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Sample description
Sample ID: 2978
Anatomical region: abdominal cavity
Organ system: alimentary system
Term: colon
Sub-term: colon (mucosa)
Sampling: 2017-10-05 / provided by Lohi lab
Transport media: Liquid nitrogen
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
443 2018-04-05 2978 (8.6.2018) 327.0 (ND) 2 mm3 100 32700.0 QIAGEN RNeasy Mini Kit 9.00 2.09 1.87
 
Applied assays   
STRT2-seq
 
Technical replicate [1036]
Other ID Platform Instrument Paired end Seq. date Strand mode Max. read length Chemistry version Laboratory Comments
STRT2_FP3_15 Illumina NextSeq 550 No Dec. 12, 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_FP3_15  STRT2_FP3_15_canine_mapped.fq.gz CanFam3.1 3.0
STRT2_FP3_15  STRT2_FP3_15_canine_mapped.bam STRT2_FP3_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_FP3_15 180,450 4,020,362 72.90