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Series GSE11674 Query DataSets for GSE11674
Status Public on Jul 06, 2008
Title Genes up-regulated by VE-cadherin expression and clustering at junctions
Organism Mus musculus
Experiment type Expression profiling by array
Summary In order to identify genes regulated by VE-cadherin expression, we compared a mouse VE-cadherin null cell line (VEC null) with the same line reconstituted with VE-cadherin wild type cDNA (VEC positive). The morphological and functional properties of these cell lines were described previously [Lampugnani,M.G. et al. Contact inhibition of VEGF-induced proliferation requires vascular endothelial cadherin, beta-catenin, and the phosphatase DEP-1/CD148. J. Cell Biol. 161, 793-804 (2003)]. By Affymetrix gene expression analysis we found several genes up-regulated by VE-cadherin, among which claudin-5 reached remarkably high levels. The up-regulation of these genes required not only VE-cadherin expression but also cell confluence suggesting that VE-cadherin clustering at junctions was needed.
 
Overall design VEC null or positive cells in the sparse and confluent conditions have been starved in MCDB 131 medium 1% BSA for 36 h. Next, RNA has been extracted with standard guanidinium isothiocyanate lysis buffer and cesium chloride ultracentrifugation. Synthesis of biotinylated cRNA targets, array hybridization (GeneChips MG_U74Av2 and MG_U74Bv2), staining and scanning were performed according to the Affymetrix standard protocols, starting from 15 μg of total RNA. Two copies of the GeneChips were hybridized with each cRNA sample. The MAS5 algorithm was used to determine the expression levels of mRNAs; the absolute analysis was performed using default parameters and scaling factor 500. Report files were extracted for each chip, and performance of labeled target was evaluated on the basis of several values (scaling factor, background and noise values, % present calls, average signal value, etc). Gene expression levels were normalized on the median over all samples. Annotation of Probe Sets is according to Affymetrix Annotation Tables (release May 31, 2007) [Vecchi,M. et al. Gene expression analysis of early and advanced gastric cancers. Oncogene 26, 4284-4294 (2007)]. We selected the genes up-regulated by VE-cadherin expression and clustering at junctions in confluent VEC positive cells.
 
Contributor(s) Taddei A, Conti A, Orsenigo F, Breviario F, Dejana E
Citation(s) 18604199
Submission date Jun 04, 2008
Last update date Feb 18, 2018
Contact name Elisabetta Dejana
E-mail(s) elisabetta.dejana@ifom-ieo-campus.it
Organization name IFOM-IEO-CAMPUS
Street address Via Adamello, 16
City Milan
ZIP/Postal code 20139
Country Italy
 
Platforms (2)
GPL81 [MG_U74Av2] Affymetrix Murine Genome U74A Version 2 Array
GPL82 [MG_U74Bv2] Affymetrix Murine Genome U74B Version 2 Array
Samples (16)
GSM296617 VEC_Null_sparse_rep1
GSM296618 VEC_Null_sparse_rep2
GSM296619 VEC_Null_confluent_rep1
Relations
BioProject PRJNA106073

Genes up-regulated by VE-cadherin expression and clustering at junctions header descriptions
FC
Symbol
Description
VEC null, Confluent
VEC positive, confluent
VEC null, sparse
VEC positive, sparse
Entrez Gene
UniGene ID
RefSeq Transcript ID
ProbeSet

Data table
FC Symbol Description VEC null, Confluent VEC positive, confluent VEC null, sparse VEC positive, sparse Entrez Gene UniGene ID RefSeq Transcript ID ProbeSet
162.7 Cldn5 claudin 5 50.5 5115.3 11.9 31.9 12741 Mm.22768 NM_013805 104516_at
96.1 Vwf Von Willebrand factor homolog 22.0 2516.5 14.5 42.1 22371 Mm.22339 NM_011708 103499_at
44.5 Lamb3 laminin, beta 3 16.6 1400.2 35.4 42.4 16780 Mm.287014 NM_008484 92759_at
20.7 Ahrr aryl-hydrocarbon receptor repressor 19.7 540.4 34.8 23.9 11624 Mm.290446 NM_009644 101709_at
18.5 Rgs2 regulator of G-protein signaling 2 319.2 3721.8 121.1 163.0 19735 Mm.28262 NM_009061 97844_at
14.9 Il13ra2 interleukin 13 receptor, alpha 2 73.3 651.7 36.3 22.1 16165 Mm.368330 NM_008356 95344_at
14.2 Col23a1 procollagen, type XXIII, alpha 1 624.6 3354.0 28.0 53.9 237759 Mm.154093 NM_153393 108983_at
13.2 Mmrn2 multimerin 2 1247.8 11459.1 255.8 1099.3 105450 Mm.272673 NM_153127 114781_at
12.8 Col15a1 procollagen, type XV 193.7 1040.6 32.4 18.0 12819 Mm.233547 NM_009928 99637_at
11.6 Slc14a1 solute carrier family 14 (urea transporter), member 1 84.1 2057.5 113.2 333.4 108052 Mm.33832 NM_028122 110850_f_at
11.5 Bgn biglycan 186.7 2633.5 236.0 264.9 12111 Mm.2608 NM_007542 96049_at
11.0 Cd200 Cd200 antigen 99.9 588.0 21.9 38.7 17470 Mm.245851 NM_010818 101851_at
10.6 Slc14a1 solute carrier family 14 (urea transporter), member 1 85.2 1329.8 96.4 193.7 108052 Mm.33832 NM_028122 110851_r_at
10.2 Sned1 sushi, nidogen and EGF-like domains 1 178.6 3164.1 184.3 568.2 208777 Mm.271897 NM_172463 109554_at
9.0 6330442E10Rik RIKEN cDNA 6330442E10 gene 164.5 854.3 60.0 59.5 268567 Mm.341747 NM_178745 103424_at
8.2 Stox2 storkhead box 2 401.3 1680.0 93.8 119.4 71069 Mm.23973 NM_175162 109365_at
7.3 Agtrl1 angiotensin receptor-like 1 1229.9 5324.5 424.7 521.2 23796 Mm.29368 NM_011784 109689_at
7.1 Crlf1 cytokine receptor-like factor 1 91.9 414.3 29.0 53.8 12931 Mm.358583 NM_018827 161046_at
7.1 2810457I06Rik RIKEN cDNA 2810457I06 gene 22.6 393.8 50.6 94.0 72828 Mm.133615 NM_176860 112830_at
6.6 Nefh neurofilament, heavy polypeptide 53.7 304.3 47.8 36.8 380684 Mm.298283 NM_010904 103234_at

Total number of rows: 85

Table truncated, full table size 8 Kbytes.




Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE11674_RAW.tar 45.3 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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