eSHAPE db-K562
A deep sequencing database of SHAPE and ∆SHAPE data
Technology Overview
Selective 2’-Hydroxyl Acylation analyzed by Primer Extension (SHAPE) is a chemical probing method that measures RNA flexibility at single nucleotide resolution. NAI adducts, formed during probing, induce a higher rate of mutations by reverse transcriptase at the modified positions during the generation of cDNA, compared to DMSO control. SHAPE technology measures local RNA flexibility both in cellular conditions (in vivo) and in purified, deproteinized RNA (in vitro), which can aid in the prediction of RNA secondary structure. In vitro SHAPE reveals flexibility information across the RNA strand while in vivo SHAPE reveals flexibility in regions not bound by proteins. The combination of in vivo and in vitro mutation rates, ∆SHAPE, can identify RNA positions that interact with proteins.
eSHAPE db-K562 is a deep sequencing database containing in vivo and in vitro SHAPE data, as well as ∆SHAPE data from the K562 cell line. The eSHAPE db-K562 is based on 6 technical replicates of polyA-selected RNA and is delivered as a data package for a single gene of interest or sets of genes at a time.
Per Gene Deliverables
| File | Description |
|---|---|
| plots | Coverage, mutation rate, and reactivity line plots across the gene and mutation rate box plot (.svg) |
| .shape | Reactivity values formatted for input to the RNAStructure algorithm to guide a fold prediction |
| metrics | Gene metrics table including total reads, coverage, uniformity and FPKM |
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300X coverage yields reactivities with high sensitivity and specificity
- Mutations generated by the NAI treatment yield valuable information on the paired or unpaired status of nucleotides.
- Minimal 300X coverage provides maximal RNA folding sensitivity and specificity.
SHAPE reactivities guide accurate RNA fold
- SHAPE reactivities produced at each nucleotide are used as input to RNA folding algorithms such as RNAStructure to guide the folding of the RNA molecule.
- SHAPE-guided RNA secondary structure predicted with >90% accuracy.
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fSHAPE predicts RBP binding
- The combination of in vivo and in vitro NAI probing datasets, footprinting SHAPE (∆SHAPE), reveals RNA nucleotides that interact with RNA binding proteins (RBPs).
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