You are logged in as AnonymousUser


 
Sample description
Sample ID: 3243
Anatomical region: head
Organ system: eye
Term: inferior rectus extraocular muscle
Sub-term: inferior rectus extraocular muscle
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
553 2017-12-13 RW589 3243 405.0 (ND) 28 mg 30 12150.0 QIAZOL + QIAGEN RNeasy Mini Kit 8.20 2.073 2.073
 
Applied assays   
STRT2-seq
 
Technical replicate [1250]
Other ID Platform Instrument Paired end Seq. date Strand mode Max. read length Chemistry version Laboratory Comments
STRT2_FP9_36 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_36  STRT2_FP9_36_canine_mapped.bam STRT2_FP9_36_canine_mapped.fq.gz CanFam3.1 3.0
STRT2_FP9_36  STRT2_FP9_36_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_36 380,962 4,685,035 70.60