title: Sample ID 05_003 primary tumor from patient with localized prostate cancer

source_name: Primary tumor sample from a patient from whom disseminated cells were also collected.

extract_protocol: The entire prostate was histologically evaluated. The area selected for molecular analysis was from the tumor, which was not multifocal. Tumor cells were isolated by laser-capture microdissection (LCM), as described previously (Lin DW, Coleman IM, Hawley S, et al. Influence of surgical manipulation on prostate gene expression: implications for molecular correlates of treatment effects and disease prognosis. J Clin Oncol 2006;24:3763-70). Two to four thousand cells were collected. DNA was isolated by the QIAamp DNA Micro Kit (Qiagen, CA). DNA was then amplified by ligation mediated pcr (as per method described in Klein CA, Schmidt-Kittler O, Schardt JA, Pantel K, Speicher MR and Riethmuller G. Comparative genomic hybridization, loss of heterozygosity, and DNA sequence analysis of single cells. Proc Natl Acad Sci U S A 1999;96: 4494-4499).

value: This sample was part of a set of nine primary tumor samples that were matched with nine disseminated cell samples from the same patient.

tag: cell id

tag: gleason grade


title: Roots of the variety ICC588 treated by dehydration for 6 hours

status: Public on Sep 26 2008

type: SAGE

anchor: NlaIII

city: Dijon

first: Carlos

middle: Mauricio

last: Molina

state: Bourgogne

address: 17 Rue Sully

department: UMRLEG

country: France

institute: INRA

description: Supersage libraries of chickpea roots were developed in control as well as 6h dehydration conditions

molecule: polyA RNA

organism: Cicer arietinum

source_name: chickpea roots of variety ICC588

extract_protocol: CTAB with LiCl precipitation

tag: chickpea variety

value: ICC588 (salt tolerant)

tag: treatment

value: dehydration

tag: time

value: 6 hours


title: Sample ID 04_139 primary tumor from patient with localized prostate cancer

status: Public on Aug 17 2008

type: genomic

city: Seattle

first: Ilona

middle: N

last: Holcomb

state: WA

address: 1100 Fairview Ave N

department: Human Biology

country: USA

institute: Fred Hutchinson Cancer Research Center

hyb_protocol: On microgram each of tumor and reference DNA labeled with Cy5 and Cy3, respectively, were combined and briefly dried by Speedvac. The samples were resuspended in hybridization mix (50% formamide, 10% dextran sulfate, 3x SSC, 1.5% SDS) and heated to 70°C for 10 minutes, followed by 1-hour incubation at 37°C to allow blocking of repetitive sequences by human Cot-1 DNA. After incubation, samples were applied to the microarray under a coverslip and hybridized at 37°C for 18 hours. After hybridization, the arrays were then washed in 50% formamide and 2x SSC (pH 7.0) for 20 minutes at 45°C, followed by a 7-minute wash at room temperature in 0.1 mol/L NaPO4 (pH 8.0) and 0.1% NP40. After washing, the arrays were dried by centrifugation at 600 rpm for 5 minutes.

scan_protocol: Arrays were scanned with a GenePix 4000A scanner (Axon Instruments, Inc., Union City, CA); fluorescence data were processed with GenePix 3.0 image analysis software (Axon Instruments, Inc.). For each spot, log2 ratio = log2(Cy5/Cy3) and average log2 intensity = [log2(Cy5) + log2(Cy3)]/2 were calculated, where Cy5 and Cy3 refer to the median foreground fluorescent signals of the tumor and reference DNA, respectively. Background subtraction was not used because it conferred no benefit in tests run on cell lines with varying numbers of X chromosome copies.

data_processing: The log2 ratios on each array were normalized and corrected for intensity-based location adjustment with a block-level loess algorithm (as described in Yang YH, Dudoit S, Luu P, Speed TP Normalization for cDNA microarray Bittner ML Chen Y Dorsel AN Dougherty ER eds. . Microarrays: optical technologies and informatics 2001141-52. SPIE, Society for Optical Engineering Bellingham, WA).

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Array CGH bioprime kit (Invitrogen)

tag: tissue

tag: tnm stage

source_name: normal female reference DNA

extract_protocol: DNA was isolated using a QIAamp DNA Blood Mini Kit (Qiagen)

value: Female peripheral blood


title: Sample ID 05_143 primary tumor from patient with localized prostate cancer


title: Sample ID 04_171 primary tumor from patient with localized prostate cancer


title: Sample ID 05_064 primary tumor from patient with localized prostate cancer

tag: gleason grade was 7


title: Sample ID 04_032 primary tumor from patient with localized prostate cancer


title: Sample ID 04_109 primary tumor from patient with localized prostate cancer


title: Sample ID 04_116 primary tumor from patient with localized prostate cancer


title: Sample ID norm1898 normal-cell sample from patient with localized prostate cancer

source_name: Normal-cell sample collected in parallel with disseminated cells from the bone marrow of a patient with localized prostate cancer.

extract_protocol: 10-20 cells from each patient were pooled and amplified by ligation mediated PCR then labeled by random priming for array CGH analysis. This sample was part of a set of nine normal-cell samples that were used for defining thresholds of chromosomal loss and gain for the disseminated cell arrays.

value: Normal cells detected by CD45 positivity and isolated by micropipetting from the bone marrow of a patient with localized prostate cancer.


title: Sample ID norm1721 normal-cell sample from patient with localized prostate cancer


title: Sample ID norm1888 normal-cell sample from patient with localized prostate cancer


title: Sample ID 04_148 primary tumor from patient with localized prostate cancer


title: Sample ID norm1719 normal-cell sample from patient with localized prostate cancer


title: Sample ID norm1720 normal cell sample from patient with localized prostate cancer


title: C-lim Anaerobic reference (pH 5) #3

status: Public on May 23 2008

type: RNA

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

description:
C-lim Anaerobic reference (pH 5) #3
DA18E

hyb_protocol: According to manufacturer's procedures

scan_protocol: Data acquisition was performed using the Affymetrix scanner 3000, quantification of array images and data filtering were performed with the Affymetrix software packages Microarray Suite v5.0, MicroDB v3.0 and Data Mining Tool v3.0.

data_processing: Chip file GCOS (Affymetrix - version 1.2.0.037)

label: biotin

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: Chemostat sample

label_protocol:
Sampling of chemostat cultures, probe preparation and hybridization to Affymetrix GeneChip microarrays was performed as described previously (Piper et al., 2002), but with the following modifications.  Double-stranded cDNA synthesis was carried out using 15 μg of total RNA and the components of the One Cycle cDNA Synthesis Kit (Affymetrix).  The double-stranded cDNA was purified (Genechip Sample Cleanup Module, Qiagen) before in vitro transcription and labeling (GeneChip IVT Labeling Kit, Affymetrix).  Finally, labeled cRNA was purified (GeneChip Sample Cleanup Module) prior to fragmentation and hybridization of 15 μg of biotinylated cRNA.
Piper MDW, Daran-Lapujade P, Bro C, Regenberg B, Knudsen S, Nielsen J & Pronk JT (2002) Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J Biol Chem 277: 37001-37008.

growth_protocol:
The laboratory reference strain CEN.PK 113-7D (MATa) was grown at 30 °C in 2-L chemostat fermentors (Applikon, Schiedam, The Netherlands) with a working volume of 1-L using an electronic level sensor to maintain a constant volume.  All cultures, including the reference, were fed with minimal medium as described by Verduyn et al. (1992) with 25 g L-1 glucose as the limiting nutrient and 0.15 ml L-1 silicone antifoam (BDH, Poole, England) to prevent excessive foaming.  The dilution rate was set to 0.10 h-1 and the pH was controlled at 5.0 with the automatic addition (ADI 1031 bio controller, Applikon) of 2 M KOH.  The stirrer speed was set at 800 RPM and anaerobicity was maintained by sparging the fermentor with N2 gas at 500 ml min-1.  To prevent diffusion of oxygen, the fermentor was equipped with Norprene tubing and Viton O-rings and the medium vessel was also flushed with N2 gas.
Verduyn C, Postma E, Scheffers WA & van Dijken JP (1992) Effect of benzoic acid on metabolic fluxes in yeast: a continuous-culture study on the regulation of respiration and alcoholic fermentation. Yeast 8: 501-517.

extract_protocol:
Sampling of chemostat cultures and probe preparation was performed as described previously (Piper et al., 2002).
Piper MDW, Daran-Lapujade P, Bro C, Regenberg B, Knudsen S, Nielsen J & Pronk JT (2002) Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J Biol Chem 277: 37001-37008.

treatment_protocol: N2 quenching

tag: Saccharomyces cerevisiae CEN.PK 113-7D (MATa)


title: C-lim Anaerobic reference (pH 5) #2

description:
C-lim Anaerobic reference (pH 5) #2
DA17E


title: Aerobic glucose limited 3

status: Public on Nov 15 2007

description:
P15
Keywords = S.cerevisiae
Keywords = chemostat
Keywords = nutrient limitation

hyb_protocol: Probe Preparation and Hybridization to Arrays-mRNA extraction, cDNA synthesis, cRNA synthesis and labeling, as well as array hybridization were performed as described in the Affymetrix usersâ€™ manual (1). Briefly, poly(A)_ RNA was enriched from total RNA in a single round using the Qiagen Oligotex kit. Double-stranded cDNA synthesis was carried out incorporating the T7 RNA-polymerase promoter in the first round. This cDNA was then used as template for in vitro transcription (ENZO BioArray High Yield IVT kit), which amplifies the RNA pool and incorporates biotinylated ribonucleotides required for the staining procedures after hybridization. 15 mg of fragmented, biotinylated cRNA was hybridized to Affymetrix yeast S98 arrays at 45 Â°C for 16 h as described in the Affymetrix usersâ€™ manual (1). Washing and staining of arrays were performed using the GeneChip Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner. (1) Affymetrix (2000) Affymetrix GeneChip Expression Analysis Technical Manual, Santa Clara, CA

data_processing:
Sample_data_processing: 	Data Acquisition and Primary Analysis
Acquisition and quantification of array images as well as primary data analysis were performed using the Affymetrix software packages: Microarray Suite version 4.0.1, MicroDB version 2.0, and Data Mining Tool version 2.0. Microsoft Excel was used for further statistical analyses. All arrays were globally scaled to a target value of 150 using the average signal from all gene features using Microarray Suite version 4.0.1. When pairwise comparisons were performed (using Microarray Suite version 4.0.1), a transcript was considered changed when a call of Increase or Decrease was made, the -fold change was at least 2, and the higher of the two average difference values was called present.

source_name: chemostat culture

label_protocol:
Probe Preparation and Hybridization to Arraysâ€”mRNA extraction, cDNA synthesis, cRNA synthesis and labeling, as well as array hybridization were performed as described in the Affymetrix usersâ€™ manual (1). Briefly, poly(A)_ RNA was enriched from total RNA in a single round using the Qiagen Oligotex kit. Double-stranded cDNA synthesis was carried out incorporating the T7 RNA-polymerase promoter in the first round. This cDNA was then used as template for in vitro transcription (ENZO BioArray High Yield IVT kit), which amplifies the RNA pool and incorporates biotinylated ribonucleotides required for the staining procedures after hybridization. 15 mg of fragmented, biotinylated cRNA was hybridized to Affymetrix yeast S98 arrays at 45 Â°C for 16 h as described in the Affymetrix usersâ€™ manual (1). Washing and staining of arrays were performed using the GeneChip Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner.
(1) Affymetrix (2000) Affymetrix GeneChip Expression Analysis Technical Manual, Santa Clara, CA

growth_protocol:
Chemostat Cultivation
Steady-state chemostat cultures were grown in Applikon laboratory fermentors of 1-liter working volume as described in detail elsewhere [van den Berg, M. A., de Jong-Gubbels, P., Kortland, C. J., van Dijken, J. P., Pronk, J. T., and Steensma, H. Y. (1996) J. Biol. Chem. 271, 28953-28959]. In brief, the cultures were fed with a defined mineral medium containing glucose as the growth-limiting nutrient [. Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1990) Microbiol.Rev. 58, 616-630]. The dilution rate (which equals the specific growth rate) in the steady-state cultures was 0.10 h_1, the temperature was 30°C, and the culture pH was 5.0.
Aerobic conditions were maintained by sparging the cultures with air (0.5 liter_min_1). The dissolved oxygen concentration, which was continuously monitored with an Ingold model 34-100-3002 probe, remained above 80% of air saturation.

treatment_protocol: Liquid N2 quenching

tag: Strain and Maintenance

tag: This study was performed with the prototrophic laboratory strain S. cerevisiae CEN.PK113-7D (MATa) [van Dijken, J. P., Bauer, J., Brambilla, L., Duboc, P., Francois, J. M., Gancedo, C., Giuseppin, M. L. F., Heinen, J. J., Hoare, M., Lange, H. C., Madden, E. A., Niederberger, P., Nielsen, J., Parrou, J. L., Petit, T., Porro, D., Reuss, M., van Riel, N., Rizzi, M., Steensma, H. Y., Verrips, C. T., Vindelov, J., and Pronk, J. T. (2000) Enz. Microb. Technol. 26, 706-714]


title: Aerobic glucose limited 2

description:
V2
Keywords = S.cerevisiae
Keywords = chemostat
Keywords = nutrient limitation

hyb_protocol: Probe Preparation and Hybridization to Arraysâ€”mRNA extraction, cDNA synthesis, cRNA synthesis and labeling, as well as array hybridization were performed as described in the Affymetrix users manual (1). Briefly, poly(A)_ RNA was enriched from total RNA in a single round using the Qiagen Oligotex kit. Double-stranded cDNA synthesis was carried out incorporating the T7 RNA-polymerase promoter in the first round. This cDNA was then used as template for in vitro transcription (ENZO BioArray High Yield IVT kit), which amplifies the RNA pool and incorporates biotinylated ribonucleotides required for the staining procedures after hybridization. 15 mg of fragmented, biotinylated cRNA was hybridized to Affymetrix yeast S98 arrays at 45 Â°C for 16 h as described in the Affymetrix users™ manual (1). Washing and staining of arrays were performed using the GeneChip Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner. (1) Affymetrix (2000) Affymetrix GeneChip Expression Analysis Technical Manual, Santa Clara, CA

data_processing:
Data Acquisition and Primary Analysis
Acquisition and quantification of array images as well as primary data analysis were performed using the Affymetrix software packages: Microarray Suite version 4.0.1, MicroDB version 2.0, and Data Mining Tool version 2.0. Microsoft Excel was used for further statistical analyses. All arrays were globally scaled to a target value of 150 using the average signal from all gene features using Microarray Suite version 4.0.1. When pairwise comparisons were performed (using Microarray Suite version 4.0.1), a transcript was considered changed when a call of Increase or Decrease was made, the -fold change was at least 2, and the higher of the two average difference values was called present.

label_protocol:
Probe Preparation and Hybridization to Arraysâ€”mRNA extraction, cDNA synthesis, cRNA synthesis and labeling, as well as array hybridization were performed as described in the Affymetrix users manual (1). Briefly, poly(A)_ RNA was enriched from total RNA in a single round using the Qiagen Oligotex kit. Double-stranded cDNA synthesis was carried out incorporating the T7 RNA-polymerase promoter in the first round. This cDNA was then used as template for in vitro transcription (ENZO BioArray High Yield IVT kit), which amplifies the RNA pool and incorporates biotinylated ribonucleotides required for the staining procedures after hybridization. 15 mg of fragmented, biotinylated cRNA was hybridized to Affymetrix yeast S98 arrays at 45 °C for 16 h as described in the Affymetrix users™ manual (1). Washing and staining of arrays were performed using the GeneChip Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner.
(1) Affymetrix (2000) Affymetrix GeneChip Expression Analysis Technical Manual, Santa Clara, CA

growth_protocol:
Chemostat Cultivation
Steady-state chemostat cultures were grown in Applikon laboratory fermentors of 1-liter working volume as described in detail elsewhere [van den Berg, M. A., de Jong-Gubbels, P., Kortland, C. J., van Dijken, J. P., Pronk, J. T., and Steensma, H. Y. (1996) J. Biol. Chem. 271, 28953-28959]. In brief, the cultures were fed with a defined mineral medium containing glucose as the growth-limiting nutrient [. Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1990) Microbiol.Rev. 58, 616-630]. The dilution rate (which equals the specific growth rate) in the steady-state cultures was 0.10 h_1, the temperature was 30 Â°C, and the culture pH was 5.0.
Aerobic conditions were maintained by sparging the cultures with air (0.5 liter_min_1). The dissolved oxygen concentration, which was continuously monitored with an Ingold model 34-100-3002 probe, remained above 80% of air saturation.

extract_protocol:
Sampling and RNA Isolation
Samples from the chemostat cultures were taken as rapidly as possible to limit any potential changes in transcript profiles during the procedure. 40-60 ml of culture broth was sampled directly from the chemostat into a beaker containing 200 ml of liquid nitrogen. With vigorous stirring, the sample froze instantly. The frozen sample was then broken into small fragments and transferred to a 50-ml centrifuge tube. The sample was then thawed at room temperature, ensuring that it remained as close to zero as possible. Cells were pelleted (5000 rpm at 0 °C for 4 min), resuspended in 2 ml of ice-cold AE buffer (50 mM sodium acetate, 10 mM EDTA, pH 5.0) and aliquoted into 5 Eppendorf tubes. This corresponded to _20 mg of dry weight per tube. For each array, total RNA was extracted from a single tube using the hot-phenol method (32) or the FastRNA kit, Red (BIO 101, Inc., Vista, CA).

treatment_protocol: Liquid N2 Quenching


title: C-lim Anaerobic reference (pH 5) #1

description:
C-lim Anaerobic reference (pH 5) #1
DA16E


title: 200cGy replicate 6

status: Public on Mar 01 2007

city: Durham

first: Holly

middle: Kloos

last: Dressman

state: NC

address: 101 Science Drive

department: Institute for Genome Sciences and Policy

institute: Duke University Medical Center

data_processing: Data was analysed with GeneSpring 7 data software package (Silicon Genetics). Each data set was filtered based on 1.5X background, thus there are missing data ( ) and normalised using  Lowess intensity-dependent normalisation.

organism: Mus musculus

source_name: 200cGy replicate 6

growth_protocol: no growth protocol

extract_protocol: Briefly, 5 x 106 MNCs were pelleted and total RNA was isolated using the RNAeasy minispin column

tag: MNCs were plelleted and total RNA was isolated via RNAeasy minispin column

source_name: Stratagene Universal Mouse reference

treatment_protocol: No treatment


title: Aerobic glucose limited 1

description:
P14
Keywords = S.cerevisiae
Keywords = chemostat
Keywords = nutrient limitation

hyb_protocol: Probe Preparation and Hybridization to Arrays—mRNA extraction, cDNA synthesis, cRNA synthesis and labeling, as well as array hybridization were performed as described in the Affymetrix users’ manual (1). Briefly, poly(A)_ RNA was enriched from total RNA in a single round using the Qiagen Oligotex kit. Double-stranded cDNA synthesis was carried out incorporating the T7 RNA-polymerase promoter in the first round. This cDNA was then used as template for in vitro transcription (ENZO BioArray High Yield IVT kit), which amplifies the RNA pool and incorporates biotinylated ribonucleotides required for the staining procedures after hybridization. 15 mg of fragmented, biotinylated cRNA was hybridized to Affymetrix yeast S98 arrays at 45 °C for 16 h as described in the Affymetrix users’ manual (1). Washing and staining of arrays were performed using the GeneChip Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner. (1) Affymetrix (2000) Affymetrix GeneChip Expression Analysis Technical Manual, Santa Clara, CA

data_processing:
Data Acquisition and Primary Analysis—
Acquisition and quantification of array images as well as primary data analysis were performed using the Affymetrix software packages: Microarray Suite version 4.0.1, MicroDB version 2.0, and Data Mining Tool version 2.0. Microsoft Excel was used for further statistical analyses. All arrays were globally scaled to a target value of 150 using the average signal from all gene features using Microarray Suite version 4.0.1. When pairwise comparisons were performed (using Microarray Suite version 4.0.1), a transcript was considered “changed” when a call of Increase or Decrease was made, the -fold change was at least 2, and the higher of the two average difference values was called present.

growth_protocol:
Chemostat Cultivation—
Steady-state chemostat cultures were grown in Applikon laboratory fermentors of 1-liter working volume as described in detail elsewhere [van den Berg, M. A., de Jong-Gubbels, P., Kortland, C. J., van Dijken, J. P., Pronk, J. T., and Steensma, H. Y. (1996) J. Biol. Chem. 271, 28953–28959]. In brief, the cultures were fed with a defined mineral medium containing glucose as the growth-limiting nutrient [. Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1990) Microbiol.Rev. 58, 616–630]. The dilution rate (which equals the specific growth rate) in the steady-state cultures was 0.10 h_1, the temperature was 30 °C, and the culture pH was 5.0.
Aerobic conditions were maintained by sparging the cultures with air (0.5 liter_min_1). The dissolved oxygen concentration, which was continuously monitored with an Ingold model 34-100-3002 probe, remained above 80% of air saturation.

extract_protocol:
Sampling and RNA Isolation—
Samples from the chemostat cultures were taken as rapidly as possible to limit any potential changes in transcript profiles during the procedure. 40–60 ml of culture broth was sampled directly from the chemostat into a beaker containing 200 ml of liquid nitrogen. With vigorous stirring, the sample froze instantly. The frozen sample was then broken into small fragments and transferred to a 50-ml centrifuge tube. The sample was then thawed at room temperature, ensuring that it remained as close to zero as possible. Cells were pelleted (5000 rpm at 0 °C for 4 min), resuspended in 2 ml of ice-cold AE buffer (50 mM sodium acetate, 10 mM EDTA, pH 5.0) and aliquoted into 5 Eppendorf tubes. This corresponded to _20 mg of dry weight per tube. For each array, total RNA was extracted from a single tube using the hot-phenol method (32) or the FastRNA kit, Red (BIO 101, Inc., Vista, CA).

treatment_protocol: liquid N2 Quenching

tag: Strain and Maintenance—

tag: This study was performed with the prototrophic laboratory strain S. cerevisiae CEN.PK113-7D (MATa) [van Dijken, J. P., Bauer, J., Brambilla, L., Duboc, P., Francois, J. M., Gancedo, C., Giuseppin, M. L. F., Heinen, J. J., Hoare, M., Lange, H. C., Madden, E. A., Niederberger, P., Nielsen, J., Parrou, J. L., Petit, T., Porro, D., Reuss, M., van Riel, N., Rizzi, M., Steensma, H. Y., Verrips, C. T., Vindelov, J., and

tag: Pronk, J. T. (2000) Enz. Microb. Technol. 26, 706–714]


title: 200cGy replicate 2

source_name: 200cGy replicate 2


title: 200cGy replicate 4

source_name: 200cGy replicate 4


title: 200cGy replicate 5

source_name: 200cGy replicate 5


title: 200cGy replicate 7

source_name: 200cGy replicate 7


title: 1000cGY replicate 1

source_name: 1000cGY replicate 1


title: 200cGy replicate 3

source_name: 200cGy replicate 3


title: 50cGy replicate 7

source_name: 50cGy replicate 7


title: 50cGy replicate 4

source_name: 50cGy replicate 4


title: 50cGy replicate 5

source_name: 50cGy replicate 5


title: 50cGy replicate 6

source_name: 50cGy replicate 6


title: Normal replicate 7

source_name: Normal replicate 7

treatment_protocol: no treatment


title: 50cGy replicate 1

source_name: 50cGy replicate 1


title: Normal replicate 6

source_name: Normal replicate 6


title: 200cGy replicate 1

source_name: 200cGy replicate 1


title: 50cGy replicate 3

source_name: 50cGy replicate 3


title: Normal replicate 5

source_name: Normal replicate 5


title: Normal replicate 4

source_name: Normal replicate 4

source_name: Stratagene Universal Mouse reference


title: Normal replicate 3

source_name: Normal replicate 3


title: 50cGy replicate 2

source_name: 50cGy replicate 2


title: Normal replicate 2

source_name: Normal replicate 2


title: Normal replicate 1

source_name: Normal replicate 1


title: Aerobic glucose limited 6

status: Public on May 23 2006

description: Sample MA55

hyb_protocol: 15 mg of fragmented, biotinylated cRNA was hybridized to Affymetrix yeast S98 arrays at 45 °C for 16 h as described in the Affymetrix users’ manual (1). Washing and staining of arrays were performed using the GeneChip Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner.(1) Affymetrix (2000) Affymetrix GeneChip Expression Analysis Technical Manual, Santa Clara, CA

scan_protocol: Data Acquisition and Primary Analysis—Acquisition and quantification of array images as well as primary data analysis were performed using the Affymetrix software packages: Microarray Suite version 4.0.1, MicroDB version 2.0, and Data Mining Tool version 2.0. Microsoft Excel was used for further statistical analyses. All arrays were globally scaled to a target value of 150 using the average signal from all gene features using Microarray Suite version 4.0.1. When pairwise comparisons were performed (using Microarray Suite version 5.0), a transcript was considered “changed” when a call of Increase or Decrease was made, the -fold change was at least 2, and the higher of the two average difference values was called present.

data_processing: MAS 5.0

source_name: chemostat culture

label_protocol: Probe Preparation and Hybridization to Arrays—mRNA extraction, cDNA synthesis, cRNA synthesis and labeling, as well as array hybridization were performed as described in the Affymetrix users’ manual (1). Briefly, poly(A)_ RNA was enriched from total RNA in a single round using the Qiagen Oligotex kit. Double-stranded cDNA synthesis was carried out incorporating the T7 RNA-polymerase promoter in the first round. This cDNA was then used as template for in vitro transcription (ENZO BioArray High Yield IVT kit), which amplifies the RNA pool and incorporates biotinylated ribonucleotides required for the staining procedures after hybridization.

growth_protocol: Chemostat Cultivation—Steady-state chemostat cultures were grown in Applikon laboratory fermentors of 1-liter working volume as described in detail elsewhere [van den Berg, M. A., de Jong-Gubbels, P., Kortland, C. J., van Dijken, J. P., Pronk, J. T., and Steensma, H. Y. (1996) J. Biol. Chem. 271, 28953–28959]. In brief, the cultures were fed with a defined mineral medium containing glucose as the growth-limiting nutrient [. Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1990) Microbiol.Rev. 58, 616–630]. The dilution rate (which equals the specific growth rate) in the steady-state cultures was 0.10 h_1, the temperature was 30 °C, and the culture pH was 5.0.Aerobic conditions were maintained by sparging the cultures with air (0.5 liter_min_1). The dissolved oxygen concentration, which was continuously monitored with an Ingold model 34-100-3002 probe, remained above 80% of air saturation.

extract_protocol: Sampling and RNA Isolation—Samples from the chemostat cultures were taken as rapidly as possible to limit any potential changes in transcript profiles during the procedure. 40–60 ml of culture broth was sampled directly from the chemostat into a beaker containing 200 ml of liquid nitrogen. With vigorous stirring, the sample froze instantly. The frozen sample was then broken into small fragments and transferred to a 50-ml centrifuge tube. The sample was then thawed at room temperature, ensuring that it remained as close to zero as possible. Cells were pelleted (5000 rpm at 0 °C for 4 min), resuspended in 2 ml of ice-cold AE buffer (50 mM sodium acetate, 10 mM EDTA, pH 5.0) and aliquoted into 5 Eppendorf tubes. This corresponded to _20 mg of dry weight per tube. For each array, total RNA was extracted from a single tube using the hot-phenol method (32) or the FastRNA kit, Red (BIO 101, Inc., Vista, CA).

tag: Strain and Maintenance—This study was performed with the prototrophic laboratory strain S. cerevisiae CEN.PK113-7D (MATa) [van Dijken, J. P., Bauer, J., Brambilla, L., Duboc, P., Francois, J. M., Gancedo, C., Giuseppin, M. L. F., Heinen, J. J., Hoare, M., Lange, H. C., Madden, E. A., Niederberger, P., Nielsen, J., Parrou, J. L., Petit, T., Porro, D., Reuss, M., van Riel, N., Rizzi, M., Steensma, H. Y., Verrips, C. T., Vindelov, J., and Pronk, J. T. (2000) Enz. Microb. Technol. 26, 706–714]


title: Anaerobic carbon limited 4

description: Sample MA72

hyb_protocol: 15 mg of fragmented, biotinylated cRNA was hybridized to Affymetrix yeast S98 arrays at 45 °C for 16 h as described in the Affymetrix users’ manual (1). Washing and staining of arrays were performed using the GeneChip Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner..

scan_protocol: Data Acquisition and Primary Analysis—Acquisition and quantificationof array images as well as primary data analysis were performed using the Affymetrix software packages: Microarray Suite version 4.0.1, MicroDB version 2.0, and Data Mining Tool version 2.0. Microsoft Excel was used for further statistical analyses. All arrays were globally scaled to a target value of 150 using the average signal from all gene features using Microarray Suite version 4.0.1. When pairwise comparisons were performed (using Microarray Suite version 4.0.1), a transcript was considered “changed” when a call of Increase or Decrease was made, the -fold change was at least 2, and the higher of the two average difference values was called present.

source_name: Chemostat culture

growth_protocol: Chemostat Cultivation—Steady-state chemostat cultures were grown in Applikon laboratory fermentors of 1-liter working volume as described in detail elsewhere [van den Berg, M. A., de Jong-Gubbels, P., Kortland, C. J., van Dijken, J. P., Pronk, J. T., and Steensma, H. Y. (1996) J. Biol. Chem. 271, 28953–28959]. In brief, the cultures were fed with a defined mineral medium containing glucose as the growth-limiting nutrient [. Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1990) Microbiol.Rev. 58, 616–630]. The dilution rate (which equals the specific growth rate) in the steady-state cultures was 0.10 h_1, the temperature was 30 °C, and the culture pH was 5.0. For anaerobic cultivation, the reservoir medium was supplemented with Tween 80 and ergosterol as described previously. Anaerobic conditions were maintained by sparging the medium reservoir and the fermentor with pure nitrogen gas (0.5 liter_min_1). Furthermore, Norprene tubing and butyl rubber septa were used to minimize oxygen of Increase or Decrease was made, the -fold change was at least 2, and the higher of the two average difference values was called present.Media—The defined mineral medium composition was based on that described by Verduyn et al [. Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1990) Microbiol.Rev. 58, 616–630]. The residual glucose concentration was targeted to 17 g_liter_1 to sustain glucose repression at the same level . For carbon limited cultivation: 5.0 g of (NH4)2SO4, 3.0 g of KH2PO4, 0.5 g of MgSO4.7H2O, and 25 g of glucose.

tag: This study was performed with the prototrophic laboratory strain S. cerevisiae CEN.PK113-7D (MATa) [van Dijken, J. P., Bauer, J., Brambilla, L., Duboc, P., Francois, J. M., Gancedo, C., Giuseppin, M. L. F., Heinen, J. J., Hoare, M., Lange, H. C., Madden, E. A., Niederberger, P., Nielsen, J., Parrou, J. L., Petit, T., Porro, D., Reuss, M., van Riel, N., Rizzi, M., Steensma, H. Y., Verrips, C. T., Vindelov, J., andPronk, J. T. (2000) Enz. Microb. Technol. 26, 706–714]


title: Aerobic glucose limited 5

description: Sample MA54


title: intermediolateral column motoneurons (IML) 29, sham-operated control

status: Public on Dec 20 2005

city: Atlanta

first: Deborah

last: Baro

state: GA

institute: Georgia State University

description:
Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5.
This sample is also known as sham mice.  Set 1 - Pair 5 - IML

source_name: adult spinal cord, sham-operated control

tag: cell type

value: intermediolateral column motoneuron (IML)


title: medial motoneurons (MMN) 28, sham-operated control

description:
Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5.
This sample is also known as sham mice. Set 2 - Pair 5 - MMN

value: medial motoneuron (MMN)


title: Aerobic glucose limited 4

description: Sample MA53


title: Anaerobic carbon limited 6

description: Sample MA74

tag: Strain and Maintenance—This study was performed with the prototrophic laboratory strain S. cerevisiae CEN.PK113-7D (MATa) [van Dijken, J. P., Bauer, J., Brambilla, L., Duboc, P., Francois, J. M., Gancedo, C., Giuseppin, M. L. F., Heinen, J. J., Hoare, M., Lange, H. C., Madden, E. A., Niederberger, P., Nielsen, J., Parrou, J. L., Petit, T., Porro, D., Reuss, M., van Riel, N., Rizzi, M., Steensma, H. Y., Verrips, C. T., Vindelov, J., andPronk, J. T. (2000) Enz. Microb. Technol. 26, 706–714]


title: medial motoneurons (MMN) 27, sham-operated control

description:
Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5.
This sample is also known as sham mice. Set 1 - Pair 5 - MMN


title: intermediolateral column motoneurons (IML) 30, sham-operated control

description:
Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5.
This sample is also known as sham mice.  Set 2 - Pair 5 - IML


title: intermediolateral column motoneurons (IML) 24, sham-operated control

description:
Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5.
This sample is also known as sham mice.  Set 2 - Pair 4 - IML


title: lateral motoneurons (LMN) 26, sham-operated control

description:
Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5.
This sample is also known as sham mice.  Set 2 - Pair 5 - LMN

value: lateral motoneuron (LMN)


title: lateral motoneurons (LMN) 25, sham-operated control

description:
Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5.
This sample is also known as sham mice.  Set 1 - Pair 5 - LMN


title: lateral motoneurons (LMN) 20, sham-operated control

description:
Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5.
This sample is also known as sham mice.  Set 2 - Pair 4 - LMN


title: medial motoneurons (MMN) 16, sham-operated control

description:
Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5.
This sample is also known as sham mice. Set 2 - Pair 3 - MMN


title: medial motoneurons (MMN) 15, sham-operated control

description:
Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5.
This sample is also known as sham mice.  Set 1 - Pair 3 - MMN


title: lateral motoneurons (LMN) 19, sham-operated control

description:
Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5.
This sample is also known as sham mice. Set 1 - Pair 4 - LMN


title: intermediolateral column motoneurons (IML) 18, sham-operated control

description:
Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5.
This sample is also known as sham mice. Set 2 - Pair 3 - IML


title: intermediolateral column motoneurons (IML) 23, sham-operated control

description:
Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5.
This sample is also known as sham mice.  Set 1 - Pair 4 - IML


title: intermediolateral column motoneurons (IML) 17, sham-operated control

description:
Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5.
This sample is also known as sham mice. Set 1 - Pair 3 - IML


title: medial motoneurons (MMN) 21, sham-operated control

description:
Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5.
This sample is also known as sham mice.  Set 1 - Pair 4 - MMN


title: medial motoneurons (MMN) 22, sham-operated control

description:
Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5.
This sample is also known as sham mice.  Set 2 - Pair 4 - MMN


title: intermediolateral column motoneurons (IML) 12, sham-operated control

description:
Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5.
This sample is also known as sham mice.  Set 2 - Pair 2 - IML


title: Anaerobic carbon limited 5

description: Sample MA73


title: lateral motoneurons (LMN) 13, sham-operated control

description:
Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5.
This sample is also known as sham mice. Set 1 - Pair 3 - LMN


title: intermediolateral column motoneurons (IML) 11, sham-operated control

description:
Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5.
This sample is also known as sham mice. Set 1 - Pair 2 - IML


title: lateral motoneurons (LMN) 14, sham-operated control

description:
Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5.
This sample is also known as sham mice.  Set 2 - Pair 3 - LMN


title: medial motoneurons (MMN) 10, sham-operated control

description:
Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5.
This sample is also known as sham mice. Set 2 - Pair 2 - MMN


title: medial motoneurons (MMN) 9, sham-operated control

description:
Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5.
This sample is also known as sham mice.  Set 1 - Pair 2 - MMN


title: lateral motoneurons (LMN) 8, sham-operated control

description:
Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5.
This sample is also known as sham mice.  Set 2 - Pair 2 - LMN


title: intermediolateral column motoneurons (IML) 5, sham-operated control

description:
Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5.
This sample is also known as sham mice. Set 1 - Pair 1 - IML


title: medial motoneurons (MMN) 4, sham-operated control

description:
Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5.
This sample is also known as sham mice. Set 2 - Pair 1 - MMN


title: lateral motoneurons (LMN) 7, sham-operated control

description:
Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5.
This sample is also known as sham mice. Set 1 - Pair 2 - LMN


title: intermediolateral column motoneurons (IML) 6, sham-operated control

description:
Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5.
This sample is also known as sham mice. Set 2 - Pair 1 - IML


title: lateral motoneurons (LMN) 1, sham-operated control

description:
Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5.
This sample is also known as sham mice. Set 1 - Pair 1 - LMN


title: medial motoneurons (MMN) 3, sham-operated control

description:
Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5.
This sample is also known as sham mice. Set 1 - Pair 1 - MMN


title: Anaerobic carbon limited 3

status: Public on Sep 03 2004

description:
P20
Keywords = S.cerevisiae
Keywords = chemostat
Keywords = nutrient limitation

hyb_protocol: Probe Preparation and Hybridization to Arrays—mRNA extraction, cDNA synthesis, cRNA synthesis and labeling, as well as array hybridization were performed as described in the Affymetrix users’ manual (1). Briefly, poly(A)_ RNA was enriched from total RNA in a single round using the Qiagen Oligotex kit. Double-stranded cDNA synthesis was carried out incorporating the T7 RNA-polymerase promoter in the first round. This cDNA was then used as template for in vitro transcription (ENZO BioArray High Yield IVT kit), which amplifies the RNA pool and incorporates biotinylated ribonucleotides required for the staining procedures after hybridization. 15 mg of fragmented, biotinylated cRNA was hybridized to Affymetrix yeast S98 arrays at 45 °C for 16 h as described in the Affymetrix users’ manual (1). Washing and staining of arrays were performed using the GeneChip Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner.

data_processing:
Data Acquisition and Primary Analysis—Acquisition and quantification
of array images as well as primary data analysis were performed using the Affymetrix software packages: Microarray Suite version 4.0.1, MicroDB version 2.0, and Data Mining Tool version 2.0. Microsoft Excel was used for further statistical analyses. All arrays were globally scaled to a target value of 150 using the average signal from all gene features using Microarray Suite version 4.0.1. When pairwise comparisons were performed (using Microarray Suite version 4.0.1), a transcript was considered “changed” when a call of Increase or Decrease was made, the -fold change was at least 2, and the higher of the two average difference values was called present.

growth_protocol:
Chemostat Cultivation—
Steady-state chemostat cultures were grown in Applikon laboratory fermentors of 1-liter working volume as described in detail elsewhere [van den Berg, M. A., de Jong-Gubbels, P., Kortland, C. J., van Dijken, J. P., Pronk, J. T., and Steensma, H. Y. (1996) J. Biol. Chem. 271, 28953–28959]. In brief, the cultures were fed with a defined mineral medium containing glucose as the growth-limiting nutrient [. Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1990) Microbiol.Rev. 58, 616–630]. The dilution rate (which equals the specific growth rate) in the steady-state cultures was 0.10 h_1, the temperature was 30 °C, and the culture pH was 5.0. For anaerobic cultivation, the reservoir medium was supplemented with Tween 80 and ergosterol as described previously. Anaerobic conditions were maintained by sparging the medium reservoir and the fermentor with pure nitrogen gas (0.5 liter_min_1). Furthermore, Norprene tubing and butyl rubber septa were used to minimize oxygen of Increase or Decrease was made, the -fold change was at least 2, and the higher of the two average difference values was called present.
Media—
The defined mineral medium composition was based on that described by Verduyn et al [. Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1990) Microbiol.Rev. 58, 616–630]. The residual glucose concentration was targeted to 17 g_liter_1 to sustain glucose repression at the same level . For carbon limited cultivation: 5.0 g of (NH4)2SO4, 3.0 g of KH2PO4, 0.5 g of MgSO4.7H2O, and 25 g of glucose.

treatment_protocol: Liquid nitrogen quenching

tag: This study was performed with the prototrophic laboratory strain S. cerevisiae CEN.PK113-7D (MATa) [van Dijken, J. P., Bauer, J., Brambilla, L., Duboc, P., Francois, J. M., Gancedo, C., Giuseppin, M. L. F., Heinen, J. J., Hoare, M., Lange, H. C., Madden, E. A., Niederberger, P., Nielsen, J., Parrou, J. L., Petit, T., Porro, D., Reuss, M., van Riel, N., Rizzi, M., Steensma, H. Y., Verrips, C. T., Vindelov, J., and Pronk, J. T. (2000) Enz. Microb. Technol. 26, 706–714]


title: lateral motoneurons (LMN) 2, sham-operated control

description:
Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5.
This sample is also known as sham mice. Set 2 - Pair 1 - LMN


title: Anaerobic carbon limited 1

description:
P16
Keywords = S.cerevisiae
Keywords = chemostat
Keywords = nutrient limitation

label_protocol: Probe Preparation and Hybridization to Arrays—mRNA extraction, cDNA synthesis, cRNA synthesis and labeling, as well as array hybridization were performed as described in the Affymetrix users’ manual (1). Briefly, poly(A)_ RNA was enriched from total RNA in a single round using the Qiagen Oligotex kit. Double-stranded cDNA synthesis was carried out incorporating the T7 RNA-polymerase promoter in the first round. This cDNA was then used as template for in vitro transcription (ENZO BioArray High Yield IVT kit), which amplifies the RNA pool and incorporates biotinylated ribonucleotides required for the staining procedures after hybridization. 15 mg of fragmented, biotinylated cRNA was hybridized to Affymetrix yeast S98 arrays at 45 °C for 16 h as described in the Affymetrix users’ manual (1). Washing and staining of arrays were performed using the GeneChip Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner.


title: Normal Adrenal Gland

status: Public on Apr 03 2005

city: Evanston

first: Xijin

last: Ge

state: IL

address: 1001 University Place

department: Center for Functional Genomics

institute: ENH Research Institute

description:
Normal human tissue:Normal Adrenal Gland
Keywords = Human, Normal Tissue, Normal Adrenal Gland

source_name: Normal Adrenal Gland, Commercial mRNA for normal human tissue


title: Anaerobic carbon limited 2

description:
P17
Keywords = S.cerevisiae
Keywords = chemostat
Keywords = nutrient limitation

scan_protocol: scanning with the Affymetrix GeneArray Scanner.


title: SAGE_Drosophila_Embryo_Radiation

status: Public on Jun 03 2005

first: San Ming

last: Wang

institute: ENH Research Institute, Northwestern University

description:
SAGE tags collected from embryo with radiation (0 to 24 hour embryos; 30 minutes after treatment with 40Gy r radiation)
Lee S et al. Detecting novel low-abundant transcripts in Drosophila. RNA. 2005 Jun;11(6):939-46.

organism: Drosophila melanogaster

source_name: Drosophila melanogaster strain (y: cn bw sp) embryo with radiation


title: norway FU40_FU 40-BE

status: Public on Sep 08 2009

city: Stanford

first: Jonathan

last: Pollack

state: CA

address: 269 Campus Drive, CCSR3245A

department: Pathology

institute: Stanford University

description:
Simple annotation: Breast, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38969.gif

hyb_protocol: not provided

scan_protocol: GenePix 4000B

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm), default computed normalization procedure, see SMD website

source_name: Normal female genomic DNA

label_protocol: not provided

extract_protocol: not provided

tag: Normal female genomic DNA

source_name: FUMI40 genomic DNA

tag: FUMI40 genomic DNA


title: OS183 replicate 2

city: Toronto

first: Bekim

last: Sadikovic

state: Ontario

address: 555 University Avenue

country: Canada

institute: The SickKids Hospital and Princess Margaret Hospital

description: The Agilent Human Genome CGH microarray 244A (Agilent Technologies, Inc., Palo Alto, USA) were used for the array-CGH experiments. Three μg of Human Genomic DNA from multiple anonymous male donors (Promega Corporation, Madison, USA) and 3 μg of test genomic DNA sample were digested with AluI (5 units) and RsaI (5 units) (Promega) for a minimum of 2 hours at 37C. Digestion quality was assessed by the DNA 1000 LabChip Kit (Agilent 2100 Bioanalyzer, Agilent Technologies). Labelling reactions were performed using the Agilent Genomic DNA Labeling Kit PLUS (Agilent Technologies, Inc., Palo Alto, USA) according to the manufacturer’s directions. Briefly, the reference and sample DNA were labelled with 1.5 - 3 mM Cy3-dUTP or Cy5-dUTP (Agilent Technologies, Inc., Palo Alto, USA), and purified using a Centricon YM-30 filter (Millipore, Billerica, USA). Probe mixture of Cy3-labelled sample DNA, Cy5-labelled reference DNA, 50 μl of 1.0mg/ ml of human Cot-1 DNA (Invitrogen, USA), 52 μl of Agilent 10X Blocking Agent and 260 μl of Agilent 2X Hybridization Buffer (Agilent Technologies, Inc.) was denatured at 100C for 1 minute 30 seconds and incubated at 37C for 30 minutes. The probe was applied to the array using an Agilent microarray hybridization chamber, and hybridized for 40 hours at 65C in a rotating oven (Robbins Scientific, Sunnyvale, USA) at 20 rpm. Arrays were washed according to the manufacturer’s recommendations; air dried, and scanned using an Agilent 2565AA DNA microarray scanner (Agilent Technologies, Inc), and processed using Agilent’s Feature Extraction software. Dye-swapped duplicate experiments were carried out.

hyb_protocol: Probe mixture of Cy3-labelled sample DNA, Cy5-labelled reference DNA, 50 μl of 1.0mg/ ml of human Cot-1 DNA (Invitrogen, USA), 52 μl of Agilent 10X Blocking Agent and 260 μl of Agilent 2X Hybridization Buffer (Agilent Technologies, Inc.) was denatured at 100C for 1 minute 30 seconds and incubated at 37C for 30 minutes. The probe was applied to the array using an Agilent microarray hybridization chamber, and hybridized for 40 hours at 65C in a rotating oven (Robbins Scientific, Sunnyvale, USA) at 20 rpm. Arrays were washed according to the manufacturer’s recommendation and air dried.

scan_protocol: Arrays were scanned using an Agilent 2565AA DNA microarray scanner (Agilent Technologies, Inc).

data_processing: Data were processed using Agilent’s Feature Extraction software protocol for array-CGH data. To analyze genomic imbalance tumour samples (2 arrays each) the  processed R signal and processed G signal columns from the Agilent  Feature Extraction-generated a-CGH .txt files were imported into PGS.  The tumour-specific signal across all probes was normalized as a ratio  to baseline using Normalise to Baseline Tool in PGS, where baseline  data corresponded to the normal human DNA. The data was then log2  transformed using the PGS Normalization and Scaling Tool. In order to  detect regions of genomic gain and loss we applied the Genomic  Segmentation tool with segmentation parameters set at: min. probes:  10, p-value threshold: 0.01, and signal to noise: 0.1. Region report  was set at values bellow -.5/+.5 (log2) and p-value threshold of 0.05  for 2/2 (replicate) arrays in individual analysis or at 40% cut-off in  cumulative analysis (i.e. 4/10 tumour samples). Regions of significant  gain or loss were annotated to the corresponding genes present on the  Affymetrix Gene 1.0 Array using the  HuGene-1_0-st-v1.na24.hg18.transcript.csv file. Visualizations and  VENN analysis were performed in PGS.

source_name: Normal Human Genomic DNA

label_protocol: Labelling reactions were performed using the Agilent Genomic DNA Labeling Kit PLUS (Agilent Technologies, Inc., Palo Alto, USA) according to the manufacturer’s directions. Briefly, DNA was labelled with 1.5 - 3 mM Cy5-dUTP (Agilent Technologies, Inc., Palo Alto, USA), and purified using a Centricon YM-30 filter (Millipore, Billerica, USA).

extract_protocol: DNA was extracted after harvesting the cells by Trypsin (Invitrogen) followed by phenol-chloroform extraction and subsequent precipitation in 100% ethanol. DNA precipitate was washed with 70% ethanol then eluted in DNAse free water.

source_name: Osteosarcoma tumor sample 183

label_protocol: Labelling reactions were performed using the Agilent Genomic DNA Labeling Kit PLUS (Agilent Technologies, Inc., Palo Alto, USA) according to the manufacturer’s directions. Briefly, DNA was labelled with 1.5 - 3 mM Cy3-dUTP (Agilent Technologies, Inc., Palo Alto, USA), and purified using a Centricon YM-30 filter (Millipore, Billerica, USA).

extract_protocol: Comercial DNA extracted as per manifacturers instructions - Human Genomic DNA from multiple anonymous male donors (Promega Corporation, Madison, USA)

tag: Paediatric Human Osteosarcoma Tissue Sample


title: Acute myeloid leukemia in remission Reference-#30-50kxba

status: Public on Sep 02 2009

city: Memphis

first: Charles

middle: G

last: Mullighan

state: TN

address: 262 Danny Thomas Place

institute: St Jude Children's Research Hospital

description: Acute myeloid leukemia in remission

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: As per manufacturer (Affymetrix)

data_processing: CEL files and TXT files (generated by Affymetrix GTYPE using the DM algorithm) were processed by dChip and model-based expression performed using the PM/MM model. Normalization was performed using the reference normalization algorithm developed at St Jude and described in Mullighan et al Nature 2007;446:758. The data matrix contains the normalized expression values produced by that algorithm.

label: Biotin

source_name: Bone marrow or peripheral blood

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cryopreserved peripheral blood or bone marrow samples obtained at remission

extract_protocol: Qiagen DNA blood mini

treatment_protocol: Samples were obtained at different stages of disease

tag: Bone marrow or peripheral blood


title: Diagnostic_acute_leukemia Hyperdip47-50-SNP-#22-250knsp

source_name: Diagnostic acute leukemia blasts

growth_protocol: Cryopreserved peripheral blood or bone marrow samples obtained at diagnosis

extract_protocol: Qiagen DNA blood mini or phenol chloroform

tag: Tissue

value: acute lymphoblastic leukemia