12 protocols
AccessionNameType
P-GSE44844-1
bioassay_data_transformation
ID_REF = VALUE = normalized log2 IP/input ratio
P-GSE44844-7
image_aquisition
standard NimbleGen protocol
P-GSE44844-8
feature_extraction
Raw signals of all channels in all replicate arrays were normalized and log2 transformed using the 'vsn' package in R/Bioconductor as described ((Prestel et al., 2010) and Tobias Straub Epigenome project PROT43, http://www.epigenesys.eu/).
P-GSE44844-6
hybridization
standard NimbleGen protocol
P-GSE44844-5
labeling
standard NimbleGen protocol
P-GSE44844-3
grow
YP lactate
P-GSE44844-10
specified_biomaterial_action
Addition of 2% Galactose (Gal-driven HO endonuclease expression) at 0hr
P-GSE44844-4
nucleic_acid_extraction
Chromatin extract preparation and chromatin immunoprecipitation were performed as described in (Kalocsay et al., 2009). Briefly, 200ml cultures of every time point were cross-linked by the addition of 1% (final concentration) formaldehyde for 16 min, and subsequent quenching with 375 mM (final concentration) glycine for at least 10 min. Cells were lysed using Silica beads, the chromatin was enriched by centrifugation and sonicated (water bath sonification: Bioruptor UCD-200, Diagenode) to shear the DNA to an average size of 250-500 bp. After RNase treatment and ligation of linker oligonucleotides, DNA was amplified two times for 14 PCR cycles (using the GenomePlex Whole Genome Amplification (WGA) and reamplifications kits (Sigma)), as described in the Farnham Lab protocol for WGA amplification of DNA (O'Geen et al., 2006). Subsequent labeling of input and IP samples (either Cy3 or Cy5), hybridization to custom-made high-density whole S. cerevisiae genome NimbleGen arrays, array scanning and raw data extraction was done by imaGenes (www.imaGenes-bio.de).
P-GSE44844-2
specified_biomaterial_action
Without addition of 2% Galactose
P-GSE44844-11
grow
SC-ADE lactate
P-GSE44844-12
specified_biomaterial_action
Addition of 2% Galactose (Gal-driven HO endonuclease expression) at 0hr; addition of 2% Glucose to shutoff HO endonuclease expression
P-GSE44844-9
specified_biomaterial_action
Addition of 2% Galactose (Gal-driven HO endonuclease expression)