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Sample description
Sample ID: 4189
Anatomical region: thoracic cavity
Organ system: cardiovascular system
Term: heart endocardium
Sub-term: aortic valve
Sampling: 2017-11-28 / provided by Lohi lab
Transport media: RNAlater
Additional info:
From subject: CLK294
Breed (variant): Collie( smooth)
Sex: Male
Age: 4y 6m
Steril./Castr.: No
Reports:  Necropsy report   Clinical test results
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
908 2020-02-26 4189 (TS26.2.2020) 115.2 (QUBIT) 2 mm3 25 2461.0 QIAZOL + QIAGEN RNeasy Mini Kit 8.00 1.95 1.58 Tissue ruptor
 
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
426 2018-06-18 4189 (25.6.2018) 103.0 (QUBIT) 2 mm3 30 2416.0 QIAZOL + QIAGEN RNeasy Mini Kit 7.80 1.94 1.92 Tissue ruptor
 
Applied assays   
STRT2-seq
 
Technical replicate [1013]
Other ID Platform Instrument Paired end Seq. date Strand mode Max. read length Chemistry version Laboratory Comments
STRT2_FP3_19 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_19  STRT2_FP3_19_canine_mapped.bam STRT2_FP3_19_canine_mapped.fq.gz CanFam3.1 3.0
STRT2_FP3_19  STRT2_FP3_19_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_19 181,898 2,960,727 71.90