|
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
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|
|
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 |