|
| Status |
Public on Jan 23, 2022 |
| Title |
PKD1 renal cyst, medium cyst_3, 20 ml |
| Sample type |
RNA |
| |
|
| Source name |
Renal cyst from PKD1 patient, medium single cyst, batch1
|
| Organism |
Homo sapiens |
| Characteristics |
diagnosis: PKD1 patient
tissue: renal cyst
|
| Treatment protocol |
All tissues were dissected within 30 minutes of nephrectomy, washed in cold phosphate-buffered saline, snapped frozen in liquid nitrogen, and stored in a -80°C freezer
|
| Growth protocol |
The nephrectomized kidneys were kept cooled on ice immediately after their removal in the operating room and through out the tissue retrieval procedure in the surgical pathology suite, where the renal capsule was striped and individual cysts identified.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA containing miRNA was extracted from each sample using miRNeasy Mini Kit (Qiagen) with an on-column DNA digestion step to minimize genomic DNA contamination
|
| Label |
biotin
|
| Label protocol |
Standard Illumina DASL label protocol
|
| |
|
| Hybridization protocol |
Standard Illumina DASL hybridisation protocol
|
| Scan protocol |
Standard Illumina DASL scanning protocol
|
| Description |
PKD1 renal cyst
MC3
|
| Data processing |
The raw data were normalized using quantile normalization with BeadStudio 3.4 (Illumina). The normalized intensities and detection p-values were exported and further adjusted for batch effect with the R package ComBat.
|
| |
|
| Submission date |
Jun 28, 2019 |
| Last update date |
Jan 23, 2022 |
| Contact name |
York PC Pei |
| E-mail(s) |
york.pei@uhn.ca
|
| Phone |
416-340-4257
|
| Organization name |
University of Toronto
|
| Department |
Department of Medicine
|
| Street address |
8N838, 585 University Avenue
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G2N2 |
| Country |
Canada |
| |
|
| Platform ID |
GPL8179 |
| Series (1) |
| GSE133530 |
microRNA (miRNA) expression data from renal cysts of autosomal dominant polycystic kidney disease (ADPKD) patients |
|
