VPS9D1-AS1

Species: Homo sapiens

Position: chr16: 89711855-89718165

Known as:

Transcript: ENST00000562866

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 GGGACGGGGTTGGGAACCGA 89712145-89712164(-) gene body (near 5') 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA2 CTGACAGTGGGAAGGTACGA 89714472-89714491(-) gene body (near 5') 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA3 TGGCCTCAGAGCAATCCGGG 89712795-89712814(-) gene body (near 5') 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA4 GCCTCTCCGGGTGTGGGACG 89712159-89712178(-) gene body (near 5') 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA5 CCCCTCGGGGACCACCAGGG 89712424-89712443(+) gene body (near 5') 20 CGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA6 GACCGCCCTGGTGGTCCCCG 89712429-89712448(-) gene body (near 5') 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA7 CATTCGAAGTCATACAGCCT 89713664-89713683(-) gene body (near 5') 20 CGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA8 GACAGCCCCTCACCGAGAGG 89712198-89712217(-) gene body (near 5') 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA9 CGGCCTCTCCGGGTGTGGGA 89712161-89712180(-) gene body (near 5') 20 CGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA10 GGGGACAGCCCCTCACCGAG 89712201-89712220(-) gene body (near 5') 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA11 TCAGTGTGGCCTTGAGCCAA 89712400-89712419(-) gene body (near 5') 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA12 CATTGTCCCTGACAGTGGGA 89714480-89714499(-) 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.