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Sample GSM1318914 Query DataSets for GSM1318914
Status Public on May 16, 2014
Title MDD matched sample pair anterior cingulate cortex MD3_ACC #30
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 22959.25942
ILMN_1343295 6638.928574
ILMN_1651199 90.08946172
ILMN_1651209 90.94084786
ILMN_1651210 91.49011057
ILMN_1651221 90.71634533
ILMN_1651228 1892.424791
ILMN_1651229 329.6952712
ILMN_1651230 85.09317105
ILMN_1651232 104.1043104
ILMN_1651235 91.67306952
ILMN_1651236 117.4983205
ILMN_1651237 86.38443039
ILMN_1651238 85.39432985
ILMN_1651249 87.26469125
ILMN_1651253 140.5149426
ILMN_1651254 563.685945
ILMN_1651259 170.6371888
ILMN_1651260 78.581633
ILMN_1651262 1666.155692

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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