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Sample description
Sample ID: 3058
Anatomical region: forelimb
Organ system: musculoskeletal system
Term: skeletal muscle
Sub-term: biceps brachii
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
786 2019-02-26 3058 (26.2.2019) 220.0 (QUBIT) 2 mm3 35 5670.0 Not specified 9.20 2.04 1.8
 
Applied assays   
STRT2-seq
 
Technical replicate [1533]
Other ID Platform Instrument Paired end Seq. date Strand mode Max. read length Chemistry version Laboratory Comments
STRT2_FP13_32 Illumina NextSeq 550 No Aug. 14, 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_FP13_32  SDID_001859_STRT2_FP13_32_canine_mapped.bam SDID_001858_STRT2_FP13_32_canine_mapped.fq.gz CanFam3.1 3.0
STRT2_FP13_32  SDID_001858_STRT2_FP13_32_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_FP13_32 152,392 3,184,755 79.40