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Sample GSM420136 Query DataSets for GSM420136
Status Public on Oct 16, 2009
Title 0,45_4h_rep2
Sample type RNA
 
Source name A549 cell line isolated from a human non small cell lung cancer, treated in vitro with various concentrations of triptolide
Organism Homo sapiens
Characteristics cell line: A549
gender: male
age: 58
tissue: lung cancer
Biomaterial provider ATCC, American Type Culture Collection: ATCC Data sheet for the A549 cell line: http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=CCL-185&Template=cellBiology
Treatment protocol A549 cells were seeded in 75cm2 plates up to 70% confluence before exposure to various concentrations of triptolide for 1, 2 and 4 hours before RNA was extracted.
Growth protocol A549 cells were cultured in RPMI 1640 medium supplemented with 10% heat-inactivated fetal calf serum, penicillin (65 µg/ml) and streptomycin (100 µg/ml).
Extracted molecule total RNA
Extraction protocol RNA extraction was performed using TRIzol reagent (Invotrogen). Total RNA were dissolved in 20 µl of Rnase-free water and qualified using the NanoDrop ND-1000 Spectrophotometer
Label Cy3
Label protocol Low RNA Input Fluorescent Linear Amplification kit (Agilent Technologies) generates fluorescent cRNA with 500ng of total RNA. In this procedure, samples are labelled with cyanine 3. A primer containing poly dT and a T7 polymerase promoter is annealed to the poly A+ RNA. Reverse transcriptase is added to the reaction to synthesize the first and second strands of cDNA. Next, cRNA are synthesized from the double-stranded cDNA using T7 RNA polymerase, which simultaneously incorporates cyanine-labelled CTP.
 
Hybridization protocol 1650 ng of cyanine 3-labelled amplified RNA are hybridised at 65°C for 17 hours
Scan protocol Scanning is performed with the Agilent scanner using default parameters for 4x44 K formats. For an XDR extraction, two image files (.tif) are generated, one noted H (high, PMT 100) and the other one noted L (low, PMT 10)
Description Sample corresponding to a treatment of 0,45µM of triptolide. Measurement after 4h. Replicate 2.
Data processing Data are extracted with the Feature Extraction 9,1 software (Agilent Technologies). This software reads and processes raw microarray image files to prepare them for analysis. Feature extraction automatically assigns a grid template and a protocol, based on the barcode of the slide. The software finds microarray grids, determines feature intensities, rejects outliers, and calculates statistical confidences
 
Submission date Jun 23, 2009
Last update date Oct 16, 2009
Contact name Stéphane VISPE
E-mail(s) stephane.vispe@pierre-fabre.com
Organization name Laboratoires Pierre Fabre
Street address 3 Rue des Satellites
City Toulouse
ZIP/Postal code 31000
Country France
 
Platform ID GPL8755
Series (1)
GSE16760 Whole genome analysis in A549 cells treated for short incubation periods with various concentrations of triptolide

Data table header descriptions
ID_REF
gMedianSignal Raw Median signal of feature in green channel
gBGMedianSignal Median background signal of feature in green channel
gIsWellAboveBG Boolean flag indicating if a feature in green channel is WellAbove Background or not
VALUE Background subtracted signal intensity

Data table
ID_REF gMedianSignal gBGMedianSignal gIsWellAboveBG VALUE
1 77675.1 58 1 77617.1
2 85.5 59 0 26.5
3 80 59 0 21
4 82 60 0 22
5 79 60 0 19
6 81 60 0 21
7 86 60 0 26
8 83 60 0 23
9 81.5 60 0 21.5
10 81 61 0 20
11 83 59 0 24
12 931 60 1 871
13 108 61 0 47
14 529 60 1 469
15 119 61 0 58
16 24520.6 61 1 24459.6
17 81.5 60 0 21.5
18 800 60 1 740
19 29332.1 61 1 29271.1
20 101 60 0 41

Total number of rows: 45015

Table truncated, full table size 900 Kbytes.




Supplementary file Size Download File type/resource
GSM420136.txt.gz 9.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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