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Sample description
Sample ID: 3226
Anatomical region: head
Organ system: eye
Term: cornea
Sub-term: cornea
Sampling: 2017-09-12 / provided by Lohi lab
Transport media: RNAlater
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
841 2019-10-29 3226 (31.10.2019) 527.0 (ND) 4 mm3 35 18469.0 QIAZOL + QIAGEN RNeasy Mini Kit 8.70 2.03 1.96 Tissue ruptor. 15min QIAZOL
 
Applied assays   
STRT2-seq
 
Technical replicate [1661]
Other ID Platform Instrument Paired end Seq. date Strand mode Max. read length Chemistry version Laboratory Comments
STRT2_FP16_3 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_3  SDID_002134_STRT2_FP16_3_canine_mapped.bam SDID_002133_STRT2_FP16_3_canine_mapped.fq.gz CanFam3.1 3.0
STRT2_FP16_3  SDID_002133_STRT2_FP16_3_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_3 28,215 8.80