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| Status |
Public on Apr 21, 2022 |
| Title |
WR3 |
| Sample type |
SRA |
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| Source name |
dorsal skin
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| Organism |
Oncorhynchus mykiss |
| Characteristics |
genotype: wild-type
phenotype: black skin (WR)
tissue: dorsal skin
age: 45 days
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| Extracted molecule |
total RNA |
| Extraction protocol |
The samples were collected immediately, then flash-frozen in liquid nitrogen,and total RNA was extracted using Trizol reagent.
Total RNA of the six libraries from dorsal skin was extracted using Trizol reagen kit (Invitrogen, Carlsbad, CA, USA), then purified RNA were ligated with 3’ and 5’ adapters.
small RNA libraries were prepared for sequencing using standard Illumina protocols
cDNA library were generated after the ligation products were reverse transcribed by PCR amplification and sequenced using Illumina HiSeq Xten by Gene Denovo Biotechnology Co. (Guangzhou, China).
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Similar to RNA-seq, quality control was conducted by removing dirty reads, including low quality reads, reads with 5’ adaptor contaminants or without 3’ adaptors, ployA in small RNA fragment and reads shorter than 18 nt.
Then, rRNA, scRNA, sonRNA, snRNA and tRNA were removed by blasting against GeneBank database (Release 209.0) and Rfam database (Release 11.0). Finally, the remaining reads were searched against miRBase database (Release 22) to identify conserved and novel miRNAs.
Genome_build: Oncorhynchus mykiss Omyk_1.0
Supplementary_files_format_and_content: tab-delimited text file includes miRNAs TPM values for each Sample
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| Submission date |
Apr 21, 2021 |
| Last update date |
Apr 21, 2022 |
| Contact name |
Pan Yu Cai |
| E-mail(s) |
pyc@guizunyu.ntesmail.com
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| Phone |
17693505396
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| Organization name |
Gansu Agricultural University
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| Department |
College of Animal Science and Technology
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| Street address |
Yin Tan Road Street, An Ning District
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| City |
Lan zhou |
| State/province |
Gansu |
| ZIP/Postal code |
730070 |
| Country |
China |
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| Platform ID |
GPL30022 |
| Series (1) |
| GSE172482 |
Integrated mRNA and miRNA expression profile analyses reveal the potential roles of miRNA–mRNA pairs in skin color variation between wild-type and yellow mutant rainbow trout |
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| Relations |
| BioSample |
SAMN18820197 |
| SRA |
SRX10651547 |
| 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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