CTD-2540B15.13

Species: Homo sapiens

Position: chr19: 33207128-33207639

Known as:

Transcript: ENST00000609744

Sequence: Download

Description:

We developed a CRISPR interference (CRISPRi) platform targeting 16,401 lncRNA loci in seven diverse cell lines, including six transformed cell lines and human induced pluripotent stem cells (iPSCs). We classified lncRNA genes as hits if their combined phenotype effect size and P value (referred to here as “screen score”) exceeded a consistent threshold applied to each screen corresponding to an empirical FDR of 5%. Large-scale screening identified 499 lncRNA loci required for robust cellular growth, of which 89% showed growth modifying function exclusively in one cell type.



sgRNAs

sgRNA_ID Sequence Position (Chr) Position (Lnc) Length PAM Type Validity Cell line Note Ref.
sgRNA1 CCAGCACCGCTCATGGACAC 33207213-33207232(+) gene body (near 5') 20 AGG CRISPRi Partial validated iPSC NA [1]
sgRNA2 GGAGCTGGGCCGTCTACCAG 33207381-33207400(-) gene body (near 3') 20 TGG CRISPRi Partial validated iPSC NA [1]
sgRNA3 CACCGGAGGTGGGACCTTCA 33207283-33207302(+) gene body (near 5') 20 GGG CRISPRi Partial validated iPSC NA [1]
sgRNA4 GCCTCGGCCGCCTCTGGAAC 33207070-33207089(+) up stream 20 CGG CRISPRi Partial validated iPSC NA [1]
sgRNA5 TCTCGCAGGCCCGAGGGCAA 33207312-33207331(-) gene body (near 5') 20 GGG CRISPRi Partial validated iPSC NA [1]
sgRNA6 GAAAGAGCCGGTTCCAGAGG 33207080-33207099(-) up stream 20 CGG CRISPRi Partial validated iPSC NA [1]
sgRNA7 TCTGGGTCTCGCAGGCCCGA 33207318-33207337(-) gene body (near 5') 20 GGG CRISPRi Partial validated iPSC NA [1]
sgRNA8 CCCGCGGCCGGTGAAAGAGC 33207092-33207111(-) up stream 20 CGG CRISPRi Partial validated iPSC NA [1]
sgRNA9 TCGCCCAGCACGGTCTGTGA 33207153-33207172(-) gene body (near 5') 20 GGG CRISPRi Partial validated iPSC NA [1]
sgRNA10 GGCCCTGAAGGTCCCACCTC 33207288-33207307(-) gene body (near 5') 20 CGG CRISPRi Partial validated iPSC NA [1]

GBrowser


Links

lncRNA Function:

sgRNA Design Tool:

Reference

1. Liu SJ, Horlbeck MA, Cho SW, Birk HS, Malatesta M, et al. (2017). CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells. Science 355(6320).