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Sample GSM4478123 Query DataSets for GSM4478123
Status Public on Apr 16, 2020
Title 2603: KSHV (+) tumor
Sample type SRA
 
Source name KSHV-positive mECK36 tumors
Organism Mus musculus
Characteristics 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 genomic DNA
Extraction protocol Genomic DNA was isolated using DNeasy Blood & Tissue Kit (QIAGEN) and sheared by sonication to fragments of ~500bp.
Methylated DNA enrichment protocol: The sheared DNA (1µg) was added to 10 µl MBD-Bead slurry (MethylMiner DNA Enrichment Kit, Invitrogen, Carlsbad, CA) and incubated on a rotating mixer for 1 hr, as described previously [49]. The DNA fragments were eluted into distinct subpopulations based on the degree of methylation; non-captured fraction (NC, representing un-methylated DNA fragments), 450 mM NaCl (representing partially methylated DNA fragments) and 2000 mM NaCl (representing methylated DNA fragments). The fractions were then ethanol precipitated and re-suspended in H2O.
MBD2 enriched methylated DNA fractions were subjected to library preparation with NEBNext® Ultra™ II DNA library prep kit for Illumina (NEB #E7645) at the next generation genomic center in the Azrieli Faculty of Medicine, Bar-Ilan University.
 
Library strategy MBD-Seq
Library source genomic
Library selection MBD2 protein methyl-CpG binding domain
Instrument model Illumina HiSeq 2000
 
Data processing The DNA libraries were sequenced on Illumina HiSeq2000, with HiSeq rapid 100PE.
Data analysis was performed on the Partek flow platform, raw reads were aligned to the mouse genome mm10 (GRCm38/mm10) with BWA
Mapped reads were analyzed with MACS2 to generate peaks and annotate differentially methylated regions. Peaks with False discovery rate (FDR) ≤5% & Fold change (FC) ≥2, were considered differentially methylated.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tab-delimited text files includes peak size, chromosome and start end locations, and fold enrichment.
 
Submission date Apr 15, 2020
Last update date Apr 16, 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 GPL13112
Series (2)
GSE148741 High-throughput sequencing analysis of a “hit and run” cell and animal model of KSHV tumorigenesis. [MBD-Seq]
GSE148742 High-throughput sequencing analysis of a “hit and run” cell and animal model of KSHV tumorigenesis.
Relations
BioSample SAMN14602488
SRA SRX8120157

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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