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| Status |
Public on Jul 16, 2019 |
| Title |
N121 |
| Sample type |
SRA |
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| Source name |
Ampulla
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| Organism |
Equus caballus |
| Characteristics |
infection status: Naïve
collection timepoint: NA
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| Treatment protocol |
Samples from the ampullae were collected at post-mortem and snap-frozen in OCT compound and stored at -80C.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 5 to 6 10um cryosections of tissue using the RNeasy Micro kit kit (Qiagen, Valencia, CA)
cDNA libraries were prepared using the TruSeq® stranded total RNA sample preparation kit with rRNA depletion (Illumina Inc., San Diego, CA) and performed by a commercial company (Exiqon Services, Vedbæk, Denmark, and Qiagen Genomic Services, Hilden Germany).
Libraries for each batch were pooled in equimolar ratios and sequenced on two High Output NextSeq500 runs with 2x50bp paired-end read length (2x30 million reads/sample) plus 2x8bp for demultiplexing. After sequencing, raw data were demultiplexed using the bcl2fastq v. 2.17 software (Illumina Inc.). FastQ for each of the two were combined and QC was performed using the FastQC software package v. 0.10.1 (Babraham Bioinformatics, Babraham Institute, Cambridge, UK).
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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 |
The sequencing results were initially trimmed for adapters and quality using TrimGalore Version 0.4.4 (Babraham Bioinformatics; www.bioinformatics.babraham.ac.uk).
The sequences were mapped to EquCab2.0 using Burrows-Wheeler Aligner (V bwa-0.7.12).
Final quantification at the gene level was performed by analyzing the BAM files in Cufflinks (2.2.1) using the Equus_caballus_ENSEMBL_88 gtf file as Guide.
normalized abundance measurements- Cufflink Gene.FPKM.Tracking
Genome_build: EquCab2.0 (GCA_000002305.1)
Supplementary_files_format_and_content: normalized abundance measurements- Cufflink Gene.FPKM.Tracking
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| Submission date |
May 29, 2018 |
| Last update date |
Jul 16, 2019 |
| Contact name |
Udeni B. R. Balasuriya |
| E-mail(s) |
ubalasuriya@uky.edu
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| Phone |
8592181124
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| Organization name |
University of Kentucky
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| Department |
Veterinary Science
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| Street address |
108 Maxwell H. Gluck Equine Research Center
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| City |
Lexington |
| State/province |
KY |
| ZIP/Postal code |
40546 |
| Country |
USA |
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| Platform ID |
GPL21401 |
| Series (1) |
| GSE114982 |
Long-term persistent infection with equine arteritis virus is associated with the upregulation of specific CD8+ T lymphocyte transcription factors, inhibitory receptors, and the CXCL16/CXCR6 axis in the ampullae of the stallion reproductive tract |
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| Relations |
| BioSample |
SAMN09273723 |
| SRA |
SRX4133131 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3161948_9-genes.fpkm_tracking.gz |
717.3 Kb |
(ftp)(http) |
FPKM_TRACKING |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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