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Sample GSM1400895 Query DataSets for GSM1400895
Status Public on May 30, 2014
Title MDD, S89.BA44.1.S
Sample type RNA
Source name Brain tissue (BA44), MDD
Organism Homo sapiens
Characteristics tissue: ventrolateral prefrontal cortex (PFC)
diagnosis: major depressive disorder
gender: male
population: French-Canadian
age: 42
ph: 6.56
rin: 7.4
Treatment protocol Post-mortem prefrontal cortex (BA44) brain tissue was obtained in collaboration with the Quebec Coroner's Office and the Suicide section of the Douglas-Bell Canada Brain Bank (Douglas Mental Health University Institute, Montreal, Quebec, Canada). A total of 25 brain samples were included in the present study. All individuals were of French-Canadian origin, a homogeneous population with a well-documented founder effect, and were matched for refrigeration delay, age and pH. Refrigeration delay refers to the difference between the estimated time of death (determined by the pathologist through external body examination details) and the time at which the body was refrigerated. Psychological autopsies were performed post-mortem on both cases and controls by a panel of psychiatrists and diagnoses were assigned based on DSM-IV criteria. The control group had no history of suicidal behavior or major mood or psychotic disorders.
Extracted molecule total RNA
Extraction protocol Total RNA (including miRNA fraction) was isolated from frozen brain using the miRNeasy Mini Kit protocol (Qiagen, Canada) with no modifications. RNA and miRNA yield and quality were determined using the Nanodrop 1000 (Thermo Scientific, USA) and Agilent 2100 Bioanalyzer (Agilent Technologies, USA), respectively.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the microRNA complete labeling and hybridization kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification. This method involves the ligation of one Cyanine 3-pCp molecule to the 3' end of a RNA molecule with greater than 90% efficiency. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
Hybridization protocol Samples were dried using a vacuum concentrator at 50°C on the medium-high heat setting for one hour. All samples were resuspended in 17 uL of nuclease-free water, 1 uL of Hyb spike-in solution, 4.5 uL of 10X GE Blocking agent and 22.5 uL of 2X Hi-RPM Hybridization Buffer , incubated at 100°C for 5 minutes followed by a 5 minute ice water bath, as suggested by the manufacturer's instructions. Samples were hybridized on Agilent-021827 slides at 55°C and rotated at 20rpm for 20 hours. After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (warmed to 37°C, Agilent) and GE Wash Buffer 2 (warmed to 37°C, Agilent) ), then dried immediately by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565C) using one color scan setting on the Unrestricted Human miRNA microarray V3 (Agilent Design ID: 021827; Product Number: G4470C). Format 8x15K, Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR low 5%.
Data processing The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. We used the AgiMicroRna package in Bioconductor to summarize the data followed by quantile normalization.
Submission date May 29, 2014
Last update date May 30, 2014
Contact name Paul Pavlidis
Organization name University of British Columbia
Department Centre for High-Throughput Biology / Psychiatry
Street address 177 Michael Smith Laboratories 2185 East Mall
City Vancouver
State/province British Columbia
ZIP/Postal code V6T 1Z4
Country Canada
Platform ID GPL18743
Series (1)
GSE58105 Prefrontal cortex microRNA expression profiling in major depression

Data table header descriptions
VALUE Normalized signal intensity, log2 transformed

Data table
bkv-miR-B1-3p 5.466624139
bkv-miR-B1-5p 5.462185712
DarkCorner 5.544239069
dmr_285 9.251513685
dmr_3 13.30018289
dmr_308 5.502665592
dmr_316 5.603718644
dmr_31a 9.662868797
dmr_6 12.56924219
ebv-miR-BART10 5.505927956
ebv-miR-BART10* 5.52722196
ebv-miR-BART11-3p 5.491087116
ebv-miR-BART11-5p 5.427304367
ebv-miR-BART12 5.602311408
ebv-miR-BART13 6.577632785
ebv-miR-BART13* 5.426016727
ebv-miR-BART1-3p 5.531477557
ebv-miR-BART14 5.470334936
ebv-miR-BART14* 5.526358581
ebv-miR-BART15 5.555699285

Total number of rows: 961

Table truncated, full table size 23 Kbytes.

Supplementary file Size Download File type/resource
GSM1400895_252182711712_1_2.txt.gz 2.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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