archetype cluster (1,2,3,4,5,6,7): 3 injpc1: -0.92357513930152 injpc2: -3.13548518314501 injpc3: -0.688374763275046 injaa (1,2,3,4,5,6): 6 in n=1526? (yes, no): yes set (66 or 1679): 1679 in n=102? (yes, no): no mmdx (abmr, pabmr, mixed, tcmr, ptcmr, nr, na): ABMR dsa (0,1): 1 rejaaclust (1,2,3,4,5,6): 4 in 1208? (1, 0): 0
Treatment protocol
The immunosuppressive treatment of the patients before the biopsy was based on individual treatment regiments; the treatment after the biopsy was adjusted based on the histopathological diagnosis.
Growth protocol
All human kidney biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.
Extracted molecule
total RNA
Extraction protocol
Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).
Label
biotin
Label protocol
Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array
Hybridization protocol
(Affymetrix, Santa Clara, CA). Amplified RNA (10ug) was hybridized for 16 hr at 45C on GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol
GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).
Description
GPL13667
Data processing
Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.
