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Sample GSM560177 Query DataSets for GSM560177
Status Public on Dec 09, 2011
Title Rhesus macaque - cerebellar cortex - 1 days old
Sample type RNA
 
Source name Dissected Rhesus macaque post-mortem cerebellar cortex
Organism Macaca mulatta
Characteristics age: 1 days
gender: m
tissue: cerebellar cortex of the brain
post-mortem interval (hours): -
rna integrity number (rin): 9.1
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 1 days old Rhesus macaque individual
Mml_1days_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 3.90634175147834
8148358 5.31464817633729
7976128 4.0640598269211
8056408 2.37424570427843
8139021 5.26841870734872
7999387 4.50458947604481
8060539 3.91624968453487
8079746 2.80212294456362
7977149 4.04363498483312
8058512 4.25773076092454
7932911 4.78684417033569
8095697 1.8238024131478
8009685 3.77640322140967
8120431 3.96853760560373
8098204 6.48576449327001
8150698 2.3093989688
8006187 2.95729056686746
8089835 3.21123506711748
7932938 4.26929915626714
8172914 5.58438626545795

Total number of rows: 13657

Table truncated, full table size 332 Kbytes.




Supplementary file Size Download File type/resource
GSM560177.CEL.gz 4.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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