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Series GSE139123 Query DataSets for GSE139123
Status Public on Oct 21, 2019
Title Next Generation Sequencing and m6A sequencing Facilitates Quantitative Analysis of Wild Type and genetic FTO knockdown ccRCC cells Transcriptomes
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: FTO is an N6-methyladenosine (m6A) RNA demethylase. The goals of this study are to to identify functional mRNA targets of FTO m6A demethylase activity in VHL deficient ccRCC cells. We performed transcriptome wide m6A sequencing and RNA sequencing analysis of two independent FTO deficient and wild type ccRCC cell lines.
Methods: We performed transcriptome wide m6A sequencing and RNA sequencing analysis of two independent FTO deficient (shFTO#2 and shFTO#5) and wild type ccRCC cell lines.
Results: Analysis using exomePeak identified a total of 20,168 m6A peaks that are different between the shFTO cells and the control cells. A total of 2,680 and 4,049 m6A peaks showed a significant increase and decrease (p < 0.05), respectively, in abundance (normalized to input), in shFTO cells relative to Ctrl_cells, and they were thus termed hyper- and hypo-methylated m6A peaks, respectively. Through integrative analysis of the RNA-seq data, we identified 459 hypermethylated m6A peaks the RNA transcripts of which were significantly (p < 0.05) downregulated (255; Hyper-down) or upregulated (204; Hyper-up) in shFTO cells relative to Ctrl cells (Figure XB).
Conclusions: Our study represents the first detailed analysis of FTO driving transcriptomes, with biologic replicates, generated by RNA-seq technology and m6A sequencing. Our results confirmed the functional role of FTO in mRNA demethylase and identify the targets of FTO. We conclude that FTO plays important role in mRNA destiny determination by m6A demethylase activity.
 
Overall design m6A-specific antibodies are used to immunoprecipitate RNA. RNA is reverse-transcribed to cDNA and deep sequenced. In paralal mRNA of UMRC2 cell transfected with shSCM, shFTO#1 and shFTO#2 were generated by deep sequencing.
 
Contributor(s) Xiao Y, Sinha S, Rankin EB
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Submission date Oct 20, 2019
Last update date Oct 21, 2019
Contact name Yiren Xiao
E-mail(s) yrxiao@stanford.edu
Phone 6504765042
Organization name Stanford University
Street address 1291 WELCH ROAD
City Stanford
State/province CA
ZIP/Postal code 94035
Country USA
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (18)
GSM4131312 UMRC2-shControl rep 1
GSM4131313 UMRC2-shControl rep 2
GSM4131314 UMRC2_shFTO#2 rep 1
Relations
BioProject PRJNA578531
SRA SRP226373

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
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Supplementary file Size Download File type/resource
GSE139123_CtrlA_peak.bedGraph.gz 190.5 Kb (ftp)(http) BEDGRAPH
GSE139123_CtrlB_peak.bedGraph.gz 112.4 Kb (ftp)(http) BEDGRAPH
GSE139123_FTP2A_peak.bedGraph.gz 114.3 Kb (ftp)(http) BEDGRAPH
GSE139123_FTP2B_peak.bedGraph.gz 101.6 Kb (ftp)(http) BEDGRAPH
GSE139123_FTP5A_peak.bedGraph.gz 937.3 Kb (ftp)(http) BEDGRAPH
GSE139123_FTP5B_peak.bedGraph.gz 134.6 Kb (ftp)(http) BEDGRAPH
GSE139123_RNA-Seq_dataset.xlsx 224.0 Kb (ftp)(http) XLSX
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Processed data are available on Series record

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