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Sample GSM880932 Query DataSets for GSM880932
Status Public on Oct 18, 2012
Title TGFb1_1
Sample type RNA
 
Source name Primary cortical astrocytes treated with TGF-b1
Organism Mus musculus
Characteristics strain: C57Bl/6
replicate: 1
tissue: Primary cortical astrocytes
treatment: TGF-b1
Treatment protocol Purified astrocyte cultures were exposed to four different experimental stimulation conditions. (i) Basal; consisting of 32hr in stimulation medium (L-glutamine-free DMEM supplemented with 5% CS, 2mM L-glutamine, 50 IU/ml penicillin, and 50μg/ml streptomycin). (ii) TGF-β1; consisting of 32hr in stimulation medium with TGF-β1 (3ng/ml; human recombinant; R&D Systems) (iii) LPS+IFNγ; consisting of 24hr in stimulation medium prior to addition of 2µg/ml LPS (E.coli 0127:B8, Sigma) and 3ng/ml IFNγ (recombinant mouse, R&D Systems) for a further 8hr. (iv) TGFβ+LPS+IFNγ; consisting of 24hr in stimulation medium with TGF-β1 prior to addition of LPS+IFNγ for a further 8hr. The 24hr duration of TGF-β1 treatment was chosen on the basis of previous experiments showing a maximal and stable effect of TGF-β on induction of iNOS and enhancement of nitric oxide production in purified astrocyte cultures over this time period (Hamby et al., 2006a).
Growth protocol Primary astrocyte cultures were prepared from cerebral cortices of postnatal (1-3 days) C57Bl/6 mice as previously described (Hamby et al., 2006a; Hamby et al., 2006b). In brief, plating media consisted of L-glutamine-free DMEM (Invitrogen) supplemented with 10% fetal bovine serum (FBS, Hyclone), 10% calf serum (CS, Hyclone), 2mM L-glutamine, 50 IU/ml penicillin, 50µg/ml streptomycin, and 10ng/ml epidermal growth factor (EGF). Upon confluence, astrocyte cultures were purified of microglia by treatment with 8µM cytosine β-D-arabinofuranoside (Ara-C; Sigma) for 5-6 days to substantially reduce microglia followed by treatment with 75mM L-leucine methyl ester (LME, Sigma; 60-90min) one day prior to experimentation to completely eradicate any residual microglia. Cells were maintained in medium consisting of L-glutamine-free DMEM, 10% CS, 2mM L-glutamine, 50 IU/ml penicillin and 50µg/ml streptomycin. All cultures were maintained at 37°C in a humidified atmosphere of 6% CO2 and used after 14-31 days in vitro.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from astrocytes using the Qiagen RNeasy Kit. RNA quantity and quality was assessed using a Nanodrop (Nanodrop Technologies) and the Agilent Bioanalyzer (Agilent Technologies), respectively. Total RNA (200ng) was amplified, biotinylated and hybridized on Illumina Mouseref-8 v2.0 BeadChip arrays. Slides were scanned using Illumina BeadStation and signal extracted using the Illumina BeadStudio software (Illumina, San Diego CA).
Label Biotin
Label protocol Illumina protocol
 
Hybridization protocol Illumina protocol
Scan protocol Illumina protocol
Description 4697095119_D
Data processing BeadStudio, quantile normalization
 
Submission date Feb 27, 2012
Last update date Oct 18, 2012
Contact name Giovanni Coppola
E-mail(s) gcoppola@ucla.edu
Phone 310-794-4172
Organization name UCLA
Department Psychiatry and Neurology
Lab Neurogenetics
Street address 1524 Gonda, 695 Charles Young Drive South
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
 
Platform ID GPL6885
Series (1)
GSE36089 Inflammatory mediators alter astrocyte genomic profiles and G-protein receptor evoked calcium signaling

Data table header descriptions
ID_REF
VALUE Log2 transformed, quantile normalized expresssion levels

Data table
ID_REF VALUE
ILMN_1212607 6.994674932
ILMN_1212612 10.76332415
ILMN_1212619 8.445348533
ILMN_1212628 7.273448789
ILMN_1212632 7.351971264
ILMN_1212636 11.93263708
ILMN_1212637 10.29443796
ILMN_1212645 6.778274635
ILMN_1212648 9.029859397
ILMN_1212653 11.4396081
ILMN_1212672 7.966960848
ILMN_1212682 6.962403112
ILMN_1212683 6.930763579
ILMN_1212685 6.907423146
ILMN_1212692 6.996583104
ILMN_1212693 9.329338138
ILMN_1212695 6.961346504
ILMN_1212698 6.743793992
ILMN_1212702 6.755232916
ILMN_1212703 7.841484745

Total number of rows: 25697

Table truncated, full table size 624 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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