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| Status |
Public on Sep 24, 2024 |
| Title |
Transcriptome-wide mapping of RNA secondary structure ensembles in a living cell |
| Organism |
Escherichia coli |
| Experiment type |
Other
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| Summary |
RNA molecules can populate an ensemble of alternative structural conformations, but the true extent of the RNA secondary structure folding space of a living cell has never been explored. We here generated the first transcriptome-wide maps of RNA secondary structure ensembles in Escherichia coli, both at physiological temperature and upon cold-shock. Our analysis revealed hundreds of novel putative conserved RNA switches.
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| Overall design |
RNA structure analysis of Escherichia coli by DMS chemical probing and mutational profiling (DMS-MaPseq)
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| Web link |
https://www.biorxiv.org/content/10.1101/2024.09.16.613214v1.full
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| Contributor(s) |
Borovska I, Morandi E, Zhang C, Petrov A, Incarnato D |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Nov 07, 2023 |
| Last update date |
Sep 25, 2024 |
| Contact name |
Danny Incarnato |
| E-mail(s) |
d.incarnato@rug.nl
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| Organization name |
University of Groningen
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| Department |
Molecular Genetics
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| Street address |
Nijenborgh 7
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| City |
Groningen |
| State/province |
Netherlands |
| ZIP/Postal code |
9747 AG |
| Country |
Netherlands |
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| Platforms (2) |
| GPL33918 |
DNBSEQ-G400 (Escherichia coli) |
| GPL33919 |
NextSeq 1000 (Escherichia coli) |
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| Samples (10)
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| GSM7885838 |
DMS-MaPseq of E. coli DH5a, exponential phase, 37°C (mRNA) |
| GSM7885839 |
DMS-MaPseq of E. coli TOP10, exponential phase, 37°C (mRNA) |
| GSM7885840 |
DMS-MaPseq of E. coli DH5a, exponential phase, 10°C cold-shock (mRNA) |
| GSM7885841 |
DMS-MaPseq of E. coli TOP10, exponential phase, 10°C cold-shock (mRNA) |
| GSM7885842 |
DMS-MaPseq of E. coli DH5a, exponential phase, in vivo, 37°C (total RNA) |
| GSM7885843 |
DMS-MaPseq of E. coli TOP10, exponential phase, in vivo, 37°C (total RNA) |
| GSM7885844 |
DMS-MaPseq of E. coli DH5a, exponential phase, ex vivo, 37°C (total RNA) |
| GSM7885845 |
DMS-MaPseq of E. coli TOP10, exponential phase, ex vivo, 37°C (total RNA) |
| GSM8335533 |
DMS-MaPseq of E. coli DH5a, in vitro refolded, 37°C (mRNA) |
| GSM8335534 |
DMS-MaPseq of E. coli TOP10, in vitro refolded, 37°C (mRNA) |
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| Relations |
| BioProject |
PRJNA1036687 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE247244_RAW.tar |
105.8 Mb |
(http)(custom) |
TAR (of WIG) |
SRA Run Selector |
| Raw data are available in SRA |
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