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Sample GSM420254 Query DataSets for GSM420254
Status Public on Nov 19, 2009
Title SH-SY5Ycells_DMSO_treated_4hours_rep2
Sample type RNA
 
Source name Human neuroblastoma SH-SY5Y cells, treated with dimethyl sulfoxide (DMSO) 0.6%, for 4 hours
Organism Homo sapiens
Characteristics cell line: SH-SY5Y
atcc: CRL-2266
cell type: neuroblastoma
treatment: DMSO
treatment time: 4 hours
Treatment protocol The growth medium was replaced with experimental medium, which was either 140 nM Bf medium (Bf 140 nM samples) or 0.6 % DMSO medium (DMSO 0.6 % samples), and cells were allowed to grow. After 4 h, cells were collected and processed for microarray analysis. Separate flasks of cells were used for each of the treatments and assays. Experiments were performed using at least three independent biological replicates.
Growth protocol SH-SY5Y human neuroblastoma cells (ATCC CRL-2266) were cultured in a humidified incubator at 37°C and 5 % CO2 in F12-EMEM (1:1) containing 15 % foetal bovine serum (FBS), 2 mM L-glutamine, 25 µg/mL gentamicin, 100 U/ml penicillin, and 100 µg/mL streptomycin at 37°C with 5 % CO2. Cells were seeded at 6 x 10e6 cells in 75 cm2 flasks and grown for 24 h (cells reached 70-80% confluence).
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the TRIzol reagent (Invitrogen) following the manufacturer’s instructions. It was then purified using the RNeasy mini kit (Qiagen). The quality of total RNA was assessed using a bioanalyzer (Agilent 2100; Agilent Technologies) and RNA was quantified by using a ND-1000 Nanodrop spectrophotometer.
Label Biotin
Label protocol 10 μg of each total RNA sample was labelled according to the standard one-cycle amplification and labelling protocol developed by Affymetrix (Santa Clara, CA).
 
Hybridization protocol Labelled cRNA was hybridized on Affymetrix GeneChip Human U133A 2.0 Arrays containing over 14,500 transcripts. Hybridized GeneChips were stained and washed using the GeneChip Fluidic Station 450.
Scan protocol GeneChips were scanned with the GeneChip Scanner 3000 7G. Cell intensity values and probe detection calls were computed from the raw array data using the Affymetrix GeneChip Operating Software (GCOS).
Description DMSO4h_5
Data processing Further data processing was performed in the R computing environment (http://www.r-project.org/, version R 2.5.0 for Windows) using packages from the BioConductor software project (http://www.bioconductor.org/). Variance-stabilizing normalization was applied, using the justvsn function from the vsn library. Normalized data were then filtered based on the Affymetrix detection call, so that only probes that had a Present call in at least one of the arrays were retained. Data were then imported in the MultiExperiment Viewer (MeV) software (version 4.0.01 for Windows XP), and statistical analysis was performed with the SAM (Significance Analysis of Microarrays) module.
 
Submission date Jun 23, 2009
Last update date Nov 19, 2009
Contact name Paola Roncaglia
Organization name SISSA/ISAS (International School for Advanced Studies)
Department Neurobiology
Street address via Bonomea 265
City Trieste
State/province TS
ZIP/Postal code 34136
Country Italy
 
Platform ID GPL571
Series (2)
GSE16767 Transcriptome analysis identifies molecular effectors of unconjugated bilirubin in human neuroblastoma SH-SY5Y cells: 4h
GSE16768 Transcriptome analysis identifies molecular effectors of unconjugated bilirubin in human neuroblastoma SH-SY5Y cells

Data table header descriptions
ID_REF
VALUE VSN signal

Data table
ID_REF VALUE
1007_s_at 9.800881942
1053_at 10.6544409
117_at 6.958982574
121_at 9.001047612
1255_g_at 8.07185785
1294_at 7.28431003
1316_at 7.15277304
1320_at 7.903984235
1405_i_at 6.275791439
1431_at 6.503468074
1438_at 7.770659166
1487_at 9.123137189
1494_f_at 7.798504286
1598_g_at 9.549859817
160020_at 7.785329953
1729_at 8.610245154
177_at 6.652345041
1773_at 8.482815707
179_at 9.425323414
1861_at 8.945582292

Total number of rows: 22277

Table truncated, full table size 496 Kbytes.




Supplementary file Size Download File type/resource
GSM420254.CEL.gz 2.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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