LINC01087

Species: Homo sapiens

Position: chr2: 131637024-131649615

Known as: LINC01087 , ENSG00000224559

Transcript: ENST00000431979

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 GCAGTGTCATACAACCCATG 131636172-131636191(-) up stream 20 AGG CRISPRko Experimental validated Huh7.5 paried with sgRNA2 [1]
sgRNA2 GATACACCACCACACAAATG 131645819-131645838(+) gene body (near 3') 20 CGG CRISPRko Experimental validated Huh7.5 paried with sgRNA1,3 [1]
sgRNA3 AAGGGTGTGCGAGAAGCTGG 131635995-131636014(-) up stream 20 TGG CRISPRko Experimental validated Huh7.5 paried with sgRNA2 [1]
sgRNA4 TACAATTCTTCGTTGCCAAG 131635553-131635572(+) up stream 20 AGG CRISPRko Experimental validated Huh7.5 paried with sgRNA5 [1]
sgRNA5 TATGACCCATGAGGCATGGA 131636802-131636821(-) up stream 20 CGG CRISPRko Experimental validated Huh7.5 paried with sgRNA4 [1]
sgRNA6 GAAGAATTGTACAGTGCCAT 131635544-131635563(-) up stream 20 AGG CRISPRko Experimental validated Huh7.5 paried with sgRNA7 [1]
sgRNA7 TATGACCCATGAGGCATGGA 131636802-131636821(-) up stream 20 CGG CRISPRko Experimental validated Huh7.5 paried with sgRNA6 [1]
sgRNA8 CCTTAGGAAAAGCAAGCAGA 131634448-131634467(+) up stream 20 TGG CRISPRko Experimental validated Huh7.5 paried with sgRNA9 [1]
sgRNA9 AATGAGCTTGAGCAAGTACA 131642906-131642925(-) gene body (near 5') 20 GGG CRISPRko Experimental validated Huh7.5 paried with sgRNA8 [1]
sgRNA10 AGAAGCCCAAGTCCCCTGGG 131636913-131636932(-) up stream 20 TGG CRISPRa Experimental validated Huh7.5 NA [1]
sgRNA11 CCACAGAAGCCCAAGTCCCC 131636917-131636936(-) up stream 20 TGG 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.