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Sample GSM7395731 Query DataSets for GSM7395731
Status Public on May 08, 2024
Title Horse 6, immune, d1pi
Sample type SRA
 
Source name nasal mucosa
Organism Equus caballus
Characteristics tissue: nasal mucosa
treatment: EHV-1 Ab4 challenge
time: d1pi
immune status: immune
breed: Icelandic
Treatment protocol All horses were intranasally infected with 1x10^7 PFU neuropathogenic EHV-1 Ab4 on d0.
Extracted molecule total RNA
Extraction protocol RNA was extracted using TRIzol LS reagent (Life Technologies Corporation, Carlsbad, CA, USA) following the manufacturer’s protocol.
RNA was processed using NEBNext Ultra II RNA Library Prep Kit (New England Biolabs, Ipswich, MA, USA) to create a cDNA library, which was quantified with a Qubit 2.0 (dsDNA HS Kit, Thermo Fisher, Waltham, MA, USA) and fragment size distribution was determined by Fragment Analyzer (Advanced Analytical, Orangeburg, NY, USA).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description NE11-Horse6-D1pi
equine_rawCounts.txt
ehv-1_rawCounts.txt
Data processing Initial processing was carried out Cornell University’s Transcriptional Regulation and Expression (TREx) facility
Reads were trimmed for loq quality and adaptor sequences using TrimGalor v0.6.0, cutadapt, and fastQC.
Equine sequences were aligned using STAR v2.7.0e, to generate a raw counts table.
SARTools and DESeq2 v1.26.0 was used to generate normalized counts and statistical analysis of differential gene expression. Raw counts were additionally analyzed in iDEP.951, to determine differential expression
Viral sequences were aligned to the EHV-1 Ab4 genome (NC_001491.2) and a raw counts table was generated usinghtseq-count (Galaxy Version 0.9.1)
Assembly: EquCab 2.0
Supplementary files format and content: tab-delimited text files include raw count values for each Sample
 
Submission date May 19, 2023
Last update date May 08, 2024
Contact name Bettina Wagner
E-mail(s) bw73@cornell.edu
Organization name Cornell University
Department Population Medicine and Diagnostic Sciences
Lab Wagner
Street address 240 Farrier Drive
City Ithaca
State/province NY
ZIP/Postal code 14815
Country USA
 
Platform ID GPL21401
Series (1)
GSE232941 Mucosal immune response against equine herpesvirus type 1
Relations
BioSample SAMN35218022
SRA SRX20440702

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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