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Sample GSM5628010 Query DataSets for GSM5628010
Status Public on Nov 02, 2021
Title SK-N-SH_haloperidol_low_rep2 [SHAP05]
Sample type genomic
 
Source name human neuroblastoma cells (SK-N-SH) with 1 uM haloperidol
Organism Homo sapiens
Characteristics cell type: human neuroblastoma cells (SK-N-SH)
treatment: Hal2
Treatment protocol We used low and high concentrations of haloperidol (1 uM and 10 uM) and risperidone (3 uM and 30 uM) based on their effective blood concentrations. The antipsychotics were dissolved in dimethyl sulfoxide (DMSO). Final concentrations of DMSO were 0.001% to 0.06%, depending on the dose of antipsychotics. The cells were cultured with or without 0.06% of DMSO as a control.
Growth protocol Human neuroblastoma SK-N-SH cells were cultured with Eagle’s minimal essential medium with 10% fetal bovine serum containing antipsychotics for 8 days.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted via standard phenol:chloroform methods. The DNA samples were subjected to bisulfite modification by the EZ DNA Methylation Kit D500 (Zymo Research,).
Label Cy5 and Cy3
Label protocol Standard Illumina Protocol was used.
 
Hybridization protocol Bisulfite converted DNA was amplified, processed and hybridized to Illumina HumanMethylation450 Beadchip using standard Illumina protocol.
Scan protocol Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.
Data processing Illumina BeadStudio was used, according to the manufacturer's instructions.
Average Beta values (Beta value was calculated according to the ratio of intensities between methylated and unmethylated alleles, as in the following formula: beta value = methylated intensity/(methylated intensity + unmethylated intensity + 100) ).
Unmethylated and methylated signal intensities (same as signalA and signalB on BeadStudio output, respectively).
 
Submission date Oct 15, 2021
Last update date Nov 02, 2021
Contact name Kazuya Iwamoto
E-mail(s) iwamotok@kumamoto-u.ac.jp
Phone +81-96-373-5054
Organization name Kumamoto University
Department Faculty of Life Sciences
Lab Department of Molecular Brain Science
Street address 1-1-1 Honjo, Chuo-ku
City Kumamoto
ZIP/Postal code 860-8556
Country Japan
 
Platform ID GPL16304
Series (1)
GSE185973 Comprehensive DNA methylation analysis of human neuroblastoma cells treated with haloperidol and risperidone

Data table header descriptions
ID_REF
VALUE Average Beta
Detection Pval

Data table
ID_REF VALUE Detection Pval
cg00000029 0.6615192 0.00
cg00000108 0.9408665 0.00
cg00000109 0.9226502 0.00
cg00000165 0.1190421 0.00
cg00000236 0.8475584 0.00
cg00000289 0.7071443 0.00
cg00000292 0.9040638 0.00
cg00000321 0.9202737 0.00
cg00000363 0.2877569 0.00
cg00000622 0.005557927 0.00
cg00000658 0.8563526 0.00
cg00000714 0.1756454 0.00
cg00000721 0.9229612 0.00
cg00000734 0.05941964 0.00
cg00000769 0.00791354 0.00
cg00000807 0.8594305 0.00
cg00000884 0.8301441 0.00
cg00000905 0.06292398 0.00
cg00000924 0.5520533 0.00
cg00000948 0.8092714 0.00

Total number of rows: 485512

Table truncated, full table size 12324 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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