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Sample description
Sample ID: 537
Anatomical region: head
Organ system: central nervous system
Term: thalamus
Sub-term: lateral geniculate nucleus
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
671 2017-03-27 537 780 (QUBIT) 22 mg 30 23700 QIAGEN RNeasy Mini Kit 8.30 2.086 1.012 WARNING: Extraction method different from other dogs.
 
Applied assays   
STRT2-seq
 
Technical replicate [937]
Other ID Platform Instrument Paired end Seq. date Strand mode Max. read length Chemistry version Laboratory Comments
STRT2_FP1_35 Illumina NextSeq 550 No April 19, 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_FP1_35  STRT2_FP1_35_canine_mapped.fq.gz — CanFam3.1 — 3.0 —
STRT2_FP1_35  STRT2_FP1_35_canine_mapped.bam STRT2_FP1_35_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_FP1_35 — — 250,274 — 104,141 19.60 — —
 
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
672 2017-03-21 537 25 (QUBIT) 25 mg 40 1000 QIAGEN RNeasy Mini Kit 9.00 2.03 1.341 WARNING: Extraction method different from other dogs.
 
Applied assays   
STRT2-seq
 
Technical replicate [1356]
Other ID Platform Instrument Paired end Seq. date Strand mode Max. read length Chemistry version Laboratory Comments
STRT2_FP11_35 Illumina NextSeq 550 No Oct. 25, 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_FP11_35  STRT2_FP11_35_canine_mapped.bam STRT2_FP11_35_canine_mapped.fq.gz CanFam3.1 — 3.0 —
STRT2_FP11_35  STRT2_FP11_35_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_FP11_35 — — 205,273 — 2,051,980 75.60 — —