|
| Status |
Public on Dec 01, 2016 |
| Title |
CRISPRi-based genome-scale identification of functional long non-coding RNA loci in human cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
|
| Summary |
The human genome produces thousands of long non-coding RNAs (lncRNAs) – transcripts >200 nucleotides long that do not encode proteins. While critical roles in normal biology and disease have been revealed for a subset of lncRNAs, the function of the vast majority remains untested. Here, we developed a CRISPR interference (CRISPRi) platform targeting 16,401 lncRNA loci in 7 diverse cell lines including 6 transformed cell lines and human induced pluripotent stem cells (iPSCs). Large-scale screening identified 499 lncRNA loci required for robust cellular growth, of which 89% showed growth modifying function exclusively in one cell type. We further found that lncRNA knockdown can perturb complex transcriptional networks in a cell type-specific manner. These data underscore the functional importance and cell type-specificity of many lncRNAs.
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| |
|
| Overall design |
96 RNA-seq samples; 16 ChIP-seq samples
|
| |
|
| Contributor(s) |
Liu SJ, Horlbeck MA, Weissman JS, Lim DA |
| Citation(s) |
27980086 |
| |
| Submission date |
Jul 29, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
John Liu |
| E-mail(s) |
john.liu@ucsf.edu
|
| Organization name |
UCSF
|
| Street address |
35 Medical Center Way
|
| City |
SAN FRANCISCO |
| State/province |
California |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
|
| Samples (112)
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|
| Relations |
| BioProject |
PRJNA335860 |
| SRA |
SRP080367 |
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