|
| Status |
Public on Aug 22, 2017 |
| Title |
Target-Enrichment Sequencing for Detailed Characterization of Small RNAs |
| Organism |
Mus musculus |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
Identification of important, functional small RNA (sRNA) species is presently hampered by the lack of reliable and sensitive methods to isolate and characterize them. We have developed a method termed Target-Enrichment of small RNAs (TEsR), which enables targeted sequencing of rare sRNAs and diverse precursor and mature forms of sRNAs not detectable by current standard sRNA sequencing methods. It is based on the amplification of full length sRNA molecules, production of biotinylated RNA probes, hybridization to one or multiple targeted RNA, removal of non-targeted sRNAs, and sequencing. By this approach, target sRNAs can be enriched by a factor of 500-30,000 while maintaining strand specificity. TEsR enriches for sRNAs irrespective of length or different molecular features, such as the presence or absence of a 5’-cap or of secondary structures or abundance levels, and allows the detection of the complete sequence (including sequence variants, 5’ and 3’ ends) of precursors, intermediate and mature forms, and all this quantitatively.
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| |
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| Overall design |
RNA extracted from mouse embryonic fibroblast cell lines (MEFs), induced or uninduced for TRF2 conditional knock out, were used for targeted enrichment sequencing of small RNA (TEsR) and MiSeq sequencing or standard TruSeq small RNA sequencing. Each treatment had at least two replicates.
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| |
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| Contributor(s) |
Nguyen Q, Aguado J, Iannelli F, Suzuki A, Rossiello F, dʼAdda di Fagagna F, Carninci P |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Aug 21, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Quan Hoang Nguyen |
| E-mail(s) |
quan.nguyen@uq.edu.au
|
| Phone |
(+61)733463147
|
| Organization name |
The University of Queensland
|
| Department |
Australian Institute for Bioengineering and Nanotechnology
|
| Lab |
Single cell and computational genomics lab
|
| Street address |
Queensland Bioscience Precinct (Building 80) The University of Queensland. 306 Carmody Road. St
|
| City |
Brisbane |
| State/province |
Queensland |
| ZIP/Postal code |
4067 |
| Country |
Australia |
| |
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| Platforms (2) |
| GPL16417 |
Illumina MiSeq (Mus musculus) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
|
| Samples (8)
|
| GSM2747111 |
MEF induced sample 1 (MiSeq TEsR sequencing) |
| GSM2747112 |
MEF induced sample 2 (MiSeq TEsR sequencing) |
| GSM2747113 |
MEF uninduced sample 1 (MiSeq TEsR sequencing) |
| GSM2747114 |
MEF uninduced sample 2 (MiSeq TEsR sequencing) |
| GSM2747115 |
MES sample 1 (MiSeq TEsR sequencing) |
| GSM2747116 |
MES sample 2 (MiSeq TEsR sequencing) |
| GSM2747117 |
MEF induced HiSeq sample 1 (HiSeq TruSeq sRNA sequencing) |
| GSM2747118 |
MEF induced HiSeq sample 2 (HiSeq TruSeq sRNA sequencing) |
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| Relations |
| BioProject |
PRJNA399091 |
| SRA |
SRP115890 |
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