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Sample description
Sample ID: 1029
Anatomical region: head
Organ system: central nervous system
Term: brainstem
Sub-term: medulla oblongata
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
192 2017-04-25 RW356 1029 120.0 (ND) 20 mg 30 3600.0 QIAGEN RNeasy Mini Kit 7.70 2.084 2.077
 
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
387 2017-04-25 RW356 1021 120 (ND) 20 mg 30 3600 Not specified 7.70 2.084 2.077
 
Applied assays   
STRT2-seq
 
Technical replicate [1070]
Other ID Platform Instrument Paired end Seq. date Strand mode Max. read length Chemistry version Laboratory Comments
STRT2_FP4_24 Illumina NextSeq 550 No May 14, 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_FP4_24  STRT2_FP4_24_canine_mapped.bam STRT2_FP4_24_canine_mapped.fq.gz CanFam3.1 3.0
STRT2_FP4_24  STRT2_FP4_24_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_FP4_24 238,810 2,426,909 68.20