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Sample description
Sample ID: 157
Anatomical region: head
Organ system: eye
Term: medial rectus extraocular muscle
Sub-term: medial rectus extraocular muscle
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
15 2017-04-03 SLK1048 157 660.0 (QUBIT) 32 mg 30 19800.0 QIAGEN RNeasy Mini Kit 6.90 2.18 2.261 —
 
Applied assays   
This sample was not sequenced yet.
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
562 2017-12-13 SLK1048 157(13.12.2017) 185.0 (QUBIT) 20 mg 30 5550.0 Not specified 8.00 2.04 2.057 —
 
Applied assays   
STRT2-seq
 
Technical replicate [1244]
Other ID Platform Instrument Paired end Seq. date Strand mode Max. read length Chemistry version Laboratory Comments
STRT2_FP9_29 Illumina NextSeq 550 No Oct. 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_FP9_29  STRT2_FP9_29_canine_mapped.bam STRT2_FP9_29_canine_mapped.fq.gz CanFam3.1 — 3.0 —
STRT2_FP9_29  STRT2_FP9_29_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_FP9_29 — — 322,111 — 6,320,611 72.40 — —