Resources introduction
ResourceNameIllustrationResource DetailsTranscript levelGene levelRegion level
CABILICabili et al. presented an integrative approach to define a reference catalog of >8000 human lincRNAs from RNA-seq data sets across 24 tissues and cell types (including Human lung fibroblasts (hLF), hLF2, Foreskin fibroblasts, Brain, HeLa, Liver, Placenta and Testes from the Rinn lab; 16 tissues from the Human Body Map 2 project).CABILI details
KELLEYKelley et al. comprehensively characterized the transposable elements content of lincRNAs which were assembled from RNA sequencing (RNA-Seq) using multiple tissues and cell lines.KELLEY details
KRETZTo define transcriptional dynamics during terminal differentiation, Kretz et al. performed paired-end, high-throughput RNA-Seq of primary human keratinocytes during days 0, 3, and 6 of calcium-induced differentiation. KRETZ details
DINGDing et al. described a comprehensive analysis of lincRNAs in twenty five pairs of snap-frozen breast cancer tissues and matched cancer adjacent tissues by RNA-Seq.DING details
KHALILKhalil et al. developed an approach for identifying large noncoding RNAs based on a distinctive chromatin signature that marks actively transcribed genes. The signature consists of a short region with histone H3 lysine 4 trimethylation (H3K4me3) (corresponding to the promoter) and a longer region with histone H3 lysine 36 trimethylation (H3K36me3, corresponding the transcribed region). They refer to this chromatin signature as a K4-K36 domain.KHALIL details
WHITEWhite et al. analyzed poly-A purified RNA-Seq data from three cohorts: LUSC cohort, LUAD cohort and adenocarcinomas and adjacent normal pairs from a Korean population.WHITE details
HEHe et al. used the lincRNA identification procedure described in Cabili et al. in the prefrontal cortex (PFC).HE details
HANGAUERHangauer et al. used de novo transcriptome assembly of a large set of RNA-seq data covering a wide array of human tissue types to discover intergenic regions encode far more lincRNAs than previously described.HANGAUER details
IYERTo delineate genome-wide lncRNA expression, Iyer et al curated 7,256 RNA sequencing (RNA-seq) libraries from tumors, normal tissues and cell lines comprising over 43 Tb of sequence from 25 independent studies. To permit sensitive detection of lineage-specific transcription, they partitioned the libraries into 18 cohorts by organ system (Skin, Blood, Cervix, Uterus, Ovary, Breast, Prostate, Bladder, Kidney, Colon, Liver, Pancreas, Stomach, Lung, Thyroid, Head andneck, Brain and Others). They applied ab initio assembly methodology to this data set, yielding a consensus human transcriptome of 91,013 expressed genes. 52,283 of genes were classified as lncRNAs after removing the transcripts of unknown coding potential (TUCP).IYER details
TRIMARCHITrimarchi et al. utilized a workflow to generate a high confidence T-ALL lncRNA annotation comprised of 6,023 isoforms derived from 1,984 unique gene loci. These ultra-high-depth RNA-sequencing (RNA-seq) data sets were generated by from T-ALL cell lines (CUTLL1 and HPBALL), two primary human thymus samples and ten primary pediatric T-ALL samples.TRIMARCHI details
MORANMoran et al. integrated sequence-based transcriptome and chromatin maps of human islets and beta-cells to define 1,128 islet lncRNA genes. We generated directional and non-directional cDNA libraries from PolyA+ and Ribo- RNA fractions of six human islets and two FACS-purified beta-cell samples, and mapped epigenetic gene landmarks in three human islet samples, including H3K4me3 which is enriched in active promoter regions. These datasets were then integrated to build strand-specific models of active human islet-cell genes with their predominant splicing patterns.MORAN details
SIGOVA1Sigova et al. compiled this catalog of lncRNA species expressed in hESCs as summarized in the figure below. Sigova1 contains a catalog of 3,548 lncRNA species expressed in hESCs.SIGOVA details
SIGOVA2Sigova et al. compiled this catalog of lncRNA species which contains a catalog of 3,986 lncRNA loci expressed in 48hr human endoderm. This catalog of lncRNAs was produced by using the criteria for generation of hESC referring Sigova1.SIGOVA details
BELLBell et al. performed RNA-seq in human coronary artery smooth muscle cell (HCASMC) as a first step toward understanding the potential role of lncRNAs in human SMC phenotypic control.BELL details
YANGDeep sequencing of RNA isolated from paired nonischemic (NICM; n=8) and ischemic (ICM; n=8) human failing LV samples collected before and after LVAD and from nonfailing human LV (n=8) was conducted by Yang et al.. YANG details
NEUsing ab initio transcript assembly of a deeply sequenced RNA data set, Nicholas E. IIott et al. examined the response of lncRNAs to TLR4 signalling through LPS stimulation.NE details
PARALKARParalkar used RNA-seq to identify 594(high + low stringency) polyadenylated lncRNAs expressed in erythroblasts of humans. PARALKAR details
SOWALSKYSowalsky et al. conducted paired-end RNA-sequencing (RNA-seq) on a panel of the bone marrow biopsy specimens of castration-resistant prostate cancer (CRPC) and performed novel lncRNA discovery using CuffLinks, accepting any novel unannotated transcript greater than 200 nucleotides with at least two exons. Finally, 2,965 novel candidate lncRNAs observed CRPC.SOWALSKY details
YANYan et al. applied single-cell RNA sequencing analysis to 124 individual cells from human preimplantation embryos and human embryonic stem cells (hESCs) at different passages.YAN details
NECSULEA1Necsulea et al. used RNA sequencing (data set was previously published and new) to determine lncRNA repertoires of human, including the polyadenylated transcriptomes of 8 organs (cortex or whole brain, cerebellum, heart, kidney, liver, placenta, ovary and testes).NECSULEA details
NECSULEA2Necsulea et al. used RNA sequencing (strand-specific data set was previously published and new) to determine lncRNA repertoires of human, including the polyadenylated transcriptomes of 8 organs (cortex or whole brain, cerebellum, heart, kidney, liver, placenta, ovary and testes).NECSULEA details
GENCODEGENCODE present and analyze the most complete human lncRNA annotation to date, produced by the GENCODE consortium within the framework of the ENCODE project and comprising 9,277 manually annotated genes producing 14,880 transcripts.GENCODE details
LNCipediaWe present LNCipedia, a novel database for human long non-coding RNA (lncRNA) transcripts and genes. LNCipedia offers 21,488 annotated human lncRNA transcripts obtained from different resources. In addition to basic transcript information and gene structure, several statistics are determined for each entry in the database, such as secondary structure information, protein coding potential and microRNA binding sites.LNCipedia details
NONCODENONCODE is an integrated knowledge database dedicated to noncoding RNAs (excluding tRNAs and rRNAs). We extracted lncRNAs from NONCODE which were collected by high-throughput RNA sequencing or microarray.NONCODE details
A comprehensive lncRNA catalog
ResourceNameIllustrationTranscript levelGene levelRegion level
Integrated resourceIt integrated all annotation resources with a relaxed filtering criterion. Transcripts/genes on the same strand and with all exons exactly matching except the first exon at the 5' end and/or the last exon at the 3' end were considered as the same transcripts/genes. As for the gene boundary level, lncRNA pairs with greater than 90% overlap were considered as the same lncRNA. The longest lncRNA satisfying the above criteria was compiled in the comprehensive lncRNA catalog. The lncRNA names begin with "LNC" (lncRNA transcripts begin with "LNCT", lncRNA genes begin with "LNCG" and lncRNA regions begin with "LNCR").