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| Status |
Public on Aug 05, 2009 |
| Title |
Toward a Better Understanding of Potential Roles of Astrocytes in HIV-1-associated Neurocognitive Disorders |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by array
|
| Summary |
We present a microarray analysis of primary mouse astrocytes exposed to HIV-1 in culture. Results are compared with previous genomic studies of HIV-1 effect in human astrocytes and human and macaque brains.
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| Overall design |
Day-two neonatal mouse astrocytes were exposed in triplicates to cell-free HIV-1/NL4-3 at m.o.i. of 1 and cultured for 24 hours. As control, cells were treated in triplicates with a mock virus concentrate at the same dilution (vol/vol) as the wild-type virus. As an example of large scale gene expression analysis we shall provide some details of the method; full description is in Kim et al. (S.-Y. Kim et al., 2004). Total RNA was prepared from cell cultures using the RNAeasy total RNA extraction kit (Qiagen, CA). RNA quality was assessed by electrophoresis and spectrophotometric analysis; between 1 and 10 µg of total RNA was used to generate a cDNA, and then 1 µg of cDNA product was used in an in vitro transcription reaction that contained biotinylated UTP and CTP. Twenty µg of full-length cRNA was fragmented and was subjected to gene expression analysis on the Affymetrix Mouse Genome 430 2.0 Array chip. Affymetrix software was used to generate CHP files. Significance analysis was performed using ArrayAssist software (Stratagene).
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| Contributor(s) |
Borjabad A, Brooks AI, Volsky DJ |
| Citation(s) |
19697136 |
| |
| Submission date |
Jul 28, 2009 |
| Last update date |
Feb 11, 2019 |
| Contact name |
Alejandra Borjabad |
| E-mail(s) |
ab2612@columbia.edu
|
| Phone |
9175574628
|
| Organization name |
St.Luke's-Roosevelt Hospital Center
|
| Department |
Medicine
|
| Lab |
Molecular Virology
|
| Street address |
432 West 58th, Street
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10019 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL1261 |
[Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array |
|
| Samples (6)
|
| GSM434350 |
Mouse astrocytes exposed to HIV-1 rep1 |
| GSM434352 |
Mouse astrocytes exposed to HIV-1 rep2 |
| GSM434353 |
Mouse astrocytes exposed to HIV-1 rep3 |
| GSM434380 |
Mouse astrocytes exposed to mock virus rep1 |
| GSM434388 |
Mouse astrocytes exposed to mock virus rep2 |
| GSM434389 |
Mouse astrocytes exposed to mock virus rep3 |
|
| Relations |
| BioProject |
PRJNA118813 |
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