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GEO help: Mouse over screen elements for information. |
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| 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
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| 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.
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| Overall design |
Transcritome-wide mapping of RNA secondary structures in mouse embryonic stem cells (mESC)
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| Web link |
http://epigenetics.hugef-research.org/data.php
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| 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
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| Organization name |
HuGeF
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| Street address |
Via Nizza 52
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| City |
Torino |
| State/province |
Italy |
| ZIP/Postal code |
10126 |
| Country |
Italy |
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| Platforms (1) |
| GPL16173 |
Illumina HiScanSQ (Mus musculus) |
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| Samples (7)
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| 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) |
| GSM1464625 |
CIRS-seq (Not treated, Replicate #2) |
| GSM1464626 |
CIRS-seq (Dimethyl sulfate, Replicate #2) |
| GSM1464627 |
CIRS-seq (N-Cyclohexyl- N’-(2-morpholinoethyl)carbodiimide metho-p-toluenesulfonate, Replicate #2) |
| GSM1464628 |
RNA-seq (Ribo-) |
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| Relations |
| BioProject |
PRJNA235209 |
| SRA |
SRP035427 |
| 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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