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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