TY - JOUR A2 - Cai, Yudong AU - Das, Shaoli AU - Ghosal, Suman AU - Chakrabarti, Jayprokas AU - Kozak, Karol PY - 2013 DA - 2013/08/29 TI - SeedSeq: Off-Target Transcriptome Database SP - 905429 VL - 2013 AB - Detection of potential cross-reaction between a short oligonucleotide sequence and a longer (unintended) sequence is crucial for many biological applications, such as high content screening (HCS), microarray nucleotide probes, or short interfering RNAs (siRNAs). However, owing to a tolerance for mismatches and gaps in base-pairing with target transcripts, siRNAs could have up to hundreds of potential target sequences in a genome, and some small RNAs in mammalian systems have been shown to affect the levels of many messenger RNAs (off-targets) besides their intended target transcripts (on-targets). The reference sequence (RefSeq) collection aims to provide a comprehensive, integrated, nonredundant, well-annotated set of sequences, including mRNA transcripts. We performed a detailed off-target analysis of three most commonly used kinome siRNA libraries based on the latest RefSeq version. To simplify the access to off-target transcripts, we created a SeedSeq database, a new unique format to store off-target information. SN - 2314-6133 UR - https://doi.org/10.1155/2013/905429 DO - 10.1155/2013/905429 JF - BioMed Research International PB - Hindawi Publishing Corporation KW - ER -