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Series GSE173221 Query DataSets for GSE173221
Status Public on Apr 30, 2021
Title Very long intergenic non-coding (vlinc) RNAs directly regulate multiple genes in cis and trans
Organism Homo sapiens
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary Majority of the human genome is transcribed in a form of long non-coding (lnc) RNAs. While these transcripts attracted considerable interest, their molecular mechanisms of function and biological significance remain controversial. Here, we present a genome-wide functional annotation strategy for lncRNAs based on integration of three distinct types of approaches: co-expression analysis, mapping of lncRNA-chromatin interactions and assaying molecular effects of lncRNA knockdowns obtained using an inducible and highly specific CRISPR/Cas13 system. We apply the strategy to annotate 407 vlincRNAs belonging to a novel widespread subclass of lncRNAs. We show that vlincRNAs appear to regulate, positively and negatively and both in trans and cis, multiple genes encoding proteins predominantly involved in RNA- and development-related functions, cell cycle and cellular adhesion via a potential mechanism involving proximity in nucleus. Finally, we show vlincRNAs and their regulatory networks potentially represent novel components of DNA damage response.
Overall design Regulatory networks for vlincRNAs were established based on co-expression analysis using 64 RNA-seq samples obtained using single-molecule sequencing (SMS, Helicos/SeqLL platform) from total RNA isolated from K562 cells perturbed with various drug treatments.
Contributor(s) Kapranov P, Cao H
Citation(s) 34016118
Submission date Apr 23, 2021
Last update date Dec 09, 2022
Contact name Huifen Cao
Phone +86 05926167250
Organization name Huaqiao University
Department School of Biomedical Sciences
Lab Institute of Genomics
Street address 668 Jimei Road
City Xiamen
State/province Fujian
ZIP/Postal code 361021
Country China
Platforms (2)
GPL14761 Helicos HeliScope (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (96)
GSM5262010 SMS.10074-G5_3h
GSM5262011 SMS.10074-G5_6h
GSM5262012 SMS.BML-277_3h
BioProject PRJNA724716
SRA SRP316065

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Supplementary file Size Download File type/resource 17.5 Mb (ftp)(http) TXT
GSE173221_RAW.tar 1.7 Gb (http)(custom) TAR (of BED)
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Raw data are available in SRA
Processed data provided as supplementary file

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