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Sample description
Sample ID: 2677
Anatomical region: head
Organ system: central nervous system
Term: piriform lobe
Sub-term: piriform lobe
Sampling: 2017-10-05 / provided by Lohi lab
Transport media: RNAlater
Additional info:
From subject: PI153
Breed (variant): German Pinscher
Sex: Female
Age: 1y 5m
Steril./Castr.: No
Reports:  Necropsy report   Clinical test results
WGS ID: PI153A1, BioProject PRJNA907518, SRR22520745
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
540 2017-12-14 PI 153 2677 285.0 (ND) 23 mg 30 8550.0 QIAGEN RNeasy Mini Kit 9.90 2.151 1.344
 
Applied assays   
STRT2-seq
 
Technical replicate [974]
Other ID Platform Instrument Paired end Seq. date Strand mode Max. read length Chemistry version Laboratory Comments
STRT2_FP2_15 Illumina NextSeq 550 No Nov. 27, 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_FP2_15  STRT2_FP2_15_canine_mapped.fq.gz CanFam3.1 3.0
STRT2_FP2_15  STRT2_FP2_15_canine_mapped.bam STRT2_FP2_15_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_FP2_15 120,704 2,822,813 71.50
Technical replicate [1223]
Other ID Platform Instrument Paired end Seq. date Strand mode Max. read length Chemistry version Laboratory Comments
STRT2_FP8_7 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_FP8_7  STRT2_FP8_7_canine_mapped.bam STRT2_FP8_7_canine_mapped.fq.gz CanFam3.1 3.0
STRT2_FP8_7  STRT2_FP8_7_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_FP8_7 36,591 836,272 69.70