RP11-723O4.9

Species: Homo sapiens

Position: chr3: 128859715-128860526

Known as:

Transcript: ENST00000567253

Sequence: Download

Description:

We report a high throughput genomic deletion strategy to screen for functional long non-coding RNAs (lncRNAs) that is based on a lentiviral paired-guide RNA (pgRNA) library. Applying our screening method, we identified 51 lncRNAs that can positively or negatively regulate human cancer cell growth. We used the MAGeCK algorithm to identify the top hits by comparing samples from day 30 with day-0 controls. The output of MAGeCK is a set of negatively (or positively) selected lncRNAs, or lncRNAs whose knockout disrupts (or stimulates) cell proliferation. In total, MAGeCK identified 43 negatively selected and 8 positively selected lncRNAs with statistical significance (false discovery rate < 0.25).



sgRNAs

sgRNA_ID Sequence Position (Chr) Position (Lnc) Length PAM Type Validity Cell line Note Ref.
sgRNA1 GTCTTGTGGATGTTCCATGG 128860332-128860351(-) gene body (near 5') 20 CGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA2 GGACATCGTCCTTTGATTAG 128865239-128865258(-) up stream 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA3 CGGCAGAAATGAAGACGTGG 128861742-128861761(+) up stream 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA4 CTCCGCAGCAGAATCAATAG 128864442-128864461(-) up stream 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA5 GCAAGCGCTGCCCAAGCCCA 128861963-128861982(-) up stream 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA6 CAGCCTCAGTCAATTAGAAG 128864398-128864417(-) up stream 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA7 TGAGCATCTACTGGTCCCTG 128863425-128863444(-) up stream 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA8 TAGAGAGGGCCTCTAATCAA 128865227-128865246(+) up stream 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA9 TGGCAAGGCCAGTAAGACCA 128861677-128861696(-) up stream 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA10 AATCGAGTTCCCCTCAAAGC 128864552-128864571(-) up stream 20 TGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA11 CCACGTCTTCATTTCTGCCG 128861742-128861761(-) up stream 20 TGG CRISPRko Partial validated Huh7.5 NA [1]

GBrowser


Links

lncRNA Function:

sgRNA Design Tool:

Reference

1. Zhu S, Li W, Liu J, Chen CH, Liao Q, et al. (2016). Genome-scale deletion screening of human long non-coding RNAs using a paired-guide RNA CRISPR-Cas9 library. Nat Biotechnol 34(12): 1279-1286.