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Series GSE102845 Query DataSets for GSE102845
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.
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.
Contributor(s) Nguyen Q, Aguado J, Iannelli F, Suzuki A, Rossiello F, dʼAdda di Fagagna F, Carninci P
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Submission date Aug 21, 2017
Last update date May 15, 2019
Contact name Quan Hoang Nguyen
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
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)
BioProject PRJNA399091
SRA SRP115890

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Supplementary file Size Download File type/resource
GSE102845_Control_SRhi10132_count_all_miRNAs_snoRNAs_rRNAs_snRNAs.txt.gz 88.0 Kb (ftp)(http) TXT
GSE102845_Count_all_miRNAs_snoRNAs_rRNAs_snRNAs.txt.gz 92.2 Kb (ftp)(http) TXT
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Processed data are available on Series record

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