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Sample GSM2417754 Query DataSets for GSM2417754
Status Public on Dec 01, 2017
Title U937 cells transduced with pCDH-MSCV-puro-DNMT3A-WT lentivirus vector_methylation
Sample type genomic
 
Source name Human promyelocytic leukemia cell line_U937_DNMT3A_wildtype
Organism Homo sapiens
Characteristics cell line: U937
cell type: Human promyelocytic leukemia cell line
tissue: Blood
Treatment protocol Cultured U937 cells were infected with lentivirus in the presence of 8 µg/ml polybrene (Sigma) and cultured for 72 hours. The infected cells were selected with 2 µg/mL puromycin for 2-weeks to obtain stable clones. DNMT3A WT/mutants expression was checked by immunoblot analysis and stable cells used for DNA extraction for methylation microarray analysis.
Growth protocol The human promyelocytic leukemia cells, U937 were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, and 1× antibiotic-antimycotic (Gibco by Life Technologies) in a humidified chamber with 5% CO2 atmosphere at 37°C
Extracted molecule genomic DNA
Extraction protocol Total DNA was isolated by standard procedures
Label Cy5 and Cy3
Label protocol Standard Illumina labelling protocol
 
Hybridization protocol Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina MethylationEPIC BeadChip microarray using standard Illumina protocol
Scan protocol Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting
Data processing Genome Studio V2011.1
 
Submission date Dec 06, 2016
Last update date Dec 01, 2017
Contact name Yun-Shien Lee
E-mail(s) bojack@mail.mcu.edu.tw
Organization name Ming Chuan Univ
Department Dept. Biotechnology
Lab GMRCL
Street address TauYau
City TauYau
State/province Taiwan
ZIP/Postal code 115
Country Taiwan
 
Platform ID GPL21145
Series (2)
GSE90933 Differential genomic-methylation profile of U937 cells transduced with WT/mutant-DNMT3A
GSE90934 Differential gene expression and genomic methylation profile of U937 cells transduced with WT/mutant-DNMT3A

Data table header descriptions
ID_REF
VALUE Normalized Average Beta
Detection Pval

Data table
ID_REF VALUE Detection Pval
cg00000029 0.2749111 0
cg00000103 0.1456588 0
cg00000109 0.8938195 0
cg00000155 0.8827544 0
cg00000158 0.8951609 0
cg00000165 0.7562652 0
cg00000221 0.5599974 0
cg00000236 0.8463273 0
cg00000289 0.7860958 0
cg00000292 0.8487425 0
cg00000321 0.7967868 0
cg00000363 0.5558169 0
cg00000540 0.8056202 0
cg00000579 0.7571473 0
cg00000596 0.1865635 0
cg00000622 0.03168723 0
cg00000658 0.7536488 0
cg00000714 0.08849303 0
cg00000721 0.8584882 0
cg00000734 0.0923624 0

Total number of rows: 866895

Table truncated, full table size 19528 Kbytes.




Supplementary file Size Download File type/resource
GSM2417754_200598790047_R02C01_Grn.idat.gz 7.1 Mb (ftp)(http) IDAT
GSM2417754_200598790047_R02C01_Red.idat.gz 7.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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