You are logged in as AnonymousUser


 
Sample description
Sample ID: 5339
Anatomical region: head
Organ system: central nervous system
Term: hippocampal formation
Sub-term: hippocampal formation
Sampling: — / provided by Lohi lab
Transport media: RNAlater
Additional info:
From subject: WLF002
Breed (variant): Wolf
Sex: Male
Age: 9y 10m
Steril./Castr.: Not specified
Reports:
WGS ID: WLF002A1, BioProject PRJNA907518, SRR22520742
Additional info: Ranua Wildlife Park
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
812 2019-04-17 5339 (24.4.2019) 230.0 (QUBIT) 2 mm3 75 12741.0 QIAZOL + QIAGEN RNeasy Mini Kit 9.90 2.07 2.05
 
Applied assays   
STRT2-seq
 
Technical replicate [1625]
Other ID Platform Instrument Paired end Seq. date Strand mode Max. read length Chemistry version Laboratory Comments
STRT2_FP15_33 Illumina NextSeq 550 No Aug. 15, 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_FP15_33  SDID_002043_STRT2_FP15_33_canine_mapped.bam SDID_002042_STRT2_FP15_33_canine_mapped.fq.gz CanFam3.1 3.0
STRT2_FP15_33  SDID_002042_STRT2_FP15_33_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_FP15_33 172,357 1,174,917 64.70