NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE179798 Query DataSets for GSE179798
Status Public on Sep 05, 2022
Title Quantitative sequencing using BID-seq uncovers abundant pseudouridines in mammalian mRNA at base resolution
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Functional characterization of pseudouridine (Ψ) in mammalian messenger RNA (mRNA) has been hampered by the lack of a quantitative method that maps pseudouridine in the whole transcriptome. We report bisulfite-induced deletion sequencing (BID-seq) that utilizes a bisulfite-mediated reaction to stoichiometrically convert pseudouridine into deletion upon reverse transcription. BID-seq enabled detection of abundant pseudouridine sites with stoichiometry information in several human cell lines and 12 different mouse tissues using 10-20 ng input RNA. We uncovered consensus sequences for pseudouridine in mammalian mRNA and assigned different ‘writer’ proteins to individual pseudouridine deposition. Our results reveal a transcript stabilization role of Ψ sites installed by TRUB1 in human cancer cells. We also detected presence of Ψ within stop codons of mammalian mRNA, and confirmed the role of Ψ in promoting stop codon read-through in vivo. This new method for sensitive and comprehensive detection of Ψ sets the stage for future investigations of the roles of Ψ in diverse biological processes.
 
Overall design [dataset1] 20 samples (Sample 1-20): "Input" and "Treated" samples in BID-seq to detect pseudouridine in polyA+ RNA from HeLa cells of shControl and 8 human PUS synthase knockdown. (5′ SR Adapter: 5′-GUUCAGAGUUCUACAGUCCGACGAUC NNNNN-3′; See instructions of each sample about 3' SR Adapter sequences)
[dataset3] 48 samples (Sample 41-88): "Input" and "Treated" samples in BID-seq to detect pseudouridine in polyA+ RNA from 12 mouse tissues. (5′ SR Adapter: 5′-GUUCAGAGUUCUACAGUCCGACGAUC NNNNN-3′; See instructions of each sample about 3' SR Adapter sequences)
[dataset4] 18 samples (Sample 89-106): "Input" and "Treated" samples in BID-seq to detect pseudouridine in polyA+ RNA from wild-type HeLa, HEK293T and A549 cells. (5′ SR Adapter: 5′-GUUCAGAGUUCUACAGUCCGACGAUC-3′; See instructions of each sample about 3' SR Adapter sequences)
 
Contributor(s) Zhang L, Dai Q, He C
Citation(s) 36302989
NIH grant(s)
Grant ID Grant title Affiliation Name
RM1 HG008935 Center for dynamic RNA epitranscriptomes - Renewal UNIVERSITY OF CHICAGO CHUAN HE
Submission date Jul 09, 2021
Last update date Nov 29, 2022
Contact name Li-Sheng Zhang
E-mail(s) [email protected]
Phone (852) 3469 2392
Organization name The University of Chicago
Department Department of Chemistry
Lab Prof. Chuan He Lab
Street address 929 E 57th St Rm E313
City Chicago
State/province IL
ZIP/Postal code 60637
Country USA
 
Platforms (2)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (86)
GSM5434326 Sample 1_HeLa_polyA-RNA_shControl_Input_rep1
GSM5434327 Sample 2_HeLa_polyA-RNA_shControl_Input_rep2
GSM5434328 Sample 3_HeLa_polyA-RNA_shControl_Treated_rep1
Relations
BioProject PRJNA745097
SRA SRP327626

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
GSE179798_A549_mRNA_WT_BID-seq.xlsx 170.5 Kb (ftp)(http) XLSX
GSE179798_HEK293T_mRNA_WT_BID-seq.xlsx 104.4 Kb (ftp)(http) XLSX
GSE179798_HeLa_mRNA_WT_BID-seq.xlsx 110.5 Kb (ftp)(http) XLSX
GSE179798_HeLa_mRNA_shControl_BID-seq.xlsx 27.3 Kb (ftp)(http) XLSX
GSE179798_Mouse_mRNA_12-Tissues_BID-seq.xlsx 3.8 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap