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| Status |
Public on Jul 09, 2021 |
| Title |
case_renal biopsy [BIOS-13-0001] |
| Sample type |
RNA |
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| Source name |
case_renal biopsy
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| Organism |
Homo sapiens |
| Characteristics |
cell type: renal, endothelial and immune cells
outcome: MVI
type of biopsy: Post kidney transplantation
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Allprep DNA/RNA/miRNA Universal Kit (Qiagen Benelux BV) on a QIAcube instrument (Qiagen Benelux BV). The quantity (absorbance at 260 nm) and purity (ratio of the absorbance at 230, 260, and 280 nm) of the isolated RNA were measured using the NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific/Life Technologies Europe BV, Ghent, Belgium). RNA integrity was evaluated with the Eukaryote nano/pico RNA Kit (Agilent Technologies Belgium NV, Diegem, Belgium) on the Bioanalyzer 2100 instrument (Agilent Technologies BelgiumNV)
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| Label |
TaqMan
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| Label protocol |
Specific reverse transcription of 150 ng of total RNA was performed using Megaplex™ RT Primers Human Pool A v2.1 (Thermo Fisher Scientific, Les Ulis, France), on a Veriti Thermal Cycler (Applied Biosystems™, Thermo Fisher Scientific). No complementary (c)DNA preamplification was required. MiRNA expression was assessed by qPCR, using TaqMan® Array Cards (Applied Biosystems™, Thermo Fisher Scientific), where the primers and probe of each miRNA were spotted and dried in duplicate wells of a microfluidic card. We used TaqMan® Array Human MicroRNA A+B Card Sets v3.0 (Thermo Fisher Scientific)
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| Hybridization protocol |
n/a
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| Scan protocol |
n/a
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| Data processing |
The normalization and all the data analysis were performed using Expression Suite software version 1.0.3. Assays with a cycle threshold (CT) values >35 were considered to be not expressed
For the normalization it uses the average of two housekeeping genes: RNU44 and RNU48
Target miRNA signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
All deltaCt based fold-change calculations from the uploaded raw threshold cycle data were calculated using R Studio.
The normalized_data.txt reports normalized signal (against housekeeping genes).
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| Submission date |
Jul 08, 2021 |
| Last update date |
Jul 09, 2021 |
| Contact name |
Baptiste Lamarthée |
| E-mail(s) |
baptiste.lamarthee@inserm.fr
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| Organization name |
Inserm U1098
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| Department |
RIGHT
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| Street address |
Bd du Mal De Lattre de Tassigny
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| City |
Dijon |
| ZIP/Postal code |
21000 |
| Country |
France |
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| Platform ID |
GPL30379 |
| Series (1) |
| GSE179772 |
Real-time quantitative PCR analysis of human renal biopsies |
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| Supplementary data files not provided |
| Processed data are available on Series record |
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