|
| Status |
Public on Aug 01, 2019 |
| Title |
Cancer-associated stroma 123_tumour |
| Sample type |
SRA |
| |
|
| Source name |
canine simple mammary carcinoma
|
| Organism |
Canis lupus familiaris |
| Characteristics |
Sex: female
age of patient (years): 14
subtype of simple carcinoma: tubular
age of sample at analysis (months): 3
breed: Maltese
|
| 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
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
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.
|
| |
|
| 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 |
SAMN12400199 |
| SRA |
SRX6623289 |
