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| Status |
Public on Jul 19, 2023 |
| Title |
T3_2 |
| Sample type |
SRA |
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| Source name |
Embryos
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| Organism |
Danio rerio |
| Characteristics |
tissue: Embryos
genotype: WT
developmental stage: 36hpf
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted from embryos at three key organogenesis stages in zebrafish using TRIzol reagent(Invitrogen, cat. NO 15596026) following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999).
2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo-off rRNA Depletion Kit (Catalog NO. MRZG12324, Illumina) and KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-T7 |
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| Data processing |
The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules
The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on DNBSEQ-T7 sequencer (MGI Tech Co., Ltd. China) with PE150 model.
Assembly: GRCz11
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
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| Submission date |
Jun 23, 2023 |
| Last update date |
Jul 19, 2023 |
| Contact name |
chune zhou |
| Organization name |
henan normal university
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| Street address |
jian she east road 46
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| City |
xinxiang |
| ZIP/Postal code |
453007 |
| Country |
China |
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| Platform ID |
GPL30277 |
| Series (1) |
| GSE235668 |
Systematic identification of long noncoding RNAs during three key organogenesis stages in zebrafish |
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| Relations |
| BioSample |
SAMN35880102 |
| SRA |
SRX20762484 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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