title: E2_T7_R1, 360 min. post rehydration

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E2_T7_R1, 360 min. post rehydration.


title: E3_T4_R1, 15 min. post rehydration

status: Public on Aug 01 2005

type: RNA

city: Blacksburg

first: Richard

middle: F.

last: Helm

state: VA

address: West Campus Drive

department: Biochemistry, Fralin Biotechnology Center

country: USA

institute: Virginia Polytechnic Institute and State University

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E3_T4_R1, 15 min. post rehydration.

molecule: total RNA

organism: Saccharomyces cerevisiae


title: E2_T7_R2, 360 min. post rehydration

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E2_T7_R2, 360 min. post rehydration.


title: E3_T3_R3, Dry

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E3_T3_R3, Dry.


title: E3_T1_R3, Control

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E3_T1_R3, Control.


title: E3_T1_R2, Control

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E3_T1_R2, Control.


title: E2_T4_R2, 15 min. post rehydration

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E2_T4_R2, 15 min. post rehydration.


title: E2_T6_R1, 90 min. post rehydration

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E2_T6_R1, 90 min. post rehydration.


title: E2_T4_R3, 15 min. post rehydration

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E2_T4_R3, 15 min. post rehydration.


title: E2_T5_R3, 45 min. post rehydration

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E2_T5_R3, 45 min. post rehydration.


title: E2_T3_R3, Dry

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E2_T3_R3, Dry.


title: E2_T4_R1, 15 min. post rehydration

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E2_T4_R1, 15 min. post rehydration.


title: E2_T5_R1, 45 min. post rehydration

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E2_T5_R1, 45 min. post rehydration.


title: E2_T5_R2, 45 min. post rehydration

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E2_T5_R2, 45 min. post rehydration.


title: E2_T3_R2, Dry

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E2_T3_R2, Dry.


title: OBX Day 7,# 3

city: Lexington

first: Ranjit

middle: S

last: Shetty

state: KY

address: 800 Rose Street

department: Physiology

institute: University of Kentucky

description:
Bilateral olfactory bulbectomies were performed on male C57Bl/6 mice(6 week old) and olfactory epithelium tissue collected 7 days post-bulbectomy. Total RNA was extracted from the olfactory epithelium tissue.  Total RNA (5µg each) was pooled from 3 mice. Target cRNA was prepared and hybridized to Mouse Genome U74Av2 GeneChip (GPL81) as per standard, commercially available Affymetrix GeneChips protocol.
Keywords = olfaction
Keywords = neurogenesis
Keywords = apoptosis
Keywords = gene silencing
Keywords = microarray, transcription factor

organism: Mus musculus

source_name: olfactory epithelium tissue


title: E2_T3_R1, Dry

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E2_T3_R1, Dry.


title: E2_T1_R2, Control

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E2_T1_R2, Control.


title: E1_T7_R1, 360 min. post rehydration

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E1_T7_R1, 360 min. post rehydration.


title: E1_T6_R3, 90 min. post rehydration

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E1_T6_R3, 90 min. post rehydration.


title: E1_T7_R2, 360 min. post rehydration

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E1_T7_R2, 360 min. post rehydration.


title: OBX Day 5,# 2

description:
Bilateral olfactory bulbectomies were performed on male C57Bl/6 mice(6 week old) and olfactory epithelium tissue collected 5 days post-bulbectomy. Total RNA was extracted from the olfactory epithelium tissue.  Total RNA (5µg each) was pooled from 3 mice. Target cRNA was prepared and hybridized to Mouse Genome U74Av2 GeneChip (GPL81) as per standard, commercially available Affymetrix GeneChips protocol.
Keywords = olfaction
Keywords = neurogenesis
Keywords = apoptosis
Keywords = gene silencing
Keywords = microarray, transcription factor


title: E2_T1_R1, Control

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E2_T1_R1, Control.


title: E1_T7_R3, 360 min. post rehydration

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E1_T7_R3, 360 min. post rehydration.


title: OBX Day 7,# 1


title: E2_T2_R1, 50% dry

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E2_T2_R1, 50% dry.


title: E2_T2_R2, 50% dry

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E2_T2_R2, 50% dry.


title: E2_T1_R3, Control

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E2_T1_R3, Control.


title: OBX Day 5,# 1


title: E1_T6_R2, 90 min. post rehydration

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E1_T6_R2, 90 min. post rehydration.


title: E2_T2_R3, 50% dry

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E2_T2_R3, 50% dry.


title: E1_T5_R1, 45 min. post rehydration

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E1_T5_R1, 45 min. post rehydration.


title: OBX Day 1,# 3

description:
Bilateral olfactory bulbectomies were performed on male C57Bl/6 mice(6 week old) and olfactory epithelium tissue collected 1 day post-bulbectomy. Total RNA was extracted from the olfactory epithelium tissue.  Total RNA (5µg each) was pooled from 3 mice. Target cRNA was prepared and hybridized to Mouse Genome U74Av2 GeneChip (GPL81) as per standard, commercially available Affymetrix GeneChips protocol.
Keywords = olfaction
Keywords = neurogenesis
Keywords = apoptosis
Keywords = gene silencing
Keywords = microarray, transcription factor


title: E1_T5_R2, 45 min. post rehydration

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E1_T5_R2, 45 min. post rehydration.


title: E1_T5_R3, 45 min. post rehydration

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E1_T5_R3, 45 min. post rehydration.


title: OBX Day 7,# 2

description:
Bilateral olfactory bulbectomies were performed on male C57Bl/6 mice(6 week old) and olfactory epithelium tissue collected 7 days post-bulbectomy. Total RNA was extracted from the olfactory epithelium tissue.  Total RNA (5µg each) was pooled from 3 mice. Target cRNA was prepared and hybridized to Mouse Genome U74Av2 GeneChip (GPL81) as per standard, commercially available Affymetrix GeneChips protocol.
Keywords = olfaction
Keywords = neurogenesis
Keywords = apoptosis
Keywords = gene silencing
Keywords = microarray, transcription factor


title: E1_T4_R2, 15 min. post rehydration

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E1_T4_R2, 15 min. post rehydration.


title: OBX Day 1,# 1


title: E1_T4_R3, 15 min. post rehydration

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E1_T4_R3, 15 min. post rehydration.


title: Sham Day 5,# 3

description:
Male C57Bl/6 mice (6 week old) were sham-operated and olfactory epithelium tissue collected 5 days post-operation. Total RNA was extracted from the olfactory epithelium tissue.  Total RNA (5µg each) was pooled from 3 mice. Target cRNA was prepared and hybridized to Mouse Genome U74Av2 GeneChip (GPL81) as per standard, commercially available Affymetrix GeneChips protocol.
Keywords = olfaction
Keywords = neurogenesis
Keywords = apoptosis
Keywords = gene silencing
Keywords = microarray, transcription factor


title: E1_T4_R1, 15 min. post rehydration

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E1_T4_R1, 15 min. post rehydration.


title: OBX Day 5,# 3

description:
Bilateral olfactory bulbectomies were performed on male C57Bl/6 mice(6 week old) and olfactory epithelium tissue collected 5 days post-bulbectomy. Total RNA was extracted from the olfactory epithelium tissue.  Total RNA (5µg each) was pooled from 3 mice. Target cRNA was prepared and hybridized to Mouse Genome U74Av2 GeneChip (GPL81) as per standard, commercially available Affymetrix GeneChips protocol.
Keywords = olfaction
Keywords = neurogenesis
Keywords = apoptosis
Keywords = gene silencing
Keywords = microarray, transcription factor


title: E1_T3_R3, Dry

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E1_T3_R3, Dry.


title: E1_T3_R2, Dry

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E1_T3_R2, Dry.


title: Sham Day 5,# 2


title: OBX Day 1,# 2


title: E1_T2_R3, 50% dry

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E1_T2_R3, 50% dry.


title: E1_T6_R1, 90 min. post rehydration

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E1_T6_R1, 90 min. post rehydration.


title: E1_T1_R2, Control

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E1_T1_R2, Control.


title: E1_T1_R3, Control

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E1_T1_R3, Control.


title: E1_T2_R2, 50% dry

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E1_T2_R2, 50% dry.


title: E1_T3_R1, Dry

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E1_T3_R1, Dry.


title: Gene expression profiling of Dysferlinopathy Patient No. 5 (B)

status: Public on Jul 28 2005

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

description: We have performed expression profiling to define the molecular changes in dysferlinopathy using a dedicated microarray platform (Human Array 1.0) made with 3’-end skeletal muscle cDNAs. Dysferlinopathy patient No. 5 has been defined by western blot, immunohistochemistry and mutation analysis and in this study has been investigated with microarray technology.

hyb_protocol: Microarray hybridisation was carried out in a dual slide chamber (HybChamber, Gene Machines, San Carlos, CA, USA) humidified with 100 µl of 3 x SSC. Labeled cDNA was dissolved in 40 µl of hybridisation buffer, denatured at 90°C for 2 min in a thermal cycler and applied directly to the slides. Microarrays were covered with 22 x 40 mm cover slip and hybridized overnight at 65°C by immersion in a high precision water bath (W28, Grant, Cambridge, UK). Post-hybridization washing was performed according to the MICROMAX TSA Detection kit (PerkinElmer).

scan_protocol: Digital images were generated in a GSI Lumonics LITE dual confocal laser scanner (ScanArray Microarray Analysis Software) and processed with QuantArray Analysis Software (GSI Lumonics, Ottawa, Canada).

data_processing: The gene expression data analysis tool SNOMAD (http://pevsnerlab.kennedykrieger.org/snomadinput.html) was used for microarray data normalization and standardization. Log2 transformation was performed for each normalized expression value.

organism: Homo sapiens

source_name: Patient No. 5 (Test)

label_protocol: Total RNA was retro-transcribed and labeled using a MICROMAX TSA Labeling Kit (PerkinElmer). Two ug of total RNA were used in each reaction but only half of the labeled cDNA was actually hybridized to the microarrays.

extract_protocol: Total RNA was purified following the TRIZOL standard protocol. A small aliquot of RNA was then used for quantification and quality control using the RNA 6000 LabChip kit and Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA). We routinely obtain a mean quantity of 0.5 mg of RNA per mg of homogenized muscle tissue.

tag: - Sex

value: male;

tag: - Muscle type

value: quadriceps femoralis;

tag: - Type 1 fibres (%)

tag: - Range diameter (um)

tag: - Degenerating fibres (%)

tag: - Foetal myosin (%)

tag: - Vimentin (%)

tag: - Laminin-A (%)

source_name: Muscles pool of vastus lateralis quadriceps femoris and deltoid (Reference)

tag: Muscle biopsies from subjects in whom a muscle disease was excluded by both clinical and histopathological criteria were used as controls. For quadriceps femoralis we used biopsies from three female and two male donors ranging between 9 and 54 years of age. For the deltoid muscle we used biopsies from three male and seven female donors ranging between 13 and 57 years of age.


title: Gene expression profiling of Dysferlinopathy Patient No. 4 (B)

description: We have performed expression profiling to define the molecular changes in dysferlinopathy using a dedicated microarray platform (Human Array 1.0) made with 3’-end skeletal muscle cDNAs. Dysferlinopathy patient No. 4 has been defined by western blot, immunohistochemistry and mutation analysis and in this study has been investigated with microarray technology.

source_name: Patient No. 4 (Test)

value: female;


title: Untreated,# 2

description:
Total RNA was extracted from olfactory epithelium tissue from male C57Bl/6 mice (6 week old). Total RNA (5µg each) was pooled from 3 mice. Target cRNA was prepared and hybridized to Mouse Genome U74Av2 GeneChip (GPL81) as per standard, commercially available Affymetrix GeneChips protocol.
Keywords = olfaction
Keywords = neurogenesis
Keywords = apoptosis
Keywords = gene silencing
Keywords = microarray, transcription factor


title: E1_T2_R1, 50% dry

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E1_T2_R1, 50% dry.


title: Gene expression profiling of Dysferlinopathy Patient No. 7 (A)

description: We have performed expression profiling to define the molecular changes in dysferlinopathy using a dedicated microarray platform (Human Array 1.0) made with 3’-end skeletal muscle cDNAs. Dysferlinopathy patient No. 7 has been defined by western blot, immunohistochemistry and mutation analysis and in this study has been investigated with microarray technology.

source_name: Patient No. 7 (Test)

value: deltoid;


title: Untreated,# 3


title: Gene expression profiling of Dysferlinopathy Patient No. 5 (A)


title: Gene expression profiling of Dysferlinopathy Patient No. 2 (A)

description: We have performed expression profiling to define the molecular changes in dysferlinopathy using a dedicated microarray platform (Human Array 1.0) made with 3’-end skeletal muscle cDNAs. Dysferlinopathy patient No. 2 has been defined by western blot, immunohistochemistry and mutation analysis and in this study has been investigated with microarray technology.

source_name: Patient No. 2 (Test)


title: Gene expression profiling of Dysferlinopathy Patient No. 7 (B)


title: Untreated,# 1


title: Gene expression profiling of Dysferlinopathy Patient No. 2 (B)


title: Gene expression profiling of Dysferlinopathy patient No. 1 (A)

description: We have performed expression profiling to define the molecular changes in dysferlinopathy using a dedicated microarray platform (Human Array 1.0) made with 3’-end skeletal muscle cDNAs. Dysferlinopathy patient No. 1 has been defined by western blot, immunohistochemistry and mutation analysis and in this study has been investigated with microarray technology.

source_name: Patient No. 1 (Test)

source_name: muscles pool of vastus lateralis quadriceps femoris and deltoid (Reference)


title: Gene expression profiling of Dysferlinopathy Patient No. 4 (A)


title: E1_T1_R1, Control

description:
Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8.  Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C.  An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C.  For more information on the unit and software, contact the corresponding author.  A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1.  Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry).  Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask.  Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092).  RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E1_T1_R1, Control.


title: Gene expression profiling of Dysferlinopathy Patient No. 1 (B)


title: Gene expression profiling of C2C12 MyoD-silenced clone at 6 days of myogenic differentiation (B)

description: RNA purified from C2C12 MyoD(-)cl.A8 at six myogenic differentiation time-points was compared with RNA from C2C12 control cells at the corresponding differentiation stages. These samples were labeled and hybridized to muscle specific microarrays produced by our group (Human Array 1.0).

source_name: C2C12 control cells (Reference)

extract_protocol: Total RNA was purified from C2C12 control cells following the standard Trizol protocol. The RNA 6000 LabChip kit (Agilent Technologies) was used for RNA quantification and quality control in conjunction with an Agilent Bioanalyzer 2001.

tag: - C2C12 cell line

tag: - Species

value: mouse, C3H; Tissue:muscle

tag: - Morphology

value: Myoblast

tag: - Depositor

value: Obtained from ATCC, USA

tag: - Properties

value: differentiation; muscle proteins express; myogenesis

tag: - Growing medium

value: DMEM + 2mM Glutamine + 10% Fetal Bovine Serum (FBS)

tag: - Differentiating medium

value: DMEM + 2mM Glutamine + 2% Horse Serum (HS)

source_name: C2C12 MyoD-silenced cells (Test)

extract_protocol: Total RNA was purified from C2C12 MyoD(-) cells (MyoD(-)cl.A8) after six days of myogenic differentiation following the standard Trizol protocol. The RNA 6000 LabChip kit (Agilent Technologies) was used for RNA quantification and quality control in conjunction with an Agilent Bioanalyzer 2001.

tag: - C2C12 MyoD-silenced cells

value: the mouse MyoD transcript was cloned in pcDNA 3.0 mammalian expression vector in antisense orientation and the construct was transfected in C2C12 cells. The cells were selected for ten days and the G-418 resistant clones were tested for MyoD silencing.

tag: - MyoD knock-down clone