|
| Status |
Public on Dec 09, 2011 |
| Title |
Chimpanzee - cerebellar cortex - 39 days old |
| Sample type |
RNA |
| |
|
| Source name |
Dissected Chimpanzee post-mortem cerebellar cortex
|
| Organism |
Pan troglodytes |
| Characteristics |
age: 39 days
gender: m
tissue: cerebellar cortex of the brain
post-mortem interval (hours): -
rna integrity number (rin): 6.6
batch: 1
|
| Biomaterial provider |
Zurich, Switzerland
|
| 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 cerebellar cortex.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA from 100 mg of tissue was performed according to the manufacturer's instructions. RNA integrity number (RIN) was measured by the Agilent® 2100 Bioanalyzer.
|
| 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. The RNA extraction and hybridization was carried out in two batches for human and macaque samples. Batches were relatively balanced with respect to age.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneChip Scanner 3000.
|
| Description |
The dataset contains two prenatal individuals; these were predicted to be ~15 and ~30 days before birth. Detailed postmortem interval (PMI) information is available only for human subjects. Macaque subjects' PMI was less than 20 minutes. Within a species, each subject used in this experiment had a unique age; samples with the same age and species identity are technical replicates.
Gene expression data from post-mortem cerebellar cortex of a 39 days old Chimpanzee individual
Ptr_39days_batch1
|
| 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 >70% of human, chimpanzee or macaque individuals.
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| |
|
| Submission date |
Jun 25, 2010 |
| Last update date |
Dec 09, 2011 |
| Contact name |
Mehmet Somel |
| E-mail(s) |
[email protected]
|
| 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 (2) |
| GSE22569 |
Gene expression in primate postnatal brain through lifespan - cerebellar cortex |
| GSE22570 |
Gene expression in primate postnatal brain through lifespan |
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