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SRX15946395: GSM6281871: H 42 ASO3 rep1; Homo sapiens; RNA-Seq
1 ILLUMINA (Illumina HiSeq 2000) run: 41.2M spots, 12.3G bases, 3.5Gb downloads

External Id: GSM6281871_r1
Submitted by: UCD Conway Institute for Biomolecular and Biomedical Research
Study: Multi-hallmark long noncoding RNA maps reveal non-small cell lung cancer vulnerabilities [ASOseries]
show Abstracthide Abstract
Long noncoding RNAs (lncRNAs) are widely dysregulated in cancer, yet their functional roles in cellular disease hallmarks remain unclear. Here we employ pooled CRISPR deletion to perturb 831 lncRNAs detected in KRAS-mutant non-small cell lung cancer (NSCLC), and measure their contribution to proliferation, chemoresistance and migration across two cell backgrounds. Integrative analysis of this data outperforms conventional “dropout” screens in identifying cancer genes, while prioritising disease-relevant lncRNAs with pleiotropic and background-independent roles. Altogether 80 high-confidence oncogenic lncRNAs are active in NSCLC, the majority identified here for the first time, and which tend to be amplified and overexpressed in tumours. A follow-up antisense oligonucleotide (ASO) screen shortlisted two candidates, Cancer Hallmarks in Lung LncRNA 1 (CHiLL 1) and GCAWKR, whose knockdown consistently suppressed cancer hallmarks in a variety of two- and three-dimension tumour models. Molecular phenotyping reveals that CHiLL 1 and GCAWKR control cellular-level phenotypes via distinct transcriptional networks converging on common oncogenic pathways. In summary, this work reveals a multi-dimensional functional lncRNA landscape underlying NSCLC that contains potential therapeutic vulnerabilities. Overall design: RNA sequencing of A549 and NCI-H460 cells treated with antisense oligonucleotides targeting two top lncRNA candidates.
Sample: H 42 ASO3 rep1
SAMN29424100 • SRS13633323 • All experiments • All runs
Organism: Homo sapiens
Library:
Name: GSM6281871
Instrument: Illumina HiSeq 2000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: RNA was extracted using the Quick-RNA MiniPrep kit (Ref R1055, ZymomResearch) according to manufacturer's protocol. Libraries were prepared using the NEBNext® Ultra RNA Library Prep Kit.
Runs: 1 run, 41.2M spots, 12.3G bases, 3.5Gb
Run# of Spots# of BasesSizePublished
SRR1990358241,158,38912.3G3.5Gb2022-07-05

ID:
22614373

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