|
Status |
Public on Aug 01, 2019 |
Title |
Cancer-associated stroma 137_tumour |
Sample type |
SRA |
|
|
Source name |
canine simple mammary carcinoma
|
Organism |
Canis lupus familiaris |
Characteristics |
Sex: female age of patient (years): 10 subtype of simple carcinoma: tubular age of sample at analysis (months): 13 breed: Chihuahua
|
Treatment protocol |
no treatment
|
Growth protocol |
spontaneous tumours from canine patients removed in the context of curative surgery
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was extracted using the optimised Covaris-FFPE RNA isolation procedure described in: Amini P, Ettlin J, Opitz L, Clementi E, Malbon A, and Markkanen, E (2017) An optimised protocol for isolation of RNA from small sections of laser-capture microdissected FFPE tissue amenable for next-generation sequencing. BMC Mol Biol 18:22. doi: 10.1186/s12867-017-0099-7 SMARTer Stranded Total RNA-seq Kit—Pico Input Mammalian from Clontech/ Takara Bio USA, using 4 ng total RNA per sample; details described in: Amini P, Ettlin J, Opitz L, Clementi E, Malbon A, and Markkanen, E (2017) An optimised protocol for isolation of RNA from small sections of laser-capture microdissected FFPE tissue amenable for next-generation sequencing. BMC Mol Biol 18:22. doi: 10.1186/s12867-017-0099-7
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
|
|
Description |
Female, neutered Cancer-associated stroma
|
Data processing |
RNAseq quantification was performed with kallisto 0.44.0 with sequence-based bias correction using transcript sequences obtained from ENSEMBLE (CanFam3.1). All other parameters were set to default when running kallisto. Kallisto's transcript-level estimates were further summarized at the gene-level using tximport 1.8.0 from Bioconductor. Genome_build: CanFam3.1 Supplementary_files_format_and_content: CSV table of raw estimated counts as obtained from tximport. Rows represent genes and columns represent samples.
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|
|
Submission date |
Jul 31, 2019 |
Last update date |
Aug 02, 2019 |
Contact name |
Enni Markkanen |
E-mail(s) |
enni.markkanen@vetpharm.uzh.ch
|
Organization name |
University of Zurich
|
Department |
Institute of Veterinary Pharmacology and Toxicology
|
Lab |
Markkanen group
|
Street address |
Winterthurerstr. 260
|
City |
Zurich |
ZIP/Postal code |
8057 |
Country |
Switzerland |
|
|
Platform ID |
GPL24229 |
Series (1) |
GSE135183 |
Next-generation RNA sequencing of FFPE subsections reveals highly conserved stromal reprogramming between canine and human mammary carcinoma |
|
Relations |
BioSample |
SAMN12400209 |
SRA |
SRX6623309 |