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Sample GSM378702 Query DataSets for GSM378702
Status Public on Mar 10, 2009
Title Human-superior frontal gyrus-25 years old
Sample type RNA
 
Source name Dissected human post-mortem superior frontal gyrus
Organism Homo sapiens
Characteristics age: 9277 days
sex: male
tissue: superior frontal gyrus of the brain
Biomaterial provider NICHDBB-Baltimore
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.
 
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 25 years old human 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.
 
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

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

Data table
ID_REF VALUE
7906878 3.65159565623426
8148358 4.66904624468799
7976128 4.84850809680769
8139021 4.87227514022883
7999387 4.02330613037204
8060539 5.31308138545456
8079746 4.56700922722468
7977149 6.18360529401189
8058512 6.07727573994333
7953032 3.47045913988716
7932911 5.26702740663467
8009685 3.40210878601501
8120431 4.74660160174872
8098204 8.05563633633248
8150698 2.23890183078794
8006187 1.89043554147402
8089835 3.06699291116566
7932938 3.02548794752547
8172914 6.37489631074254
7985089 6.70265717074533

Total number of rows: 11818

Table truncated, full table size 287 Kbytes.




Supplementary file Size Download File type/resource
GSM378702.CEL.gz 3.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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