Table 1.

Large-Scale Efforts to Catalog lincRNA Loci and Transcripts

Reference	Data for Transcript Reconstruction	Genomic Features and Filters	Coding-Potential Filters	Number of lincRNAs
Mouse
Ravasi et al., 2006	cDNAs		Manual curation, ORF length, CRITICA	13,502 transcripts
Ponjavic et al., 2007	cDNAs, CAGE		Manual curation, ORF length, BLAST, CRITICA	3,122 transcripts
Guttman et al., 2009	Chromatin marks, tiling arrays	Collection of approximate exonic regions, chromatin domain ≥5 kb	CSF	1,675 loci (1,250 conservatively defined)
Guttman et al., 2010	RNA-seq	Multi-exon only	CSF	1,140 lincRNA transcripts
Sigova et al., 2013	RNA-seq, cDNAs, chromatin marks,	Antisense overlap with mRNA introns allowed, ≥100 nt mature length	CPC	1,664 loci

Human
Khalil et al., 2009	Chromatin marks, tiling arrays	Collection of approximate exonic regions, chromatin domain ≥ 5 kb	CSF	3,289 loci
Jia et al., 2010	cDNAs	Overlap with mRNAs allowed		5,446 transcripts
Ørom et al., 2010	cDNAs	Restricted to loci >1 kb away from known protein-coding genes, ≥200 nt mature length	Manual curation based on length, conservation and other characteristics of the ORFs	3,019 transcripts from 2,286 loci
Cabili et al., 2011	RNA-seq	Multi-exon only, ≥200 nt mature length	PhyloCSF, Pfam	8,195 transcripts (4,662 in the stringent set)
Derrien et al., 2012	cDNAs	Overlap with mRNAs allowed (intergenic transcripts reported separately), ≥200 nt mature length	Manual curation based on length, conservation and other characteristics of the ORFs	14,880 transcripts from 9,277 loci, including 9,518 intergenic transcripts
Sigova et al., 2013	RNA-seq, cDNAs, chromatin marks,	Antisense overlap with mRNA introns allowed, ≥100 nt mature length	CPC	3,548 loci from embryonic stem cells, and 3,986 loci from endodermal cells

Frog
Tan et al., 2013	RNA-Seq	>25 kb away from known protein- coding genes or on a different strand from the neighboring genes, ≥200 nt mature length	ORF length, BLAST, Pfam	6,686 transcripts from 3,859 loci

Zebrafish
Ulitsky et al., 2011	RNA-seq, cDNAs, 3P-seq, chromatin marks	Antisense overlap with mRNA introns allowed, ≥200 nt mature length	CPC	691 transcripts from 567 loci
Pauli et al., 2012	RNA-seq	Stringent criteria for single exon, intron overlap with mRNA allowed, ≥160 nt mature length	ORF length, PhyloCSF, BLAST, Pfam	397 intergenic and 184 intronic overlapping transcripts

Fly
Tupy et al., 2005	cDNA		Manual curation based on ORF length, conservation and other characteristics, K_a/K_s test, QRNA	17 transcripts
Young et al., 2012	RNA-seq	≥200 nt locus length		1,119 trancripts

Nematode
Nam and Bartel, 2012	RNA-seq, 3P-seq	≥100 nt mature length	CPC, RNAcode, ribosome profiling, polysome association	262 lincRNA transcripts from 170 loci

Arabidopsis
Liu et al., 2012a	cDNA, tiling arrays, RNA-seq	In part a collection of approximate exonic regions, >500 bp away from protein-coding genes, no overlap with transposable elements allowed, ≥200 nt mature length	ORF length	6,480 transcription units from tiling arrays, 278 transcripts from RNA-seq

Maize
Boerner and McGinnis, 2012	cDNA	Both sense overlap with introns and antisense overlap with mRNA or introns allowed, ≥200 nt mature length	ORF length	2,492 transcripts

Plasmodium falciparum
Broadbent et al., 2011	Tiling arrays	Collection of approximate exonic regions, ≥200 nt mature length	BLAST	60 transcripts

Transcripts overlapping protein-coding sequences on either strand were excluded unless noted otherwise. Coding-potential filters included: ORF length; similarity to known protein-coding regions (BLAST); substitution patterns in whole-genome alignments, quantified by CRITICA (Badger and Olsen, 1999), CSF (Lin et al., 2007), PhyloCSF (Lin et al., 2011), QRNA (Rivas and Eddy, 2001; Rivas et al., 2001), or RNAcode (Washietl et al., 2011), as indicated; the CPC algorithm, which evaluates ORF properties and similarity to known proteins (Kong et al., 2007); the HMMER algorithm, which tests for potential to encode a known protein domain (Pfam); ribosome profiling, and polyribosome association. Criteria used to define the lincRNA collection (and not those used only for characterization) are listed.