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Sample GSM1207735 Query DataSets for GSM1207735
Status Public on Aug 13, 2013
Title plasma samples from normal individual 5
Sample type RNA
 
Source name plasma samples from normal individual 5
Organism Homo sapiens
Characteristics gender: Female
age: 68 years
disease state: non-cardiac chest pain (control)
tissue: plasma
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from plasma or tissues using miRNeasy Mini Kit (Qiagen, Valencia, CA). 250 µl of EDTA-plasma were mixed with 700 µl Qiazol, incubated for 5 min at room temperature and subsequently mixed with 140 µl chloroform. The organic and aqueous phase was separated by centrifugation at 12,000 g for 15 min. The upper aqueous phase was collected and the RNA was precipitated by adding 100% ethanol. The mixture was applied to a miRNeasy Mini spin column. After washed several times, the RNA was eluted in 25 µl RNase-free water.
Label FAM
Label protocol Five ul total RNA per sample was reverse-transcribed using Megaplex primers, sets A and B (Applied Biosystems). cDNA was pre-amplified for twelve cycles with Mexaplex Pre-Amp primers, sets A and B (Applied Biosystems), then diluted to 100 ul. Manufacturer's protocol was followed throughout.
Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TLDA cards (2 per sample). Quantitative real-time PCR was performed for 768 features, 754 of which represent primate miRNAs
For each of two cards per sample (A and B), nine ul of pre-amplified, diluted sample was mixed with TaqMan reaction mix (Applied Biosystems) and loaded into miRNA TLDA cards (Applied Biosystems) by centrifugation. Cards were sealed, and qRT-PCR was performed with a real-time thermocycler (ABI-7900, Applied Biosystems) per manufacturer's recommendations.
 
Hybridization protocol n/a
Scan protocol n/a
Description SAMPLE 5
Data processing SDS software (Applied Biosystems) was used to collect data.
Threshold intensities were set, visually and individually confirmed, and standardized with RQ Manager (Applied Biosystems). Data were processed using DataAssist (Applied Biosystems).
For the normalization it uses Mamm U6 as housekeeping gene.
Raw miRNA expression CT values were normalized to the endogenous housekeeping gene MammU6; 2^-deltaCt, where deltaCt = (Ct_Target - Ct_Mamm U6)
 
Submission date Aug 13, 2013
Last update date Aug 13, 2013
Contact name Hong Chen
E-mail(s) chenhongbj@medmail.com.cn
Phone 1088325349
Organization name Peking University People’s Hospital
Department Dept. of Cardiology
Street address Xizhimen South Street 11, Xicheng District, Beijing
City Beijing
State/province China
ZIP/Postal code 100044
Country China
 
Platform ID GPL15467
Series (1)
GSE49823 miRNA profiling of plasma samples: patients with unstable coronary artery disease and controls

Data table header descriptions
ID_REF
VALUE Target gene normalized signal (against housekeeping gene).

Data table
ID_REF VALUE
1
2 0.0055
3 0.0218
4 0.1648
5
6 0.0054
7
8
9 0.0056
10
11
12
13
14 0.0217
15 0.6922
16 0.6904
17 0.0003
18
19 0.085
20 1.3807

Total number of rows: 768

Table truncated, full table size 4 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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