HM13-AS1

Species: Homo sapiens

Position: chr20: 31567706-31573263

Known as:

Transcript: ENST00000412178

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 ATCTGAAAGTAATCTATGGG 31576700-31576719(-) up stream 20 TGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA2 GCAAGAGTCGGCCATTCAGG 31572841-31572860(+) gene body (near 5') 20 AGG CRISPRko Experimental validated Huh7.5 NA [1]
sgRNA3 GTAACACTCAGATGCAGAGG 31577208-31577227(+) up stream 20 TGG CRISPRko Experimental validated Huh7.5 NA [1]
sgRNA4 ACAAGGCTATCTTCATGTGA 31576873-31576892(+) up stream 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA5 GCCCTAGTCCGCTGCTCCGG 31570991-31571010(-) gene body (near 5') 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA6 TCAAATGGCTATCAGGGGCG 31572936-31572955(+) gene body (near 5') 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA7 GCCACCTCAGCCTCTGCCGG 31570909-31570928(-) gene body (near 5') 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA8 GATCCCGGTCAGGCAGAAAG 31577305-31577324(-) up stream 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA9 CTGGTAACACTCAGATGCAG 31577205-31577224(+) up stream 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA10 ACCGTAAGGGCGGGCCCAGG 31572398-31572417(+) gene body (near 5') 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA11 TCCCATGGAAAAATGGCACC 31571166-31571185(+) gene body (near 5') 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA12 CCAACTGGGCTGATCCCAGG 31576982-31577001(-) up stream 20 GGG CRISPRko Experimental validated Huh7.5 NA [1]
sgRNA13 TATCAAATGGCTATCAGGGG 31572934-31572953(+) gene body (near 5') 20 CGG CRISPRko Experimental validated Huh7.5 NA [1]
sgRNA14 TGAGGGCAAGGAATATACAA 31574279-31574298(+) up stream 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA15 GCGTCGCTGAGCTGGCGGGC 31573248-31573267(-) gene body (near 5') 20 GGG CRISPRko Experimental validated Huh7.5 NA [1]
sgRNA16 CAAACGCAGGGCGGGGAGGC 31572977-31572996(-) gene body (near 5') 20 AGG CRISPRko Experimental validated Huh7.5 NA [1]
sgRNA17 TTGGGACAATCCTGAGGGCC 31574010-31574029(+) up stream 20 TGG CRISPRko Experimental validated Huh7.5 NA [1]
sgRNA18 GAGGGAATCCAAACGCAGGG 31572986-31573005(-) gene body (near 5') 20 CGG CRISPRko Experimental validated Huh7.5 NA [1]
sgRNA19 TTTGAGTAAATTTGAGGGCA 31574267-31574286(+) up stream 20 AGG CRISPRko Experimental validated Huh7.5 NA [1]
sgRNA20 GACACGATCGTAGGAACCGG 31572801-31572820(-) gene body (near 5') 20 AGG CRISPRko 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.