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| Status |
Public on Sep 18, 2024 |
| Title |
zebrafish embryo, 5dpf, sas10 mutant, rep 2 |
| Sample type |
SRA |
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| Source name |
embryo
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| Organism |
Danio rerio |
| Characteristics |
tissue: embryo
genotype: sas10 mutant
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from WT and sas10zju2/zju2 mutant embryos at 5dpf using TRIpure Reagent (Aidlab, RN0102), with three independent biological repeats each, and was treated with DNase I (New England Biolabs, M0303S) to remove genomic DNA contamination.
Total RNA for each sample was ligated with 3'RACE_adapter, followed by 3'RACE_adapter specific RT primer's reverse transcription. Sequencing libraries were derived from PCR amplification using forward primer containing zebrafish 5'ETS sequence and reverse primers (Illumina RPIs).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
RACE |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Sequence reads were trimmed of adapter sequences and low quality sequences using Cutadpat.
Trimmed sequences were deduplicated, zebrafish 5'ETS sequence searched, and mapped to zebrafish pre-rRNA reference sequence to analyze the 3' end of each read.
Assembly: GRCz11
Supplementary files format and content: tab-delimited text file including each read's relative postion in pre-rRNA, corresponding sequence, modification status and modification size.
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| Submission date |
Mar 28, 2024 |
| Last update date |
Sep 18, 2024 |
| Contact name |
Shuyi Zhao |
| E-mail(s) |
[email protected]
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| Organization name |
Zhejiang University
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| Department |
College of Animal Sciences
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| Lab |
MOE Key Laboratory for Molecular Animal Nutrition
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| Street address |
866 Yuhangtang Road
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| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310058 |
| Country |
China |
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| Platform ID |
GPL24995 |
| Series (1) |
| GSE262698 |
Effect of depletion of Sas10 in pre-rRNA processing |
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| Relations |
| BioSample |
SAMN40646976 |
| SRA |
SRX24092863 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8174002_RACE_S_2.txt.gz |
4.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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