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Sample description
Sample ID: 1104
Anatomical region: head
Organ system: eye
Term: lateral rectus extraocular muscle
Sub-term: lateral rectus extraocular muscle
Sampling: 2017-04-11 / provided by Lohi lab
Transport media: RNAlater
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
749 2017-07-31 1104 (19.2.2019) 213.0 (QUBIT) 25 mg 30 4800.0 QIAZOL + QIAGEN RNeasy Mini Kit 8.50 2.042 2.137
 
Applied assays   
STRT2-seq
 
Technical replicate [1486]
Other ID Platform Instrument Paired end Seq. date Strand mode Max. read length Chemistry version Laboratory Comments
STRT2_FP12_27 Illumina NextSeq 550 No April 30, 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_FP12_27  SDID_001753_STRT2_FP12_27_canine_mapped.bam SDID_001752_STRT2_FP12_27_canine_mapped.fq.gz CanFam3.1 3.0
STRT2_FP12_27  SDID_001752_STRT2_FP12_27_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_FP12_27 100,180 45,609 5.20
Technical replicate [1657]
Other ID Platform Instrument Paired end Seq. date Strand mode Max. read length Chemistry version Laboratory Comments
STRT2_FP16_19 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_19  SDID_002102_STRT2_FP16_19_canine_mapped.bam SDID_002101_STRT2_FP16_19_canine_mapped.fq.gz CanFam3.1 3.0
STRT2_FP16_19  SDID_002101_STRT2_FP16_19_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_19 6,809,890 77.60