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Sample description
Sample ID: 530
Anatomical region: head
Organ system: central nervous system
Term: cerebellum vermis
Sub-term: cerebellum vermis
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
332 2017-06-12 JPK344 530 325.0 (ND) 18 mg 30 9750.0 QIAZOL + QIAGEN RNeasy Mini Kit 7.80 2.134 2.414 —
 
Applied assays   
CAGE-seq
 
Technical replicate [1454]
Other ID Platform Instrument Paired end Seq. date Strand mode Max. read length Chemistry version Laboratory Comments
CAGE_L_00142.BC1 Illumina HiSeq 2500 No Jan. 28, 2019 SR 1x50bp 50 bp Hi-Seq High Output v4 Daub lab 10% Phi-X spike in added for CAGE set 05
Sequencing information
Sequencing data
Seq. ID Files Derived from Mapped genome Command Freeze version Comments
CAGE_L_00142.BC1  CAGE_L_00142.BC01_qfilter_trimBC.fq.gz — CanFam4 — 4 —
CAGE_L_00142.BC1  CAGE_L_00142.BC1_yeast_unAl — CanFam3.1 — 4 —
CAGE_L_00142.BC1  CAGE_L_00142.BC01.sorted.tar.gz CAGE_L_00142.BC1_yeast_unAl CanFam4 — 4 —
 
Sequencing quality data
Other ID Pool name BC reads Spike-in mapped reads Spike-in mapped % Canine mapped reads Canine mapped % Unmapped reads % Comments
CAGE_L_00142.BC1 Cerebellum pool Cerebellum pool 30,058,014 — — 27,151,642 90.33 7.37 —