RP11-374P20.4

Species: Homo sapiens

Position: chr9: 134054289-134058805

Known as:

Transcript: ENST00000412181

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 GCAGACCCAAACACGGTGCG 134054088-134054107(+) up stream 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA2 CACCGTGGCTGTCCACGCAT 134054019-134054038(-) up stream 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA3 ATCCTGACGGCAGCATAAGC 134055881-134055900(-) gene body (near 5') 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA4 CAACGTCGCCCAGGCAGAGA 134061734-134061753(+) down stream 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA5 GACGTTTGCAGACCCAAACA 134054081-134054100(+) up stream 20 CGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA6 CACCTTCCCTCCAAGCACAG 134056876-134056895(+) gene body (near 3') 20 TGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA7 CACTTCCTAAAACAAAGCTG 134062946-134062965(+) down stream 20 CGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA8 GCCCCAGGGTGTGGCATTGG 134061216-134061235(-) down stream 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA9 GACCCGGTGCTCACAGCCCC 134055066-134055085(+) gene body (near 5') 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA10 TTGCAGACCCAAACACGGTG 134054086-134054105(+) up stream 20 CGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA11 GAGTCGACCCCACGAGTGGG 134053946-134053965(-) up stream 20 TGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA12 GCTGTGTTGGGCCCGCACCG 134054034-134054053(-) up stream 20 TGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA13 CCGACAGCCTCTCACCTGGG 134053731-134053750(-) up stream 20 TGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA14 AGCCTTCAGGCACTCCACAG 134061172-134061191(+) down stream 20 AGG 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.