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| Status |
Public on Apr 13, 2023 |
| Title |
Reactivity-Based RNA Profiling (RBRP) determined transcriptome interactions of small molecule drugs |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We developed Reactivity-Based RNA Profiling (RBRP) approach to determine the off-target transcriptome interactions of small molecule drugs. Deep sequencing was used to locate and quantify drug-promoted acylation of RNA 2ยด-hydroxyl groups as a proxy of RNA-drug interaction in HEK293.
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| Overall design |
The sequencing experiments were performed in two biological replicates. Comparative analysis of deep sequencing data using a customized pipeline identifies drug binding events.
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| Contributor(s) |
Fang L, Kool E |
| Citation(s) |
37917579 |
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| Submission date |
Apr 10, 2023 |
| Last update date |
Dec 06, 2023 |
| Contact name |
Linglan Fang |
| Organization name |
Stanford University
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| Street address |
369 N-S AXIS STAUFFER I, RM-107-CHEMISTRY-KOOL LAB
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| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platforms (1) |
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| Samples (28)
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| GSM7158909 |
Das-comp-2, RBRP |
| GSM7158910 |
DMSO-1, RBRP |
| GSM7158911 |
DMSO-2, RBRP |
| GSM7158912 |
Exp-Das-1, RNA-seq |
| GSM7158913 |
Exp-Das-2, RNA-seq |
| GSM7158914 |
Exp-DMSO-1, RNA-seq |
| GSM7158915 |
Exp-DMSO-2, RNA-seq |
| GSM7158916 |
Exp-HCQ-1, RNA-seq |
| GSM7158917 |
Exp-HCQ-2, RNA-seq |
| GSM7158918 |
Exp-Lev-1, RNA-seq |
| GSM7158919 |
Exp-Lev-2, RNA-seq |
| GSM7158920 |
HCQ-1, RBRP |
| GSM7158921 |
HCQ-2, RBRP |
| GSM7158922 |
HCQ-comp-1, RBRP |
| GSM7158923 |
HCQ-comp-2, RBRP |
| GSM7158924 |
Lev-1, RBRP |
| GSM7158925 |
Lev-2, RBRP |
| GSM7158926 |
Lev-comp-1, RBRP |
| GSM7158927 |
Lev-comp-2, RBRP |
| GSM7158928 |
Lev-diazirine-1 |
| GSM7158929 |
Lev-diazirine-2 |
| GSM7158930 |
Lev-diazirine-comp-1 |
| GSM7158931 |
Lev-diazirine-comp-2 |
| GSM7158932 |
Linker-1, RBRP |
| GSM7158933 |
Linker-2, RBRP |
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| Relations |
| BioProject |
PRJNA954018 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE229331_RNA-seq_Das.txt.gz |
179.6 Kb |
(ftp)(http) |
TXT |
| GSE229331_RNA-seq_HCQ.txt.gz |
168.1 Kb |
(ftp)(http) |
TXT |
| GSE229331_RNA-seq_Lev.csv.gz |
207.6 Kb |
(ftp)(http) |
CSV |
| GSE229331_Results_Lev_diazirine.csv.gz |
137.5 Kb |
(ftp)(http) |
CSV |
| GSE229331_diff_RBRP_Das.sim.bw |
2.9 Mb |
(ftp)(http) |
BW |
| GSE229331_diff_RBRP_HCQ.sim.bw |
719.1 Kb |
(ftp)(http) |
BW |
| GSE229331_diff_RBRP_Lev.sim.bw |
2.4 Mb |
(ftp)(http) |
BW |
| GSE229331_neglog10P-value_Das.sim.bw |
2.4 Mb |
(ftp)(http) |
BW |
| GSE229331_neglog10P-value_HCQ.sim.bw |
234.8 Kb |
(ftp)(http) |
BW |
| GSE229331_neglog10P-value_Lev.sim.bw |
2.2 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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