13 protocols
AccessionNameType
P-TABM-3864
image_acquisition
Scanning was performed with an Agilent 2565 BA DNA Microarray scanner using defaults parameters (100 PMT, 10 um resolution, at 20 °C in low ozone concentration environment. Microarray images were alysed by using Feature Extraction software version A.8.5.1 from Agilent technologies. Defaults settings were used.
P-TABM-3866
transformation
Lowess normalized data files from the Agilent Feature Extraction software were then imported into GS7.3 for filtering flagged spots, controls and low fluorescence spots then averaging the replicate probes with the same id.
P-TABM-3857
hybridization
Agilent 60mer oligo microarray processing protocol v 4.1 (SSC Wash). Chamber type: Agilent SureHyb Chamber; Quantity of each labelled extract: 750 ng; duration: 17 hours; volume: 500 ul ; Temperature in C: 60;
P-TABM-3855
labeling
(500 ng). Agilent oligo Cy5 probes labeling protocol. Kit used for probe labeling: Agilent Fluorescent Low RNA Input Linear Amplification kit (500 ng total RNA per reaction).
P-TABM-3862
pool
pool of normal colon tissue RNAs obtained from 68 individuals total of 526 μl of a mixture of RNAs at a concentration of 753 ng/ul and good quality RIN=8.7,
P-TABM-3854
labeling
(500 ng). Agilent oligo Cy3 probes labeling protocol. Kit used for probe labeling: Agilent Fluorescent Low RNA Input Linear Amplification kit (500 ng total RNA per reaction).
P-TABM-3860
nucleic_acid_extraction
RNA was extracted directly from the frozen samples using TRIZOL (Invitrogen, Carlsbad, CA) and a homogenizer (Ultraturrax T8-S8N-5G Rose Scientific Ltd, Canada). Afterwards RNA was treated with DNAse using RNeasy Microkit (Qiagen GmbH, Germany). RNA quality was measure with Agilent Bioanalyzer 2100 (Agilent technologies, Palo Alto U.S.A) and only good quality samples, RIN (RNA Integrity Number) higher than 7.5, were selected for the analysis.
P-TABM-3863
dissect
isolated from colon s surgery removed tissue
P-TABM-3865
image_acquisition
Scanning was performed with an Agilent 2565 BA DNA Microarray scanner using defaults parameters (100% PMT & 10% PMT, 5 um resolution, at 20 °C in low ozone concentration environment. Microarray images were alysed by using Feature Extraction software version A.9.5.1 from Agilent technologies. Defaults settings were used. Lowess normalization calculated by Agilent's Feature Extraction
P-TABM-3858
hybridization
Agilent 60mer oligo microarray processing protocol v 5.5. Chamber type: Agilent SureHyb Chamber; Quantity of each labelled extract: 750 ng; duration: 17 hours; volume: 500 ul ; Temperature in C: 65;
P-TABM-3856
hybridization
Agilent 60mer oligo microarray processing protocol v 2.1 (SSPE Wash). Chamber type: Agilent SureHyb Chamber; Quantity of each labelled extract: 750 ng; duration: 17 hours; volume: 500 ul ; Temperature in C: 60;
P-TABM-3859
hybridization
Agilent 60mer oligo microarray processing protocol v 5.5. Chamber type: Agilent SureHyb Chamber; Quantity of each labelled extract: 825 ng; duration: 17 hours; volume: 110 ul ; Temperature in C: 65;
P-TABM-3861
dissect
isolated from normal colon surgery removed tissue