RNA extraction, gene chip hybridization and Northern analysis To minimize the chance of RNA degradation, frozen biomass was directly ground in liquid nitrogen and subsequently total RNA was isolated using the Trizol reagent according to the manufacturers instructions. promotion information Prior to gene chip hybridization, sam ples were puri?ed on NucleoSpin RNA II Inhibitors,Modulators,Libraries columns including a DNAse I treatment. Lab on chip quality control, labeling, A?ymetrix chip hybridization and scanning were performed at ServiceXS according to the GeneChip Expression Analysis Technical Manual. Northern analysis using dCTP labelled probes was performed as previously described by Damveld et al. using 1. 8 ug of RNA per sample. A stan dard loading control such as 18S rRNA was not used. Equal loading was concluded from smoothly increasing decreasing time course pro?les.

Transcriptome data Inhibitors,Modulators,Libraries analysis RNA samples from four cultivation phases were sub jected to genome wide transcriptional pro?ling, Expo nential growth Inhibitors,Modulators,Libraries phase, 16 hours, 60 hours and 140 hours post carbon depletion. While the expression data for the exponential growth phase was derived from triplicate cultures, expression data for the three post exponential time points was obtained from duplicate cultures. Transcriptomic data were analyzed with the statistical programming language R. The following packages of the open source and open develop ment project Bioconductor were used, a?y, a?y coretools, a?yPLM and limma. A?ymetrix probe level data was imported from. CEL ?les and pre processed with the Robust Multi array Average Inhibitors,Modulators,Libraries algorithm as implemented in the a?y package.

To improve background correction Inhibitors,Modulators,Libraries and data normalization, six additional. CEL ?les corresponding to day 2 and day 8 of carbon limited retentostat cultivations of A. niger, available at the Gene Expression Omnibus database under accession number, GSE21752, were included in the RMA preprocessing step. Prior to the computation of di?eren tially expressed genes, 65 A?ymetrix control probes and 204 probes targeting genetic elements were removed from the expression matrix. For 277 transcripts targeted by multiple probes, mean expression values were calculated from the RMA expression data of all associated probes. Subsequently, KPT-330 buy RMA expression data for the 13,989 tran scripts were analyzed with the limma package comparing day 1, 3 and 6 of carbon starvation with the exponential growth phase. The Benjamini Hochberg False Discov ery Rate was controlled at 0. 005. Because fold changes are not necessarily related to biological relevance, a minimal fold change criterion was not applied.