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Sample description
Sample ID: 1599
Anatomical region: thoracic cavity
Organ system: cardiovascular system
Term: pericardium
Sub-term: pericardium
Sampling: 2016-09-20 / provided by Lohi lab
Transport media: RNAlater
Additional info: This was originally a training dog.
From subject: BC1642
Breed (variant): Border Collie
Sex: Male
Age: 6y 11m
Steril./Castr.: Not specified
Reports:  Necropsy report 
WGS ID: BC1642A1, BioProject PRJNA907518, SRR22520746
Additional info: This was originally a training dog. Epilepsy (cortex, hippocampus) + degenerative changes in large brain (mild neuronal loss, prominent capilaries, lipofuscinosis).
Study: Study of gene expression across dog tissues
Description: This project will generate the critical resources to better utilize various canine models to advance both dog and human health.
Status / Visibility: Submitted / Public
Publication: The DoGA consortium expression atlas of promoters and genes in 100 canine tissues. Nat. Commun. 2024, 15(1):9082 (PMID: 39433728)
Other IDs: PRJNA907518
Additional info:
 
Sample processing
RNA extraction
ID Date Bioanalizer ID Stock Conc.
(ng/µl)
Tissue ammount Sample volume RNA amount
(ng)
Extraction method RIN Ratio
A260/A280
Ratio
A260/A230
Comments
738 2019-02-21 1599 (22.2.2019_10-18-59) 45.0 (QUBIT) 2 mm3 50 1850.0 QIAZOL + QIAGEN RNeasy Mini Kit 7.50 1.98 1.12
 
Applied assays   
STRT2-seq
 
Technical replicate [1470]
Other ID Platform Instrument Paired end Seq. date Strand mode Max. read length Chemistry version Laboratory Comments
STRT2_FP12_23 Illumina NextSeq 550 No April 30, 2019 SR 1x75bp 75bp NextSeq High Output FuGU lab Phi-X spike in added to each STRT2 library for sequencing (20%).
Sequencing information
Sequencing data
Seq. ID Files Derived from Mapped genome Command Freeze version Comments
STRT2_FP12_23  SDID_001745_STRT2_FP12_23_canine_mapped.bam SDID_001744_STRT2_FP12_23_canine_mapped.fq.gz CanFam3.1 3.0
STRT2_FP12_23  SDID_001744_STRT2_FP12_23_canine_mapped.fq.gz CanFam3.1 3.0
 
Sequencing quality data
Other ID Pool name BC reads Spike-in mapped reads Spike-in mapped % Canine mapped reads Canine mapped % Unmapped reads % Comments
STRT2_FP12_23 142,125 1,239,106 43.20