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Sample GSM4225036 Query DataSets for GSM4225036
Status Public on Mar 30, 2020
Title ShLy75-S
Sample type SRA
 
Source name Ovarian cancer
Organism Homo sapiens
Characteristics cell line: SKOV3
treatment: LY75 suppression shRNA
Growth protocol Cells were passed in RPMI culture media supplemented with 10% fetal bovine serum
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from SKOV3 (M) and (E) clones with Blood & Cell Culture DNA Mini Kit (Qiagen)
100ng genomic DNA was then digested using the methylation-insensitive enzyme MspI, fragment ends were filled in and adapters were ligated. After size selection by AMPure XP beads, fragments were subjected for bisulfite conversion. Samples were sequenced on an Illumina platform, Single-Read, read length 50 bp (SR50). The adapter sequences and low-quality base calls (< 30) were trimmed from the 3’ end using Trimmomatic programm. The bisulfite converted sequencing reads were then aligned to the human reference genome using Bismark program. Differentially methylated regions (DMRs) were determined.
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection Reduced Representation
Instrument model Illumina HiSeq 3000
 
Data processing Sequencing was performed on an Illumina HiSeq 3000.
Quality control of sequencing reads was performed using FastQC.
Adapter removal was perfomed using Trim Galore 0.4.1
Reads were aligned using Bismark v0.16.1 and followed by methylation calling using the corresponding bismark functionality
The methylKit package ( (Altuna Akalin, (2012). " Genome Biology , 13:R87) was used for data processing and analysis
Genome_build: hg19
Supplementary_files_format_and_content: csv file including tthe output of methylKit (DMR, CpGs minimum per tile, q-value < 0.01 and ≥25% average differences)
 
Submission date Dec 18, 2019
Last update date Mar 30, 2020
Contact name Clémence Belleannee
Organization name CHU de Québec-Université Laval Research Center
Street address 2705 Bd Laurier
City Québec
ZIP/Postal code G1V 4G2
Country Canada
 
Platform ID GPL21290
Series (1)
GSE142310 LY75 ablation mediates mesenchymal-epithelial transition (MET) in epithelial ovarian cancer (EOC) cells associated with aberrant DNA methylation alterations implicated in EOC dissemination
Relations
BioSample SAMN13630660
SRA SRX7411574

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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