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Sample GSM838429 Query DataSets for GSM838429
Status Public on Nov 24, 2011
Title HL60, replicate A2
Sample type RNA
Source name HL60 AML cells
Organism Homo sapiens
Characteristics cell line: HL-60
treatment: DMSO
leukemia type: promyelocytic AML
Treatment protocol Cells were treated with DMSO
Growth protocol HL-60 cells were cultivated in RPMI medium with 10 % FCS, 1 % penecillin and 1 % streptavidin at 37°C and 5 % CO2
Extracted molecule total RNA
Extraction protocol TriZol extraction of total RNA was performed according to the manufacturer's instructions.
Label Biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
Hybridization protocol The cDNA was fragmented, labeled and hybridized to Affymetrix U133A microarrays (Affymetrix, Santa Clara, CA)
Scan protocol standard Affymetrix protocol
Data processing The data was processed using Bioconductor (affy package 1.30.0) by reading CEL files with default 'ReadAffy()' function. Data was background corrected with RMA, normalized by quantiles method, PM only correction, and then median polished. To account for batch variation, the log2 values were adjusted using ComBat (version 2) in GenePattern with a parametric Empirical Bayes priors distribution estimation method and without covariate analysis.
Submission date Nov 22, 2011
Last update date Nov 28, 2011
Contact name Kolja Eppert
Organization name University Health Network
Street address 101 College St., rm 8-301
City Toronto
State/province Ontario
ZIP/Postal code M5G 1L7
Country Canada
Platform ID GPL571
Series (1)
GSE33892 Comparison of TEX and M9-ENL1 cell lines to HL60 and THP1 cell lines
Reanalysis of GSM405502

Data table header descriptions
VALUE log2 transformed intensity value

Data table
1007_s_at 6.417001267
1053_at 8.292638994
117_at 6.189998625
121_at 8.330502733
1255_g_at 4.360595879
1294_at 7.248941015
1316_at 5.576926115
1320_at 4.935186303
1405_i_at 7.045061209
1431_at 4.897739305
1438_at 6.193919476
1487_at 8.126283711
1494_f_at 6.315828683
1598_g_at 7.871471818
160020_at 7.202996857
1729_at 7.292189094
177_at 5.858114221
1773_at 6.569380963
179_at 8.487054761
1861_at 6.392184144

Total number of rows: 22277

Table truncated, full table size 496 Kbytes.

Supplementary file Size Download File type/resource
GSM838429_GSM405502.CEL.gz 1.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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