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| Status |
Public on Nov 24, 2008 |
| Title |
Expression from control subplate neurons with few synapses and cocultured subplate neurons with induced synaptogenesis |
| Organism |
Rattus norvegicus |
| Experiment type |
Expression profiling by array
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| Summary |
The transcriptional events accompanying synaptogenesis are largely unknown, or have been studied in systems in which synapse formation occurs gradually over time. With a system in which synaptogenesis is synchronized and controllable, molecular or biochemical techniques can be used to examine cellular events across cultures on a wide scale, as synapses develop.
Here, we have triggered synaptogenesis in immunopurified subplate neurons by coculturing with cortical feeder layers and have used microarrays to investigate the transcriptional events occuring in this more defined and controllable system.
Keywords: treatment type comparison, time course
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| Overall design |
Affymetrix rat GeneChip microarrays were used to assess whether coculturing induces transcriptional changes in subplate neurons. Subplate synapses develop rapidly following coculturing; an exposure to the feeder layer of only 48 hours is sufficient to detect a significant increase in the density of synapses, and is as effective as longer durations. Within the first few minutes or hours of a cell's response to an exogenous signal, any primary transcriptional events are expected to involve activation of immediate early genes (IEGs), often transcription factors themselves, which may then turn on downstream target response genes encoding factors to be delivered to sites of action, such as synapses. With the aim of searching for such downstream genes, microarrays were performed after 24 hours of coculturing, an intermediate timepoint between the likely phase of IEG transcription and the large wave of synaptogenesis seen between 24 and 48 hours of coculturing. Additional microarrays were also performed after 96 hours of coculturing to assess transcriptional changes that might occur over longer timescales. Five biological replicates of control and cocultured neurons at 24 and 96 hours were used, for a total of 20 microarrays.
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| Contributor(s) |
McKellar CE, Shatz CJ |
| Citation(s) |
19029062 |
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| Submission date |
Jun 28, 2007 |
| Last update date |
Jul 31, 2017 |
| Contact name |
Claire McKellar |
| Organization name |
HHMI Janelia Farm Research Campus
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| Street address |
19700 Helix Drive
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| City |
Ashburn |
| State/province |
VA |
| ZIP/Postal code |
20147 |
| Country |
USA |
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| Platforms (1) |
| GPL1355 |
[Rat230_2] Affymetrix Rat Genome 230 2.0 Array |
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| Samples (20)
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| GSM206257 |
cocultured 96h, biological rep1 |
| GSM206258 |
control 24h, biological rep2 |
| GSM206259 |
cocultured 24h, biological rep2 |
| GSM206260 |
control 96h, biological rep2 |
| GSM206261 |
cocultured 96h, biological rep2 |
| GSM206262 |
control 24h, biological rep3 |
| GSM206263 |
cocultured 24h, biological rep3 |
| GSM206264 |
control 96h, biological rep3 |
| GSM206265 |
cocultured 96h, biological rep3 |
| GSM206266 |
control 24h, biological rep4 |
| GSM206267 |
cocultured 24h, biological rep4 |
| GSM206268 |
control 96h, biological rep4 |
| GSM206269 |
cocultured 96h, biological rep4 |
| GSM206270 |
control 24h, biological rep5 |
| GSM206271 |
cocultured 24h, biological rep5 |
| GSM206272 |
control 96h, biological rep5 |
| GSM206273 |
cocultured 96h, biological rep5 |
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| Relations |
| BioProject |
PRJNA101299 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE8318_RAW.tar |
52.3 Mb |
(http)(custom) |
TAR (of CEL) |
| GSE8318_genes_expressed_in_subplate_cultures_annotated.txt |
5.2 Mb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
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