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Sample GSM1072302 Query DataSets for GSM1072302
Status Public on Mar 08, 2013
Title DKO1-SAHA-1
Sample type RNA
 
Source name DKO1 Cell Line
Organism Homo sapiens
Characteristics treatment: SAHA treated
cell line: DKO1 Cell Line
Treatment protocol Cells were treated with 0.3 uM Aza and harvested after 72 hours or with 1 uM SAHA treatment and harvested after 24hours
Growth protocol Cells were grown under standard conditions
Extracted molecule total RNA
Extraction protocol RNA was extracted using standard TRIzol procedure.
Label biotin
Label protocol Standard Illumina labeling protocol
 
Hybridization protocol RNA was amplified, fragmented and hybridized to the Illumina bead array using standard Illumina protocols
Scan protocol Beadchips were imaged using Illumina BeadArray Reader using standard recommended Illumina scanner setting.
Description male, derivative of HCT116, engineerd disruption of DNA methyltransferase DNMT1 and DNMT3B, SAHA treated
Data processing Raw signal intensities for each probe were obtained using Illumina Beadstudio data analysis software and imported to the Bioconductor lumi package for data transformation and normalization. Probes with all samples ‘‘absent’’ (near or below background levels) were filtered. Loess normalization was performed
 
Submission date Jan 29, 2013
Last update date Mar 08, 2013
Contact name Kurinji Pandiyan
Organization name University of Southern California
Department Department of Urology - Norris Comprehensive Cancer Center
Street address 1441 Eastlake Avenue NOR 7344
City Los Angeles
ZIP/Postal code 90033
Country USA
 
Platform ID GPL10904
Series (2)
GSE38858 AcceSssIble Assay to Study the Chomatin Accessibility and DNA Methylation
GSE43852 Functional DNA methylation is accompanied by chromatin accessibility [gene expression]

Data table header descriptions
ID_REF
VALUE Standard Lumi normalized expression values obtained

Data table
ID_REF VALUE
A1BG 8.20573131
A1CF 8.059359705
A26C3 8.248161785
A2LD1 8.650082223
A2ML1 9.29878926
A4GALT 9.99614236
A4GNT 8.247978426
AAAS 9.216735385
AACS 9.12326235
AACSL 8.347356944
AADACL1 9.598782681
AADAT 9.416724207
AAGAB 11.07522651
AAK1 8.364665409
AAMP 10.39977603
AARS 13.46251562
AARS2 9.910389907
AARSD1 10.57291779
AASDH 9.520408448
AASDHPPT 10.65211307

Total number of rows: 19160

Table truncated, full table size 364 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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