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Sample GSM386248 Query DataSets for GSM386248
Status Public on Mar 26, 2009
Title Untreated PBMCs, replicate 2
Sample type RNA
 
Source name Untreated PBMCs, replicate 2
Organism Homo sapiens
Characteristics cell type: peripheral blood mononuclear cells
Treatment protocol Cells from donors 1-6 were grown in vehicle, the IC90 (0.2 uM R547) and 3xIC90 (0.6 uM R547) dose of R547 for 2 or 24 hours. Donor 7 was used as the untreated zero hour time-point
Growth protocol Human peripheral blood mononuclear cells (PBMCs) were separated from whole blood of seven healthy donors and cultured in six T75 flasks per donor at 10^7 cells per flask in 10% heat-inactivated FBS in RPMI medium
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from cells using the Qiagen RNeasy Mini Kit
Label biotin
Label protocol RNA was converted into cDNA and cRNA according to the manufacturer’s recommendation and using manufacturer’s kits (Affymetrix, Santa Clara, CA). 15 ug of total RNA was converted to cDNA with the One-cycle cDNA Synthesis Kit with the addition of reagents from the Poly-A RNA Control Kit. cRNA was produced with the IVT Labeling Kit
 
Hybridization protocol Hybridization Mix contained, in addition to cRNA, reagents from the Hybridization Control Kit and Control Oligo B2. Staining and washing steps were performed as suggested by the manufacturer (Affymetrix, Santa Clara, CA).
Scan protocol Each hybridized Affymetrix GeneChip array was scanned with a GeneChip Scanner 3000 7G (Agilent/Affymetrix).
Description n/a
Data processing Affymetrix gene expression microarray data was first background corrected and normalized via the RMA procedure followed by QQ normalization (R/Bioconductor)
 
Submission date Mar 25, 2009
Last update date Aug 28, 2018
Contact name James Rosinski
E-mail(s) jim.rosinski@gmail.com
Organization name Roche
Department In Silico Sciences
Street address 340 Kingsland St
City Nutley
State/province NJ
ZIP/Postal code 07110
Country USA
 
Platform ID GPL570
Series (2)
GSE15389 Peripheral blood mononuclear cells treated with a CDK inhibitor
GSE15396 Peripheral blood mononuclear, DU145, and HCT116 cells treated with a CDK inhibitor
Relations
Reanalyzed by GSE119087

Data table header descriptions
ID_REF
VALUE QQ normalized RMA signal

Data table
ID_REF VALUE
1007_s_at 98.415726
1053_at 74.757774
117_at 123.341652
121_at 128.393372
1255_g_at 7.011007
1294_at 342.293274
1316_at 38.532959
1320_at 17.862991
1405_i_at 4157.640625
1431_at 8.918756
1438_at 19.2927
1487_at 149.954361
1494_f_at 29.263149
1552256_a_at 48.691738
1552257_a_at 197.744202
1552258_at 20.870396
1552261_at 16.357819
1552263_at 317.870605
1552264_a_at 530.089783
1552266_at 11.064643

Total number of rows: 54675

Table truncated, full table size 1108 Kbytes.




Supplementary file Size Download File type/resource
GSM386248.CEL.gz 4.7 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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