8 protocols
AccessionType
bioassay_data_transformation
ID_REF =
VALUE = Normalized log2 ratio IP Cy5 /Input Cy3
hybridization
At least 2 independent hybridization experiments were performed on biological replicates of the untagged control and Mit1-GFP and Yhr177w and Yhr177w deletion control. One experiment was performed on Wor1 overexpressing cells in a mit1/Yhr177w deletion, with vector control. Protocol is available in Hernday et al. (Methods Enzymol. 2010;470:737-58).
labeling
IP genomic DNA samples were labeled with Cy5 and input genomic DNA samples were labeled with Cy3. Protocol is available in Hernday et al. (Methods Enzymol. 2010;470:737-58).
image_aquisition
Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol.
grow
Cells were grown overnight to an OD of low/mid log phase (.3- 1) in YPD or appropriate selectable media.
specified_biomaterial_action
Cells were fixed, lysed, immunoprecipitated with antibody and genomic DNAs were sheared by sonication.
feature_extraction
Normalized enrichment values were determined for every probe on the microarray by LOWESS normalization using Agilent Chip Analytics Version 1.2 software (Tuch et al., 2008), followed by visualization and additional analysis using MochiView v.1.39 (http://johnsonlab.ucsf.edu/).
nucleic_acid_extraction
Genomic DNA extracted using protocol in Methods Enzymol. 2010;470:737-58.