Chunk #39 — Materials and Methods — LincRNA Discovery — Transcripts annotated in public databases and literature sources that could be lincRNAs were compiled
Ensembl v61 “processed_transcript” and “lincRNA” categories, GENCODE v6 “processed_transcript” and “lincRNA” categories, RefSeq NR and XR genes, H-Invitational “noncoding” transcripts, ultra conserved elements (UCEs), and published lincRNAs from Khalil et al. [18] and Cabili et al. [16]. LiftOver was used to map hg19 coordinates to hg18 for Ensembl, GENCODE, H-Invitational and Cabili et al. [16] transcripts. RefSeq XR sequences in hg19 were aligned to hg18 with BLAT v34 and the top scoring alignment was used. Ultra conserved elements sequences were retrieved from http://biodev.cbm.fvg.it, aligned to hg18 with BLAT v34 and the top scoring alignment was used. Khalil et al. [18] exons were grouped by their overlapping defined transcribed regions to build transcript structures.
