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Sample GSM718412 Query DataSets for GSM718412
Status Public on Jul 01, 2012
Title Expt 1 - RA and TNF - repeat 3 - mAdbID:68685
Sample type RNA
 
Source name THP-1 RA and TNF
Organism Homo sapiens
Characteristics tissue: bone marrow
cell line: THP-1 cells
cell type: human myeloid cells
Treatment protocol Treatment type: compound
Agent: at-RA (All-trans-Retinoic acid); TNF-alpha (tumor necrosis factor)
Treatment dose: 20 nM; 5ng/ml
Treatment time: 40 hours
In-vitro treatment: THP-1 cells were treated with 20 nM of RA for 16 hours, followed by treatment with 20nM of RA and 5 ng/ml of TNF-alpha for 24 hours. All cells were harvested at the 40 hour time point.
Extracted molecule total RNA
Extraction protocol RNA was prepared using Trizol extraction.
Label biotin
Label protocol Affymetrix labeling protocol: cDNA was synthesized, labeled, and purified according to vendor's (Affymetrix Inc., Santa Clara, CA) instructions.
 
Hybridization protocol Affymetrix Hybridization Protocol: The arrays were hybridized overnight at 45°C and washed using the fluidics station, then stained with streptavidin-phycoerythrin using the standard antibody amplification protocol (GeneChip Expression Analysis Technical Manual, Affymetrix, Santa Clara, CA).
Scan protocol Affymetrix Scanning Protocol: The arrays were scanned at 488 nm at 11-micron resolution using an Affymetrix Gene Chip Scanner.
Description mAdb experiment ID: 68685
Data processing Data were acquired using Genechip Operating Software (GCOS, Affymetrix) and uploaded onto the NCI website mAdb (http://nciarray.nci.nih.gov/). Data were analyzed by setting the signal floor value to 1 and centering each array to the median signal intensity. The results were expressed as log 2-transformed signal intensities and the log 2 of the median intensity for each array was set to 0.
 
Submission date Apr 30, 2011
Last update date Jul 01, 2012
Contact name A. Catharine Ross
E-mail(s) acr6@psu.edu
Phone 814 865 4721
Fax 814 863 6103
URL http://nutrition.hhdev.psu.edu/faculty/profiles.cfm?facultyid=23
Organization name Penn State
Department Nutritional Sciences
Street address 110 Chandlee Laboratory
City University Park
State/province PA
ZIP/Postal code 16802
Country USA
 
Platform ID GPL570
Series (1)
GSE28995 THP-1 cell study: RA and TNF Treatments; RA time course

Data table header descriptions
ID_REF Affymetrix ID
VALUE see Data Processing Protocol

Data table
ID_REF VALUE
117_at -0.020
121_at 2.600
177_at 0.020
179_at 2.224
320_at 1.672
336_at -0.657
564_at 1.263
632_at 2.692
823_at -2.126
1053_at 3.857
1294_at 2.690
1316_at 0.324
1320_at -2.992
1431_at -1.008
1438_at 0.016
1487_at 3.909
1729_at 1.330
1773_at 1.289
1861_at 2.242
243_g_at 3.637

Total number of rows: 54675

Table truncated, full table size 924 Kbytes.




Supplementary file Size Download File type/resource
GSM718412_68685.CEL.gz 3.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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