NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1318927 Query DataSets for GSM1318927
Status Public on May 16, 2014
Title Control matched sample pair anterior cingulate cortex MD3_ACC #21
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 22574.42112
ILMN_1343295 7610.334596
ILMN_1651199 104.9085017
ILMN_1651209 108.7585068
ILMN_1651210 92.54178559
ILMN_1651221 97.55846214
ILMN_1651228 1999.511274
ILMN_1651229 631.6924892
ILMN_1651230 100.9084965
ILMN_1651232 104.5085012
ILMN_1651235 103.9585005
ILMN_1651236 105.3085022
ILMN_1651237 98.40845325
ILMN_1651238 92.15844509
ILMN_1651249 101.275097
ILMN_1651253 147.991858
ILMN_1651254 506.7256261
ILMN_1651259 153.4585651
ILMN_1651260 91.64178441
ILMN_1651262 1659.46083

Total number of rows: 48803

Table truncated, full table size 1186 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap