You are logged in as AnonymousUser


 
Sample description
Sample ID: 1434
Anatomical region: head
Organ system: central nervous system
Term: cerebellum vermis
Sub-term: cerebellum vermis
Sampling: 2016-09-20 / provided by Lohi lab
Transport media: RNAlater
Additional info: This was originally a training dog.
From subject: BC1642
Breed (variant): Border Collie
Sex: Male
Age: 6y 11m
Steril./Castr.: Not specified
Reports:  Necropsy report 
WGS ID: BC1642A1, BioProject PRJNA907518, SRR22520746
Additional info: This was originally a training dog. Epilepsy (cortex, hippocampus) + degenerative changes in large brain (mild neuronal loss, prominent capilaries, lipofuscinosis).
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
707 2017-02-01 5. (6.2.2017) 230 (ND) 20 mg 40 9200 QIAGEN RNeasy Mini Kit 8.70 2.178 2.166 —
 
Applied assays   
STRT2-seq
 
Technical replicate [1277]
Other ID Platform Instrument Paired end Seq. date Strand mode Max. read length Chemistry version Laboratory Comments
STRT2_FP9_8 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_8  STRT2_FP9_8_canine_mapped.bam STRT2_FP9_8_canine_mapped.fq.gz CanFam3.1 — 3.0 —
STRT2_FP9_8  STRT2_FP9_8_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_8 — — 229,432 — 774,033 58.70 — —
 
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
408 2017-08-22 BC1642 1434 465 (ND) 22 mg 30 13950 QIAZOL + QIAGEN RNeasy Mini Kit 7.50 2.07 2.197 —
 
Applied assays   
This sample was not sequenced yet.