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Sample GSM359440 Query DataSets for GSM359440
Status Public on Jun 01, 2009
Title cell-line MBMEC - 3
Sample type RNA
 
Source name b.End5 cell-line
Organism Mus musculus
Characteristics b.End5 endothelioma cultures from mouse brain microvascular cells
Treatment protocol as above
Growth protocol mouse brain microvascular endothelial cells were isolated with or without culture as described above
Extracted molecule total RNA
Extraction protocol RNA was extracted using RNAready kit (BioDiagnostik, University Bern, Bern, Switzerland) according to the manufacturer protocol including an on-column DNase digestion
Label biotin
Label protocol cDNAs were prepared by reverse transcription (RT) (WT-Ovation Pico System, NuGEN) according to the manufacturer’s protocol from total isolated RNAs. Fragmented and biotin labelled single-stranded cDNA targets were generated with the FL-Ovation cDNA Biotin Module V2 (NuGEN, 4200-12) according to the manufacturer’s protocol.
 
Hybridization protocol The biotin-labelled cDNA targets were mixed in 220 µL of Hybridization Mix (Affymetrix Inc., P/N 9007200) containing Hybridization controls and Control Oligonucleotide B2 (Affymetrix Inc., P/N 900454). Samples were hybridized to GeneChip® arrays for 18 h at 45 ºC
Scan protocol An Affymetrix GeneChip® Scanner 3000 (Affymetrix Inc.) was used to measure fluorescent intensities emitted by labelled targets and signals were saved to a CEL file format.
Description gene expression from b.End5 endothelioma cultures
Data processing CEL file date were normalized using RMAExpress 0.5 (Robust Multichip Average) (Bolstad et al 2003) and Custom CDF version 10 (Mm430_Mm_REFSEQ.cdf) (Dai et al 2005). The RMAExpress options background-adjustment and quantile normalization were enabled. To exclude probe sets in the lower end of the signal range which have large signal variation, a cutoff value was defined as the maximal signal value obtained from non-murine Affymetrix-control probe sets multiplied by a factor of 1.2. In this data set, the cutoff value was log25.78. Probe sets with a signal below cutoff in every array of the corresponding comparison, as well as Affymetrix control probe sets (prefix of “AFFX”) were excluded from further analysis.
 
Submission date Jan 12, 2009
Last update date Jan 12, 2009
Contact name Francois Verrey
E-mail(s) verrey@access.uzh.ch
Phone +41 44 635 50 44
Fax +41 44 635 68 14
Organization name University of Zurich
Department Institute of Physiology
Street address Winterthurerstr. 190
City Zurich
ZIP/Postal code CH-8057
Country Switzerland
 
Platform ID GPL8059
Series (1)
GSE14375 Culture induced changes in Blood-Brain Barrier transcriptome: implications for amino acid transporters in vivo

Data table header descriptions
ID_REF
VALUE RMA signal

Data table
ID_REF VALUE
NM_001001144_at 8.286368
NM_001001152_at 7.443263
NM_001001160_at 5.515811
NM_001001176_at 8.856983
NM_001001177_at 6.167031
NM_001001180_at 5.069633
NM_001001181_at 10.981056
NM_001001182_at 10.800493
NM_001001183_at 11.991408
NM_001001184_at 7.928253
NM_001001295_at 8.585575
NM_001001297_at 6.751873
NM_001001309_at 11.346186
NM_001001321_at 8.474394
NM_001001326_at 10.782869
NM_001001333_at 7.278338
NM_001001335_at 6.97644
NM_001001447_at 6.359169
NM_001001454_at 5.876975
NM_001001488_at 9.454789

Total number of rows: 21625

Table truncated, full table size 479 Kbytes.




Supplementary file Size Download File type/resource
GSM359440.CEL.gz 3.8 Mb (ftp)(http) CEL
GSM359440.CHP.gz 388.9 Kb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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