|
| Status |
Public on Oct 01, 2022 |
| Title |
Peripheral blood mononuclear cells_Kidney transplanted patient 1_Time 0_outcome EGF |
| Sample type |
RNA |
| |
|
| Source name |
Peripheral blood mononuclear cells Time 5
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: Male patient, 58 years old, kidney transplantation, outcome EGF
|
| Growth protocol |
Twenty ml of whole blood were harvested from the selected patients at the time of transplantation, before the administration of induction therapy. PBMCs were isolated by density separation over a Ficoll-PaqueTM (GE healthcare, Uppsala, Sweden).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini Kit (Qiagen AG, Basel, Switzerland) and qualitatively and quantitatively analyzed through Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA). Only samples with good quality, indicated by a RIN> 8, were used in the microarray experiment.
|
| Label |
Biotin
|
| Label protocol |
The One-Cycle cDNA Synthesis Kit (Affymetrix) was used. Starting from 1.5 micrograms of total RNA we performed the in vitro transcription (IVT) reaction for complementary RNA (cRNA) amplification and biotin labeling, according to the manufacturer’s instructions.The biotinylated cRNA targets were then cleaned up, fragmented, and hybridized to GeneChip brand expression arrays.
|
| |
|
| Hybridization protocol |
Total RNA was hybridized on to the GeneChip Human Genome U133A Array (Affymetrix, Santa Clara, CA) according to the manufacture's instructions
|
| Scan protocol |
We used the default settings of GCOS software to scan the chips.
|
| Description |
Peripheral blood mononuclear cells_Kidney transplanted patient 1_Time 0_outcome EGF
|
| Data processing |
We used the default settings of Affymetrix Microarray Suite software version 5 (MAS 5.0; Affymetrix) to calculate scaled gene expression values. R 2.0.1 statistical software was used to perform the normalization of the data according to R. A. Irizarryet al, Biostatistics, 2003. Differentially expressed genes were identified using GeneSpring GX software (Agilent, Palo Alto, CA), by applying a moderated t-test with Storey with bootstrapping multiple testing correction.
We selected the differentially expressed genes using a q-value cut-off of 0.05
|
| |
|
| Submission date |
Oct 19, 2020 |
| Last update date |
Oct 01, 2022 |
| Contact name |
Paola Pontrelli |
| E-mail(s) |
paola.pontrelli@uniba.it
|
| Phone |
+390805478868
|
| Organization name |
University of Bari
|
| Department |
Dept. of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J)
|
| Lab |
Nephrology Unit
|
| Street address |
Piazza G.Cesare 11
|
| City |
Bari |
| ZIP/Postal code |
70124 |
| Country |
Italy |
| |
|
| Platform ID |
GPL96 |
| Series (1) |
| GSE159636 |
Pre-Transplant recipients’ gene expression profiles in peripheral blood mononuclear cells correlate with the development of delayed graft function in kidney transplantation |
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