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Sample GSM434655 Query DataSets for GSM434655
Status Public on Jul 18, 2011
Title 6h EGF replicate 3 repetition (IMPPC)
Sample type RNA
 
Source name Cervical cancer cell line (HeLa)
Organism Homo sapiens
Characteristics cell line: HeLa
treatment: serum deprived for 24 hours, followed by exposure to EGF for 6 hours
Treatment protocol For treatments, the cells were transferred to 60 mm dishes and cultured for 48h in complete growth medium, after which they were starved for 24h in DMEM containing 2% FBS. After serum deprivation cells were stimulated with EGF (150 ng/ml) for the indicated times. Three biological replicate experiments were performed, each comparing EGF treated with untreated control HeLa cells.
Growth protocol HeLa cells were cultured at 37ºC in a 95/5 Air/CO2 water saturated atmosphere in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% heat inactivated foetal bovine serum (FBS), 2 mM L-glutamine and 100U/ml Penicilin/streptomycine (complete growth medium).
Extracted molecule total RNA
Extraction protocol Total RNA from HeLa cells was extracted using the RNeasy RNA Isolation kit (Qiagen) followed by treatment with RNase-free DNase I (Ambion, Austin, TX) following manufacturer's instructions. RNA quantification was performed with a Nanodrop spectrophotometer, and the RNA integrity was assessed using the Bioanalyzer 2100 nanoelectrophoresis Lab-on-a–chip system (Agilent, Wilmington, DE). All RNAs used had RIN (RNA integrity number) ranging between 9.3 and 10, and 28S/18S ratios between 1.67 and 2.07.
Label biotin / streptavidin-phycoerythrin
Label protocol 5 µg of total RNA was converted into double-stranded cDNA using the Superscript II system for cDNA synthesis (Invitrogen). Double-stranded cDNA was purified and in vitro transcribed. Biotinylated cRNA was purified and fragmented randomly to an average length of ~100 nt by incubating at 94°C for 35 min.
 
Hybridization protocol Microarrays were hybridized with 15 µg of fragmented cRNA. Hybridizations were carried out at 45°C for 16 h without agitation. Arrays were washed and the hybridized RNA was fluorescence-stained by incubating with streptavidin–phycoerythrin.
Scan protocol Detection and feature readout were performed using the CCD-based detection system of the Geniom device (Cy3 filter set).
Description HeLa cells, serum deprived for 24 hours, followed by exposure to EGF for 6 hours
6h time point, EGF, biological replicate 3 of 3. Technical replicate 2 of 2.
Data processing Extracted raw data were filtered and normalized using the Limma package developed within the Bioconductor project in the R statistical programming environment. The single channel intensity data were quantile normalized to scaling across chips. Differentially expressed genes for each time point were chosen using as cut off criteria a SAM FDR of 5% and an average absolute fold change (|FC|) above 1.2 .
 
Submission date Jul 29, 2009
Last update date Jul 18, 2011
Contact name Lauro Sumoy
E-mail(s) lsumoy@igtp.cat
Organization name IGTP
Department High Content Genomics and Bioinformatics
Street address Ctra. Can Ruti, Camí de les escoles s/n
City Badalona
State/province Barcelona
ZIP/Postal code 08916
Country Spain
 
Platform ID GPL8948
Series (1)
GSE17403 Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis

Data table header descriptions
ID_REF
VALUE Normalized intensity

Data table
ID_REF VALUE
1 438.04
2 375.17
3 346.09
4 569.61
5 7259.87
6 3855.48
7 1245.88
8 1279.56
9 8339.30
10 806.69
11 1423.12
12 1084.50
13 956.71
14 487.64
15 3340.61
16 3707.54
17 1039.89
18 4704.68
19 3245.18
20 5488.80

Total number of rows: 6776

Table truncated, full table size 81 Kbytes.




Supplementary file Size Download File type/resource
GSM434655_F-00006621_A8_H2_D1.tsv.gz 303.9 Kb (ftp)(http) TSV
Processed data included within Sample table

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