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Sample GSM378698 Query DataSets for GSM378698
Status Public on Mar 10, 2009
Title Human-superior frontal gyrus-0.1 years old
Sample type RNA
 
Source name Dissected human post-mortem superior frontal gyrus
Organism Homo sapiens
Characteristics age: 34 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 0.1 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) [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 (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 3.42298242296906
8148358 4.99909474535497
7976128 4.41150320019078
8139021 5.57587890795672
7999387 4.03157566004181
8060539 5.53875992273968
8079746 4.73804055322146
7977149 5.60647853160682
8058512 5.55419533508057
7953032 2.88591604153484
7932911 5.30242573038035
8009685 3.1554651316969
8120431 5.475341935227
8098204 8.07880126615968
8150698 3.78210180041247
8006187 2.85632663730718
8089835 3.53588108283148
7932938 3.7781541874269
8172914 6.22611098863898
7985089 6.48407963570966

Total number of rows: 11818

Table truncated, full table size 287 Kbytes.




Supplementary file Size Download File type/resource
GSM378698.CEL.gz 3.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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