RP11-680A11.5

Species: Homo sapiens

Position: chr12: 53298654-53300314

Known as:

Transcript: ENST00000550263

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 CTTCAAAAAACAGCTGACCG 53301505-53301524(+) up stream 20 TGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA2 GCAGTTAGGTGCAGCAGCAA 53300582-53300601(-) up stream 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA3 ACGCGGACTACGGCAGTGGA 53300331-53300350(-) up stream 20 TGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA4 GCTGACGCGGACTACGGCAG 53300335-53300354(-) up stream 20 TGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA5 TGGGTAATCGAAGTCATTGG 53302543-53302562(-) up stream 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA6 GGTGTGGTATAATTGAGGGA 53301336-53301355(-) up stream 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA7 TTGCTGCTGCACCTAACTGC 53300582-53300601(+) up stream 20 TGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA8 GACATGAAATCCCAGAGGAT 53301216-53301235(-) up stream 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA9 TTAGGCTGTAAATATTGGGA 53301459-53301478(-) up stream 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.