title: Gene expression upon nitrogen starvation, 3hrs (F250)

description: Comparing between vegetatively-growing control cells (Cy3) and cells 3 hrs after nitrogen starvation (Cy5).

hyb_protocol: The labeled targets were added to the hybridization solution to contain an equal amount of the Cy3 and Cy5, and then were hybridized onto DNA on the microarray, using Genomic solutions GeneTac Hybridization Station, for four hours at 40｡C in Genomic solutions GeneTac Hyb buffer 120microl (including 42% formamide ). The slides after hybridization were washed in the following sequence: (1) 2xSSC 0.1%SDS at 40｡C for 5min, (2) 0.2xSSC at 25｡C for 1min, and (3) 0.1xSSC at 25｡Cfor 1min.

data_processing: Measured fluorescent intensity, I, was corrected as follows to give a corrected intensity, C:C = I-M, (for I>M+2s), C = I*2s/(M+2s), (for I<M+2s) where M and s are an average and a standard deviation of I of negative control spots for each wave length respectively. When I = M+2s, that is C=2s, it was set to be a detection limit. When C for either Cy3 or Cy5 or both were greater than 2s, the values were considered to be effective data. VALUE (Expression ratio r') of the each effective detection spot obtained thus was scaled as follows: r'=r-m, r=logR(base is 2), R=(Ccy5/Ccy3), m is an average of r of all effective detection spots.

extract_protocol: Total RNA was isolated by acid phenol methods described Sanger S. pombe post-genomics website, and then polyA-RNA was purified by Oligotex-dT30<super>mRNA purification kit (Takara).

treatment_protocol: A single colony of S. pombe cells on a YES plate was inoculated into YES liquid medium to grow to 5x(the 6th power of 10)cell/ml at 30｡C. After two washes in EMM2-N (EMM2 depleted of nitrogen sources), cells were transferred to EMM2-N and further incubated at 30｡C. Cells were collected 3 hrs after the nitrogen starvation.


title: DLBCL biopsy, sample 2141

status: Public on Apr 10 2009

type: RNA

city: New York

first: Laura

last: Pasqualucci

state: NY

address: 1130 St Nicholas Avenue

department: Institute for Cancer Genetics

country: USA

institute: Columbia University

description:
frozen biopsy of lymph node tumor
Gene expression data from primary DLBCL biopsy

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for at least 16 hr at 45C on GeneChip Human Genome Array U133Plus_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000A.

data_processing: Data were normalized using MAS5 and subsequently log2 transformed. For Gene Set Enrichment Analysis (GSEA), probesets were first filtered out if mean, mu<50, or coeffient of variation, CV<0.3 (as assessed in 259 B cell-related gene expression profiles from U133Plus_2 arrays) ; these probes do not appear in the attached Matrix.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: DLBCL frozen biopsy

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Lymphoma biopsies were snap frozen in liquid nitrogen or embedded in OCT compound followed by flash freezing in liquid nitrogen

extract_protocol: Tissue samples were homogenized in Trizol and extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Not applicable

tag: tissue

value: lymph node tumor


title: Gene expression upon nitrogen starvation, 3hrs (F249)

status: Public on Sep 29 2009

city: Kobe

first: Atsushi

last: Matsuda

address: 588-2, Iwaoka, Iwaoka-cho, Nishi-ku

country: Japan

institute: National Institute of Information and Communications Technology

scan_protocol: Microarrays were scanned using an ArraywoRx arrayscanner, and the acquired data was analyzed by a SoftwoRx software (Applied Precision, Inc., Seattle, WA). Fluorescent intensity in each spot circle (150microm diameter) was measured by Softworx tracker.

molecule: polyA RNA

organism: Schizosaccharomyces pombe

source_name: h- rhb1-DA8, 3hrs after nitorogen starvation

label_protocol: The polyA-RNA (3-6microg) was labeled by CyScribe Post-Labeling Kit (Amasham Pharmacia) with Cy5 with Oligo dT primer.

tag: h- rhb1-DA8

source_name: h- rhb1-DA8, logarithmically growing

label_protocol: The polyA-RNA (3-6microg) was labeled by CyScribe Post-Labeling Kit (Amasham Pharmacia) with Cy3 with Oligo dT primer.

treatment_protocol: A single colony of S. pombe cells on a YES plate was inoculated into YES liquid medium. Cells were collected at 5x(the 6th power of 10)cell/ml at 30｡C.


title: Gene expression upon nitrogen starvation, 3hrs (F122)

source_name: h- rhb1-DA4, 3hrs after nitorogen starvation

tag: h- rhb1-DA4

source_name: h- rhb1-DA4, logarithmically growing


title: Gene expression upon nitrogen starvation, 3hrs (D151)

description: Comparing between vegetatively-growing control cells (Cy3) and cells at each time point after nitrogen starvation (Cy5).

hyb_protocol: The labeled targets were added to the hybridization solution to contain an equal amount of the Cy3 and Cy5, and then were hybridized onto DNA on the microarray, using Genomic solutions GeneTac Hybridization Station, for four hours at 40°C in Genomic solutions GeneTac Hyb buffer 120microl (including 42% formamide ). The slides after hybridization were washed in the following sequence: (1) 2xSSC 0.1%SDS at 40°C for 5min, (2) 0.2xSSC at 25°C for 1min, and (3) 0.1xSSC at 25°C for 1min.

data_processing: Measured fluorescent intensity, I, was corrected as follows to give a corrected intensity, C:C = I-M,  (for I>M+2s), C = I*2s/(M+2s),  (for I<M+2s) where M and s are an average and a standard deviation of I of negative control spots for each wave length respectively. When I = M+2s, that is C=2s, it was set to be a detection limit. When C for either Cy3 or Cy5 or both were greater than 2s, the values were considered to be effective data. VALUE (Expression ratio r') of the each effective detection spot obtained thus was scaled as follows: r'=r-m, r=logR(base is 2), R=(Ccy5/Ccy3), m is an average of r of all effective detection spots.

source_name: L972, 3hrs after nitorogen starvation

extract_protocol: Total RNA was isolated by acid phenol methods described in http://www.sanger.ac.uk/PostGenomics/S_pombe/, and then polyA-RNA was purified by Oligotex-dT30<super>mRNA purification kit (Takara).

treatment_protocol: A single colony of S. pombe cells on a YES plate was inoculated into YES liquid medium to grow to 5x(the 6th power of 10)cell/ml at 30°C. After two washes in EMM2-N (EMM2 depleted of nitrogen sources), cells were transferred to EMM2-N and further incubated at 30°C. Cells were collected at each time point after the nitrogen starvation.

tag: L972 h- wild type

source_name: L972, logarithmically growing


title: Gene expression upon nitrogen starvation, 3hrs (F248)


title: Gene expression upon nitrogen starvation, 3hrs (D169)

source_name: AE509, 3hrs after nitorogen starvation

tag: AE509 h- tsc2::ura4+ ura4-D18

source_name: AE509, logarithmically growing


title: DLBCL biopsy, sample 2132


title: Gene expression upon nitrogen starvation, 3hrs (F116)


title: DLBCL biopsy, sample 2178


title: DLBCL biopsy, sample 2153


title: 3 mo left lung control biorep 13

status: Public on Mar 16 2011

city: North Grafton

first: Julia

middle: A

last: Paxson

state: MA

address: 200 Westboro Road

department: Clinical Sciences

institute: Tufts Cummings School of Veterinary Medicine

description: Replicate 1 - pooled RNA sample from the left lungs of mouse 13a and 13b

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Probe sets were background corrected and summarized using the RMA algorithm along with quantile normalization, all of which are available in BioConductor's lumi package. Quality control on the arrays was performed by again using the lumi package to visualize intensity distributions, percentage present calls, and correlations between arrays; none of which turned up any reasons for concern and resulted in the inclusion of all arrays in the analysis. Following quality inspection, probe sets were filtered to include only those detected on all arrays. This step eliminated all probes with signal intensities reported at background level and resulted in the inclusion of roughly 17,500 probe sets for further analysis. Data analysis of the filtered probe set can be described in two steps. First, differential gene expression was calculated between pneumonectomy and control samples for the animals within each age group and at each time point following surgery. This was accomplished using the limma (Linear Modeling for Microarray Data) package in BioConductor, with pneumonectomy and control sample pairings built into the model. Fold-change and p-values for each probe set were calculated using a moderated t-statistic, with the variance estimate being adjusted by incorporating global variation measures for the complete set of probes on the array. The P-value data were then corrected for multiple hypothesis testing using the Benjamini and Hochberg method. This analysis resulted in unique sets of differentially expressed genes for each age group and time point. An absolute fold-change value ≥ 1.5 and adjusted P-value < 0.05 were used as criteria for defining a set of genes for further exploration. Following completion of this analysis, second analysis addressed the question of how differential gene expression differed between the aged and young age groups. To determine differences in differential gene expression between the aged and young animals, individual pair-wise fold-changes were calculated for each of the groups analyzed in step 1, providing threefold-change values per group (one for each paired replicate sample). This allowed for groups of fold-change values for a given time point in the aged group to be directly compared to those in the young group, again using the t-statistic. An absolute fold-change value ≥ 1.5 in at least one of the groups tested (i.e. either 3 month or 9 month groups) and adjusted P-value < 0.05 were used as criteria for defining a set of genes for further exploration. Results of this analysis provided genes showing significant differential expression specific to the aged group compared to the young group with baseline differences subtracted.

organism: Mus musculus

source_name: Mouse left lung

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with Purelink RNA mini kit (Invitrogen #12183-018A) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Two samples were obtained from each mouse; the left lung was removed at day 0 during the pneumonectomy surgery and processed as a control sample; then, the remaining lung tissue was removed at one of three time points post-pneumonectomy (1 day, 3 days, or 7 days). For each of the three time points, two groups of mice were used: (1) aged and (2) young, with six animals in each group. For the microarray experiment, equal amounts of RNA from 2 animals (control and PNX samples) were pooled, resulting in a total of 3 control and 3 PNX microarray samples at each time point.

value: left lung

tag: strain

tag: Sex

value: female

tag: age

value: 3 months

tag: group

tag: day

value: Young

value: Control

tag: sample

tag: biorep

tag: condition


title: DLBCL biopsy, sample 2125


title: DLBCL biopsy, sample 2157


title: DLBCL biopsy, sample 2195


title: DLBCL biopsy, sample 2138


title: DLBCL biopsy, sample 2134


title: DLBCL biopsy, sample 2184A


title: DLBCL biopsy, sample 2160


title: DLBCL biopsy, sample 2152


title: DLBCL biopsy, sample 2162


title: DLBCL biopsy, sample 2144


title: DLBCL biopsy, sample 2127


title: DLBCL biopsy, sample 2148


title: DLBCL biopsy, sample 2126


title: DLBCL biopsy, sample 2163


title: DLBCL biopsy, sample 2183


title: DLBCL biopsy, sample 2135


title: DLBCL biopsy, sample 2112


title: DLBCL biopsy, sample 2113


title: DLBCL biopsy, sample 2105


title: DLBCL biopsy, sample 2100


title: DLBCL biopsy, sample 2110


title: DLBCL biopsy, sample 2103


title: DLBCL biopsy, sample 2104


title: DLBCL biopsy, sample 2091


title: DLBCL biopsy, sample 2094


title: DLBCL biopsy, sample 2087


title: DLBCL biopsy, sample 2069


title: DLBCL biopsy, sample 2072


title: DLBCL biopsy, sample 2097


title: DLBCL biopsy, sample 2085


title: DLBCL biopsy, sample 2078


title: DLBCL biopsy, sample 2089


title: DLBCL biopsy, sample 2096


title: DLBCL biopsy, sample 2065


title: DLBCL biopsy, sample 2109


title: DLBCL biopsy, sample 2108


title: DLBCL biopsy, sample 2106


title: DLBCL biopsy, sample 2064


title: DLBCL biopsy, sample 2093


title: DLBCL biopsy, sample 2082


title: DLBCL biopsy, sample 2102


title: DLBCL biopsy, sample 2083


title: DLBCL biopsy, sample 2067


title: DLBCL biopsy, sample 2073


title: DLBCL biopsy, sample 2063


title: DLBCL biopsy, sample 2062


title: DLBCL biopsy, sample 2057


title: DLBCL biopsy, sample 2034


title: DLBCL biopsy, sample 2043


title: DLBCL biopsy, sample 2060


title: DLBCL biopsy, sample 2044


title: DLBCL biopsy, sample 2040


title: DLBCL biopsy, sample 2041


title: DLBCL biopsy, sample 2027

description:
frozen biopsy of cutaneous tumor
Gene expression data from primary DLBCL biopsy

value: cutaneous tumor


title: DLBCL biopsy, sample 2032


title: DLBCL biopsy, sample 2026


title: DLBCL biopsy, sample 2029


title: DLBCL biopsy, sample 2023


title: DLBCL biopsy, sample 2046


title: DLBCL biopsy, sample 2025


title: DLBCL biopsy, sample 2019


title: Germinal Center Centrocytes, sample 5

description:
CD10-positive CD77-negative B-cells purified by magnetic cell separation.
Gene expression data from purified germinal center centrocytes

source_name: Germinal Center Centrocytes from human tonsil

tag: cell type

value: CD10-positive cell type:CD77-negative B-cells purified by magnetic cell separation.


title: DLBCL biopsy, sample 2020

description:
frozen biopsy of splenic tumor
Gene expression data from primary DLBCL biopsy

value: splenic tumor


title: Germinal Center Centrocytes, sample 4


title: Germinal Center Centrocytes, sample 2


title: DLBCL biopsy, sample 2024


title: Germinal Center Centrocytes, sample 1


title: DLBCL biopsy, sample 2012


title: DLBCL biopsy, sample 2015


title: Germinal Center Centrocytes, sample 3


title: DLBCL biopsy, sample 2017


title: DLBCL biopsy, sample 2033


title: DLBCL biopsy, sample 2016


title: Germinal Center Centroblasts, sample 5

description:
CD77-positive B-cells from human tonsil, purified by magnetic cell separation.
Gene expression data from purified germinal center centroblasts

source_name: Germinal Center Centroblasts from human tonsil

value: CD77-positive B-cells from human tonsil


title: Germinal Center Centroblasts, sample 4


title: Germinal Center Centroblasts, sample 2


title: Gene expression of the partial aneuploid bearing Ch16 and S28. (D108)

status: Public on Dec 01 2007

description: Comparing between wild type haploid (Cy3) and partial aneuploid bearing Ch16 amd S28 (Cy5).

source_name: CRLb35, logarithmically growing

growth_protocol: A white single colony of S. pombe cells on a YE plate was inoculated into YES liquid medium to grow to 5x(the 6th power of 10)cell/ml at 30°C.

growth_protocol: A single colony of S. pombe cells on a YES plate was inoculated into YES liquid medium to grow to 5x(the 6th power of 10)cell/ml at 30°C.


title: Gene expression of the partial aneuploid bearing Ch10. (D254)

description: Comparing between wild type haploid (Cy3) and partial aneuploid bearing Ch10.

source_name: CRLe70, logarithmically growing

source_name: CRLe72, logarithmically growing


title: Gene expression of the partial aneuploid bearing Ch10. (D129)


title: Comparative genome hybridization of partial aneuploid bearing Ch16 and S28 (D249)

type: genomic

description: Comparing between wild type haploid (Cy3) and partial aneuploid bearing Ch16 (Cy5).

data_processing: Measured fluorescent intensity, I, was corrected as follows to give a corrected intensity, C:C = I-M,  (for I>M+2s), C = I*2s/(M+2s),  (for I<M+2s) where M and s are an average and a standard deviation of I of negative control spots for each wave length respectively. When I = M+2s, that is C=2s, it was set to be a detection limit. When C for either Cy3 or Cy5 or both were greater than 2s, the values were considered to be effective data. VALUE (Copy ratio r') of the each effective detection spot obtained thus was scaled as follows: r'=r-m, r=logR(base is 2), R=(Ccy5/Ccy3), m is an average of r of all effective detection spots.

molecule: genomic DNA

label_protocol: The isolated genome DNA was divided into 3 aliquots. They were digested with AluI, RsaI, and Sau3AI, respectively, and then were mixed. After short DNA fragments (16bp or less) were excluded by CENTRI-SEP Span column (Applied Biosystems) and were labeled with Cy5-dUTP by Oligotailing kit (Rochediagnostics). After once purification with CENTRI-SEP Span column, 1-1.5µg labeled targets were added to the hybridization solution.

extract_protocol: Genome DNA was isolated from the S.pombe cell nuclei according to Matsumoto et al., 1987, Mol. Cell. Biol. vol.7 pp 4424-4430.

label_protocol: The isolated genome DNA was divided into 3 aliquots. They were digested with AluI, RsaI, and Sau3AI, respectively, and then were mixed. After short DNA fragments (16bp or less) were excluded by CENTRI-SEP Span column (Applied Biosystems) and were labeled with Cy3-dUTP by Oligotailing kit (Rochediagnostics). After once purification with CENTRI-SEP Span column, 1-1.5µg labeled targets were added to the hybridization solution.


title: Germinal Center Centroblasts, sample 3


title: DLBCL biopsy, sample 2165


title: Germinal Center Centroblasts, sample 1

description:
CD77-positive B-cells from human tonsil, purified by magnetic cell separation.
Gene expression data from purified germinal center centroblasts.


title: Lymphoma lambda MYCtg/IµHABCL6KI/AIDKO 2

status: Public on Nov 01 2007

description: Gene expression data from nodal B-NHL of lMYC transgenic/IµHABCL6 Knock-in/AIDKO mouse

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for at least 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The data were analyzed with MAS5 in the Affymetrix GeneChip Operating Software (GCOS v1.2) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 250.

source_name: nodal B-NHL from lambda MYC transgenic/IµHABCL6 Knock-in/AIDKO mouse 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Anymals were monitored biweekly and sacrificed upon evidence of tumor formation.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Nodal tumors were isolated,frozen in dry ice and stored at -80C.

tag: Strain

value: mixed C57BL/6xSv129

tag: Tissue

value: frozen biopsy of lymph node tumor


title: Lymphoma lambda MYCtg/IµHABCL6KI/AIDKO 6

source_name: nodal B-NHL from lambda MYC transgenic/IµHABCL6 Knock-in/AIDKO mouse 6


title: Gene expression of the partial aneuploid bearing Ch16 and S28. (D237)


title: Chromatin immunoprecipitation with anti Swi6 aintibody in wild type (E112)

description: Comparing between genomic DNA (Cy3) and DNA from immunoprecipitates with anti Swi6(Cy5) of wild type haploid.

data_processing: Measured fluorescent intensity, I, was corrected as follows to give a corrected intensity, C:C = I-M, (for I>M+2s), C = I*2s/(M+2s), (for I<M+2s) where M and s are an average and a standard deviation of I of negative control spots for each wave length respectively. When I = M+2s, that is C=2s, it was set to be a detection limit. When C for either Cy3 or Cy5 or both were greater than 2s, the values were considered to be effective data. VALUE (Copy ratio r') of the each effective detection spot obtained thus was scaled as follows: r'=r-m, r=logR(base is 2), R=(Ccy5/Ccy3), m is an average of r of all effective detection spots.

source_name: CRLf90, logarithmically growing

label_protocol: The amplified DNA were labeled with Cy5-dUTP by Oligotailing kit (Rochediagnostics).

extract_protocol: DNA isolated from immunoprecipitates was amplified according to methods in (Katou et al., 2003, Nature vol424, pp1078-1083). In the first round of amplification, A primer (GGAATTCCAGCTGACCACCNNNNNNNNN) and the template DNA were incubated in reaction mixture of Sequenase Ver2.0 T7 DNA polymerase (USB). In the second round of amplification, B primer (GGAATTCCAGCTGACCACC) and product of the first round was incubated in reaction mixture of Ex Taq polymerase (TAKARA).

label_protocol: The amplified DNA were labeled with Cy3-dUTP by Oligotailing kit (Rochediagnostics).

extract_protocol: Genome DNA was isolated from the S.pombe cell nuclei according to Matsumoto et al., 1987, Mol. Cell. Biol. vol.7 pp 4424-4430. The isolated genomic DNA was amplified according to methods in (Katou et al., 2003, Nature vol424, pp1078-1083). In the first round of amplification, A primer (GGAATTCCAGCTGACCACCNNNNNNNNN) and the template DNA were incubated in reaction mixture of Sequenase Ver2.0 T7 DNA polymerase (USB). In the second round of amplification, B primer (GGAATTCCAGCTGACCACC) and product of the first round was incubated in reaction mixture of Ex Taq polymerase (TAKARA).


title: Lymphoma lambda MYCtg/IµHABCL6KI/AIDKO 5

source_name: nodal B-NHL from lambda MYC transgenic/IµHABCL6 Knock-in/AIDKO mouse 5


title: Lymphoma lambda MYCtg/IµHABCL6KI 12

description: Gene expression data from nodal B-NHL of lMYC transgenic/IµHABCL6 Knock-in  mouse

source_name: nodal B-NHL from lambda MYC transgenic/IµHABCL6 Knock-in  mouse 12


title: Lymphoma lambda MYCtg/IµHABCL6KI/AIDKO 4

source_name: nodal B-NHL from lambda MYC transgenic/IµHABCL6 Knock-in/AIDKO mouse 4


title: Chromatin immunoprecipitation with anti Swi6 aintibody in wild type (CEN002)

hyb_protocol: The labeled targets (~100ng) were added to the hybridization solution to hybridize to the DNA probes on the microarray, using Genomic solutions GeneTac Hybridization Station, for four hours at 40°C in Genomic solutions GeneTac Hyb buffer (120µl; including 42% formamide). After hybridization, the slides were washed in the following sequence: (1) 2xSSC 0.1%SDS at 40°C for 5min, (2) 0.2xSSC at 25°C for 1min, and (3) 0.1xSSC at 25°C for 1min.

scan_protocol: Microarrays were scanned using an ArrayWoRx array scanner, and the acquired data was analyzed by ArrayWoRx software (Applied Precision, Inc.). The fluorescence intensity of each spot circle (150µm diameter) was measured using SoftWorx tracker.

data_processing:
The measured fluorescent intensity, designated by I, was corrected as follows to give a corrected intensity designated by C:C=I-M in case of I>M+2s, C=I*2s/(M+2s) in case of I<M+2s. M and s are the average and standard deviation of I of negative control spots for each wave length, respectively. When I = M+2s, that is C=2s, it was set as the detection limit.  When C for either Cy3 or Cy5, or both, was greater than 2s, the values were considered to be effective data. The value r' of the each effective detection spot obtained was calculated as follows:
r'=r-m, r=logR(the base of 2), R=(Ccy5/Ccy3), m is the average of r for  the unique region , which is on the outside of cen1.

label_protocol: The amplified DNA, from the immunoprecipitates, was labeled with Cy5-dUTP, using an Oligotailing kit (Roche Diagnostics).

extract_protocol: The DNA, isolated from immunoprecipitates, was amplified according to previously described methods (Katou et al., 2003. Nature v424, pp 1078-1083). In the first round of amplification, primer A (GGAATTCCAGCTGACCACCNNNNNNNNN) and the template DNA were incubated in reaction mixture containing Sequenase Ver2.0 T7 DNA polymerase (USB). In the second round of amplification, primer B (GGAATTCCAGCTGACCACC) and the product of the first round were incubated in reaction mixture with Ex Taq polymerase (TAKARA).

label_protocol: The amplified DNA, from the whole nuclei was labeled with Cy3-dUTP, using an Oligotailing kit (Roche Diagnostics).

extract_protocol: Genomic DNA was isolated from S. pombe using the methods described in Matsumoto et al., 1987,  Mol. Cell. Biol. vol.7 pp 4424-4430. Genomic DNA, isolated from nuclei  was amplified according to previously described methods (Katou et al., 2003 Nature v424, pp 1078-1083). In the first round of amplification, primer A (GGAATTCCAGCTGACCACCNNNNNNNNN) and the template DNA were incubated in reaction mixture containing Sequenase Ver2.0 T7 DNA polymerase (USB). In the second round of amplification, primer B (GGAATTCCAGCTGACCACC) and the product of the first round were incubated in reaction mixture with Ex Taq polymerase (TAKARA).


title: Chromatin immunoprecipitation with anti Swi6 aintibody in partial aneuploid bearing Ch10 (CEN003)


title: Gene expression of the partial aneuploid bearing Ch16. (D107)

source_name: AY238-8B, logarithmically growing


title: Lymphoma lambda MYCtg/IµHABCL6KI/AIDKO 3

source_name: nodal B-NHL from lambda MYC transgenic/IµHABCL6 Knock-in/AIDKO mouse 3


title: Relative amounts of mRNA for each ORF

status: Public on Apr 01 2009

type: mixed

description: Comparing between genome DNA (Cy3) and mRNA (Cy5) of wild type haploid.

data_processing: Measured fluorescent intensity, I, was corrected as follows to give a corrected intensity, C:C = I-M,  (for I>M+2s), C = I*2s/(M+2s),  (for I<M+2s) where M and s are an average and a standard deviation of I of negative control spots for each wave length respectively. When I = M+2s, that is C=2s, it was set to be a detection limit. When C for either Cy3 or Cy5 or both were greater than 2s, the values were considered to be effective data. Copy ratio r' of the each effective detection spot obtained thus was scaled as follows: r'=r-m, r=logR(base is 2), R=(Ccy5/Ccy3), m is an average of r of all effective detection spots. VALUE(E=the copy number of mRNA) was calculated as follows: E=(R'/S)*100,000, r'=logR'(base is 2), S=SUM(R' of all 4932 ORFs), where the total mRNA number in the cell  was estimated at 100,000 copies.

source_name: L972, logarithmically growing

treatment_protocol: A single colony of S. pombe cells on a YES plate was inoculated into YES liquid medium to grow to 5x(the 6th power of 10)cell/ml at 30°C.


title: Chromatin immunoprecipitation with anti Swi6 aintibody in partial aneuploid bearing Ch10 (E113)

description: Comparing between genomic DNA (Cy3) and DNA from immunoprecipitates with anti Swi6(Cy5) of partial aneuploid bearing Ch10.


title: Lymphoma lambda MYCtg/IµHABCL6KI 8

source_name: nodal B-NHL from lambda MYC transgenic/IµHABCL6 Knock-in  mouse 8


title: Comparative genome hybridization of partial aneuploid bearing Ch16 (D247)


title: Lymphoma lambda MYCtg/IµHABCL6KI 11

source_name: nodal B-NHL from lambda MYC transgenic/IµHABCL6 Knock-in  mouse 11


title: Gene expression of the partial aneuploid bearing Ch16. (D235)


title: Lymphoma lambda MYCtg/IµHABCL6KI/AIDKO 1

source_name: nodal B-NHL from lambda MYC transgenic/IµHABCL6 Knock-in/AIDKO mouse 1


title: Lymphoma lambda MYCtg/IµHABCL6KI 10

source_name: nodal B-NHL from lambda MYC transgenic/IµHABCL6 Knock-in  mouse 10


title: Lymphoma lambda MYCtg/IµHABCL6KI 9

source_name: nodal B-NHL from lambda MYC transgenic/IµHABCL6 Knock-in  mouse 9


title: Lymphoma lambda MYCtg/IµHABCL6KI 4

source_name: nodal B-NHL from lambda MYC transgenic/IµHABCL6 Knock-in  mouse 4


title: Lymphoma lambda MYCtg/IµHABCL6KI 2

source_name: nodal B-NHL from lambda MYC transgenic/IµHABCL6 Knock-in  mouse 2


title: Lymphoma lambda MYCtg/IµHABCL6KI 7

source_name: nodal B-NHL from lambda MYC transgenic/IµHABCL6 Knock-in  mouse 7


title: Lymphoma lambda MYCtg/AIDKO 5

description: Gene expression data from nodal B-NHL of lMYC transgenic/AIDKO  mouse

source_name: nodal B-NHL from lambda MYC transgenic/AIDKO  mouse 5


title: Lymphoma lambda MYCtg/AIDKO 3

source_name: nodal B-NHL from lambda MYC transgenic/AIDKO  mouse 3


title: Lymphoma lambda MYCtg/IµHABCL6KI 6

source_name: nodal B-NHL from lambda MYC transgenic/IµHABCL6 Knock-in  mouse 6


title: Lymphoma lambda MYCtg 4

description: Gene expression data from nodal B-NHL  of lMYC mouse

source_name: nodal B-NHL from lambda MYC transgenic mouse 4


title: Lymphoma lambda MYCtg/IµHABCL6KI 5

source_name: nodal B-NHL from lambda MYC transgenic/IµHABCL6 Knock-in  mouse 5


title: Lymphoma lambda MYCtg/IµHABCL6KI 1

source_name: nodal B-NHL from lambda MYC transgenic/IµHABCL6 Knock-in  mouse 1


title: Lymphoma lambda MYCtg/AIDKO 4

source_name: nodal B-NHL from lambda MYC transgenic/AIDKO  mouse 4


title: Lymphoma lambda MYCtg/IµHABCL6KI 3

source_name: nodal B-NHL from lambda MYC transgenic/IµHABCL6 Knock-in  mouse 3


title: Lymphoma lambda MYCtg 5

source_name: nodal B-NHL from lambda MYC transgenic mouse 5


title: Lymphoma lambda MYCtg/AIDKO 2

source_name: nodal B-NHL from lambda MYC transgenic/AIDKO  mouse 2


title: Lymphoma lambda MYCtg 2

source_name: nodal B-NHL from lambda MYC transgenic mouse 2


title: Lymphoma lambda MYCtg/AIDKO 1

source_name: nodal B-NHL from lambda MYC transgenic/AIDKO  mouse 1


title: Lymphoma lambda MYCtg 1

source_name: nodal B-NHL from lambda MYC transgenic mouse 1


title: Lymphoma lambda MYCtg 3

source_name: nodal B-NHL from lambda MYC transgenic mouse 3


title: Gene expression in mmi1-ts3 mutant cells

status: Public on Jul 06 2006

description: Comparing between vegetatively-growing control cells and cells at 30minutes  after shift to the restrictive temperature.

hyb_protocol: The labeled targets were added to the hybridization solution to contain an equal amount of the Cy3 and Cy5, and then were hybridized onto DNA on the microarray, using Genomic solutions GeneTac Hybridization Station, for four hours at 40°C in Genomic solutions GeneTac Hyb buffer 120 microl (including 42% formamide ). The slides after hybridization were washed in the following sequence: (1) 2xSSC 0.1%SDS at 40°C for 5min, (2) 0.2xSSC at 25°C for 1min, and (3) 0.1xSSC at 25°C for 1min.

data_processing: RNA from vegetatively-growing control cells were labeled with Cy3, and RNA from cells in each experimental condition were labeled with Cy5. Measured fluorescent intensity, I, was corrected as follows to give a corrected intensity, C:C = I-M, (for IA°U¨M+2s), C = I*2s/(M+2s), (for IA°O¨M+2s) where M and s are an average and a standard deviation of I of negative control spots for each wave length respectively. When I = M+2s, that is C=2s, it was set to be a detection limit. When C for either Cy3 or Cy5 or both was greater than 2s, the values were considered to be effective data. VALUE (Expression ratio r') of the each effective detection spot obtained thus was scaled as follows: r'=r-m, r=logR(base is 2), R=(Ccy5/Ccy3), m is an average of r of all effective detection spots.

source_name: JV565, 30minutes after temperature shift

treatment_protocol: A single colony of S. pombe cells on a YES plate was inoculated into YES liquid medium to grow to 5x(the 6th power of 10) cell/ml at 25°C. Cells were shifted to 36°C and collected after further incubation for 30minutes.

tag: JV565 h- mmi1-ts3-adhT<<kanr ade6-M216 leu1

source_name: JV565, logarithmically growing

treatment_protocol: A single colony of S. pombe cells on a YES plate was inoculated into YES liquid medium. Cells were collected at 5x(the 6th power of 10) cell/ml at 25°C.


title: Gene expression upon nitrogen replenishment, 3.5 hr.(D260)

status: Public on Mar 31 2007

description: Comparing the growth-resuming cells at 2 hr after nitrogen replenishment (Cy5) with cells at nitrogen-starved G0 state (Cy3).

hyb_protocol: The labeled targets were added to the hybridization solution to contain an equal amount of the Cy3 and Cy5, and then were hybridized onto DNA on the microarray, using Genomic solutions GeneTac Hybridization Station, for four hours at 40°C in Genomic solutions GeneTac Hyb buffer 120microl (including 42% formamide ). The slides after hybridization were washed in the following sequence: (1) 2xSSC 0.1%SDS at 40°C for 5min, (2) 0.2xSSC at 25°C for 1min, and (3) 0.1xSSC at 25°Cfor 1min.

source_name: L972, 3.5 hr after nitrogen replenishment to nitrogen-starved G0 state.

treatment_protocol: A single colony of S. pombe cells on a YPD plate was inoculated into EMM2 liquid medium to grow to 2x(the 6th power of 10)cell/ml at 26C. After two washes in EMM2-N (EMM2 depleted of nitrogen sources), cells were transferred to EMM2-N with the concentration of 2x(the 7th power of 10)cell/ml and further incubated at 26C for 48 hr. During this incubation, most cells divided twice, nearly reached to 8x(the 7th power of 10)cell/ml in the first 6 hr and arrested at G0 state. After 48 hr incubation in EMM2-N, 4 volumes of fresh EMM2 liquid media was added to the culture for the nitrogen replenishment. Cells were collected at 3.5 hr after the replenishment.

source_name: L972, nitrogen-starved for 48 hrs, arrested at G0 state

treatment_protocol: A single colony of S. pombe cells on a YPD plate was inoculated into EMM2 liquid medium to grow to 2x(the 6th power of 10)cell/ml at 26C. After two washes in EMM2-N (EMM2 depleted of nitrogen sources), cells were transferred to EMM2-N with the concentration of 2x(the 7th power of 10)cell/ml and further incubated at 26C for 48 hr. During this incubation, cells divided twice and reached to 8x(the 7th power of 10)cell/ml in the first 6 hr and arrested at G0 state.


title: Gene expression in proliferating cells and in G0-arrested cells(D262)

source_name: L972, logarithmically growing

treatment_protocol: A single colony of S. pombe cells on a YPD plate was inoculated into EMM2 liquid medium to grow to 2x(the 6th power of 10)cell/ml at 26C.


title: Gene expression in mmi1-ts3 mutant cells (E140)


title: Gene expression in wild-type cells

source_name: JV558, 30minutes after temperature shift

tag: JV558 h- mmi1-adhT<<kanr ade6-M216 leu1

source_name: JV558, logarithmically growing


title: Gene expression upon nitrogen starvation, 3hrs (D168)

status: Public on Jun 13 2006

description: Comparing between vegetatively-growing control cells (Cy3) and cells 3 hrs after nitrogen starvation (Cy5).

source_name: AE411, 3hrs after nitorogen starvation

growth_protocol: A single colony of S. pombe cells on a YES plate was inoculated into YES liquid medium to grow to 5x(the 6th power of 10)cell/ml at 30｡C. After two washes in EMM2-N (EMM2 depleted of nitrogen sources), cells were transferred to EMM2-N and further incubated at 30｡C. Cells were collected  3 hrs after the nitrogen starvation.

tag: AE411 h- tsc1::ura4+ ura4-D18

source_name: AE411, logarithmically growing

growth_protocol: A single colony of S. pombe cells on a YES plate was inoculated into YES liquid medium. Cells were collected at 5x(the 6th power of 10)cell/ml at 30｡C.


title: Gene expression upon nitrogen starvation, 3hrs (D169)

source_name: AE509, 3hrs after nitorogen starvation

source_name: AE509, logarithmically growing


title: Gene expression upon nitrogen replenishment, 6 hr.(D261)

source_name: L972, 6 hr after nitrogen replenishment to nitrogen-starved G0 state.

treatment_protocol: A single colony of S. pombe cells on a YPD plate was inoculated into EMM2 liquid medium to grow to 2x(the 6th power of 10)cell/ml at 26C. After two washes in EMM2-N (EMM2 depleted of nitrogen sources), cells were transferred to EMM2-N with the concentration of 2x(the 7th power of 10)cell/ml and further incubated at 26C for 48 hr. During this incubation, most cells divided twice, nearly reached to 8x(the 7th power of 10)cell/ml in the first 6 hr and arrested at G0 state. After 48 hr incubation in EMM2-N, 4 volumes of fresh EMM2 liquid media was added to the culture for the nitrogen replenishment. Cells were collected at 6 hr after the replenishment.


title: Gene expression in wild-type cells (E139)


title: Gene expression upon nitrogen replenishment, 1 hr.

description: Comparing the growth-resuming cells at 1 hr after nitrogen replenishment (Cy5) with cells at nitrogen-starved G0 state (Cy3).

source_name: L972, 1 hr after nitrogen replenishment to nitrogen-starved G0 state.

treatment_protocol: A single colony of S. pombe cells on a YPD plate was inoculated into EMM2 liquid medium to grow to 2x(the 6th power of 10)cell/ml at 26C. After two washes in EMM2-N (EMM2 depleted of nitrogen sources), cells were transferred to EMM2-N with the concentration of 2x(the 7th power of 10)cell/ml and further incubated at 26C for 48 hr. During this incubation, most cells divided twice, nearly reached to 8x(the 7th power of 10)cell/ml in the first 6 hr and arrested at G0 state. After 48 hr incubation in EMM2-N, 4 volumes of fresh EMM2 liquid media was added to the culture for the nitrogen replenishment. Cells were collected at 1 hr after the replenishment.


title: Gene expression upon nitrogen replenishment, 2 hr.

source_name: L972, 2 hr after nitrogen replenishment to nitrogen-starved G0 state.

treatment_protocol: A single colony of S. pombe cells on a YPD plate was inoculated into EMM2 liquid medium to grow to 2x(the 6th power of 10)cell/ml at 26C. After two washes in EMM2-N (EMM2 depleted of nitrogen sources), cells were transferred to EMM2-N with the concentration of 2x(the 7th power of 10)cell/ml and further incubated at 26C for 48 hr. During this incubation, most cells divided twice, nearly reached to 8x(the 7th power of 10)cell/ml in the first 6 hr and arrested at G0 state. After 48 hr incubation in EMM2-N, 4 volumes of fresh EMM2 liquid media was added to the culture for the nitrogen replenishment. Cells were collected at 2 hr after the replenishment.


title: Gene expression upon nitrogen starvation and P-factor treatment, 8hrs (D164)

status: Public on Apr 20 2006

description: Comparing between vegetatively-growing control cells (Cy3) and cells at at each time point after nitrogen starvation with P-factor (Cy5).

hyb_protocol: The labeled targets were added to the hybridization solution to contain an equal amount of the Cy3 and Cy5, and then were hybridized onto DNA on the microarray, using Genomic solutions GeneTac Hybridization Station, for four hours at 40C in Genomic solutions GeneTac Hyb buffer 120microl (including 42% formamide ). The slides after hybridization were washed in the following sequence: (1) 2xSSC 0.1%SDS at 40C for 5min, (2) 0.2xSSC at 25C for 1min, and (3) 0.1xSSC at 25Cfor 1min.

source_name: CRL672, 8hrs after nitorogen starvation and P-factor treatment

treatment_protocol: A single colony of S. pombe cells on a YES plate was inoculated into YES liquid medium to grow to 5x(the 6th power of 10)cell/ml at 30C. After two washes in EMM2-N (EMM2 depleted of nitrogen sources), cells were transferred to EMM2-N with 0.5microg/ml synthetic P-factor and further incubated at 30C. Cells were collected at each time point  after the nitrogen starvation with P-factor.

tag: CRL672 h- ura4-D18, sxa2D::ura4+

source_name: CRL672, logarithmically growing

treatment_protocol: A single colony of S. pombe cells on a YES plate was inoculated into YES liquid medium. Cells were collected at 5x(the 6th power of 10)cell/ml at 30C.


title: Gene expression upon nitrogen starvation and P-factor treatment, 4hrs (D160)

source_name: CRL672, 4hrs after nitorogen starvation and P-factor treatment


title: Gene expression upon nitrogen starvation and P-factor treatment, 5hrs (D161)

source_name: CRL672, 5hrs after nitorogen starvation and P-factor treatment


title: Gene expression upon nitrogen starvation, 6hrs (D154)

description: Comparing between vegetatively-growing control cells (Cy3) and cells at each time point after nitrogen starvation (Cy5).

source_name: L972, 6hrs after nitorogen starvation

treatment_protocol: A single colony of S. pombe cells on a YES plate was inoculated into YES liquid medium to grow to 5x(the 6th power of 10)cell/ml at 30C. After two washes in EMM2-N (EMM2 depleted of nitrogen sources), cells were transferred to EMM2-N and further incubated at 30C. Cells were collected  cells at each time point after the nitrogen starvation.

tag: L972 h- wild type


title: Gene expression upon nitrogen starvation and P-factor treatment, 7hrs (D163)

source_name: CRL672, 7hrs after nitorogen starvation and P-factor treatment


title: Gene expression upon nitrogen starvation, 5hrs (D153)

source_name: L972, 5hrs after nitorogen starvation


title: Gene expression upon nitrogen starvation, 7hrs (D155)

source_name: L972, 7hrs after nitorogen starvation

source_name: L972, logarithmically growing


title: Gene expression upon nitrogen starvation, 3hrs (D151)

source_name: L972, 3hrs after nitorogen starvation


title: Gene expression upon nitrogen starvation and P-factor treatment, 3hrs (D159)

source_name: CRL672, 3hrs after nitorogen starvation and P-factor treatment


title: Gene expression upon nitrogen starvation and P-factor treatment, 2hrs (D158)

source_name: CRL672, 2hrs after nitorogen starvation and P-factor treatment


title: Gene expression upon nitrogen starvation and P-factor treatment, 6hrs (D133)

source_name: CRL672, 6hrs after nitorogen starvation and P-factor treatment


title: Gene expression upon nitrogen starvation and P-factor treatment, 7hrs (D132)


title: Gene expression upon nitrogen starvation, 1hr (D149)

source_name: L972, 1hr after nitorogen starvation


title: Gene expression upon nitrogen starvation and P-factor treatment, 1hr (D157)

source_name: CRL672, 1hr after nitorogen starvation and P-factor treatment


title: Gene expression upon nitrogen starvation, 2hrs (D150)

source_name: L972, 2hrs after nitorogen starvation


title: Gene expression upon nitrogen starvation and P-factor treatment, 5hrs (D134)


title: Gene expression upon nitrogen starvation and P-factor treatment, 6hrs (D162)


title: Gene expression upon nitrogen starvation and P-factor treatment, 2hrs (D140)


title: Gene expression upon nitrogen starvation, 8hrs (D156)

source_name: L972, 8hrs after nitorogen starvation


title: Gene expression upon nitrogen starvation, 4hrs (D152)

source_name: L972, 4hrs after nitorogen starvation


title: Gene expression upon nitrogen starvation and P-factor treatment, 1hr (D141)

source_name: CRL672, logarithmically growing


title: Gene expression upon nitrogen starvation and P-factor treatment, 8hrs (D131)

source_name: CRL672, 8hrs after nitorogen starvation and P-factor treatment


title: Gene expression upon nitrogen starvation, 8hrs (D220)


title: Gene expression upon nitrogen starvation, 5hrs (D222)


title: Gene expression upon nitrogen starvation, 7hrs (D221)


title: Gene expression upon nitrogen starvation and P-factor treatment, 3hrs (D139)


title: Gene expression upon nitrogen starvation and P-factor treatment, 4hrs (D138)

source_name: CRL672, 4hrs after nitorogen starvation and P-factor treatment


title: Gene expression upon nitrogen starvation, 6hrs (D216)

source_name: L972, 6hrs after nitorogen starvation


title: Gene expression upon nitrogen starvation, 2hrs (D213)


title: Gene expression upon nitrogen starvation, 3hrs (D223)


title: Gene expression upon nitrogen starvation, 4hrs (D215)


title: Gene expression upon nitrogen starvation, 1hr (D224)

treatment_protocol: A single colony of S. pombe cells on a YES plate was inoculated into YES liquid medium to grow to 5x(the 6th power of 10)cell/ml at 30C. After two washes in EMM2-N (EMM2 depleted of nitrogen sources), cells were transferred to EMM2-N and further incubated at 30C. Cells were collected at 1 hour after the nitrogen starvation.