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Sample GSM1318943 Query DataSets for GSM1318943
Status Public on May 16, 2014
Title MDD matched sample pair anterior cingulate cortex MD3_ACC #11
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 24714.6588
ILMN_1343295 7363.950463
ILMN_1651199 106.9219086
ILMN_1651209 108.5553112
ILMN_1651210 110.4719144
ILMN_1651221 93.80525713
ILMN_1651228 1247.640472
ILMN_1651229 634.8227709
ILMN_1651230 102.6219015
ILMN_1651232 124.7053376
ILMN_1651235 105.1053056
ILMN_1651236 108.6219113
ILMN_1651237 111.5553161
ILMN_1651238 104.1886041
ILMN_1651249 94.30525795
ILMN_1651253 129.3386452
ILMN_1651254 915.0066285
ILMN_1651259 135.7719557
ILMN_1651260 97.07193247
ILMN_1651262 1552.34097

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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