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Sample GSM1240321 Query DataSets for GSM1240321
Status Public on Dec 19, 2013
Title THP-1_24h_50µg/mL_of_empty_ENP_rep2
Sample type RNA
 
Source name THP-1, 24 h, 50 µg/mL of empty ENP, replicate 2
Organism Homo sapiens
Characteristics tissue: peripheral blood
gender: male
age: 1-y-old
time: 24 h
treatment: 50 µg/mL of empty ENP
cell line: THP-1
Treatment protocol THP-1 cells at a density of 3 x 105 cells / mL were incubated without (control) or with 50 µg / mL of empty polymeric Eudragit® RL nanoparticles (empty ENP; 50 µg/mL) for 24 h. Eudragit® RL PO [CAS number: 33434-24-1], an acrylic polycationic copolymer of acrylic and methacrylic acid esters with a proportion of quaternary ammonium groups (0.5-0.8%), was a gift from Evonik polymers (Darmstadt, Germany).
Growth protocol THP-1 human monocyte cell line is derived from a blood sample of a one-year old child suffering from acute monocytic leukemia and was obtained from American Type Culture Collection (ATCC, TIB-202TM, Manassas, VA, USA). Cells were grown in RPMI 1640 medium (GIBCO, Invitrogen, Cergy Pontoise, France) supplemented with 10 % of heat-inactivated fetal bovine serum (Eurobio, Les Ullis, France), as well as 100 U/mL of penicillin, 100 µg/mL of streptomycin and 0.25 µg/mL of amphotericin B (all from Sigma, Saint Quentin Fallavier, France). Cells were incubated at 37°C to an atmosphere composed of 95 % air, 5 % CO2 and diluted by half every 3 days.
Extracted molecule total RNA
Extraction protocol The quality of the RNA extracted by TRIzol® Reagent (Invitrogen, La Jolla, CA) was determined by spectrophotometry (A260nm/A280nm > 1.8, BioSpec-nano, Shimadzu) and by capillary electrophoresis using RNA 6000 Nano® (RIN > 9, Agilent 2100 Bioanalyser, Santa Clara, CA, USA).
Label CTP-Cy3
Label protocol CTP-cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Microarray-Based Gene Expression Analysis (Agilent, version 6.6) according to manufacturer's instructions, followed by chromatographic purification (RNeasy Mini kit, QIAGEN). Dye incorporation and cRNA yield and quality were checked by spectrophotometry (BioSpec-nano, Shimadzu) and by electrophoresis (Agilent 2100 Bioanalyser).
 
Hybridization protocol Six hundred ng of CTP-Cy3-labelled cRNA (specific activity > 10 pmol Cy3 / µg cRNA) was fragmented at 60°C for 30 min in a reaction volume of 25 µL containing 25 x Agilent fragmentation buffer and 10 x Agilent blocking agent following the manufacturer’s instructions. On cRNA fragmentation completion, 25 µL of 2 x Agilent hybridization buffer were added to the fragmentation mixture and cRNA were hybridized to SurePrint G3 Human GE v2 8x60K (Agilent) for 17 h at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with GE Wash Buffer 1TM and 1 min with 37°C GE Wash buffer 2TM (Agilent), and immediately dried by brief immersion in acetonitrile.
Scan protocol Slides were scanned immediately after washing using Agilent DNA Microarray Scanner (G2505C) by setting: (i) one color scan channel for 8x60k array slides, (ii) scan area of 61x21.6 mm, (iii) scan resolution of 3 µm, (iv) dye channel to Green, (v) Tiff file dynamic range of 20 bits and (vi) Green PMT to 100 %.
Description Gene expression in THP-1 cells after 24 h in presence of empty ENP exposure (50 µg/mL)
Data processing The scanned images were analyzed by Feature Extraction version 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 039494_D_F_20120628) to subtract background and to obtain spatially detrended processed signal intensities. Features flagged in Feature Extraction as Non-uniform outliers Feature were excluded.
 
Submission date Sep 25, 2013
Last update date Dec 19, 2013
Contact name Olivier Joubert
E-mail(s) olivier.joubert@univ-lorraine.fr
Phone 0372742694
Organization name Université de lorraine
Department Dpt 4
Lab Nanomatériaux et santé
Street address 2 allée guinier
City nancy
ZIP/Postal code 54011
Country France
 
Platform ID GPL16699
Series (1)
GSE51186 Transcriptome study of THP-1 human monocytes following exposure for 4 h or 24 h to 50 uM S-Nitrosoglutathione, 50 and 200 ug/ml S-Nitrosoglutathione-loaded polymeric and empty Eudragit RL nanoparticles

Data table header descriptions
ID_REF
VALUE Lowess normalized signal intensity

Data table
ID_REF VALUE
1 1.22E+05
2 1.05E+01
3 3.18E+00
4 2.47E+03
5 2.39E+01
6 3.26E+00
7 2.60E+01
8 8.03E+01
9 2.04E+05
10 4.04E+03
11 1.97E+03
12 9.99E+03
13 2.86E+02
14 2.16E+01
15 7.70E+00
16 3.39E+00
17 5.40E+02
18 5.20E+02
19 3.30E+01
20 3.28E+03

Total number of rows: 62976

Table truncated, full table size 911 Kbytes.




Supplementary file Size Download File type/resource
GSM1240321_F_11_Feature_extraction.txt.txt.gz 12.4 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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