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| Status |
Public on Aug 28, 2011 |
| Title |
Integrative Annotation of Human Large Intergenic Non-Coding RNAs Reveals Global Properties and Specific Subclasses |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Large intergenic non-coding RNAs (lincRNAs) are emerging as key regulators of diverse cellular processes. Determining the function of individual lincRNAs remains a challenge. Recent advances in RNA sequencing (RNA-Seq) and computational methods allow for an unprecedented analysis of such transcripts. Here, we present an integrative approach to define a reference catalogue of over 8,000 human lincRNAs. Our catalogue unifies previously existing annotation sources with transcripts we assembled from RNA-Seq data collected from ~4 billion RNA-Seq reads across 24 tissues and cell types. We characterize each lincRNA by a panorama of more than 30 properties, including sequence, structural, transcriptional, and orthology features. We find that lincRNA expression is strikingly tissue specific compared to coding genes, and that they are typically co-expressed with their neighboring genes, albeit to a similar extent to that of pairs of neighboring protein-coding genes. We distinguish an additional sub-set of transcripts that have high evolutionary conservation but may include short open reading frames, and may serve either as lincRNAs or as small peptides. Our integrated, comprehensive, yet conservative reference catalogue of human lincRNAs reveals the global properties of lincRNAs and will facilitate experimental studies and further functional classification of these genes.
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| Overall design |
We extracted profiled the transcriptome expression polyadenylated mRNA-Seq. We then used these to reconstruct the transcriptome using de-novo assemblers and identify long non coding RNAs and their expression.
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| Contributor(s) |
Cabili MN, Trapnell C, Goff L, Tazon-Vega B, Koziol M, Regev A, Rinn JL |
| Citation(s) |
21890647 |
| Submission date |
Jul 11, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Nataly Moran Cabili |
| E-mail(s) |
nmcabili@fas.harvard.edu
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| Organization name |
Broad Institute ; Harvard University
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| Street address |
7 Cambridge Center
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platforms (1) |
| GPL9115 |
Illumina Genome Analyzer II (Homo sapiens) |
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| Samples (9)
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| Relations |
| SRA |
SRP007494 |
| BioProject |
PRJNA144473 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE30554_RAW.tar |
19.9 Gb |
(http)(custom) |
TAR (of BAM) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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