|
| Status |
Public on May 16, 2014 |
| Title |
MDD matched sample pair amygdala MD3_AMY #16 |
| Sample type |
RNA |
| |
|
| Source name |
MDD sample, brain amygdala
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: brain amygdala
disease state: MDD case
|
| Treatment protocol |
not applicable
|
| Growth protocol |
not applicable
|
| Extracted molecule |
total RNA |
| Extraction protocol |
1µg of total high quality total RNA was reverse transcribed into single stranded cDNA, that was then converted into double stranded cDNA and purified using the Illumina TotalPrep RNA Amplification Kit. An in vitro transcription reaction was carried out overnight in the presence of biotinylated UTP and CTP to obtain biotin-labeled cRNA from the double stranded cDNA. The cRNA was purified using the same Amplification Kit, and quality control was assessed.
|
| Label |
biotin
|
| Label protocol |
standard Illumina protocol
|
| |
|
| Hybridization protocol |
The sections were then hybridized with [35S]-labeled riboprobes (10^6 cpm/uL) in hybridization buffer at 56 °C for 16h. The hybridization buffer contained 50% formamide, 0.75 M NaCl, 20 mM 1,4-piperazine diethane sulfonic acid, pH 6.8, 10 mM ethylenediaminetetraacetic acid (EDTA), 10% dextran sulfate, 5X Denhardt’s solution (0.2 mg/mL Ficoll, 0.2 mg/mL polyvinylpyrrolidone, 0.2 mg/mL bovine serum albumin), 50 mM dithiothreitol, 0.2% sodium dodecyl sulfate, and 100 ug/mL yeast transfer RNA.
|
| Scan protocol |
DirecHyb Gene Expression. iScan Control Software 1.3.10+
|
| Description |
dissected from frozen coronal blocks ~2 cm caudal to the temporal pole
|
| Data processing |
Probeset signals were extracted with the Beadarray software following the default quality control parameters and batch-normalized.
GenomeStudio Gene Expression Module v1.6+
|
| |
|
| Submission date |
Jan 30, 2014 |
| Last update date |
May 16, 2014 |
| Contact name |
Etienne Sibille |
| E-mail(s) |
etienne.sibille@camh.ca
|
| Phone |
412-624-0804
|
| Organization name |
University of Pittsburgh
|
| Department |
Psychiatry
|
| Street address |
450 Technology Drive, Suite 231
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15219 |
| Country |
USA |
| |
|
| Platform ID |
GPL6947 |
| Series (1) |
| GSE54564 |
Expression data from human brain amygdala - including control samples and samples with major depression disorders (42 samples MD3_AMY) |
|
