|
| Status |
Public on Feb 02, 2012 |
| Title |
Macaque-PFC-fetal-30d |
| Sample type |
RNA |
| |
|
| Source name |
Dissected macaque post-mortem superior frontal gyrus
|
| Organism |
Macaca mulatta |
| Characteristics |
gender: male
age: 30 days before birth
tissue: superior frontal gyrus of the brain
|
| Treatment protocol |
Rhesus macaque samples were obtained from the Suzhou Experimental Animal Center, China. All individuals used in this study suffered sudden deaths for reasons other than their participation in this study and without any relation to the tissue used.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA from 100 mg of tissue was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared from 2 microg. total RNA following standard Affymetrix protocols.
|
| |
|
| Hybridization protocol |
Hybridization to Affymetrix Human Gene 1.0 ST arrays was carried out following standard Affymetrix protocols.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneChip Scanner 3000.
|
| Description |
Gene expression data from post-mortem superior frontal gyrus of a macauqe with 30 days before birth
|
| Data processing |
Affymetrix microarray image data were collected with Affymetrix GeneChip Operating Software version 1.1 using default parameters. To identify array probes that contain mismatches among species, we mapped HuGene-1_0-st probe sequences (http://www.affymetrix.com/Auth/analysis/downloads/na23/wtgene/HuGene-1_0-st-v1.probe.tab.zip) to the human (hg18), chimpanzee (panTro2), and rhesus macaque (rheMac2) genomes using BLAT (http://genome.ucsc.edu/FAQ/FAQblat.html). Based on these alignments, we only included probes which matched all three genomes perfectly and at a single location (27% of the original array probes). Intensities of probes that passed this mask were corrected for background using the antigenomic probes with the same GC content; the latter are used as an estimator of the unspecific background hybridization (http://www.affymetrix.com/support/technical/whitepapers/exon_background_correction_whitepaper.pdf). Probe intensities were then log-transformed and quantile normalized. Intensity values per transcript were calculated by median polishing. To determine whether the signal intensity of a given probe was above the expected level of background noise, we compared each probe's signal intensity to a distribution of signal intensities of the antigenomic probes with the same GC content (a GC-bin). For each GC-bin, except the ones with the most extreme GC content, the numbers of antigenomic probes are close to 1,000. We considered a probe signal as detected if its intensity is higher than 95% of the background probes' intensities (see PMID: 17456239). In each array, we considered a transcript as “detected” if more than 50% of probes and at least 8 probes per transcript were detected. We considered a transcript as “expressed” if it was detected in >1/3 of human or chimpanzee individuals. For further analysis, we mapped the transcript IDs to Ensemble Genes using the table provided at the Affymetrix support site (“http://www.affymetrix.com/analysis/downloads/na26/wtgene/HuGene-1_0-st-v1.na26.hg18.transcript.csv.zip”). For 127 expressed genes with multiple transcripts, we calculated the means across transcripts.
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| |
|
| Submission date |
May 09, 2011 |
| Last update date |
Feb 02, 2012 |
| Contact name |
Xiling Liu |
| Organization name |
Partner Institute for Computational Biology
|
| Street address |
320 Yue Yang Road
|
| City |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
| |
|
| Platform ID |
GPL6244 |
| Series (2) |
| GSE29138 |
The mRNA expression patterns in macaque brains from prenatal to neonatal |
| GSE29140 |
An extreme human-specific delay in cortical synaptic development |
|
