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| Status |
Public on Mar 10, 2009 |
| Title |
Chimpanzee-superior frontal gyrus-35 years old |
| Sample type |
RNA |
| |
|
| Source name |
Dissected chimpanzee post-mortem superior frontal gyrus
|
| Organism |
Pan troglodytes |
| Characteristics |
age: 12784 days
sex: male
tissue: superior frontal gyrus of the brain
|
| Biomaterial provider |
Zurich
|
| Treatment protocol |
All human postmortem brain tissue samples were obtained from the NICHD Brain and Tissue Bank for Developmental Disorders (NICHDBB)(Baltimore, MD, USA). All subjects were defined as normal controls by forensic pathologists at the NICHDBB. No subjects with prolonged agonal state were used. Chimpanzee samples were obtained from the Yerkes Primate Center (Atlanta, GA, USA), from the Biomedical Primate Research Centre (Rijswijk, Netherlands) and from the Anthropological Institute of the University of Zurich (Switzerland). Rhesus macaque brains were obtained from the SuZhou Experimental Animal Center (SuZhou, China). The dissections were made from the cortical region approximately corresponding to Brodmann area 9 of the prefrontal cortex (the superior frontal gyrus). We aimed to make dissections that contain 2:1 grey:white matter (60-70% grey matter).
|
| 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.
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| |
|
| 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 35 years old chimpanzee individual
|
| 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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| |
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| Submission date |
Mar 09, 2009 |
| Last update date |
Mar 09, 2009 |
| Contact name |
Mehmet Somel |
| E-mail(s) |
somel@eva.mpg.de
|
| Phone |
+49-(0)341-3550-530
|
| Fax |
+49-(0)341-3550-555
|
| Organization name |
Max Planck Institute for Evolutionary Anthropology
|
| Department |
Evolutionary Genetics
|
| Street address |
Deutscher Platz 6
|
| City |
Leipzig |
| ZIP/Postal code |
D-04103 |
| Country |
Germany |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE15163 |
Gene expression data from primate postnatal brain development - superior frontal gyrus |
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