SHAPE db-K562

A deep sequencing database of SHAPE and fSHAPE 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, fSHAPE, can identify RNA positions that interact with proteins.

SHAPE db-K562 is a deep sequencing database containing in vivo and in vitro SHAPE data, as well as fSHAPE data from the K562 cell line. The SHAPE 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.

Data Deliverables

File Description
.bam SHAPE db-K562 DMSO reads aligned to the genome and intersected with a gene of interest
SHAPE db-K562 NAI reads aligned to the genome and intersected with a gene of interest
.bed Gene annotation file used for SHAPE db-K562 data calculations
.shape Reactivity values formatted for input to the RNAStructure algorithm to guide a fold prediction
.bedgraph Reactivity score at each position across the gene with >300x coverage for genome visualization
metrics Gene metrics table including total reads, coverage, uniformity and FPKM
plots Coverage, mutation rate, and reactivity line plots across the gene and mutation rate box plot (.svg)

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300X coverage yields reactivities with high sensitivity and specificity

SHAPE reactivities guide accurate RNA fold

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fSHAPE predicts RBP binding

RESOURCES

rbp eclip 4

Learn More About SHAPE db-K562

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