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Sample GSM1318954 Query DataSets for GSM1318954
Status Public on May 16, 2014
Title MDD matched sample pair amygdala MD3_AMY #20
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 108.0173522
ILMN_2055271 106.017355
ILMN_1736007 117.0173398
ILMN_2383229 104.0173577
ILMN_1806310 102.0173605
ILMN_1779670 127.0173259
ILMN_2321282 107.0173536
ILMN_1671474 105.0173564
ILMN_1772582 122.0173328
ILMN_1735698 128.0173245
ILMN_1653355 133.0173176
ILMN_1717783 131.0173204
ILMN_1705025 114.0173439
ILMN_1814316 608.0166605
ILMN_2359168 571.0167117
ILMN_1731507 157.0172844
ILMN_1787689 114.0173439
ILMN_1745607 1266.01575
ILMN_2136495 130.0173218
ILMN_1668111 92.01737434

Total number of rows: 48803

Table truncated, full table size 1187 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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