A deep sequencing database of SHAPE and fSHAPE data
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.
|.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)|
Learn More About SHAPE db-K562
Schedule a meeting with Eclipsebio’s RNA experts today.