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| Status |
Public on Oct 29, 2019 |
| Title |
S8: Bronchial lymph node |
| Sample type |
SRA |
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| Source name |
Bronchial lymph node
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| Organism |
Bos taurus |
| Characteristics |
tissue: Bronchial lymph node
treatment: BRSV challenged
house: B
breed: Holstein-Friesian
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| Extracted molecule |
total RNA |
| Extraction protocol |
Bronchial lymph nodes were removed, flash frozen on dry ice, and RNA was harvested using the Qiagen RNeasy Plus Universal Mini Kit (Qiagen LTD, Manchester, UK). Extracted RNA was shipped frozen at -80oC on dry ice to the University of Missouri’s DNA Core Facility for RNA-Seq library preparation (Illumina TruSeq stranded mRNA Kit).
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Adapter trimmed sequence reads were received in FASTQ format and assessed for quality using FastQC (version 0.11.7) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads were aligned to the bovine genome UMD3.1 using the Spliced Transcripts Alignment to a Reference (STAR) aligner (version 2.5.2b) (Dobin et al., 2013).
Read counts were generated by converting aligned reads into counts per gene using the Spliced Transcripts Alignment to a Reference (STAR) aligner (version 2.5.2b) (Dobin et al., 2013).
Genome_build: UMD3.1
Supplementary_files_format_and_content: Microsoft excel comma separated values file containing raw counts of sequencing reads for the features of interest
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| Submission date |
May 20, 2019 |
| Last update date |
Oct 29, 2019 |
| 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 |
GPL23055 |
| Series (1) |
| GSE131452 |
Elucidation of the host transcriptomic response to bovine respiratory syncytial virus |
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| Relations |
| BioSample |
SAMN11775974 |
| SRA |
SRX5865495 |
| 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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