|
| Status |
Public on Dec 31, 2020 |
| Title |
FIP-FCoV+1 |
| Sample type |
SRA |
| |
|
| Source name |
mesenteric lymph node
|
| Organism |
Felis catus |
| Characteristics |
age: 1 y
breed: Maine Coon
fip status: Neg
fcov infection: FCoV+
disease in non-fip: Connective tissue abnormality and pleural effusion (FCoV RT-qPCR negative) => in paper just effusion in Thesis also connective tissue problem
tissue: mesenteric lymph node
|
| Treatment protocol |
NA - all natural infections and clinical cases
|
| Growth protocol |
NA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extracted with Qiagen RNeasy Mini Kit, then remaining DNA removed with ezDNase (Thermo Fisher Scientific).
TruSeq RNA stranded
PolyA, TruSeq RNA Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
G1_Pos_1
|
| Data processing |
bcl2Fastq v2.19 software used for demultiplexing + basecalling.
reads trimmed with trimmomatic, options: ILLUMINACLIP:adapters.fa:1:20:7:5:true AVGQUAL:10 MINLEN:20
reads mapped with STAR v2.7.1, options: --sjdbOverhang 150 --twopassMode None --runThreadN 8 --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outMultimapperOrder Random --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted
count: FeatureCounts (Bioconductor), options: allowMultiOverlap = true; countPrimaryAlignmentsOnly= true; minFeatureOverlap=10; minMapQuality= 10 ; keepMultiHits=true
differential expression analysis: EdgeR, options: normMethod = TMM; backgroundExpression =10; testMethod = glm; deTest =QL
Genome_build: Relis Catus, Ensembl, 6.2
Supplementary_files_format_and_content: tad-delimited, raw counts
|
| |
|
| Submission date |
Jun 17, 2020 |
| Last update date |
Jan 01, 2021 |
| Contact name |
giancarlo russo |
| E-mail(s) |
giancarlo.russo@fgcz.ethz.ch
|
| Organization name |
ETH/University of Zurich
|
| Department |
Functional Genomics Center Zurich
|
| Street address |
winterthurerstrasse 190
|
| City |
Zurich |
| State/province |
Schweiz |
| ZIP/Postal code |
8057 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL23056 |
| Series (1) |
| GSE152676 |
The effect of natural feline coronavirus infection on the host immune response: a whole-transcriptome analysis on the mesenteric lymph nodes of cats with and without feline infectious peritonitis |
|
| Relations |
| BioSample |
SAMN15297659 |
| SRA |
SRX8564839 |
