|
| Status |
Public on Feb 05, 2021 |
| Title |
Group2-1 |
| Sample type |
SRA |
| |
|
| Source name |
Bovine serum
|
| Organism |
Bos taurus |
| Characteristics |
breed: Holstein
tissue: Whole blood
condition: MAP infection
fecal pcr: Positive
elisa: Positive
clinical sign: Negative
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Small RNA was extracted from bovine serum using the miRNeasy Serum/Plasma Kit (Qiagen, Germany) according to the manufacturer's instruction.
The libraries were prepared for 50bp single-end sequencing using the NEXTflex Small RNA-Seq Kit (Bioo Scientific Corp.).
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
fecal PCR(+), ELISA(+), Clinical sign(-)
Small RNA
miRNA_expression_norm.txt
|
| Data processing |
Low quality bases or reads were trimmed using the Cutadapt tool (Marcel Martin, 2011).
Filtered reads were mapped to the reference genome of the related species using the aligner Bowtie.
The expression estimation find by mirdeep2 tool.
The variant calling was performed by the GATK to search variants in the miRNA seed region.
miRNA level count data were generated using mirdeep2.
Genome_build: UMD3.1.83
Supplementary_files_format_and_content: miRNA_expression_norm.txt: Tab-delimited text file includes abundance measurements.
|
| |
|
| Submission date |
Feb 04, 2021 |
| Last update date |
Feb 06, 2021 |
| Contact name |
Sungwoon Choi |
| E-mail(s) |
chltjddns7@gmail.com
|
| Phone |
01020167484
|
| Organization name |
Seoul National University
|
| Department |
Veterinary Medicine
|
| Lab |
Infectious Disease
|
| Street address |
1. Gwanak-ro
|
| City |
Seoul |
| State/province |
Gwanak-gu |
| ZIP/Postal code |
ASI/KR/KS013 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL26012 |
| Series (1) |
| GSE166230 |
miRNA profiling of putative biomarker candidates in Mycobacterium avium subsp. paratuberculosis-infected cattle |
|
| Relations |
| BioSample |
SAMN17804098 |
| SRA |
SRX10033774 |
