You are logged in as AnonymousUser


 
Sample description
Sample ID: 3780
Anatomical region: thoracic cavity
Organ system: cardiovascular system
Term: cardiac muscle tissue
Sub-term: interventricular septum muscular part
Sampling: 2017-11-01 / provided by Lohi lab
Transport media: RNAlater
Additional info:
From subject: AM398
Breed (variant): Alaskan Malamute
Sex: Female
Age: 7y 1m
Steril./Castr.: No
Reports:  Necropsy report 
WGS ID:
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
760 2019-04-12 3780 (15.4.2019) 284.0 (QUBIT) 2 mm3 30 6450.0 QIAGEN RNeasy Mini kit + Proteinase K 9.40 2.08 1.91
 
Applied assays   
STRT2-seq
 
Technical replicate [1517]
Other ID Platform Instrument Paired end Seq. date Strand mode Max. read length Chemistry version Laboratory Comments
STRT2_FP13_39 Illumina NextSeq 550 No Aug. 14, 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_FP13_39  SDID_001873_STRT2_FP13_39_canine_mapped.bam SDID_001872_STRT2_FP13_39_canine_mapped.fq.gz CanFam3.1 3.0
STRT2_FP13_39  SDID_001872_STRT2_FP13_39_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_FP13_39 156,744 8,159 4.30
Technical replicate [1689]
Other ID Platform Instrument Paired end Seq. date Strand mode Max. read length Chemistry version Laboratory Comments
STRT2_FP16_27 Illumina NextSeq 550 No Dec. 23, 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_FP16_27  SDID_002120_STRT2_FP16_27_canine_mapped.bam SDID_002119_STRT2_FP16_27_canine_mapped.fq.gz CanFam3.1 3.0
STRT2_FP16_27  SDID_002119_STRT2_FP16_27_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_FP16_27 24,615 5.70
Technical replicate [1685]
Other ID Platform Instrument Paired end Seq. date Strand mode Max. read length Chemistry version Laboratory Comments
STRT2_FP16_43 Illumina NextSeq 550 No Dec. 23, 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_FP16_43  SDID_002138_STRT2_FP16_43_canine_mapped.bam SDID_002137_STRT2_FP16_43_canine_mapped.fq.gz CanFam3.1 3.0
STRT2_FP16_43  SDID_002137_STRT2_FP16_43_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_FP16_43 29,682 6.30