially available library preparation methods: (1) Novex TBE PAGE gel; (2) Pippin Prep automated gel system; and (3) AMPure XP beads. We describe our bioinformatics pipeline, provide recommendations for sequencing coverage, and describe in detail the expression and distribution of all sncRNAs in four human tissues: whole-blood, brain, heart and liver.
Conclusions: Ultimately this study provides tools and outcome metrics that will aid researchers and clinicians in choosing an appropriate and effective high-throughput sequencing quantification method for various study designs, and overall generating valuable information that can contribute to our understanding of small ncRNAs as potential biomarkers and mediators of biological functions and disease.
Overall design Quantification of microRNAs and other small non-coding RNAs using next generation sequencing for Biomarker discovery
Contributor(s) Lopez JP, Ernst C
Citation(s) 26130076
Submission date Jun 12, 2015
Last update date May 15, 2019
Contact name Juan Pablo Lopez
Phone 514 7616131
Organization name McGill University
Department Human Genetics
Lab McGill Group for Suicide Studies (MGSS)
Street address 6875 La Salle Blvd
City Montreal
State/province Quebec
ZIP/Postal code H4H1R3
Country Canada
Platforms (2)
GPL15520 Illumina MiSeq (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (71)
GSM1709641 HiSeq_A1
GSM1709642 HiSeq_A2
GSM1709643 HiSeq_A3
BioProject PRJNA286878
SRA SRP059434

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE69825_HiSeq2500.txt.gz 23.3 Kb (ftp)(http) TXT
GSE69825_Library_Preparation.txt.gz 17.7 Kb (ftp)(http) TXT
GSE69825_MiSeq.txt.gz 11.7 Kb (ftp)(http) TXT
GSE69825_RNA_Degradation.txt.gz 26.7 Kb (ftp)(http) TXT
GSE69825_RNA_Input.txt.gz 11.9 Kb (ftp)(http) TXT
GSE69825_ncRNA_Expression.txt.gz 16.2 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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