LINC00882

Species: Homo sapiens

Position: chr3: 106836810-107240641

Known as: LINC00882 , ENSG00000242759

Transcript: ENST00000484698 , ENST00000479612 , ENST00000473636 , ENST00000477210

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 CAGGTGTATTGGAACGGTG 107130143-107130161(+) gene body (near 5') 19 TGG CRISPRko Experimental validated Huh7.5 paried with sgRNA2 [1]
sgRNA2 TTACCATGGAATTATCCAT 107129500-107129518(-) gene body (near 5') 19 AGG CRISPRko Experimental validated Huh7.5 paried with sgRNA1 [1]
sgRNA3 AGCGTGAATAAGTGTGGGT 107130417-107130435(+) gene body (near 5') 19 AGG CRISPRko Experimental validated Huh7.5 paried with sgRNA4 [1]
sgRNA4 GTTTAACGTTCAAAAGAAG 107129694-107129712(-) gene body (near 5') 19 AGG CRISPRko Experimental validated Huh7.5 paried with sgRNA3 [1]
sgRNA5 AGTTGGAAGTTTCCTCAGG 107113086-107113104(-) gene body (near 5') 19 TGG CRISPRko Experimental validated Huh7.5 paried with sgRNA6 [1]
sgRNA6 TGCATGAGGGTTTGCACTA 107110484-107110502(-) gene body (near 5') 19 GGG CRISPRko Experimental validated Huh7.5 paried with sgRNA5 [1]
sgRNA7 GGCAGAAGAAGCGCATTGCG 107240738-107240757(-) up stream 20 CGG CRISPRa Experimental validated Huh7.5 NA [1]
sgRNA8 CTCACTGCGCACGCGCCGGT 107240661-107240680(+) up stream 20 CGG CRISPRa Experimental 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.