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Sample GSM880939 Query DataSets for GSM880939
Status Public on Oct 18, 2012
Title TGFb1_3
Sample type RNA
 
Source name Primary cortical astrocytes treated with TGF-b1
Organism Mus musculus
Characteristics strain: C57Bl/6
replicate: 3
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 4700266112_C
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 7.122201153
ILMN_1212612 10.72588751
ILMN_1212619 8.514270941
ILMN_1212628 6.966081972
ILMN_1212632 7.201782325
ILMN_1212636 11.74734189
ILMN_1212637 9.522950646
ILMN_1212645 6.919900165
ILMN_1212648 9.29545712
ILMN_1212653 11.25981514
ILMN_1212672 7.782642518
ILMN_1212682 7.371920065
ILMN_1212683 6.729012602
ILMN_1212685 7.003941993
ILMN_1212692 7.064776516
ILMN_1212693 9.802130034
ILMN_1212695 6.93514791
ILMN_1212698 6.846101972
ILMN_1212702 7.027054252
ILMN_1212703 7.896505299

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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