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Sample GSM547670 Query DataSets for GSM547670
Status Public on Oct 19, 2011
Title NCI-H292-pcHO1_TNF_rep3
Sample type RNA
 
Source name NCI-H292 cells, pcHO1, 24hr, TNF treated, replicate 3
Organism Homo sapiens
Characteristics cell line: NCI-H292
overexpression: HO-1
treatment: TNF
Treatment protocol NCI-H292 cells, control and overexpressing HO-1, after reaching the confluence were treated with TNF (30 ng/ml) dissolved in RPMI 1640 medium deprived of serum. The cultures were incubated for 24 hours at 37 ºC in a humidified incubator with 5% CO2.
Growth protocol NCI-H292 cells were cultured in RPMI-1640 medium suplemented with fetal bovine serum to a final concentration of 10%, at 37.0°C in 5% of CO2
Extracted molecule total RNA
Extraction protocol RNA was prepared using the QIAzol Lysis Reagent (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.4 ug cDNA (reversely transcribed from RNA) using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
Hybridization protocol Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven (10 rpm). After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B US22502687) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel was set to Green and Green PMT. Two readings were performed: XDR Hi 100% and XDR Lo 10%).
Description Gene expression after 24hr in treated with TNF NCI-H292 cells overexpressing HO-1
Data processing The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 014850_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
 
Submission date May 27, 2010
Last update date Oct 19, 2011
Contact name Slawomir Golda
Organization name Jagiellonian University
Department Faculty of Biochemistry, Biophysics adn Biotechnology
Street address Gronostajowa 7
City Krakow
ZIP/Postal code 30-387
Country Poland
 
Platform ID GPL4133
Series (1)
GSE22030 HO-1 modulates the expression of genes involved in inflammation, angiogenesis, proliferation, apoptosis and cell adhesion in human lung cancer cells.

Data table header descriptions
ID_REF
VALUE Log2 of bakcground adjusted signal (gBGSubSignal column from raw datafile), quantile normalized (R, preprocessCore package)

Data table
ID_REF VALUE
1 17.268
2 null
3 null
4 null
5 null
6 null
7 null
8 null
9 null
10 null
11 null
12 8.947
13 5.603
14 8.389
15 4.682
16 12.830
17 3.334
18 7.464
19 15.595
20 4.047

Total number of rows: 45015

Table truncated, full table size 519 Kbytes.




Supplementary file Size Download File type/resource
GSM547670_12-pcHO1+TNF.txt.gz 7.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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