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| Status |
Public on Dec 17, 2022 |
| Title |
Effect of reduced glucocorticoid receptor-RNA affinity on dexamethasone treatment |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The RNA binding ability of the glucocorticoid receptor (GR) remains an understudied area of GR regulation. Through in vitro binding assays, we identified a separation-of-function mutation (SoF) in the DNA-binding domain that greatly reduces RNA affinity with a slight reduction in DNA affinity. To study the effects of RNA binding on GR function, we first generated stable U2OS cells expressing wild-type GR-HaloTag, the SoF mutant, or a control (Ctrl) mutant that mimics the SoF's reduction in DNA affinity without impairing RNA affinity. We then treated the cells with dexamethsone every hour over three hours with 4-thiouridine labeling, isolated the labeled RNAs, and used deep sequencing to measure changes in the dexamethasone-driven transcriptome.
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| Overall design |
4sU-seq to measure differences in the transcriptome between glucocorticoid receptor constructs in U2OS over 3 hours of 100 nM dexamethasone treatment.
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| Contributor(s) |
Lammer NC, Allen MA, Wuttke DS, Batey RT |
| Citation(s) |
37296231, 37608297 |
| Submission date |
Oct 21, 2022 |
| Last update date |
Sep 14, 2023 |
| Contact name |
Nickolaus Charles Lammer |
| E-mail(s) |
nickolaus.lammer@colorado.edu
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| Organization name |
University of Colorado, Boulder
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| Department |
Biochemistry
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| Lab |
Deborah S. Wuttke Lab
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| Street address |
3415 Colorado Ave
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| City |
Boulder |
| State/province |
Colorado |
| ZIP/Postal code |
80303 |
| Country |
USA |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (24)
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| GSM6670643 |
U2OS, wt GR-HaloTag, 1hdex, rep2 |
| GSM6670644 |
U2OS, wt GR-HaloTag, 2hdex, rep1 |
| GSM6670645 |
U2OS, wt GR-HaloTag, 2hdex, rep2 |
| GSM6670646 |
U2OS, wt GR-HaloTag, 3hdex, rep1 |
| GSM6670647 |
U2OS, wt GR-HaloTag, 3hdex, rep2 |
| GSM6670648 |
U2OS, SoF K492A GR-HaloTag, 0hdex, rep1 |
| GSM6670649 |
U2OS, SoF K492A GR-HaloTag, 0hdex, rep2 |
| GSM6670650 |
U2OS, SoF K492A GR-HaloTag, 1hdex, rep1 |
| GSM6670651 |
U2OS, SoF K492A GR-HaloTag, 1hdex, rep2 |
| GSM6670652 |
U2OS, SoF K492A GR-HaloTag, 2hdex, rep1 |
| GSM6670653 |
U2OS, SoF K492A GR-HaloTag, 2hdex, rep2 |
| GSM6670654 |
U2OS, SoF K492A GR-HaloTag, 3hdex, rep1 |
| GSM6670655 |
U2OS, SoF K492A GR-HaloTag, 3hdex, rep2 |
| GSM6670656 |
U2OS, Ctrl R470A GR-HaloTag, 0hdex, rep1 |
| GSM6670657 |
U2OS, Ctrl R470A GR-HaloTag, 0hdex, rep2 |
| GSM6670658 |
U2OS, Ctrl R470A GR-HaloTag, 1hdex, rep1 |
| GSM6670659 |
U2OS, Ctrl R470A GR-HaloTag, 1hdex, rep2 |
| GSM6670660 |
U2OS, Ctrl R470A GR-HaloTag, 2hdex, rep1 |
| GSM6670661 |
U2OS, Ctrl R470A GR-HaloTag, 2hdex, rep2 |
| GSM6670662 |
U2OS, Ctrl R470A GR-HaloTag, 3hdex, rep1 |
| GSM6670663 |
U2OS, Ctrl R470A GR-HaloTag, 3hdex, rep2 |
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| Relations |
| BioProject |
PRJNA893006 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE216337_4su_exon_stranded_counts.csv.gz |
1.4 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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