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Sample description
Sample ID: 787
Anatomical region: abdominal cavity
Organ system: alimentary system
Term: pancreas
Sub-term: pancreas left lobe
Sampling: 2017-03-06 / provided by Lohi lab
Transport media: RNAlater
Additional info: List of tissues was modified from previous necropsy.
From subject: JPK344
Breed (variant): Swedish Elkhound
Sex: Female
Age: 3y 5m
Steril./Castr.: No
Reports:  Necropsy report   Clinical test results
WGS ID: JPK344A1, BioProject PRJNA907518, SRR22520748
Additional info: Two generalized epileptic seizures.
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
278 2017-05-02 JPK344 787 910.0 (QUBIT) 15 mg 50 48250.0 QIAGEN RNeasy Mini Kit 8.00 2.115 2.246
 
Applied assays   
STRT2-seq
 
Technical replicate [1578]
Other ID Platform Instrument Paired end Seq. date Strand mode Max. read length Chemistry version Laboratory Comments
STRT2_FP14_5 Illumina NextSeq 550 No May 2, 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_FP14_5  SDID_001983_STRT2_FP14_5_canine_mapped.bam SDID_001982_STRT2_FP14_5_canine_mapped.fq.gz CanFam3.1 3.0
STRT2_FP14_5  SDID_001982_STRT2_FP14_5_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_FP14_5 110,046 3,962,007 66.50
Technical replicate [1185]
Other ID Platform Instrument Paired end Seq. date Strand mode Max. read length Chemistry version Laboratory Comments
STRT2_FP7_5 Illumina NextSeq 550 No Aug. 16, 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_FP7_5  STRT2_FP7_5_canine_mapped.bam STRT2_FP7_5_canine_mapped.fq.gz CanFam3.1 3.0
STRT2_FP7_5  STRT2_FP7_5_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_FP7_5 68,266 2,348,469 66.30