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Sample GSM1089029 Query DataSets for GSM1089029
Status Public on Apr 29, 2014
Title Control_2h_rep2
Sample type RNA
 
Source name hCMEC/D3
Organism Homo sapiens
Characteristics tissue: Brain endothelium
cell line: hCMEC/D3
treatment: control
time: 2 h
Treatment protocol hCMEC/D3 cells were seeded onto collagen-coated tissue culture plate supplied by Greiner Bio-one (Gloucestershire, UK) and maintained for 72 h after confluence. Culture media was then changed to EGM-2 media without VEGF. Cells were left untreated or treated with TNFα and IFNγ at the concentrations and times indicated for each experiment.
Growth protocol hCMEC/D3 cells were cultured in EGM-2 MV medium (Lonza, Slough Wokingham, UK) and supplemented with the following components obtained from the manufacturer: 0.025 % (v/v) rhEGF, 0.025 % (v/v) VEGF, 0.025 % (v/v) IGF, 0.1 % (v/v) rhFGF, 0.1 % (v/v) gentamycin, 0.1 % (v/v) ascorbic acid, 0.04 % (v/v) hydrocortisone and 2.5 % (v/v) foetal bovine serum (FBS) (hereafter referred to as EGM-2 medium).
Extracted molecule total RNA
Extraction protocol Total RNA of hCMEC/D3 cells were isolated using miRNeasy mini kit (Qiagen, Sussex, UK) according to the manufacturer’s protocols. The quantity (NanoDrop 1000 spectrophotometer) and the quality (2100 Bioanalyzer, RNA 6000 Pico LabChip; Agilent, Palo Alto, CA, USA) of the total RNA were analyzed prior to determination of mRNA levels
Label Cy3
Label protocol Total RNA (100 ng) was labelled with pCp-Cy3 using T4 RNA ligase (GE healthcare, Amersham, UK)
 
Hybridization protocol Total RNA including miRNA (100 ng) was first dephosphorylated with calf intestine alkaline phosphatase (GE healthcare, Amersham, UK), denatured with dimethyl sulfoxide, and labeled with pCp-Cy3 to the 3’-ends using T4 RNA ligase (GE healthcare, Amersham, UK). The labeled RNAs were hybridized to Agilent human miRNA microarray (Santa Clara, CA). Design ID(AMADID)=021827.
Standard Agilent’s miRNA microarray hybridization protocol
Scan protocol Standard Agilent scaning protocol
Description Gene expression contol 2h pair to T2F-T
Data processing standard Agilent Feature Extraction protocol
 
Submission date Feb 26, 2013
Last update date Aug 29, 2016
Contact name Miguel Alejandro Lopez-Ramirez
E-mail(s) malopezramirez@ucsd.edu
Phone 858-822-6487
Organization name University of California, San Diego
Department School of Medicine
Street address 9500 Gilman Drive
City La Jolla
State/province California/San Diego
ZIP/Postal code 92093
Country USA
 
Platform ID GPL14767
Series (2)
GSE44692 MiR-155 promotes blood-brain barrier dysfunction in neuroinflammation (part 1)
GSE44694 MiR-155 promotes blood-brain barrier dysfunction in neuroinflammation

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
1 2.04E+02
2 1.65E+00
3 1.08E+04
4 2.98E-01
5 -8.23E-02
6 4.09E+00
7 2.85E-01
8 3.10E+00
9 1.68E+00
10 -9.72E-01
11 -1.41E+00
12 -7.50E-01
13 1.50E+00
14 -5.70E+00
15 -8.28E+00
16 -1.98E+00
17 -1.33E+00
18 -1.05E+00
19 8.49E-01
20 -2.93E+00

Total number of rows: 15739

Table truncated, full table size 226 Kbytes.




Supplementary file Size Download File type/resource
GSM1089029_252182710988_S01_1_3.txt.gz 2.0 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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