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| Status |
Public on Nov 06, 2024 |
| Title |
60nt_mix_32nt_oligo, CMC_treated, blocked, XRN1_treated_30min, rep1 |
| Sample type |
SRA |
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| Source name |
60nt mix 32nt oligo
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| Organism |
synthetic construct |
| Characteristics |
treatment1: CMC_treated
treatment2: blocked
treatment3: XRN1_treated_30min
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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 |
SRX19919342 |
| BioSample |
SAMN34131438 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7158854_60nt_mix_32nt_oligo.CMC_treated.blocked.XRN1_treated_30min.rep1.stoprate.txt.gz |
1.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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