GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM2038486 Query DataSets for GSM2038486
Status Public on Jan 14, 2016
Title LOD-rem_10
Sample type RNA
Source name leukocytes
Organism Homo sapiens
Characteristics gender: Male
diagnosis: Major depressive disorder
state: Remission
age: 51
Treatment protocol The blood samples were obtained between 9:00 and 12:00, and then heparinized.
Extracted molecule total RNA
Extraction protocol The total RNA was extracted using the QIAmp RNA Blood Mini Kit (QIAGEN K.K., Tokyo, Japan) according to the manufacturer’s instructions. The eluted samples were processed with the standard method of ethanol precipitation, and the RNA pellet was dissolved in RNase-free water. The RNA quantity and quality were assessed using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific Inc., Waltham, MA, USA) and an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) as recommended.
Label Cy3
Label protocol Total RNA was amplified and labeled with Cyanine 3 (Cy3) using a one-color Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer’s instructions. Briefly, 100 ng of total RNA was reverse-transcribed to obtain double-stranded cDNA using a poly dT-T7 promoter primer. The primer, template RNA, and quality-control transcripts of known concentrations and quality were first denatured at 65°C for 10 min and then incubated for 2 h at 40°C with 5× first-strand buffer, 0.1 M dithiotreitol, 10 mM dNTP mix, and AffinityScript RNase Block Mix. The AffinityScript enzyme was then inactivated at 70°C for 15 min. The cDNA products were used as templates for in vitro transcription to generate fluorescent cRNA. The cDNA products were mixed with a transcription master mix in the presence of T7 RNA polymerase and Cy3-labeled CTP and then incubated at 40°C for 2 h. The labeled cRNAs were purified using Qiagen’s RNeasy mini spin columns and eluted using 30 µl of nuclease-free water. After cRNA was amplified and labeled, the cRNA quantity and cyanine incorporation were determined using a NanoDrop ND-1000 spectrophotometer and an Agilent Bioanalyzer.
Hybridization protocol For each hybridization, 600 ng of Cy3-labeled cRNA was fragmented and hybridized at 65°C for 17 h to the Agilent SurePrint G3 Human GE 8×60K v2 Microarray (Design ID: 039494).
Scan protocol After washing, the microarrays were scanned using an Agilent DNA microarray scanner.
Data processing The intensity values of each scanned feature were quantified using Agilent feature extraction software version, which performs background subtractions. The normalization was performed using Agilent GeneSpring GX version 11.0.2 (per chip: normalization to the 75th percentile shift; per gene: none). The probes that were declared as “present” in all the assayed samples and that displayed a raw intensity value above 50 in at least 2 samples were used for the following statistical analyses.
Submission date Jan 13, 2016
Last update date Jan 14, 2016
Contact name Shigeo Miyata
Organization name Gunma University Graduate School of Medicine
Street address 3-39-22 Showa-machi
City Maebashi
ZIP/Postal code Gunma 371-8511
Country Japan
Platform ID GPL17077
Series (1)
GSE76826 Blood transcriptomic markers in patients with late-onset major depressive disorder

Data table header descriptions
VALUE Normalized signal intensity

Data table
GE_BrightCorner 8.16673851 P
DarkCorner -6.173989773 A
A_23_P117082 3.076434612 P
A_33_P3246448 -6.141059399 A
A_33_P3318220 -6.133972645 A
A_33_P3236322 -5.935294628 A
A_33_P3319925 -4.151418686 A
A_21_P0000509 -0.916760445 P
A_21_P0000744 1.225778103 P
A_24_P215804 0.672959805 P
A_23_P110167 2.361951351 P
A_33_P3211513 1.66660738 P
A_23_P103349 -5.869724274 A
A_32_P61480 -6.096856117 A
A_33_P3788124 -6.095798492 A
A_33_P3414202 0.793314457 P
A_33_P3316686 2.907091618 P
A_33_P3300975 -0.743702412 P
A_33_P3263061 2.431171894 P
A_33_P3261373 -6.094820976 A

Total number of rows: 50739

Table truncated, full table size 1395 Kbytes.

Supplementary file Size Download File type/resource
GSM2038486_LOD-rem_10.txt.gz 12.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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