|
| Status |
Public on Oct 07, 2020 |
| Title |
TNBC, T4h (RNA-seq) |
| Sample type |
SRA |
| |
|
| Source name |
TNBC, T4h
|
| Organism |
Canis lupus familiaris |
| Characteristics |
cell type: TNBC
infection: vaccinia infected
time: T4h
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Poly(A) RNAs were purified using a Dynabeads mRNA purification kit (Invitrogen) and fragmented for 7 min at 95 °C.
Libraries were then generated with the Ion Total RNA seq kit V2 (life technologies) and sequenced on the Ion Proton system with P1 chip V3 following the manufacturer’s instructions.
instrument model: AB Ion Proton
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
TableCount_logCPM.txt
|
| Data processing |
Prinseq-lite-0.20.4 to remove reads size < 35b
Mapping with STAR_2.4.0a then bowtie2-2.2.4 versus canFam3 build + vaccina virus NC_006998 sequence
Bam files merging using MergeSamFiles.jar (picard-tools-1.119) then counting with HTSeq-0.6.1 "--minaqual=0 --mode=intersection-nonempty" parameters
Raw counts were coverted to counts per million (CPM) and log-transformed
Genome_build: CanFam3
Supplementary_files_format_and_content: tab-delimited text file including log2 counts per million for each sample.
|
| |
|
| Submission date |
Dec 17, 2019 |
| Last update date |
Oct 07, 2020 |
| Contact name |
Kevin Lebrigand |
| Organization name |
IPMC/CNRS
|
| Lab |
Functional Genomics Platform of Nice-Sophia-Antipolis, France.
|
| Street address |
660 route des lucioles
|
| City |
Valbonne - Sophia-Antipolis |
| ZIP/Postal code |
06560 |
| Country |
France |
| |
|
| Platform ID |
GPL27923 |
| Series (2) |
| GSE142180 |
RNAseq profiling of dog primary mammary triple-negative breast cancer cells infected or not with a vaccinia virus deleted for the thymidine kinase gene |
| GSE142185 |
Expression profiling of dog primary mammary triple-negative breast cancer cells infected or not with a vaccinia virus deleted for the thymidine kinase gene |
|
| Relations |
| BioSample |
SAMN13614498 |
| SRA |
SRX7396978 |
