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| Status |
Public on May 08, 2024 |
| Title |
Horse 24, immune, d5pi |
| Sample type |
SRA |
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| Source name |
nasal mucosa
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| Organism |
Equus caballus |
| Characteristics |
tissue: nasal mucosa
treatment: EHV-1 Ab4 challenge
time: d5pi
immune status: immune
breed: Icelandic
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| Treatment protocol |
All horses were intranasally infected with 1x10^7 PFU neuropathogenic EHV-1 Ab4 on d0.
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| 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).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
NE32-Horse24-D5pi
ehv-1_rawCounts.txt
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| 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
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| Submission date |
May 19, 2023 |
| Last update date |
May 08, 2024 |
| Contact name |
Bettina Wagner |
| E-mail(s) |
bw73@cornell.edu
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| Organization name |
Cornell University
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| Department |
Population Medicine and Diagnostic Sciences
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| Lab |
Wagner
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| Street address |
240 Farrier Drive
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| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14815 |
| Country |
USA |
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| Platform ID |
GPL21401 |
| Series (1) |
| GSE232941 |
Mucosal immune response against equine herpesvirus type 1 |
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| Relations |
| BioSample |
SAMN35218001 |
| SRA |
SRX20440723 |
| 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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