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Sample GSM560172 Query DataSets for GSM560172
Status Public on Dec 09, 2011
Title Rhesus macaque - cerebellar cortex - 151 days old
Sample type RNA
 
Source name Dissected Rhesus macaque post-mortem cerebellar cortex
Organism Macaca mulatta
Characteristics age: 151 days
gender: m
tissue: cerebellar cortex of the brain
post-mortem interval (hours): -
rna integrity number (rin): 9
batch: 2
Biomaterial provider SuZhou, China
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 151 days old Rhesus macaque individual
Mml_151days_batch2
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.
 
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

Data table header descriptions
ID_REF
VALUE Quantile normalized log2-transformed signal intensities

Data table
ID_REF VALUE
7906878 3.65873515253199
8148358 4.67927636439996
7976128 4.01271721246275
8056408 1.48481727503104
8139021 5.07373131855846
7999387 5.70257789837858
8060539 4.0499109756009
8079746 3.11265460091446
7977149 4.12233921478772
8058512 4.54101230699038
7932911 4.79252590581184
8095697 2.14903010825249
8009685 4.03121172581556
8120431 3.65838802763805
8098204 6.61261599376265
8150698 3.10962539639823
8006187 3.0715035235777
8089835 2.89254038032082
7932938 4.29723268968435
8172914 5.61044461777497

Total number of rows: 13657

Table truncated, full table size 332 Kbytes.




Supplementary file Size Download File type/resource
GSM560172.CEL.gz 4.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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