7 protocols
AccessionType
bioassay_data_transformation
ID_REF = VALUE = normalized
feature_extraction
The data were analyzed and normalized with GeneSpring software (v.11.5). After normalization, the data was baseline transformed to the median of all samples and filtered on expression (20-100 percentile), on flags (detected), on error (CV50%), and stats (One way ANOVA P<0.01) to compare among groups (Sham+Normal as control, Clip, ClipR-14).
image_aquisition
Slides were scanned with an Agilent DNA Microarray Scanner model G2539.
hybridization
1.65 ug of Cy3-labeled cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 16 hours in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol prior to washing.
labeling
500 ng of total RNA was amplified and labeled using the Quick Amp Labeling kit (Agilent Technologies) according to the manufacturer's protocol.
nucleic_acid_extraction
Left Kidney was dissected out. Total RNA of whole kidney was extracted using ISOGEN (Nippon Gene). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
specified_biomaterial_action
Left ureter was obstructed by vascular clip for 2 days (Clip) and removed for 12 days (ClipR-14).