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Sample GSM593080 Query DataSets for GSM593080
Status Public on Oct 17, 2010
Title DG_4B (MDD) vs. 4D (Control)
Sample type RNA
 
Channel 1
Source name DG_MDD 4B
Organism Homo sapiens
Characteristics sample id: 4B
disease state: MDD
tissue: Dentate Gyrus (DG)
age: 54
gender (sex): M
race: C
Cause of death: suicide, CO
pmi: 23
ph: 6.24
toxicology: CO, phenobarbital, phenytoin
medications: sertraline
depressive features: Chronic, Moderate severity, Nonpsychotic, without melancholia
axix i comorbidity: none
Extracted molecule total RNA
Extraction protocol Total RNA from the dentate gyrus granule and CA1 pyramidal cell layer punches was extracted using RNAqueous kit (Ambion, Austin, TX), followed by cleanup with RNeasy MinElute kit (Qiagen, Valencia, CA) according to the manufacturer's protocol.
Label Cy5
Label protocol Total RNA (RIN > 4.8, A260/280 > 1.9) from MDD and matched control human samples (n = 15) were reverse-transcribed into cDNA and indirectly labeled with highly sensitive fluorescent technology (Genisphere, Hatfield, PA)
 
Channel 2
Source name DG_Control 4D
Organism Homo sapiens
Characteristics sample id: 4D
disease state: control
tissue: Dentate Gyrus (DG)
age: 56
gender (sex): M
race: C
Cause of death: hypertrophic cardiomyopathy
pmi: 25
ph: 6.14
toxicology: ND
Extracted molecule total RNA
Extraction protocol Total RNA from the dentate gyrus granule and CA1 pyramidal cell layer punches was extracted using RNAqueous kit (Ambion, Austin, TX), followed by cleanup with RNeasy MinElute kit (Qiagen, Valencia, CA) according to the manufacturer's protocol.
Label Cy3
Label protocol Total RNA (RIN > 4.8, A260/280 > 1.9) from MDD and matched control human samples (n = 15) were reverse-transcribed into cDNA and indirectly labeled with highly sensitive fluorescent technology (Genisphere, Hatfield, PA)
 
 
Hybridization protocol In a two-step process, array chips were initially hybridized to cDNA overnight, followed by a series of stringent washes to reduce nonspecific probe binding, and then post-stained with fluorescent Cy5 (MDD) and Cy3 (Control) dendrimers (Genisphere, Hatfield, PA)
Scan protocol Scanned on GenePix scanner (Axon Instruments, Union City, CA)
Description VDUR_303642 (4B+4D).gpr
DG_4B+4D
Data processing Data from all 30 two-channel arrays were analyzed using R/Bioconductor. First, probes with more than three missing values out of 30 (10%) were dropped. Data were normalized using linear-Log normalization to stabilize the variance of low expressing genes, and then spatial plus intensity based LOWESS to remove spatial and intensity related biases, using the MAANOVA library. P values were then adjusted to control false discovery rate (FDR) at 0.05 using the Q-value package. P values were calculated using distributions generated using permutation methods and standard error estimates were therefore not used in the P value calculations.
We can not provide a list of normalized values for each individual hybridization (per chip), but rather have a list of average expression values for all hybridizations used in the experiment (n=15). See supplementary files on Series record.
 
Submission date Sep 13, 2010
Last update date Sep 30, 2010
Contact name Vanja Duric
Organization name Yale University
Street address 34 Park Street
City New Haven
State/province CT
ZIP/Postal code 06508
Country USA
 
Platform ID GPL10907
Series (1)
GSE24095 Human postmortem hippocampus: Major depressive disorder (MDD) vs. Control

Supplementary file Size Download File type/resource
GSM593080.gpr.gz 5.4 Mb (ftp)(http) GPR
Processed data are available on Series record

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