PXN-AS1

Species: Homo sapiens

Position: chr12: 120201290-120212919

Known as:

Transcript: ENST00000542265

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 GGGTTATTAATTGGGGGAGC 120213719-120213738(-) down stream 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA2 AAGAGATCTCGGGTGTCCGC 120207565-120207584(-) gene body (near 3') 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA3 CGTGCCGACTATGCCCACCT 120212651-120212670(-) gene body (near 3') 20 CGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA4 AACTGCCTTCGGCAGGGAAG 120209941-120209960(+) gene body (near 3') 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA5 ACCTTTCAGGATCCACAGCA 120207374-120207393(-) gene body (near 3') 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA6 AAGGCAGTTACTTACAGTTG 120209930-120209949(-) gene body (near 3') 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA7 AATGAGCGTTTAGGACAACA 120212712-120212731(-) gene body (near 3') 20 CGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA8 CTGGACACCTTTACAATCAG 120206600-120206619(+) gene body (near 5') 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA9 GCATTCTGGGGGCCCCACAG 120213481-120213500(-) down stream 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA10 CAAATCCGGACATGACGACG 120209887-120209906(+) gene body (near 3') 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA11 TGATCCAGCTGCATCTGGGG 120210366-120210385(+) gene body (near 3') 20 TGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA12 CGTGGGCTTTGCTCCTGCCT 120210251-120210270(-) gene body (near 3') 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA13 GAGCTGCACCCTGTGTGATG 120212625-120212644(+) gene body (near 3') 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA14 CCAATTAATAACCCCAAATG 120213725-120213744(+) 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.