NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4041357 Query DataSets for GSM4041357
Status Public on Aug 22, 2019
Title Targeted_Bisulfite_GSK343_rep2
Sample type SRA
 
Source name Neuroblastoma
Organism Homo sapiens
Characteristics tissue: Neuroblastoma
cell line: SH-SY5Y
treatment: GSK343
Treatment protocol SH-SY5Y cells (density of 0.5~0.6 x 106 cells/ml) were treated with either DMSO or 5 uM GSK343 (an inhibitor of H3K27me3-specific HMTase) for 72hours.
Growth protocol SH-SY5Y (Korean Cell Line Bank, 22266) were maintained in DMEM/F12 (Gibco, 11320033) supplemented with 10% fetal bovine serum (Welgene, S001-01) and Penicillin/Streptomycin (Lonza, 17-602E) at 5% CO2 in 37°C.
Extracted molecule genomic DNA
Extraction protocol SH-SY5Y cells were washed with 10ml of PBS and genomic DNA were prepared using AccuPrep Genomic DNA Extraction Kit (Bioneer, K-0332).
Targeted Bisulfite-Seq library were prepared using the SureSelectXT Methyl-Seq Target Enrichment System for Illumina Multiplexed Sequencing (Agilent Technologies). Briefly, 3μg of genomic DNA per sample was fragmented to median size of 150bp, repaired, and ligated with adapters. The prepared gDNA library was hybridized using SureSelectXT methyl-Seq capture reagent, followed by bisulfite conversion using EZ DNA Methylation-Gold kit (ZymoResearch, Cat #D5005). After desulphonation, the sequence-modified, target-enriched library were amplified and uniquely indexed by PCR. The indexed libraries were pooled and multiplexed into 4 separate lanes using 100 bp paired-end sequencing (Illumina HiSeq2500).
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 2500
 
Data processing The targeted bisulfite sequencing library were aligned to Homo sapiens (hg19) using Bowtie2.
Genome_build: hg19
Supplementary_files_format_and_content: After deduplication (deduplicate_bismark), methylation levels (bismark_methylation_extractor) were estimated using bismark tools with default parameters.
 
Submission date Aug 21, 2019
Last update date Aug 22, 2019
Contact name Wooje Lee
E-mail(s) ntinamu001@gmail.com
Organization name Chosun University
Department Cellular and Molecular Medicine
Street address 309, Pilmun-daero, Dong-gu
City Gwangju
ZIP/Postal code 61452
Country South Korea
 
Platform ID GPL16791
Series (2)
GSE122366 MeCP2 regulates genome-wide gene expression through recognition of H3K27me3
GSE136119 MeCP2 regulates gene expression through direct interaction with H3K27me3 [Targeted_BS_seq: DMSO_vs_GSK343]
Relations
BioSample SAMN12616436
SRA SRX6748006

Supplementary file Size Download File type/resource
GSM4041357_GSK343_re2_bismark_bt2_pe.deduplicated.CX_report.txt.gz 4.1 Gb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap