Time shift

Other Datasets Available

Cell cycle (alpha factor arrest and release)

Time points 18 Time unit 7 min

Description

A MATa strain was grown to logarithmic (asynchronous) growth, then arrested at G1 phase by the addition of alpha factor. After 2 hours, cells were shifted into medium without alpha factor, and samples were taken every seven minutes for 119 minutes. A control sample was prepared from asynchronously growing cells of the same strain in the same medium, untreated with alpha factor. Transcript abundances were determined for each time point relative to the control, by hybridization to a cDNA microarray.

Reference

Spellman, P. T., Sherlock, G., Zhang, M. Q., Iyer, V. R., Anders, K., Eisen, M. B., Brown, P. O., Botstein, D., and Futcher, B. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9, 3273-97 (1998).

Cell cycle (cdc15 arrest and release)

Time points 24 Time unit 20 min

Description

cdc15-2ts cells were grown at 23 degrees in YPD to 2.5e6 cells/ml and moved to 37 degrees for 3.5 hours to synchronize them in late M (and having reached 6.6E6 cells/ml). The culture was then transferred to a 23 deg water bath, to release the cell cycle block, and sampled every 10 minutes up to 290 minutes (three cell cycles). An untreated culture grown at 23 deg to 1e7 cells/ml was used as a control. mRNA transcript abundances were assessed for over 6000 genes. The values graphed are log of the ratio of expression in the 37 deg blocked-and-released cells (red dye) over expression in the asynchronous cells (green dye).

Reference

Spellman, P. T., Sherlock, G., Zhang, M. Q., Iyer, V. R., Anders, K., Eisen, M. B., Brown, P. O., Botstein, D., and Futcher, B. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9, 3273-97 (1998).

Cell cycle (cell size selection and release)

Time points 14 Time unit 30 min

Description

Cells were grown at 25 degrees in YP+ethanol to 1.5e7 cells/ml and small, unbudded G1 cells were selected by elutriation. These cells were released at 2.3e7 cells/ml and sampled every 30 minutes up to 390 minutes (one cell cycle). An untreated culture grown at 25 degrees to log-phase was used as a control. mRNA transcript abundances were assessed for over 6000 genes. The values graphed are log of the ratio of expression in the selected and synchronized cells (red dye) over expression in the asynchronous cells (green dye).

Reference

Spellman, P. T., Sherlock, G., Zhang, M. Q., Iyer, V. R., Anders, K., Eisen, M. B., Brown, P. O., Botstein, D., and Futcher, B. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9, 3273-97 (1998).

DNA damage by MMS (timecourse)

Time points 4 Time unit 0, 10, 30, 60 min

Description

Cells in logarithmic growth were treated with 0.1% methyl methanesulfonate (MMS) for 10, 30 or 60 minutes. A control sample of the same strain growing under the same conditions was not treated. Transcript abundances were determined relative to the control, by hybridization to an oligonucleotide microarray.

Reference

Jelinsky, S. A., Estep, P., Church, G. M., and Samson, L. D. Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiae cells: Rpn4 links base excision repair with proteasomes. Mol Cell Biol 20, 8157-8167 (2000).

Diauxic shift

Time points 7 Time unit 2 hr

Description

mRNA expression levels for 6116 yeast genes were studied during the period of diauxic shift from fermentation to respiration. Expression during the period from 9 to 21 hours after inoculation was compared to initial levels (at 9 hours). The expression ratios are shown as fold induction (positive numbers, graphed above the baseline) or fold repression (negative, below the baseline).

Reference

DeRisi, J. L., Iyer, V. R., and Brown, P. O. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278, 680-686 (1997).

Histone H4 depletion

Time points 7 Time unit 0, 0.5, 1, 1.5, 2, 4, 6 hr

Description

Yeast strain UKY403, carrying a single copy of the histone H4 gene under the GAL1-10 promoter, was grown in galactose-containing medium, then switched to medium containing glucose. A control strain carrying a wild-type histone H4 gene was grown similarly. Samples were taken at 0, 0.5, 1, 1.5, 2, 4 and 6 hours after glucose repression of histone H4 expression. Transcript abundances were determined for 6175 yeast genes by hybridization to an oligonucleotide microarray. The expression ratios are graphed as fold induction (positive numbers, graphed above the baseline) or fold repression (negative, below the baseline). This analysis reveals that depletion of histone H4 caused the increased expression of 15% and 10 decrease expression of 10% of the genes; the expression of 75% of the genes was unaffected. Notably the expression of telomere-proximal gene (a region of roughly 20 kb) was also increased, suggesting that histones perform telomere silencing functions.

Reference

Wyrick, J. J., Holstege, F. C. P., Jennings, E. G., Causton, H. C., Shore, D., Grunstein, M., Lander, E. S., and Young, R. A. Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast. Nature 402, 418-421 (1999).

Meiosis and sporulation

Time points 7 Time unit 0, 0.5, 2, 5, 7, 9, 11.5 hr

Description

mRNA expression levels for 6118 yeast genes were studied during course of meiosis and spore formation. Wild-type cells were transferred to sporulation-inducing medium and samples were taken after 0, 0.5, 2, 5, 7, 9 and 11.5 hours. A control sample was prepared at the initial time point. Transcript abundances were determined for each time point relative to the control, by hybridization to a cDNA microarray. The expression ratios for the 7 time points are graphed as fold induction (positive numbers, graphed above the baseline) or fold repression (negative, below the baseline).

Reference

Chu, S., DeRisi, J., Eisen, M., Mulholland, J., Botstein, D., Brown, P. O., and Herskowitz, I. The transcriptional program of sporulation in budding yeast. Science 282, 699-705 (1998).

alpha-factor response in bni1 null mutant cells (time course)

Time points 3 Time unit 30 min

Description

Yeast cells carrying a bni1 deletion were grown to mid-logarithmic phase, then incubated in the absence or presence of 50 nM alpha-factor for 60, 90 or 120 minutes. Transcript abundances were assessed by two-fluor simultaneous hybridization to cDNA microarrays. The reported ratios of treated to untreated cells represent the average of at least two hybridizations which include reversal of the fluors of the control and experimental samples.

Reference

Roberts, C. J., Nelson, B., Marton, M. J., Stoughton, R., Meyer, M. R., Bennett, H. A., He, Y. D. D., Dai, H. Y., Walker, W. L., Hughes, T. R., Tyers, M., Boone, C., and Friend, S. H. Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science 287, 873-880 (2000).

alpha-factor response in tec1 null mutant cells compared to wild-type cells treated with alpha-factor

Time points 2 Time unit 30, 120 min

Description

tec1 null mutant and wild-type cells were grown to mid-logarithmic phase, then incubated in the presence of 50 nM alpha-factor for 30 or 120 minutes. Transcript abundances were assessed by two-fluor simultaneous hybridization to cDNA microarrays. The reported ratios of mutant to wild-type cells (both treated with alpha-factor) represent the average of at least two hybridizations that include reversal of the fluors of the control and experimental samples.

Reference

Roberts, C. J., Nelson, B., Marton, M. J., Stoughton, R., Meyer, M. R., Bennett, H. A., He, Y. D. D., Dai, H. Y., Walker, W. L., Hughes, T. R., Tyers, M., Boone, C., and Friend, S. H. Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science 287, 873-880 (2000).

alpha-factor response in wild-type cells (time course)

Time points 7 Time unit 0, 15, 30, 45, 60, 90, 120 min

Description

Wild-type (a mating-type) cells were grown to mid-logarithmic phase, then incubated in the presence of 50 nM alpha-factor for varied times. Transcript abundances were assessed by two-fluor simultaneous hybridization to cDNA microarrays. The reported ratios are relative to the untreated cells, and represent the average of at least two hybridizations which include reversal of the fluor of the control and experimental samples.

Reference

Roberts, C. J., Nelson, B., Marton, M. J., Stoughton, R., Meyer, M. R., Bennett, H. A., He, Y. D. D., Dai, H. Y., Walker, W. L., Hughes, T. R., Tyers, M., Boone, C., and Friend, S. H. Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science 287, 873-880 (2000).

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Cell cycle (alpha factor arrest and release)
Time points	18	Time unit	7 min
Description
A MATa strain was grown to logarithmic (asynchronous) growth, then arrested at G1 phase by the addition of alpha factor. After 2 hours, cells were shifted into medium without alpha factor, and samples were taken every seven minutes for 119 minutes. A control sample was prepared from asynchronously growing cells of the same strain in the same medium, untreated with alpha factor. Transcript abundances were determined for each time point relative to the control, by hybridization to a cDNA microarray.
Reference
Spellman, P. T., Sherlock, G., Zhang, M. Q., Iyer, V. R., Anders, K., Eisen, M. B., Brown, P. O., Botstein, D., and Futcher, B. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9, 3273-97 (1998).
Cell cycle (cdc15 arrest and release)
Time points	24	Time unit	20 min
Description
cdc15-2ts cells were grown at 23 degrees in YPD to 2.5e6 cells/ml and moved to 37 degrees for 3.5 hours to synchronize them in late M (and having reached 6.6E6 cells/ml). The culture was then transferred to a 23 deg water bath, to release the cell cycle block, and sampled every 10 minutes up to 290 minutes (three cell cycles). An untreated culture grown at 23 deg to 1e7 cells/ml was used as a control. mRNA transcript abundances were assessed for over 6000 genes. The values graphed are log of the ratio of expression in the 37 deg blocked-and-released cells (red dye) over expression in the asynchronous cells (green dye).
Reference
Spellman, P. T., Sherlock, G., Zhang, M. Q., Iyer, V. R., Anders, K., Eisen, M. B., Brown, P. O., Botstein, D., and Futcher, B. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9, 3273-97 (1998).
Cell cycle (cell size selection and release)
Time points	14	Time unit	30 min
Description
Cells were grown at 25 degrees in YP+ethanol to 1.5e7 cells/ml and small, unbudded G1 cells were selected by elutriation. These cells were released at 2.3e7 cells/ml and sampled every 30 minutes up to 390 minutes (one cell cycle). An untreated culture grown at 25 degrees to log-phase was used as a control. mRNA transcript abundances were assessed for over 6000 genes. The values graphed are log of the ratio of expression in the selected and synchronized cells (red dye) over expression in the asynchronous cells (green dye).
Reference
Spellman, P. T., Sherlock, G., Zhang, M. Q., Iyer, V. R., Anders, K., Eisen, M. B., Brown, P. O., Botstein, D., and Futcher, B. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9, 3273-97 (1998).
DNA damage by MMS (timecourse)
Time points	4	Time unit	0, 10, 30, 60 min
Description
Cells in logarithmic growth were treated with 0.1% methyl methanesulfonate (MMS) for 10, 30 or 60 minutes. A control sample of the same strain growing under the same conditions was not treated. Transcript abundances were determined relative to the control, by hybridization to an oligonucleotide microarray.
Reference
Jelinsky, S. A., Estep, P., Church, G. M., and Samson, L. D. Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiae cells: Rpn4 links base excision repair with proteasomes. Mol Cell Biol 20, 8157-8167 (2000).
Diauxic shift
Time points	7	Time unit	2 hr
Description
mRNA expression levels for 6116 yeast genes were studied during the period of diauxic shift from fermentation to respiration. Expression during the period from 9 to 21 hours after inoculation was compared to initial levels (at 9 hours). The expression ratios are shown as fold induction (positive numbers, graphed above the baseline) or fold repression (negative, below the baseline).
Reference
DeRisi, J. L., Iyer, V. R., and Brown, P. O. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278, 680-686 (1997).
Histone H4 depletion
Time points	7	Time unit	0, 0.5, 1, 1.5, 2, 4, 6 hr
Description
Yeast strain UKY403, carrying a single copy of the histone H4 gene under the GAL1-10 promoter, was grown in galactose-containing medium, then switched to medium containing glucose. A control strain carrying a wild-type histone H4 gene was grown similarly. Samples were taken at 0, 0.5, 1, 1.5, 2, 4 and 6 hours after glucose repression of histone H4 expression. Transcript abundances were determined for 6175 yeast genes by hybridization to an oligonucleotide microarray. The expression ratios are graphed as fold induction (positive numbers, graphed above the baseline) or fold repression (negative, below the baseline). This analysis reveals that depletion of histone H4 caused the increased expression of 15% and 10 decrease expression of 10% of the genes; the expression of 75% of the genes was unaffected. Notably the expression of telomere-proximal gene (a region of roughly 20 kb) was also increased, suggesting that histones perform telomere silencing functions.
Reference
Wyrick, J. J., Holstege, F. C. P., Jennings, E. G., Causton, H. C., Shore, D., Grunstein, M., Lander, E. S., and Young, R. A. Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast. Nature 402, 418-421 (1999).
Meiosis and sporulation
Time points	7	Time unit	0, 0.5, 2, 5, 7, 9, 11.5 hr
Description
mRNA expression levels for 6118 yeast genes were studied during course of meiosis and spore formation. Wild-type cells were transferred to sporulation-inducing medium and samples were taken after 0, 0.5, 2, 5, 7, 9 and 11.5 hours. A control sample was prepared at the initial time point. Transcript abundances were determined for each time point relative to the control, by hybridization to a cDNA microarray. The expression ratios for the 7 time points are graphed as fold induction (positive numbers, graphed above the baseline) or fold repression (negative, below the baseline).
Reference
Chu, S., DeRisi, J., Eisen, M., Mulholland, J., Botstein, D., Brown, P. O., and Herskowitz, I. The transcriptional program of sporulation in budding yeast. Science 282, 699-705 (1998).
alpha-factor response in bni1 null mutant cells (time course)
Time points	3	Time unit	30 min
Description
Yeast cells carrying a bni1 deletion were grown to mid-logarithmic phase, then incubated in the absence or presence of 50 nM alpha-factor for 60, 90 or 120 minutes. Transcript abundances were assessed by two-fluor simultaneous hybridization to cDNA microarrays. The reported ratios of treated to untreated cells represent the average of at least two hybridizations which include reversal of the fluors of the control and experimental samples.
Reference
Roberts, C. J., Nelson, B., Marton, M. J., Stoughton, R., Meyer, M. R., Bennett, H. A., He, Y. D. D., Dai, H. Y., Walker, W. L., Hughes, T. R., Tyers, M., Boone, C., and Friend, S. H. Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science 287, 873-880 (2000).
alpha-factor response in tec1 null mutant cells compared to wild-type cells treated with alpha-factor
Time points	2	Time unit	30, 120 min
Description
tec1 null mutant and wild-type cells were grown to mid-logarithmic phase, then incubated in the presence of 50 nM alpha-factor for 30 or 120 minutes. Transcript abundances were assessed by two-fluor simultaneous hybridization to cDNA microarrays. The reported ratios of mutant to wild-type cells (both treated with alpha-factor) represent the average of at least two hybridizations that include reversal of the fluors of the control and experimental samples.
Reference
Roberts, C. J., Nelson, B., Marton, M. J., Stoughton, R., Meyer, M. R., Bennett, H. A., He, Y. D. D., Dai, H. Y., Walker, W. L., Hughes, T. R., Tyers, M., Boone, C., and Friend, S. H. Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science 287, 873-880 (2000).
alpha-factor response in wild-type cells (time course)
Time points	7	Time unit	0, 15, 30, 45, 60, 90, 120 min
Description
Wild-type (a mating-type) cells were grown to mid-logarithmic phase, then incubated in the presence of 50 nM alpha-factor for varied times. Transcript abundances were assessed by two-fluor simultaneous hybridization to cDNA microarrays. The reported ratios are relative to the untreated cells, and represent the average of at least two hybridizations which include reversal of the fluor of the control and experimental samples.
Reference
Roberts, C. J., Nelson, B., Marton, M. J., Stoughton, R., Meyer, M. R., Bennett, H. A., He, Y. D. D., Dai, H. Y., Walker, W. L., Hughes, T. R., Tyers, M., Boone, C., and Friend, S. H. Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science 287, 873-880 (2000).