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| Status |
Public on May 05, 2021 |
| Title |
S12 BRSV challenged |
| Sample type |
SRA |
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| Source name |
whole blood
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| Organism |
Bos taurus |
| Characteristics |
treatment: BRSV challenged
breed: Holstein-Friesian
shed: B
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Tempus™ Spin RNA Isolation Kit (Bio-Sciences LTD, Dublin, Ireland), according to the manufacturer's instructions.
RNA-Seq library preparation was performed using the TruSeq stranded mRNA Kit (Illumina, San Diego, California, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
counts.txt
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| Data processing |
The 3' end of the sequence reads were trimmed for Illumina adapters, low quality reads (quality score < 20), ambiguous nucleotides, and poly-G artefacts resulting from the NextSeq’s two-colour chemistry, using CutAdapt (version 1.18).
The cleaned sequence reads were evaluated for quality using FastQC.
Reads were aligned to the UMD3.1 bovine reference genome and read counts were generated by converting aligned reads into counts per gene using the Spliced Transcripts Alignment to a Reference (STAR) aligner (version 2.6.1b)
Genome_build: UMD3.1
Supplementary_files_format_and_content: TXT file of raw counts table of sequenced reads
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| Submission date |
Jun 22, 2020 |
| Last update date |
May 05, 2021 |
| Contact name |
Dayle Johnston |
| Organization name |
Teagasc
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| Department |
Animal and Bioscience Research Department
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| Lab |
Teagasc Grange
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| Street address |
AGRIC
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| City |
Dunsany |
| State/province |
Ireland |
| ZIP/Postal code |
C15 PW93 |
| Country |
Ireland |
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| Platform ID |
GPL26012 |
| Series (1) |
| GSE152959 |
Messenger RNA Biomarkers of Bovine Respiratory Syncytial Virus Infection in whole blood of dairy calves |
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| Relations |
| BioSample |
SAMN15340200 |
| SRA |
SRX8594779 |
| 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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