GSE145805
GSE GEO Potentially relatedRNA secondary structome of different cell lines
Summary
we resolved the RNA secondary structure of human (HEK293, HeLa, K562, HepG2, H9) and mouse (mES) cells based on optimized in vivo click selective 2'-hydroxyl acylation and profiling experiment (icSHAPE). we describe a deep discriminative neural network (PrismNet) that integrates big data of RBP binding and RNA secondary structure from matched living cells and accurately models the RNA sequence and structural preferences of protein-RNA interactions in vivo, enabling precise prediction of the perturbation effects of genetic variants.
Overall Design
Libraries of 7 cell lines (human: HEK293, HeLa, K562, HepG2, H9 and mouse : mES) were constructed as the optimized icSHAPE protocol. The RNA structure in vivo was calculated based on DMSO samples (D), in vivo NAI-N3 treatment samples (N) by the new protocol icSHAPE-pipe.
Analysis
View Data ProcessingSupplementary Files (1)
SRA Experiments (12) and Runs (24)
Total: 234448 MBPotentially Related Publications (1)
This accession was text-mined from the PMC full text of these publications. It may be referenced for comparison or reused from another study rather than generated for them.
Data Files (24)
| Accession | File Name | Stored Type | Output Type | Mapping Assembly | Size | Download | |
|---|---|---|---|---|---|---|---|
| — | SRR11164860_GSM4333255 | OTHER | 6.4 GB | link | |||
| — | SRR11164861_GSM4333255 | OTHER | 7.1 GB | link | |||
| — | SRR11164862_GSM4333256 | OTHER | 14.4 GB | link | |||
| — | SRR11164863_GSM4333256 | OTHER | 13.7 GB | link | |||
| — | SRR11164864_GSM4333257 | OTHER | 8.8 GB | link | |||
| — | SRR11164865_GSM4333257 | OTHER | 7.2 GB | link | |||
| — | SRR11164866_GSM4333258 | OTHER | 12.6 GB | link | |||
| — | SRR11164867_GSM4333258 | OTHER | 17.4 GB | link | |||
| — | SRR11164868_GSM4333259 | OTHER | 5.4 GB | link | |||
| — | SRR11164869_GSM4333259 | OTHER | 4.8 GB | link | |||
| — | SRR11164870_GSM4333260 | OTHER | 11.3 GB | link | |||
| — | SRR11164871_GSM4333260 | OTHER | 12.2 GB | link | |||
| — | SRR11164872_GSM4333261 | OTHER | 1.7 GB | link | |||
| — | SRR11164873_GSM4333261 | OTHER | 1.9 GB | link | |||
| — | SRR11164874_GSM4333262 | OTHER | 13.0 GB | link | |||
| — | SRR11164875_GSM4333262 | OTHER | 12.3 GB | link | |||
| — | SRR11164876_GSM4333263 | OTHER | 6.6 GB | link | |||
| — | SRR11164877_GSM4333263 | OTHER | 6.3 GB | link | |||
| — | SRR11164878_GSM4333264 | OTHER | 14.2 GB | link | |||
| — | SRR11164879_GSM4333264 | OTHER | 12.9 GB | link | |||
| — | SRR11164880_GSM4333265 | OTHER | 7.4 GB | link | |||
| — | SRR11164881_GSM4333265 | OTHER | 6.4 GB | link | |||
| — | SRR11164882_GSM4333266 | OTHER | 11.3 GB | link | |||
| — | SRR11164883_GSM4333266 | OTHER | 13.8 GB | link |