|
| Status |
Public on Jun 04, 2024 |
| Title |
Sample DM-026-A - PDM2 - 3 |
| Sample type |
RNA |
| |
|
| Source name |
Whole blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Whole blood
group: PDM2
age: 56
Sex: male
glucose (mg/dl): 292
%hba1c: 10.77
|
| Treatment protocol |
null
|
| Growth protocol |
null
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Whole blood samples were obtained from each participant in vacutainer-EDTA tubes and then mixed with RNAlater (Thermo Fisher Scientific, USA) in a 5:1 proportion and stored at -70°C until use. The Trizol-Chloroform method (Invitrogen) was used, in conjunction with the QIAmp column protocol (Qiagen Inc., USA), to process frozen blood samples. RNA concentration and purity were determined using ND-1000 nanodrop (Thermo Fisher Scientific, USA). The RNA integrity number (RIN) was determined using the RNA 6000 Nano kit (Agilent Technologies, USA) on a Bioanalyzer-2100 equipment (Agilent Technologies Genomics, USA) following the manufacturer's instructions. RNA samples at a concentration of 50 ng/ul were stored at -70°C until use.
|
| Label |
Cy3
|
| Label protocol |
200 ng of whole RNA samples with 260/280> 2 and RIN> 6 were used to synthesize of complementary Cy3-labeled copy RNA (cRNA) according to the standard low input Quick Amp labelling protocol (Agilent Technologies, USA).
|
| |
|
| Hybridization protocol |
1.65 ug of cRNA (specific activity > 9.0 pmol of Cy3 per µg) by sample were hybridized to high-density human GE 4X44K v2 microarrays (Part Number: G4845A, Agilent Technologies, USA) for 17 h at 65°C, according to the manufacturer´s instructions.
|
| Scan protocol |
The mean fluorescence intensity (MFI) values of each probe on the chip were obtained using the SureScan Microarray Scanner laser reader (G4900DA, Agilent Technologies, USA) and validated using the Agilent Feature Extraction program (Agilent Technologies, USA).
|
| Description |
L5 refers to slide 5 of 5
|
| Data processing |
Statistical processing of the microarray raw data was performed within the R (RRID:SCR_001905) environment (R Foundation for Statistical Computing, 2016) applying the functions from Bioconductor Limma R-packages . The raw data were corrected with the 'norm exp' function. The 'quantile' function was applied to normalize and correct the batch effect among the arrays. The 'aver exp' function was applied to produce the average between the arrays, which was used as input to fit the linear regression models, considering the comparisons at the disease level. Then, the empirical Bayes function (eBayes), which was applied to the resulting linear contrast models, allowed the determination of induced and repressed genes, based on the fold change values extracted from the 'decide test' function (Smyth 2004). This function used a p-value < 0.05 and a logarithm of Fold Change > |1|.
Normalized signal intensity: AverExp of 446 genes having a p-value < 0.05 and a logarithm of Fold Change > |1| for the total of comparisons at the disease level.
|
| |
|
| Submission date |
Nov 30, 2023 |
| Last update date |
Jun 04, 2024 |
| Contact name |
José Antonio Enciso-Moreno |
| E-mail(s) |
enciso_2000@yahoo.com
|
| Organization name |
Instituto Mexicano del Seguro Social
|
| Department |
Unidad de Investigación Biomédica de Zacatecas
|
| Lab |
Unidad de Investigación Biomédica de Zacatecas
|
| Street address |
Interior de la Alameda 45
|
| City |
Zacatecas |
| State/province |
Zacatecas |
| ZIP/Postal code |
98000 |
| Country |
Mexico |
| |
|
| Platform ID |
GPL10332 |
| Series (1) |
| GSE249102 |
Whole RNA profiling of Tuberculosis-diabetes comorbidity linked to diabetes with poor glycemic control |
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