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Sample GSM3161942 Query DataSets for GSM3161942
Status Public on Jul 16, 2019
Title L141
Sample type SRA
 
Source name Ampulla
Organism Equus caballus
Characteristics infection status: Short-term carrier
collection timepoint: 726 days post-infection
Treatment protocol Samples from the ampullae were collected at post-mortem and snap-frozen in OCT compound and stored at -80C.
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).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
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
 
Submission date May 29, 2018
Last update date Jul 16, 2019
Contact name Udeni B. R. Balasuriya
E-mail(s) ubalasuriya@uky.edu
Phone 8592181124
Organization name University of Kentucky
Department Veterinary Science
Street address 108 Maxwell H. Gluck Equine Research Center
City Lexington
State/province KY
ZIP/Postal code 40546
Country USA
 
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
Relations
BioSample SAMN09273729
SRA SRX4133125

Supplementary file Size Download File type/resource
GSM3161942_3-genes.fpkm_tracking.gz 740.3 Kb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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