RP11-195M16.1

Species: Homo sapiens

Position: chr1: 109884175-109886264

Known as:

Transcript: ENST00000415166

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 CCAGATCCTGCCTGCAGAGA 109886459-109886478(-) up stream 20 CGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA2 GCAATAACATGAATCAGAAC 109890858-109890877(-) up stream 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA3 AAAGCTCCTGCAGCTAGATG 109886297-109886316(-) up stream 20 TGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA4 GAGCAATGAGAGTTTGGACA 109885875-109885894(-) gene body (near 5') 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA5 TTTCTCCACCATAACGCAAG 109886190-109886209(-) gene body (near 5') 20 TGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA6 CTGATAGCCCCTCTGTGGGA 109886850-109886869(-) up stream 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA7 CAGGCCTCGCTACTGAAGTG 109887396-109887415(-) up stream 20 CGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA8 ACCACGATGTGCCTAAGTGG 109887607-109887626(-) up stream 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA9 TGTTAAGCTTGTTCTGGTGA 109885017-109885036(-) gene body (near 3') 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA10 GTCTGGTCCCCAACCTTCGC 109886670-109886689(-) up stream 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA11 TTTCTGCAAACTACCAGCGC 109884506-109884525(-) gene body (near 3') 20 TGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA12 CTGCTGGCCCTGTTATGCAA 109884306-109884325(-) gene body (near 3') 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA13 TTTGACTGCAAGCCACCCGG 109885040-109885059(-) gene body (near 3') 20 TGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA14 TTATGCAAGGGACTTTGTGT 109884294-109884313(-) gene body (near 3') 20 GGG 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.