LINC00883

Species: Homo sapiens

Position: chr3: 107240691-107248348

Known as:

Transcript: ENST00000466734

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 ATTAGTTAATCCCAAGGGGA 107235263-107235282(+) up stream 20 AGG CRISPRko Experimental validated Huh7.5 NA [1]
sgRNA2 TGCTCCTTTGCGATCCGCCG 107240851-107240870(+) gene body (near 5') 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA3 TGGGCACACTGGCTTCACGC 107241036-107241055(+) gene body (near 5') 20 CGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA4 AGCCCTCAGAGTCTAAAACG 107235306-107235325(+) up stream 20 TGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA5 CCTTATTAGTTAATCCCAAG 107235259-107235278(+) up stream 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA6 GCACCTCTGCTCCTCCCCCT 107241459-107241478(+) gene body (near 5') 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA7 CTAGGCAATCCAGCATCGCG 107241001-107241020(+) gene body (near 5') 20 TGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA8 CCATTTGGGCACCCCTGCCC 107240894-107240913(+) gene body (near 5') 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA9 ATATCCAGCCAAATTGCTG 107245889-107245907(+) gene body (near 3') 19 AGG CRISPRko Experimental validated Huh7.5 NA [1]
sgRNA10 TAACCTAGATTAAAACAGT 107246164-107246182(-) gene body (near 3') 19 GGG CRISPRko Experimental validated Huh7.5 NA [1]
sgRNA11 GAAGGTATACTAATAATGC 107249114-107249132(-) down stream 19 AGG CRISPRko Experimental validated Huh7.5 NA [1]
sgRNA12 GGAGCAGCCCTCAACACAC 107246448-107246466(-) gene body (near 3') 19 AGG CRISPRko Experimental validated Huh7.5 NA [1]
sgRNA13 GGAACGTAATTGACTGGGG 107249230-107249248(-) down stream 19 GGG CRISPRko Experimental 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.