NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1318951 Query DataSets for GSM1318951
Status Public on May 16, 2014
Title MDD matched sample pair amygdala MD3_AMY #17
Sample type RNA
 
Source name MDD sample, brain amygdala
Organism Homo sapiens
Characteristics tissue: brain amygdala
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)
GSE54564 Expression data from human brain amygdala - including control samples and samples with major depression disorders (42 samples MD3_AMY)

Data table header descriptions
ID_REF
VALUE quantile normalized signal

Data table
ID_REF VALUE
ILMN_1762337 104.0035065
ILMN_2055271 140.0034964
ILMN_1736007 94.00350927
ILMN_2383229 104.0035065
ILMN_1806310 100.0035076
ILMN_1779670 123.0035012
ILMN_2321282 106.0035059
ILMN_1671474 101.0035073
ILMN_1772582 113.003504
ILMN_1735698 97.00350843
ILMN_1653355 143.0034956
ILMN_1717783 116.0035031
ILMN_1705025 108.0035054
ILMN_1814316 681.0033456
ILMN_2359168 731.0033316
ILMN_1731507 137.0034973
ILMN_1787689 133.0034984
ILMN_1745607 573.0033757
ILMN_2136495 169.0034884
ILMN_1668111 111.0035045

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