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Sample GSM1318957 Query DataSets for GSM1318957
Status Public on May 16, 2014
Title MDD matched sample pair amygdala MD3_AMY #24
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 116.0081727
ILMN_2055271 107.0081795
ILMN_1736007 108.0081788
ILMN_2383229 102.0081833
ILMN_1806310 101.008184
ILMN_1779670 120.0081697
ILMN_2321282 118.0081712
ILMN_1671474 108.0081788
ILMN_1772582 114.0081742
ILMN_1735698 109.008178
ILMN_1653355 131.0081614
ILMN_1717783 94.00818932
ILMN_1705025 112.0081757
ILMN_1814316 725.0077135
ILMN_2359168 735.0077059
ILMN_1731507 222.0080928
ILMN_1787689 131.0081614
ILMN_1745607 1053.007466
ILMN_2136495 125.0081659
ILMN_1668111 107.0081795

Total number of rows: 48803

Table truncated, full table size 1182 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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