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| Status |
Public on Dec 31, 2020 |
| Title |
FIP+9 |
| Sample type |
SRA |
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| Source name |
mesenteric lymph node
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| Organism |
Felis catus |
| Characteristics |
age: 12y
breed: ESH
fip status: Pos
tissue: mesenteric lymph node
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| Treatment protocol |
NA - all natural infections and clinical cases
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| Growth protocol |
NA
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
G2_8
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| 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
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| Submission date |
Jun 17, 2020 |
| Last update date |
Jan 01, 2021 |
| Contact name |
giancarlo russo |
| E-mail(s) |
giancarlo.russo@fgcz.ethz.ch
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| Organization name |
ETH/University of Zurich
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| Department |
Functional Genomics Center Zurich
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| Street address |
winterthurerstrasse 190
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| City |
Zurich |
| State/province |
Schweiz |
| ZIP/Postal code |
8057 |
| Country |
Switzerland |
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| Platform ID |
GPL28702 |
| 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 |
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| Relations |
| BioSample |
SAMN15297640 |
| SRA |
SRX8564853 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4623174_G2_8.txt.gz |
94.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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