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Sample description
Sample ID: 53
Anatomical region: head
Organ system: central nervous system
Term: thalamus
Sub-term: lateral geniculate nucleus
Sampling: 2017-02-16 / provided by Lohi lab
Transport media: RNAlater
Additional info: Dissection date 16.2.2017
From subject: SLK1048
Breed (variant): Finnish Lapphund
Sex: Female
Age: 6y 6m
Steril./Castr.: Yes
Reports:  Necropsy report   Clinical test results
WGS ID: SLK1048A1, BioProject PRJNA907518, SRR22520749
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
83 2017-03-06 53 (13.3.2017) 88.0 (QUBIT) 15 mg 40 3560.0 QIAZOL + QIAGEN RNeasy Mini Kit 8.60 2.059 0.783
 
Applied assays   
STRT2-seq
 
Technical replicate [927]
Other ID Platform Instrument Paired end Seq. date Strand mode Max. read length Chemistry version Laboratory Comments
STRT2_FP1_12 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_12  STRT2_FP1_12_canine_mapped.bam STRT2_FP1_12_canine_mapped.fq.gz CanFam3.1 3.0
STRT2_FP1_12  STRT2_FP1_12_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_12 117,374 850,266 60.40
Technical replicate [1336]
Other ID Platform Instrument Paired end Seq. date Strand mode Max. read length Chemistry version Laboratory Comments
STRT2_FP11_12 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_12  STRT2_FP11_12_canine_mapped.bam STRT2_FP11_12_canine_mapped.fq.gz CanFam3.1 3.0
STRT2_FP11_12  STRT2_FP11_12_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_12 227,357 4,228,627 75.80