RP11-128M1.1

Species: Homo sapiens

Position: chr20: 2207216-2213151

Known as:

Transcript: ENST00000447956

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 GTGGCCGTGCGCCTCTGCTC 2207639-2207658(+) gene body (near 5') 20 CGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA2 CTTGATAATGCTACTTGGGC 2208967-2208986(+) gene body (near 5') 20 AGG CRISPRko Experimental validated Huh7.5 NA [1]
sgRNA3 ATAATTACTATTTCAACCGA 2202970-2202989(+) up stream 20 TGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA4 ACGCAAACAACTTAGGATGG 2204060-2204079(+) up stream 20 TGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA5 CGTCTGCTACCCACAGCCTG 2207049-2207068(+) up stream 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA6 GGTCAGTGTCGCTCAGCGAC 2206878-2206897(+) up stream 20 AGG CRISPRko Experimental validated Huh7.5 NA [1]
sgRNA7 GTCGTGGCTGGGAGCTGCCG 2207612-2207631(+) gene body (near 5') 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA8 GCACCGACGGCGGGAAAACG 2207165-2207184(+) up stream 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA9 CACCATGGCAACTCGGGCGT 2207424-2207443(+) gene body (near 5') 20 CGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA10 CCTCGTGCAAACCCACCCCG 2206912-2206931(+) up stream 20 AGG CRISPRko Experimental validated Huh7.5 NA [1]
sgRNA11 GTCCAGATCTGGAGAAGCCG 2207756-2207775(+) gene body (near 5') 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA12 CAAGGCCCGGGCGGCGGCAG 2207676-2207695(+) gene body (near 5') 20 GGG CRISPRko Experimental validated Huh7.5 NA [1]
sgRNA13 GACGGCGGGAAAACGAGGAC 2207170-2207189(+) up stream 20 CGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA14 GAGGTTATCAACTCATCAAC 2202293-2202312(+) up stream 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA15 TGGGCTGCGAGCCGAGTGGG 2207452-2207471(+) gene body (near 5') 20 TGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA16 GCGTCCAGATCTGGAGAAGC 2207754-2207773(+) gene body (near 5') 20 CGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA17 TGTCGCTCAGCGACAGGGCT 2206884-2206903(+) up stream 20 CGG CRISPRko Experimental validated Huh7.5 NA [1]
sgRNA18 AGCGTGGGCTGCGAGCCGAG 2207448-2207467(+) gene body (near 5') 20 TGG CRISPRko Experimental validated Huh7.5 NA [1]
sgRNA19 GCCAGGAGTGTGCGGTCACG 2206941-2206960(+) up stream 20 AGG CRISPRko Experimental validated Huh7.5 NA [1]
sgRNA20 ACGAGAAGTGACGCAGGTGA 2207504-2207523(+) gene body (near 5') 20 CGG CRISPRko Experimental validated Huh7.5 NA [1]
sgRNA21 CGTCGCCACTCTCCTGCCCC 2207068-2207087(-) up stream 20 AGG CRISPRko Experimental validated Huh7.5 NA [1]
sgRNA22 GCGGGGTCTCTGGGTGGTCG 2207596-2207615(+) 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.