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| Status |
Public on Jun 11, 2011 |
| Title |
Ramified microglia from 4-week rat brain biological rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Ramified microglia from 4-week rat brain
|
| Organism |
Rattus norvegicus |
| Characteristics |
age: Postnatal day 28
tissue origin: brain
tissue type: corpus callosum
cell type: Microglia
cell morphology: Ramified (RMC)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 600 microglia cells isolated by Laser-capture microdissection using RNeasy micro kit according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Total RNA (15ng) was reverse transcripted into the first-strand cDNA using a T7-Oligo (dT) Primer (Two-Cycle Target Labeling and Control Reagent package, Affymetrix, CA, USA). After second-strand cDNA synthesis, the double-stranded cDNA was purified and served as a template in the first cycle of in vitro transcription (IVT) reaction. The unlabeled cRNA was then reverse transcripted into the first-strand cDNA of the second cycle using random primers. Subsequently, the T7-Oligo(dT) Promoter Primer was used in the second-strand cDNA synthesis to generate double-stranded cDNA template containing T7 promoter sequences. Then the double-stranded cDNA was amplified and labeled using a biotinylated nucleotide analog/ribonucleotide mix in the second IVT reaction.
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| |
|
| Hybridization protocol |
The labeled cRNA was then cleaned up, fragmented, and hybridized to Rat Genome 230 2.0 Array (Cat. No. 900506, Affymetrix, CA, USA).
|
| Scan protocol |
The arrays were stained according to the manufacturer's protocols and then scanned with the Genechip scanner (Affymetrix, CA, USA).
|
| Description |
Gene expression data from ramified microglia isolated from corpus callosum of 4-week rat brain
|
| Data processing |
CEL files were exported to Affymetrix Expression Console Version 1.1 and RMA normalization was carried out. [The data were also analyzed with Microarray Suite version 5.0 (MAS 5.0) using GeneChip Operating Software (GCOS, Affymetrix, CA, USA). For absolute analysis, each chip was normalized to a target intensity of 500, and probe sets were assigned a signal intensity and detection call of Present, Marginal or Absent (See MAS5_GCOS_analyzed.txt on GSE29885)]
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| |
|
| Submission date |
Jun 10, 2011 |
| Last update date |
Jun 11, 2011 |
| Contact name |
S Thameem Dheen |
| E-mail(s) |
[email protected]
|
| Organization name |
National University of Singapore
|
| Street address |
Medical Drive 10
|
| City |
Singapore |
| ZIP/Postal code |
117597 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL1355 |
| Series (1) |
| GSE29885 |
Expression data from amoeboid and ramified microglia isolated from the corpus callosum of 5-day and 4-week old rat brain |
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