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Sample GSM1318956 Query DataSets for GSM1318956
Status Public on May 16, 2014
Title MDD matched sample pair amygdala MD3_AMY #23
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)

Data table header descriptions
ID_REF
VALUE quantile normalized signal

Data table
ID_REF VALUE
ILMN_1762337 108.9927058
ILMN_2055271 136.9927278
ILMN_1736007 123.9927176
ILMN_2383229 96.99269639
ILMN_1806310 105.9927035
ILMN_1779670 113.9927097
ILMN_2321282 107.992705
ILMN_1671474 99.99269874
ILMN_1772582 99.99269874
ILMN_1735698 104.9927027
ILMN_1653355 175.9927584
ILMN_1717783 91.99269246
ILMN_1705025 101.9927003
ILMN_1814316 1015.993418
ILMN_2359168 948.9933657
ILMN_1731507 253.9928197
ILMN_1787689 134.9927262
ILMN_1745607 747.9932078
ILMN_2136495 147.9927365
ILMN_1668111 98.99269796

Total number of rows: 48803

Table truncated, full table size 1185 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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