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Sample GSM1318900 Query DataSets for GSM1318900
Status Public on May 16, 2014
Title MDD matched sample pair anterior cingulate cortex MD3_ACC #16
Sample type RNA
 
Source name MDD sample, brain anterior cingulate cortex
Organism Homo sapiens
Characteristics tissue: brain anterior cingulate cortex
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)
GSE54563 Expression data from human brain anterior cingulate cortex - including control samples and samples with major depression disorders (50 samples MD3_ACC)

Data table header descriptions
ID_REF
VALUE quantile normalized signal

Data table
ID_REF VALUE
ILMN_1343291 22844.67163
ILMN_1343295 8032.966285
ILMN_1651199 113.7366764
ILMN_1651209 144.6366604
ILMN_1651210 106.9366799
ILMN_1651221 99.03671399
ILMN_1651228 1005.835916
ILMN_1651229 526.3865632
ILMN_1651230 105.6200806
ILMN_1651232 98.37005433
ILMN_1651235 100.920083
ILMN_1651236 107.2366798
ILMN_1651237 101.4033828
ILMN_1651238 115.0700757
ILMN_1651249 98.73671414
ILMN_1651253 121.8700722
ILMN_1651254 532.60316
ILMN_1651259 228.8533169
ILMN_1651260 90.50338839
ILMN_1651262 1673.119571

Total number of rows: 48803

Table truncated, full table size 1186 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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