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Sample GSM359436 Query DataSets for GSM359436
Status Public on Jun 01, 2009
Title co-cultured pMBMEC - 2
Sample type RNA
 
Source name co-cultured mouse brain endothelial cells
Organism Mus musculus
Characteristics for each preparation cortices from ten 4 week old female C57BL/6 mice (Charles River, L’Arbresle, France)
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 5 day cultures on transwell filters of mouse brain microvascular endothelial cells co-cultured with 3 week mouse brain glial cultures in the lower well in non-contact
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 8.349593
NM_001001152_at 5.122518
NM_001001160_at 5.338649
NM_001001176_at 8.694864
NM_001001177_at 5.714083
NM_001001180_at 4.213581
NM_001001181_at 11.526273
NM_001001182_at 10.114906
NM_001001183_at 12.027335
NM_001001184_at 6.768469
NM_001001295_at 8.532019
NM_001001297_at 5.964259
NM_001001309_at 7.903938
NM_001001321_at 8.350514
NM_001001326_at 10.568556
NM_001001333_at 6.390027
NM_001001335_at 6.89573
NM_001001447_at 6.465898
NM_001001454_at 5.701248
NM_001001488_at 10.138956

Total number of rows: 21625

Table truncated, full table size 479 Kbytes.




Supplementary file Size Download File type/resource
GSM359436.CEL.gz 3.8 Mb (ftp)(http) CEL
GSM359436.CHP.gz 389.8 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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