JRK

Species: Homo sapiens

Position: chr8: 142666414-142681968

Known as:

Transcript: ENST00000591357

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 CTGGGGAGCAGCGGGATCCG 142681901-142681920(-) gene body (near 5') 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA2 CAGGATTGCAAGCAGTGCGA 142681784-142681803(-) gene body (near 5') 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA3 GAGCTTCCCTGGAGGAGCGG 142680703-142680722(-) gene body (near 5') 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA4 GGGACTCTAGAGCATTAGGC 142681817-142681836(+) gene body (near 5') 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA5 CAGAAAGATTAATAGTTCAG 142681477-142681496(-) gene body (near 5') 20 TGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA6 TGCAGGTGCGGGACGGGTCG 142681541-142681560(-) gene body (near 5') 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA7 TAATGCTCTAGAGTCCCCCT 142681814-142681833(-) gene body (near 5') 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA8 CAAGCCCCGGTCACAGGGGA 142680757-142680776(-) gene body (near 5') 20 CGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA9 TGCCCTGTTTAGTCCCTCGG 142681130-142681149(-) gene body (near 5') 20 TGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA10 GTGGGGGGACGACAGCCGCC 142681439-142681458(+) gene body (near 5') 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA11 CGTGCCAAGAGCTTCCCTGG 142680711-142680730(-) gene body (near 5') 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA12 AGGGGGCCGTGAAGATGGGG 142681170-142681189(+) gene body (near 5') 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA13 CCTGCCGTCCCCTGTGACCG 142680750-142680769(+) gene body (near 5') 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA14 GCCTCCATGGCGGTGGCCTG 142681231-142681250(-) gene body (near 5') 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA15 GGGAAGCTCTTGGCACGACC 142680714-142680733(+) gene body (near 5') 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA16 GTGACCGTGTGTTTCAGAAG 142681099-142681118(-) gene body (near 5') 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.