Author: Timothy A. Dinh; Ramja Sritharan; F. Donelson Smith; Adam B. Francisco; Rosanna K. Ma; Rodica P. Bunaciu; Matt Kanke; Charles G. Danko; Andrew P. Massa; John D. Scott; Praveen Sethupathy
Title: Hotspots of aberrant enhancer activity in fibrolamellar carcinoma reveal molecular mechanisms of oncogenesis and intrinsic drug resistance Document date: 2020_1_18
ID: bf4qpsy7_53
Snippet: Small RNA sequencing was performed as previously described (Dinh et al., 2019) . Briefly, reads were trimmed using Cutadapt and mapped to the genome using Bowtie (Langmead et al., 2009) . Perfectly aligned reads represented miRNA loci and then imperfectly mapped reads (derived from isomiRs) were re-aligned to these loci using SHRiMP (Rumble et al., 2009) . Aligned reads were quantified and normalized using reads per million mapped to miRNAs. Data.....
Document: Small RNA sequencing was performed as previously described (Dinh et al., 2019) . Briefly, reads were trimmed using Cutadapt and mapped to the genome using Bowtie (Langmead et al., 2009) . Perfectly aligned reads represented miRNA loci and then imperfectly mapped reads (derived from isomiRs) were re-aligned to these loci using SHRiMP (Rumble et al., 2009) . Aligned reads were quantified and normalized using reads per million mapped to miRNAs. Data are available from the Gene Expression Omnibus (GEO): accession number GSE114974.
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