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Sample GSM7158845 Query DataSets for GSM7158845
Status Public on Nov 06, 2024
Title 60nt_oligo, no_CMC_treated, not_blocked, no_XRN1_treated, rep2
Sample type SRA
 
Source name 60nt oligo
Organism synthetic construct
Characteristics treatment1: no_CMC_treated
treatment2: not_blocked
treatment3: no_XRN1_treated
Extracted molecule other
Extraction protocol The oligonucleotides were purchased.
RNA oligonucleotides were RNA was reverse transcribed by Superscript III reverse transcriptase (Thermo scientific). The 5’ adaptor was ligated by T4 RNA ligase high concentration 1 (NEB). The amplification cycles of the cDNA were determined by qPCR (generally 10-15 cycles). The cDNA was amplified by PCR with Q5 High-Fidelity 2×Master Mix (NEB). Library PCR products were purified twice by 0.9x XP beads (Beckman).
 
Library strategy OTHER
Library source other
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing Adapters in raw reads were trimmed, and reads shorter than 20 were filtered with Trim Galore (v0.6.1).
Then reads were mapped to 60-nt and 32-nt oligonucleotides sequences with bowtie2 (v2.4.1).
RT-stop rates of all bases in oligonucleotides sequences were calculated using custom scripts.
Assembly: 60nt_mix_32nt_oligonucleotide
Supplementary files format and content: txt, RT-stop rate result
 
Submission date Apr 10, 2023
Last update date Nov 06, 2024
Contact name Ziang Lu
E-mail(s) zianglu@whu.edu.cn
Organization name Wuhan University
Street address Wuhan University, No.299, Bayi Road, Wuchang District
City Wuhan
ZIP/Postal code 430072
Country China
 
Platform ID GPL26526
Series (1)
GSE229317 Exonuclease-assisted identification of pseudouridine sites in single-stranded RNA
Relations
SRA SRX19919333
BioSample SAMN34131447

Supplementary file Size Download File type/resource
GSM7158845_60nt_oligo.no_CMC_treated.not_blocked.no_XRN1_treated.rep2.stoprate.txt.gz 881 b (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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