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Sample GSM1318978 Query DataSets for GSM1318978
Status Public on May 16, 2014
Title Control matched sample pair amygdala MD3_AMY #24
Sample type RNA
 
Source name Control sample, brain amygdala
Organism Homo sapiens
Characteristics tissue: brain amygdala
disease state: Control
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 90.99541806
ILMN_2055271 128.9954371
ILMN_1736007 114.9954301
ILMN_2383229 92.99541906
ILMN_1806310 101.9954236
ILMN_1779670 117.9954316
ILMN_2321282 102.9954241
ILMN_1671474 108.9954271
ILMN_1772582 109.9954276
ILMN_1735698 100.9954231
ILMN_1653355 125.9954356
ILMN_1717783 93.99541957
ILMN_1705025 101.9954236
ILMN_1814316 684.9957162
ILMN_2359168 794.9957714
ILMN_1731507 197.9954718
ILMN_1787689 122.9954341
ILMN_1745607 936.9958427
ILMN_2136495 113.9954296
ILMN_1668111 96.99542107

Total number of rows: 48803

Table truncated, full table size 1190 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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