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Sample description
Sample ID: 1161
Anatomical region: thoracic cavity
Organ system: respiratory system
Term: bronchus
Sub-term: right main bronchus
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
519 2017-12-04 RW356 1161 (5.12) 145.0 (QUBIT) 25 mg 30 4650.0 QIAZOL + QIAGEN RNeasy Mini Kit 7.80 2.074
 
Applied assays   
STRT2-seq
 
Technical replicate [1571]
Other ID Platform Instrument Paired end Seq. date Strand mode Max. read length Chemistry version Laboratory Comments
STRT2_FP14_42 Illumina NextSeq 550 No May 2, 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_FP14_42  SDID_001969_STRT2_FP14_42_canine_mapped.bam SDID_001968_STRT2_FP14_42_canine_mapped.fq.gz CanFam3.1 3.0
STRT2_FP14_42  SDID_001968_STRT2_FP14_42_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_FP14_42 103,457 3,235,870 71.30
 
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
269 2017-04-25 RW356 1161 90.0 (QUBIT) 20 mg 30 2700.0 QIAGEN RNeasy Mini Kit 6.20 2.07 1.592
 
Applied assays   
STRT2-seq
 
Technical replicate [1143]
Other ID Platform Instrument Paired end Seq. date Strand mode Max. read length Chemistry version Laboratory Comments
STRT2_FP6_7 Illumina NextSeq 550 No June 15, 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_FP6_7  STRT2_FP6_7_canine_mapped.bam STRT2_FP6_7_canine_mapped.fq.gz CanFam3.1 3.0
STRT2_FP6_7  STRT2_FP6_7_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_FP6_7 47,629 441,632 62.90