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Sample GSM1318941 Query DataSets for GSM1318941
Status Public on May 16, 2014
Title Control matched sample pair anterior cingulate cortex MD3_ACC #35
Sample type RNA
 
Source name Control sample, brain anterior cingulate cortex
Organism Homo sapiens
Characteristics tissue: brain anterior cingulate cortex
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 Jan 26, 2015
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)
Relations
Reanalyzed by GSE65314

Data table header descriptions
ID_REF
VALUE quantile normalized signal

Data table
ID_REF VALUE
ILMN_1343291 23859.71219
ILMN_1343295 6940.389503
ILMN_1651199 95.25809266
ILMN_1651209 102.3806323
ILMN_1651210 99.96312962
ILMN_1651221 98.26299346
ILMN_1651228 1935.679187
ILMN_1651229 406.5009532
ILMN_1651230 76.96810795
ILMN_1651232 97.45141429
ILMN_1651235 97.6357881
ILMN_1651236 103.5086116
ILMN_1651237 89.87562504
ILMN_1651238 79.1644521
ILMN_1651249 81.75102307
ILMN_1651253 144.3839699
ILMN_1651254 613.1415488
ILMN_1651259 146.3860366
ILMN_1651260 94.38130421
ILMN_1651262 1761.103493

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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