You are logged in as AnonymousUser


 
Sample description
Sample ID: 826
Anatomical region: abdominal cavity
Organ system: alimentary system
Term: jejunum
Sub-term: jejunum (mucosa)
Sampling: 2017-03-06 / provided by Lohi lab
Transport media: RNAlater
Additional info: List of tissues was modified from previous necropsy.
From subject: JPK344
Breed (variant): Swedish Elkhound
Sex: Female
Age: 3y 5m
Steril./Castr.: No
Reports:  Necropsy report   Clinical test results
WGS ID: JPK344A1, BioProject PRJNA907518, SRR22520748
Additional info: Two generalized epileptic seizures.
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
151 2017-04-12 826 400.0 (ND) 13 mg 60 24000.0 QIAGEN RNeasy Mini Kit 7.00 2.161 2.027
 
Applied assays   
STRT2-seq
 
Technical replicate [1582]
Other ID Platform Instrument Paired end Seq. date Strand mode Max. read length Chemistry version Laboratory Comments
STRT2_FP14_2 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_2  SDID_001942_STRT2_FP14_2_canine_mapped.fq.gz CanFam3.1 3.0
STRT2_FP14_2  SDID_001943_STRT2_FP14_2_canine_mapped.bam SDID_001942_STRT2_FP14_2_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_2 113,865 2,504,460 62.90
Technical replicate [1182]
Other ID Platform Instrument Paired end Seq. date Strand mode Max. read length Chemistry version Laboratory Comments
STRT2_FP7_2 Illumina NextSeq 550 No Aug. 16, 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_FP7_2  STRT2_FP7_2_canine_mapped.bam STRT2_FP7_2_canine_mapped.fq.gz CanFam3.1 3.0
STRT2_FP7_2  STRT2_FP7_2_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_FP7_2 66,480 1,210,496 67.10