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Status |
Public on Oct 17, 2010 |
Title |
DG_23B (MDD) vs. 17D (Control) |
Sample type |
RNA |
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Channel 1 |
Source name |
DG_MDD 23B
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Organism |
Homo sapiens |
Characteristics |
sample id: 23B disease state: MDD tissue: Dentate Gyrus (DG) age: 68 gender (sex): M race: C Cause of death: suicide, CO pmi: 4 ph: 6.21 toxicology: CO medications: none depressive features: Single Episode, Moderate severity, secondary Nonpsychotic. axix i comorbidity: Parkinson’s disease
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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.
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Label |
Cy5
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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)
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Channel 2 |
Source name |
DG_Control 17D
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Organism |
Homo sapiens |
Characteristics |
sample id: 17D disease state: control tissue: Dentate Gyrus (DG) age: 70 gender (sex): M race: C Cause of death: CVD pmi: 20 ph: 6.81 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)
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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)
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Scan protocol |
Scanned on GenePix scanner (Axon Instruments, Union City, CA)
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Description |
VDUR_211411 (23B+17D).gpr DG_23B+17D
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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.
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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 |
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Platform ID |
GPL10907 |
Series (1) |
GSE24095 |
Human postmortem hippocampus: Major depressive disorder (MDD) vs. Control |
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