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Sample description
Sample ID: 5739
Anatomical region: forelimb
Organ system: integumental system
Term: skin
Sub-term: skin (fibroblast)
Sampling: 2017-09-12 / provided by Lohi lab
Transport media: Not specified
Additional info:
From subject: RW589
Breed (variant): Rottweiler
Sex: Male
Age: 5y 1m
Steril./Castr.: No
Reports:  Necropsy report   Clinical test results
WGS ID: RW589A1, BioProject PRJNA907518, SRR22520744
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
631 2018-03-01 RW589 RNA E1 (8.6.2018) 151.0 (ND) 30 4530.0 QIAGEN RNeasy Mini Kit 10.00 2.1 1.79 Amount of cells at 80% confluence in 10cm PD. RNA sample RUN OUT !!! (11.2.2020)
 
Applied assays   
STRT2-seq
 
Technical replicate [1660]
Other ID Platform Instrument Paired end Seq. date Strand mode Max. read length Chemistry version Laboratory Comments
STRT2_FP16_20 Illumina NextSeq 550 No Dec. 23, 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_FP16_20  SDID_002106_STRT2_FP16_20_canine_mapped.bam SDID_002105_STRT2_FP16_20_canine_mapped.fq.gz CanFam3.1 3.0
STRT2_FP16_20  SDID_002105_STRT2_FP16_20_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_FP16_20 381,466 42.90