Dynamic transcriptome profiling with metabolic labeling (4tU) (Sun et al. Genome Research 2012) was applied to synchronized S.cerevisiae cells to estimate labeled and total mRNA levels every 5 minutes for three complete cell cycles. The dataset comprises two time series from independent biological replicates for each  mRNA fraction (total, labeled).

Periodic mRNA synthesis and degradation co-operate during cell cycle gene expression

Affymetrix GeneChip Yeast Genome 2.0 Array [Yeast_2]

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treatment

Transcription profiling by array of Saccharomyces cerevisiae cells to estimate labeled and total mRNA levels every 5 minutes for three complete cell cycles

Dynamic transcriptome profiling with metabolic labeling (4tU) (Sun et al. Genome Research 2012) was applied to synchronized S.cerevisiae cells to estimate labeled and total mRNA levels every 5 minutes for three complete cell cycles. The dataset comprises two time series from independent biological replicates for each  mRNA fraction (total, labeled).


P-AFFY-3

P-MTAB-35162

The BAR1 deletion strain was generated from wt strain BY4741 (MATa, his3delta1, leu2delta0, met15delta0, ura3delta0) by replacing the BAR1 open reading frame from its start- to stop- codon with a KanMX module. The deltabar1 strain was inoculated from a fresh overnight culture at OD600 0.1.

P-MTAB-35163

At OD600 0.4 alpha factor (Bachem) was added at a final concentration of 600 ng/mL for 2 hours. Synchronization was followed visually by counting the number of budding cells under the microscope. Cells were centrifuged for 2 min at 1600 x g at 30C and washed once with 3 x the original culture volume prewarmed YPD.  Cells were then resuspended in the original culture volume with prewarmed YPD.  41 consecutive samples were labeled for 5 min with 4-thiouracil every 5 min for 200 min.  Labeling and sample processing was performed as described (Sun et al, 2012). Total RNA purification, separation of labeled RNA as well as sample hybridization and microarray scanning were carried out as previously described (Sun et al., 2012).  The quantification of labeled and total mRNA time courses was performed in two independent biological replicates.

P-MTAB-35164

Total RNA was extracted with the RiboPure-Yeast Kit (Ambion/Applied Biosystems), following the manufacturers protocol. 

P-MTAB-35165

Labeling of samples for array analysis was performed using the GeneChip 3’IVT labeling assay (Affymetrix) with 100 ng input RNA.

P-MTAB-35166

Total RNA is labeled for 5 min with the nucleotide analog 4-thiouracil (4tU). 4tU-RNA is chemically biotinylated and purified using strepatavidin-coated magnetic beads as described in (Dolken, et al., 2008, RNA 14, 1959-1972).

Transcription profiling by array of Saccharomyces cerevisiae cells to estimate labeled and total mRNA levels every 5 minutes for three complete cell cycles

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