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| Status |
Public on Nov 29, 2022 |
| Title |
C48HKs-3 |
| Sample type |
SRA |
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| Source name |
head kidney tissues
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| Organism |
Oncorhynchus mykiss |
| Characteristics |
tissue: head kidney tissues
treatment: control
phenotype: wild-type
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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.
miRNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Reads obtained from the sequencing machines included dirty reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get clean tags, raw reads were further filtered according to the following rules: 1) Removing low quality reads containing more than one low quality (Q-value≤20) base or containing unknown nucleotides (N); 2) Removing reads without 3’adapters; 3) Removing reads containing 5’adapters; 4) Removing reads containing 3’ and 5’ adapters but no small RNA fragment between them; 5) Removing reads containing ployA in small RNA fragment; 6) Removing reads shorter than 18nt (not include adapters).
All of the clean tags were aligned with small RNAs in GeneBank database (Release 209.0) and in Rfam database (Release 11.0) to identify and remove ribosomal RNA (rRNA), small conditional RNA (scRNA), small nucleolar RNA (snoRNA), small nuclear RNA (snRNA), and transfer RNA (tRNA).
The enriched clean tags were also aligned with reference genome. Those mapped to exons or introns might be fragments from mRNA degradation, so these tags were removed. The tags mapped to repeat sequences were also removed. The remaining tags were searched against miRBase database (Release 22) to identify known miRNAs.
All the unannotated tags were clustered and defined as novel miRNA candidates according to their genome positions and hairpin structures predicted by the software Mireap_v0.2.
Assembly: rainbow trout
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
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| Submission date |
Nov 25, 2022 |
| Last update date |
Nov 29, 2022 |
| Contact name |
jinqiang huang |
| E-mail(s) |
huangjq@gsau.edu.cn
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| Organization name |
Gansu Agricultural University
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| Street address |
Yintanlu Stress
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| City |
Lanzhou |
| ZIP/Postal code |
730070 |
| Country |
China |
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| Platform ID |
GPL30022 |
| Series (1) |
| GSE218752 |
Integrative mRNA-miRNA interaction analysis associated with the immune response in the head kidney of rainbow trout (Oncorhynchus mykiss) after infectious hematopoietic necrosis virus infection |
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| Relations |
| BioSample |
SAMN31872148 |
| SRA |
SRX18377973 |
| 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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