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Sample GSM1318942 Query DataSets for GSM1318942
Status Public on May 16, 2014
Title MDD matched sample pair anterior cingulate cortex MD3_ACC #3
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 26254.92418
ILMN_1343295 6306.517054
ILMN_1651199 95.79876835
ILMN_1651209 111.7654716
ILMN_1651210 96.98209859
ILMN_1651221 101.3487695
ILMN_1651228 2055.699174
ILMN_1651229 480.882148
ILMN_1651230 95.26543824
ILMN_1651232 104.9154702
ILMN_1651235 104.6487702
ILMN_1651236 112.6487718
ILMN_1651237 104.1154701
ILMN_1651238 101.5820695
ILMN_1651249 95.81543835
ILMN_1651253 133.2320761
ILMN_1651254 544.3488612
ILMN_1651259 175.2654848
ILMN_1651260 90.04876716
ILMN_1651262 1240.382005

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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