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Sample description
Sample ID: 4602
Anatomical region: thoracic cavity
Organ system: cardiovascular system
Term: vena cava
Sub-term: vena cava
Sampling: 2018-02-07 / provided by Lohi lab
Transport media: RNAlater
Additional info: Not all the tissues were collected from this dog.
From subject: VEO010
Breed (variant): East-European Shepherd
Sex: Female
Age: 2y 10m
Steril./Castr.: Not specified
Reports:  Necropsy report 
WGS ID:
Additional info:
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
432 2018-08-24 4602 (12.9.2018) 80 (ND) 2 mm3 30 2415 QIAZOL + QIAGEN RNeasy Mini Kit 8.00 1.86 1.38
 
Applied assays   
This sample was not sequenced yet.
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
677 2018-06-18 4602 (25.6.2018) 99.0 (QUBIT) 2 mm3 30 2452.5 QIAZOL + QIAGEN RNeasy Mini Kit 7.50 1.91 1.66
 
Applied assays   
STRT2-seq
 
Technical replicate [1004]
Other ID Platform Instrument Paired end Seq. date Strand mode Max. read length Chemistry version Laboratory Comments
STRT2_FP3_31 Illumina NextSeq 550 No Dec. 12, 2018 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_FP3_31  STRT2_FP3_31_canine_mapped.bam STRT2_FP3_31_canine_mapped.fq.gz CanFam3.1 3.0
STRT2_FP3_31  STRT2_FP3_31_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_FP3_31 188,078 879,356 63.60