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| Status |
Public on May 31, 2024 |
| Title |
milk EVs, control 6 |
| Sample type |
SRA |
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| Source name |
milk
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| Organism |
Bos taurus |
| Characteristics |
tissue: milk
treatment: Control
sample type: EV
condition: subclinical mastitis
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| Extracted molecule |
total RNA |
| Extraction protocol |
The RNA was isolated from the EV using the miRNeasy Mini Kit (cat. No. 217004, QIAGEN, Germany). The isolation process followed the manufacturer’s protocol. Briefly, EV samples were first lysed and homogenized in a highly denaturing guanidine-thiocyanate-containing buffer, which immediately inactivated RNases, ensuring the purification of intact RNA. By mixing with ethanol, the samples were loaded into an RNeasy Mini spin column. The total RNA bound to the membrane and contaminants were washed away. The eluted, high-quality RNA was collected and stored at -80 °C for further analysis.
Briefly, libraries were subjected to reverse transcription and amplification by connecting 3’ and 5’ adapters to the ends of RNA molecules using T4 RNA Ligase (catalog no. LR2D1132K, Epicentre, US). cDNA constructs were purified and recovered, and the libraries were subsequently checked and normalized.
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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 |
c6
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| Data processing |
In brief, raw data were converted from basic reads by base calling. Reads with 3’ adapters, without 5’ primer contaminants and poly (A), and ranging between 15 nt and 41 nt were kept to obtain clean reads. The Fastx_toolkit (version 0.0.13) was used to control the quality of the read. The NGSQC Toolkit (version 2.3.2) was used to filter reads containing N bases. Non-coding RNAs, including ribosomal RNAs, other small RNAs, and small nucleolar RNAs, were annotated by searching against the Rfam (v.10.1). The miRBase (v.21) database was used to identify miRNA and analyze their expression patterns.
Assembly: NCBI assembly Bos taurus (assembly ARS-UCD1.2), mirbase-22-release
Supplementary files format and content: miRNA.csv
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| Submission date |
Feb 23, 2024 |
| Last update date |
May 31, 2024 |
| Contact name |
Wanjie Yu |
| E-mail(s) |
Wanjie.Yu@student.uliege.be
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| Organization name |
Institute of Animal Science, Chinese Academy of Agricultural Sciences
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| Street address |
No. 2 Yuanmingyuan West Road
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| City |
Beijing |
| ZIP/Postal code |
100193 |
| Country |
China |
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| Platform ID |
GPL26012 |
| Series (1) |
| GSE256521 |
Effect of inulin on extracellular vesicles microRNAs in milk from dairy cows with sub-clinical mastitis |
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| Relations |
| BioSample |
SAMN40089555 |
| SRA |
SRX23724161 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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