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Sample description
Sample ID: 334
Anatomical region: abdominal cavity
Organ system: alimentary system
Term: duodenum
Sub-term: duodenum serosa
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
62 2017-03-14 SLK1048 334 60.0 (QUBIT) 22 mg 40 3200.0 QIAGEN RNeasy Mini Kit 8.20 2.078 2.209
 
Applied assays   
STRT2-seq
 
Technical replicate [1589]
Other ID Platform Instrument Paired end Seq. date Strand mode Max. read length Chemistry version Laboratory Comments
STRT2_FP14_10 Illumina NextSeq 550 No May 2, 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_FP14_10  SDID_001902_STRT2_FP14_10_canine_mapped.fq.gz CanFam3.1 3.0
STRT2_FP14_10  SDID_001903_STRT2_FP14_10_canine_mapped.bam SDID_001902_STRT2_FP14_10_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_FP14_10 100,581 2,090,494 58.30
Technical replicate [1197]
Other ID Platform Instrument Paired end Seq. date Strand mode Max. read length Chemistry version Laboratory Comments
STRT2_FP7_10 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_FP7_10  STRT2_FP7_10_canine_mapped.bam STRT2_FP7_10_canine_mapped.fq.gz CanFam3.1 3.0
STRT2_FP7_10  STRT2_FP7_10_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_FP7_10 81,485 2,458,649 70.50