|
| Status |
Public on Feb 20, 2020 |
| Title |
VASCULAR SURGERY T1 [N072] |
| Sample type |
RNA |
| |
|
| Source name |
URINE
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
age: 65
|
| Treatment protocol |
Approximately 50mL Urine was spun down at 1500g for 30 min at 4 degrees Celsius. Pellet was collected, lysed using 1mL RLT lysis buffer with 10uL β-mercaptoethanol from the kit and processed according the manufacturer's protocol.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted from the urine of patients using Qiagen RNeasy mini kit (250) Catalog Number - 74106 according the manufacturer's protocol.
|
| Label |
biotin
|
| Label protocol |
cDNA was amplified using GeneChip™ WT PLUS Reagent Kit, from ThermoFisher Scientific following manufacturers instructions.Amplified cDNA was fragmented with UDG and APE1 enzymes according to ThermoFisher Scientific instructions. Labeling was performed with TdT with biotin reagent followed by streptavidin/phycoerythrin.
|
| |
|
| Hybridization protocol |
Labeled cDNA was hybridized to GeneChip™ Human Transcriptome 2.0 arrays according to ThermoFisher Scientific instructions, 16 hours at 45C at 60 rpm.
|
| Scan protocol |
Arrays were scanned GeneChip Scanner 3000 7G using AGCC software
|
| Description |
VASCULAR SURGERY DAY 1
|
| Data processing |
Background Correction, Normalization and Summarization were done by RMA using Transcriptome Analysis Console (TAC) software provided by Affymetrix. Statistical comparison was done using empirical Bayes method in Linear Models for Microarray Analysis (LIMMA) using TAC. Significance threshold was adjusted for multiple testing using Benjamini-Hochberg false discovery rate (FDR).
|
| |
|
| Submission date |
May 03, 2019 |
| Last update date |
Feb 20, 2020 |
| Contact name |
Azra Bihorac |
| E-mail(s) |
abihorac@ufl.edu
|
| Phone |
3522739009
|
| Organization name |
University of Florida
|
| Department |
Medicine
|
| Street address |
1600 SW Archer Road
|
| City |
Gainesville |
| State/province |
FL |
| ZIP/Postal code |
32610 |
| Country |
USA |
| |
|
| Platform ID |
GPL17586 |
| Series (2) |
| GSE112098 |
Discovery and validation of urinary molecular signature of early sepsis (validation cohort) |
| GSE112100 |
Discovery and validation of urinary molecular signature of early sepsis |
|
