NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE179741 Query DataSets for GSE179741
Status Public on Jul 09, 2021
Title RNA sequencing of wildtype and catalytic knockouts of TUT4/7
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary TUT4 and TUT7 are terminal uridyl transferases that adds uridine bases to the 3′ end of RNAs such as miRNAs and mRNAs. The overall aim of this experiment was to identify differentially regulated mRNAs and miRNAs in catalytic knockouts of TUT4/7 relative to the wildtype. Catalytic mutants of TUT4/7 was generated in the prostate cancer cell line DU145 and the ovarian cancer cell line IGROV1. As the miRNA regulation by TUT4/7 depends on the oncoprotein LIN28A, LIN28A was lentivirally integrated in the LIN28A- DU145-derived lines and control. IGROV1 endogenously expresses LIN28A. We report that excluding the let-7 family, miRNAs do not depend on LIN28A for TUT4/7-mediated regulation. As the entire miRNA is captured in a read, we provide the isomiR landscape in the presence and absence of TUT4/7. Loss of uridylated isomiRs results in a simultaneous gain in adenylated isomiRs. Finally, we report cell line specific miRNA-mRNA regulation.
 
Overall design Identification differentially regulated genes and comparison of isomiR profiles in TUT4/7 catalytic knockouts and the wildtypes of DU145 and IGROV1 cell lines
Web link https://www.biorxiv.org/content/10.1101/2021.07.12.451846v2
 
Contributor(s) Medhi R, Price J, Miska EA
Citation(s) 34949722
Submission date Jul 08, 2021
Last update date Mar 09, 2022
Contact name Jonathan Lewis Price
Organization name University of Cambridge
Department The Gurdon Inst.
Lab Miska Lab
Street address The Gurdon Inst. Tennis Court Road
City cambridge
ZIP/Postal code CB2 1QN
Country United Kingdom
 
Platforms (1)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (72)
GSM5430294 RNA DU145-LIN28A overexpressing-wildtype-rep1
GSM5430295 miRNA DU145-LIN28A overexpressing-wildtype-rep1
GSM5430296 RNA DU145-LIN28A overexpressing-wildtype-rep2
Relations
BioProject PRJNA744885
SRA SRP327508

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE179741_RAW.tar 9.5 Mb (http)(custom) TAR (of TXT)
GSE179741_miRNAs_expressed_all_samples_12_02_2020_t_08_52_18combined.mirdeep.arf.csv.gz 208.6 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap