CKMT2-AS1

Species: Homo sapiens

Position: chr5: 81237827-81301555

Known as:

Transcript: ENST00000501927

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 TCAGTTCGCAGTGTACTCAT 81243263-81243282(-) gene body (near 3') 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA2 AAAAGGGGCAGGCCGAGTGC 81237206-81237225(+) down stream 20 TGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA3 CCAGAGACTTCCTGACAGGC 81234483-81234502(+) down stream 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA4 TTTAGAAGTCATATGCCCTG 81236162-81236181(+) down stream 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA5 CAACAGAGTCCAAACGGTAG 81243374-81243393(+) gene body (near 3') 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA6 ACGTAGACCAGAAGCACAGG 81206367-81206386(-) down stream 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA7 AGAGACTCATTCAAAAAAGG 81237503-81237522(+) down stream 20 TGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA8 GTTTGTGATGTGTTAGCAAC 81202468-81202487(+) down stream 20 TGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA9 AGGGTAAGATCATTGAGAAG 81204844-81204863(+) down stream 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA10 GTTAAAGAAAGGAACCCTTG 81201707-81201726(+) down stream 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA11 CTAAAATTGGCAGAATACCT 81235883-81235902(-) down stream 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA12 GCTGTGGTGCGAGGGGCCCG 81245788-81245807(+) gene body (near 3') 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA13 ATAGTCCACACTCTTAACCA 81239795-81239814(-) gene body (near 3') 20 CGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA14 GATGTTTATTCTTCACTGGA 81248907-81248926(+) gene body (near 3') 20 TGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA15 CAGAGAAGAGCATTAAGACC 81235661-81235680(+) down stream 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA16 AGCAGGGTTCCTACACCTAG 81237415-81237434(+) down stream 20 CGG 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.