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Series GSE54106 Query DataSets for GSE54106
Status Public on Oct 01, 2014
Title Genome-wide profiling of mouse RNA secondary structures reveals key features of the mammalian transcriptome
Organism Mus musculus
Experiment type Other
Expression profiling by high throughput sequencing
Summary By using a novel high-throughput method, named chemical inference of RNA structures (CIRS-seq), that uses dimethyl sulfate (DMS), and N-cyclohexyl-N'-(2-morpholinoethyl)carbodiimide metho-p-toluenesulfonate (CMCT) to modify RNA residues in single-stranded conformation within native RNA secondary structures, we investigated the structural features of mouse embryonic stem cell (ESC) transcripts. Our analysis revealed an unexpected higher structuring of the 5' and 3' untranslated regions (UTRs) compared to the coding regions, a reduced structuring at the Kozak sequence and stop codon, and a three-nucleotide periodicity across the coding region of messenger RNAs. We also observed that ncRNAs exhibit a higher degree of structuring with respect to protein coding transcripts. Moreover, we found that the Lin28a binding protein binds selectively to RNA motifs with a strong preference toward a single stranded conformation.
 
Overall design Transcritome-wide mapping of RNA secondary structures in mouse embryonic stem cells (mESC)
Web link http://epigenetics.hugef-research.org/data.php
 
Contributor(s) Incarnato D, Neri F, Anselmi F, Oliviero S
Citation(s) 25323333
Submission date Jan 15, 2014
Last update date Dec 09, 2016
Contact name Francesco Neri
E-mail francesco.neri@hugef-torino.org
Organization name HuGeF
Street address Via Nizza 52
City Torino
State/province Italy
ZIP/Postal code 10126
Country Italy
 
Platforms (1)
GPL16173 Illumina HiScanSQ (Mus musculus)
Samples (7)
GSM1464622 CIRS-seq (Not treated, Replicate #1)
GSM1464623 CIRS-seq (Dimethyl sulfate, Replicate #1)
GSM1464624 CIRS-seq (N-Cyclohexyl- N’-(2-morpholinoethyl)carbodiimide metho-p-toluenesulfonate, Replicate #1)
Relations
BioProject PRJNA235209
SRA SRP035427

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE54106_CIRS-seq_CMCT_combined_rawcounts.bed.gz 62.1 Mb (ftp)(http) BED
GSE54106_CIRS-seq_DMS_combined_rawcounts.bed.gz 57.1 Mb (ftp)(http) BED
GSE54106_CIRS-seq_NT_combined_rawcounts.bed.gz 39.9 Mb (ftp)(http) BED
GSE54106_CIRS-seq_Reactivity_combined.wig.gz 45.0 Mb (ftp)(http) WIG
GSE54106_CIRS-seq_Reactivity_rep1.wig.gz 35.5 Mb (ftp)(http) WIG
GSE54106_CIRS-seq_Reactivity_rep2.wig.gz 32.8 Mb (ftp)(http) WIG
GSE54106_RAW.tar 691.4 Mb (http)(custom) TAR (of BED, WIG)
Raw data are available in SRA
Processed data provided as supplementary file
Processed data is available on Series record

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