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Sample description
Sample ID: 5740
Anatomical region: forelimb
Organ system: integumental system
Term: skin
Sub-term: skin (fibroblast)
Sampling: 2017-04-11 / provided by Lohi lab
Transport media: Not specified
Additional info:
From subject: RW356
Breed (variant): Rottweiler
Sex: Male
Age: 6y 2m
Steril./Castr.: No
Reports:  Necropsy report   Clinical test results
WGS ID: RW356A1, BioProject PRJNA907518, SRR22520747
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
630 2018-04-05 RW356 RNA T4 (8.6.2018) 281.0 (ND) 100 28136.0 QIAGEN RNeasy Mini Kit 10.00 2.08 1.72 Amount of cells: 10 cm PD 70% confluence. Same elution volume going twice through the column
 
Applied assays   
STRT2-seq
 
Technical replicate [1659]
Other ID Platform Instrument Paired end Seq. date Strand mode Max. read length Chemistry version Laboratory Comments
STRT2_FP16_21 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_21  SDID_002108_STRT2_FP16_21_canine_mapped.bam SDID_002107_STRT2_FP16_21_canine_mapped.fq.gz CanFam3.1 3.0
STRT2_FP16_21  SDID_002107_STRT2_FP16_21_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_21 1,617,367 59.70