Description

This track contains information that appears in the paper by DaSilva L.F. et al. (2018) Chromatin landscape distinguishes the genomic loci of hundreds of androgen-receptor-associated lincRNAs from the loci of non-associated lincRNAs. Front. Genet. 9:132 https://doi.org/10.3389/fgene.2018.00132.

Tracks described in the above paper

• ARA_lincRNAs: Immunoprecipitation of Androgen Receptor (AR), followed by large-scale sequencing of co-immunoprecipitated RNAs (RIP-seq) has identified in the LNCaP cell line a total of 619 lincRNAs that were significantly enriched (FDR ≤ 10%, DESeq2) in the anti-Androgen Receptor (antiAR) fraction in relation to the control fraction (non-specific IgG), and they were named Androgen-Receptor-Associated lincRNAs (ARA-lincRNAs). This data can be browsed in this track and can be downloaded from http://verjolab.usp.br/tracks/hg/hg19/genes/.


• Comprehensive_LNCaP_transcriptome: Deep RNA-seq data from four replicates of LNCaP cell cultures were trimmed of low-quality reads and clipped of sequencing adaptors with Trimmomatic (Bolger et al., 2014). Trimmed reads were aligned to hg19 version of the human genome with TopHat2 (Kim et al., 2013), followed by an assembly using the Cufflinks 2.2 tool (Trapnell et al., 2013) with the default parameters. For the alignment and assembly, a comprehensive_reference_transcriptome custom GTF file was used (see below). Transcriptome assemblies were generated for each of the four samples separately, and then Cuffmerge (Trapnell et al., 2013) was used to combine the transcripts from all samples. The resulting merged GTF file is deposited at NCBI in the GEO repository under Accession number GSE100710. Next, both GTF files mentioned above were merged to generate a comprehensive_LNCaP_transcriptome GTF file, which can be browsed in this track and can be downloaded from http://verjolab.usp.br/tracks/hg/hg19/genes/.


• LNCaP_lincRNAs: All lincRNA transcripts detected as expressed with FPKM ≥ 1 in the deep RNA-seq data from four replicates of LNCaP cell cultures were kept in this dataset. Previously annotated lncRNAs in the comprehensive reference transcriptome (custom GTF) were identified; next, novel transcripts were identified in these analyses (class code "u" identified by Cuffmerge—putative novel intergenic transcripts). All transcripts with a length ≤ 200 nt were removed. All transcripts with coding potential, as assessed by the Coding Potential Calculator (CPC version 0.9-r2) (Kong et al., 2007) were discarded, thus resulting in the set of all lincRNAs expressed in LNCaP with FPKM ≥ 1. A GTF file with these LNCaP_lincRNAs can be browsed in this track and can be downloaded from http://verjolab.usp.br/tracks/hg/hg19/genes/.


• Comprehensive_reference_transcriptome: This data set is comprised of the human transcripts from GENCODE v19 (Harrow et al., 2012) plus the lincRNAs already annotated in three other publications (Cabili et al., 2011; Prensner et al., 2011; Hangauer et al., 2013). This custom GTF can be browsed in this track and can be downloaded from http://verjolab.usp.br/tracks/hg/hg19/genes/.