NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM573729 Query DataSets for GSM573729
Status Public on Jul 23, 2013
Title OCILY18-LT20-4h-rep1
Sample type RNA
 
Source name Human cell line, 4h
Organism Homo sapiens
Characteristics cell line: Oci-Ly18
treatment: LT20
dose: 10
unit: µg/ml
Treatment protocol cells were treated for 4h
Growth protocol standard procedures of cell culture according to the guidelines of suppliers
Extracted molecule total RNA
Extraction protocol Extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
Description Gene expression data from human cell lines
Data processing The MAS5.0 normalized data for each unicate provided in the Sample table.
The data were further analyzed with In-house tools. We generated data sets consisting of "mean values" for the three replicates and "change factors" to the appropriate control experiment supplied in the GSE23394_Matrix_triplicates.xls file. Our in-house tool is called Race-A (Roche Affymetrix Chip Experiment - Analysis). The method is MAS5.0 and the scaling factor was adjusted for a scaling mean of 158. The CHGF=change factors are relative ratios (-1 for up regulation and +1 for down regulation to avoid the gap between -1 and +1), i.e. chgf=1 means double signal, chgf=-1 means half signal.
 
Submission date Aug 03, 2010
Last update date Jul 23, 2013
Contact name Helmut Burtscher
E-mail(s) helmut.burtscher@roche.com
Organization name Roche Pharma
Street address Nonnenwald 2
City Penzberg
ZIP/Postal code 82377
Country Germany
 
Platform ID GPL570
Series (1)
GSE23394 Expression data from human NHL cell lines treated with agonistic antibodies

Data table header descriptions
ID_REF
VALUE MAS5.0 signal intensity

Data table
ID_REF VALUE
200825_s_at 729.73
200826_at 5022.77
200827_at 60.58
200828_s_at 2269.98
200829_x_at 2480.18
200830_at 1685.27
200831_s_at 345.13
200832_s_at 1461.30
200833_s_at 2171.76
200834_s_at 7554.35
200835_s_at 33.04
200836_s_at 78.94
200837_at 281.80
200838_at 51.40
200839_s_at 145.03
200840_at 4477.54
200841_s_at 163.39
200842_s_at 1383.28
200843_s_at 1237.33
200844_s_at 1181.34

Total number of rows: 54675

Table truncated, full table size 890 Kbytes.




Supplementary file Size Download File type/resource
GSM573729.CEL.gz 5.2 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap