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| Status |
Public on Feb 16, 2024 |
| Title |
high BFI 1 |
| Sample type |
SRA |
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| Source name |
sperm
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| Organism |
Bos taurus |
| Characteristics |
tissue: sperm
bull fertility: high
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| Treatment protocol |
no extra treatment
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| Extracted molecule |
total RNA |
| Extraction protocol |
Sperm RNA was exreacted via miRNeasy Mini Kit (QIAGEN, Toronto, ON, Canada, Cat. # 217004)
NEBnext RNA library preparation kit (Catalog#: E7530L) was used for small RNA library construction and illumine sequencing
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
fertility_associated_tsRNAs.xlsx
miRNAs_that_associated_with_bull_fertility.xlsx
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| Data processing |
Sperm RNA was exreacted via miRNeasy Mini Kit (QIAGEN, Toronto, ON, Canada, Cat. # 217004)
NEBnext RNA library preparation kit (Catalog#: E7530L) was used for small RNA library construction and illumine sequencing
small rna library was cut then sent for sequencing.
The trimmomatic v0.39(Bolger, 2014) had been used for data trimming of the fastq file, and mapping had been made with the star v2.7.10b(Dobin, 2013).
The index was built with mature miRNA fasta from Mirbase. The differentially expression analysis had been made with the DESeq2 v1.34.0(Love, 2014).tRAX was used for tsRNAs analysis, and for analyzing tRNA-derived small RNAs,tRAX groups the sequencing reads into different tRNA fragment types(Holmes, 2022).
Assembly: miRbase and tsRNA analysis of eXpression(tRAX) was used, briefly, the custom tRNA reference database(built by tRAX) including all trna
Supplementary files format and content: miRNAs that associated with bull fertility(excel format),miRNAs that associated with daughter fertility(excel format);fertility associated tsRNAs(excel format).
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| Submission date |
Feb 21, 2023 |
| Last update date |
Feb 16, 2024 |
| Contact name |
Marc-André Sirard |
| E-mail(s) |
Marc-Andre.Sirard@fsaa.ulaval.ca
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| Organization name |
Université Laval
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| Department |
Sciences Animales
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| Street address |
Offfice 2732, 2440 Hochelaga Blvd.
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| City |
Québec City |
| State/province |
Quebec |
| ZIP/Postal code |
G1V 0A6 |
| Country |
Canada |
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| Platform ID |
GPL26012 |
| Series (1) |
| GSE225705 |
Sperm-borne tsRNAs and microRNA analysis in relation to dairy cattle fertility |
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| Relations |
| BioSample |
SAMN33392758 |
| SRA |
SRX19452737 |
| 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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