LINC00176

Species: Homo sapiens

Position: chr20: 64034343-64039001

Known as:

Transcript: ENST00000444463

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 GTTCAGGGGATACTTCCTGC 64035001-64035020(+) gene body (near 5') 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA2 CCTGGGGTCTGAGTGCAAAC 64033445-64033464(+) up stream 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA3 CCATGTCTTGGGACCTGCTG 64035731-64035750(+) gene body (near 5') 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA4 CAGTCGTTGAGGCCAGCGGG 64034088-64034107(+) up stream 20 CGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA5 GTTGAGGCCAGCGGGCGGGG 64034093-64034112(+) up stream 20 AGG CRISPRko Experimental validated Huh7.5 NA [1]
sgRNA6 TCATGTGCGTGGCCTGCTGG 64036270-64036289(+) gene body (near 5') 20 CGG CRISPRko Experimental validated Huh7.5 NA [1]
sgRNA7 ATCCCTGCCTGCACGTGGGG 64034348-64034367(+) gene body (near 5') 20 CGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA8 CTCCTGGGTATCTTTACGGC 64035614-64035633(+) gene body (near 5') 20 AGG CRISPRko Experimental validated Huh7.5 NA [1]
sgRNA9 TCACAGAGGAGGCACTGTGG 64033249-64033268(+) up stream 20 AGG CRISPRko Experimental validated Huh7.5 NA [1]
sgRNA10 GTCGTTGAGGCCAGCGGGCG 64034090-64034109(+) up stream 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA11 GTGACAGTGTCACCAGTAAG 64033530-64033549(+) up stream 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA12 GAGCCAGCTGGTTCTTGTGT 64034009-64034028(+) up stream 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA13 AGCCCTGGATCCCCTGGGAG 64036002-64036021(+) gene body (near 5') 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA14 GCGACAGCAGCCAAGGATCG 64035579-64035598(+) gene body (near 5') 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA15 GCTGGTTCTTGTGTAGGCCG 64034015-64034034(+) up stream 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA16 GACATGGTCAATCCCGGGCA 64034431-64034450(+) gene body (near 5') 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA17 CGTTGATCACCCGAGAGACT 64033912-64033931(+) up stream 20 TGG CRISPRko Experimental validated Huh7.5 NA [1]
sgRNA18 TGGGGTCCAGCTCAAATCGT 64034514-64034533(+) gene body (near 5') 20 TGG CRISPRko Experimental validated Huh7.5 NA [1]
sgRNA19 CAGCTGGTTCTTGTGTAGGC 64034013-64034032(+) up stream 20 CGG CRISPRko Experimental validated Huh7.5 NA [1]
sgRNA20 GAGCCAGCCCGGCCCTGTAC 64034768-64034787(+) gene body (near 5') 20 AGG CRISPRko Experimental validated Huh7.5 NA [1]
sgRNA21 ATCTGGCTGGAGGTCATGGC 64034046-64034065(+) up stream 20 TGG CRISPRko Experimental validated Huh7.5 NA [1]
sgRNA22 AGCCCGGCCCTGTACAGATG 64034722-64034741(+) gene body (near 5') 20 TGG 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.