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Sample GSM1264039 Query DataSets for GSM1264039
Status Public on Nov 17, 2014
Title V_H004
Sample type RNA
 
Source name Human THP-1 cells
Organism Homo sapiens
Characteristics treatment: treatment with DMSO and LPS stimulation
Treatment protocol Human THP-1 cells were pretreated with vehicle or PBHA (10 μM) before LPS stimulation (50 ng/ml). After 8 hours, the total cellular RNAs were manipulated for microarray assay.
Growth protocol Human monocytic cells (THP-1, ATCC) were cultured in RPMI medium 1640 supplemented with 10% heat-inactivated fetal bovine serum (FBS), 100 U/ml penicillin, 100 microg/ml streptomycin and 18 mM HEPES, pH 7.4. Cells were used at 90% confluence, and following treatments were handled in the same medium with 0.5% FBS (Chou et al., 2011).
Extracted molecule total RNA
Extraction protocol RNA extraction by RNeasy Mini kit (Qiagen, Valencia, CA, USA). RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧8).
Label Cy5
Label protocol 1 µg of total RNA was reverse-transcribed and amplified using Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dyes (Amersham Pharmacia, Piscataway, NJ, USA).
 
Hybridization protocol Fluorescent targets were hybridized to the Human Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization at 50 ℃, non-specific binding targets were washed away by three different washing steps (WashⅠ 42 ℃ 5 mins;Wash Ⅱ 42 ℃, 5 mins, 25 ℃ 5 mins; Wash Ⅲ rinse 20 times)
Scan protocol The arrays were scanned by G2505C (ScanPower=100 n/a, PMTGain=0 n/a) and quantify the fluoresence intensity.
Data processing The signal intensity of each spot was loaded into Rosetta Resolver System® (Rosetta Biosoftware) to process data analysis. The error model of Rosetta Resolver System® could remove both systematic and random errors form the data. We filtered out spots that the flag is less than 0. Spots that passed the criteria were normalized by 50% media scaling normalization method.Normalize intensities: Median scaling performed on data set without flagged and control data. Merge technical replicate data: Average intensity values calculated on technical replicates.
Calculate average ratios of the hybridization replicates and find significant values for each gene by pairwise comparision (Ranking and hypothesis testing).
 
Submission date Nov 14, 2013
Last update date Nov 17, 2014
Contact name George Hsiao
E-mail(s) geohsiao@tmu.edu.tw
Phone +886-2-27374622
Organization name Taipei Medical University
Department Pharmacology
Street address No. 250, Wu-Hsing Str
City Taipei
ZIP/Postal code 110
Country Taiwan
 
Platform ID GPL16951
Series (1)
GSE52365 Microarray analysis of gene expression profiles in PBHA-treated THP-1 cells after LPS stimulation

Data table header descriptions
ID_REF
VALUE Normalize intensities

Data table
ID_REF VALUE
PH_hs_0000002 211
PH_hs_0000003 154
PH_hs_0000004 612
PH_hs_0000005 4
PH_hs_0000006 1034
PH_hs_0000007 1429
PH_hs_0000008 1044
PH_hs_0000009 4226
PH_hs_0000010 10284
PH_hs_0000011 329
PH_hs_0000012 212
PH_hs_0000013 1144
PH_hs_0000014 176
PH_hs_0000015 36
PH_hs_0000016 31
PH_hs_0000017 15
PH_hs_0000018 566
PH_hs_0000019 18
PH_hs_0000021 71
PH_hs_0000022 4

Total number of rows: 31741

Table truncated, full table size 545 Kbytes.




Supplementary file Size Download File type/resource
GSM1264039_H004-1101006567.gpr.gz 1.3 Mb (ftp)(http) GPR
Processed data included within Sample table
Processed data are available on Series record

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