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Sample GSM3391999 Query DataSets for GSM3391999
Status Public on Apr 23, 2019
Title Mock-infected mouse spinal cord at 35 days pi_5
Sample type SRA
 
Source name Mock-infected mouse spinal cord at 35 days pi
Organism Mus musculus
Characteristics strain: SJL/J
Sex: Female
infection: Intracerebral injection of PBS
time: 35 days p.i.
tissue: Spinal cord
Treatment protocol Female 5-week-old SJL/J mice (Jackson Laboratory, Bar Harbor, ME) were infected intracerebrally with 2 x 10^5 plaque forming units (PFU) of the Daniels (DA) strain of TMEV.
Extracted molecule total RNA
Extraction protocol RNA was isolated using Tri-Reagent and RNeasy Mini Kit (QIAGEN). Illumina TruSeq Stranded Total RNA LT Sample Prep kit - Set A with Ribo-Zero Gold was used with 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description SO256
Data processing Basecalls performed using CASAVA
The raw sequence data were aligned to reference genome, Mus musculus GRCm38.75, downloaded from ENSEMBLE, using the Spliced Transcripts Alignment to a Reference (STAR)
The read count data were normalized with two methods: 1) read counts per kilobase (RPK) and 2) DEG elimination strategy (DEGES), using “R” and the package “tag count comparison (TCC)”
Genome_build: mm10
Supplementary_files_format_and_content: Normalized read counts
 
Submission date Sep 17, 2018
Last update date Apr 23, 2019
Contact name Seiichi Omura
E-mail(s) omura.s@hotmail.com
Organization name Kindai University Faculty of Medicine
Department Department of Microbiology
Street address 377-2 Ohnohigashi
City Osakasayama
State/province Osaka
ZIP/Postal code 589-8511
Country Japan
 
Platform ID GPL19057
Series (2)
GSE120041 Theiler’s Virus-Mediated Immunopathology in the CNS and Heart: Roles of Organ-Specific Cytokine and Lymphatic Responses [RNA-Seq]
GSE120042 Theiler’s Virus-Mediated Immunopathology in the CNS and Heart: Roles of Organ-Specific Cytokine and Lymphatic Responses
Relations
BioSample SAMN10077626
SRA SRX4702810

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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