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Sample GSM4222235 Query DataSets for GSM4222235
Status Public on Oct 07, 2020
Title TNBC, NT0 (RNA-seq)
Sample type SRA
 
Source name TNBC, NT0
Organism Canis lupus familiaris
Characteristics cell type: TNBC
infection: control
time: T0
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 SAMN13614496
SRA SRX7396980

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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