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Sample GSM4279924 Query DataSets for GSM4279924
Status Public on Jan 23, 2020
Title KSHV (+) tumors [DS007accepted_hitsmouse]
Sample type SRA
 
Source name KSHV (+) tumors
Organism Mus musculus
Characteristics tissue/cell type: KSHV-positive mECK36 tumors
Growth protocol mECK36 cells KSHV (+) were obtained and cultured as previously described (Mutlu et al., 2007). mECK36 KSHV (+) tumors were obteined as previously described (Mutlu et al., 2007). KSHV (-) tumor cells were obtained from mECK36 tumor explants after Bac36 episome loss achieved by growth without hygromycin selection as previously described (Mutlu et al., 2007). KSHV (-) tumors were obteined by subcutaneous injection of KSHV (-) tumor cells in nude mice as previously described (Ma et a., 2013).
Extracted molecule polyA RNA
Extraction protocol RNA was isolated and purified using the RNeasy mini kit (Qiagen). RNA concentration and integrity were measured on an Agilent 2100 Bioanalyzer (Agilent Technologies). Only RNA samples with RNA integrity values (RIN) over 8.0 were considered for subsequent analysis.
mRNA from cell lines and tumor samples were processed for directional mRNA-seq library construction using the Preparation Kit according to the manufacturer's protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description DS007accepted
Data processing We performed 76 nt paired-end sequencing using an Illumina NextSeq500 platform.
Illumina Casava software was used for basecalling.
The short-read sequences were mapped to the mouse reference genome (GRCm38.82) by the splice junction aligner TopHat V2.1.0.
The number of reads mapped to each gene based on the TxDb. Mmusculus gene ensembls were counted, reported and annotated using the Rsamtools, GenomicFeatures, GenomicAlignments packages.
Genome_build: GRCm38.82
Supplementary_files_format_and_content: Tab-delimited text files include log2 count per million values for each Sample
 
Submission date Jan 22, 2020
Last update date Jan 25, 2020
Contact name Martin Carlos Abba
E-mail(s) mcabba@gmail.com
Phone 054-221-4236711
Organization name School of Medical Sciences - UNLP
Lab CINIBA
Street address 60 y 120
City La Plata
State/province Buenos Aires
ZIP/Postal code 1900
Country Argentina
 
Platform ID GPL19057
Series (2)
GSE144101 High-throughput sequencing analysis of a “hit and run” cell and animal model of KSHV tumorigenesis. [RNA-Seq]
GSE148742 High-throughput sequencing analysis of a “hit and run” cell and animal model of KSHV tumorigenesis.
Relations
BioSample SAMN13906975
SRA SRX7620796

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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