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Status |
Public on Nov 06, 2024 |
Title |
60nt_oligo, CMC_treated, blocked, no_XRN1_treated, rep2 |
Sample type |
SRA |
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Source name |
60nt oligo
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Organism |
synthetic construct |
Characteristics |
treatment1: CMC_treated treatment2: blocked treatment3: no_XRN1_treated
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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).
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Library strategy |
OTHER |
Library source |
other |
Library selection |
other |
Instrument model |
Illumina NovaSeq 6000 |
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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
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Submission date |
Apr 10, 2023 |
Last update date |
Nov 06, 2024 |
Contact name |
Ziang Lu |
E-mail(s) |
zianglu@whu.edu.cn
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Organization name |
Wuhan University
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Street address |
Wuhan University, No.299, Bayi Road, Wuchang District
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City |
Wuhan |
ZIP/Postal code |
430072 |
Country |
China |
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Platform ID |
GPL26526 |
Series (1) |
GSE229317 |
Exonuclease-assisted identification of pseudouridine sites in single-stranded RNA |
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Relations |
SRA |
SRX19919339 |
BioSample |
SAMN34131441 |
Supplementary file |
Size |
Download |
File type/resource |
GSM7158851_60nt_oligo.CMC_treated.blocked.no_XRN1_treated.rep2.stoprate.txt.gz |
892 b |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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