title: Top1 distribution in HU(ChIP fraction), in HU for 2h

description: Top1 bunding profile in HU after 2h.

source_name: Chromatin-immunoprecipitated DNA by Top1

tag: Strain expressing 10XFLAG tagged Top1 was used. Cells were arrested by HU for 2hrs


title: 8 year old male with classic medulloblastoma of Mstage 0, Philadelphia protocol (1M21)

status: Public on Aug 01 2007

type: genomic

city: Heidelberg

first: Stefan

middle: M

last: Pfister

address: INF 580

department: Molecular Genetics

country: Germany

institute: German Cancer Research Center

description: Comparison of tumor DNA (Cy3-labeled) vs. normal DNA (Cy5-labeled). Whole-genome screening of DNA copy-number aberrations using array-CGH

hyb_protocol: Ten micrograms each of tumor and reference DNA were combined with 300µg of human Cot-1 DNA (Roche Diagnostics, Mannheim, Germany) and suspended in 125µl of UltrahybTM hybridization buffer (Ambion, Bad Soden, Germany). Denaturation of combined DNA was performed at 75°C for 10 min, followed by preannealing at 37°C for 30 min. Hybridization was carried out in a GeneTAC Hybridization Station (Genomic Solutions, Oberhaching, Germany) for 36 hr at 37°C. Slides were washed with 2× SSC/0.05% Tween-20 at 37°C for 1 cycle, 2× SSC/0.05% Tween-20 at 44°C for 2 cycles, 50% formamide/2× SSC/0.1% Tween-20 at 44°C for 3 cycles, 2× SSC/0.05% Tween-20 at 44°C for 2 cycles, and finally 1× PBS/0.05% Tween-20 at 25°C for 2 cycles. Slides were dried by centrifugation at 54 g for 1 min, followed by centrifugation at 216 g for 1 min in a clinical centrifuge.

scan_protocol: Arrays were scanned at a 5µm resolution with an Axon 4000B scanner (Axon Instruments, Burlingame, USA) and images analyzed using GenePix Pro 6.0 software (Axon Instruments). Results files containing all relevant raw data were processed by use of ChipYard microarray analysis platform software (developed in-house), the statistical programming language R, and packages of the Bioconductor project; Ihaka and Gentleman, 1996).

data_processing: Fluorescence intensities of all spots were filtered consistently (intensity/local background >3; mean/median intensity <1.3; standard deviation of clone log2 ratios <0.2) and globally normalized using the printtip-loess algorithm (Smyth and Speed, 2003).

molecule: genomic DNA

organism: Homo sapiens

source_name: tumor DNA

label_protocol: Genomic DNA (300-500 ng) was labeled with Cy3-labeled dCTP (tumor) or Cy5-conjugated dCTP (control) by use of a BioPrime DNA Labeling Kit (Invitrogen, Karlsruhe, Germany). Unincorporated nucleotides, random primers, and dyes were removed by use of MicroCon YM30 Spin Columns (Millipore, Schwalbach, Germany). Incorporation of dyes into the labeled DNA was determined by UV spectrophotometry.

extract_protocol: Genomic DNA from tumor tissue was isolated using the Blood and Cell Culture Kit (Qiagen,Hilden, Germany) following the instructions of the suppliers.  Genomic DNA from peripheral blood mononuclear cells of healthy donors was isolated by use of the Quiagen DNA Blood Midi-Kit (Hilden, Germany).

tag: tissue

value: 8 years old male patient with classic medulloblastoma of Mstage 0 ,treated postoperatively with Philadelphia protocol

source_name: Pooled lymphocyte DNA from 10 healthy individuals (age 25-40 years)

value: pooled DNA from peripheral blood mononuclear cells of ten healthy donors


title: Top1 distribution in HU(ChIP fraction) on early origins deleted chromosome VI

city: Bunkyo-ku

first: Katsuhiko

last: Shirahige

state: Tokyo

address: 1-1-1 Yayoi

department: Research Center for Epigenetic Disease

country: Japan

institute: The University of Tokyo

description: Top1 distribution on early origins deleted chromosome VI under HU.

hyb_protocol: Hybridization, blocking and washing steps were carried out as previously described by Winzeler et al. (Science. 281, 1194-1197, 1998). Each sample was hybridized to the array in 150ul containing 6XSSPE, 0.005% TritonX-100, 15ug fragmented denatured salmon sperm DNA (Gibco-BRL), and 1nmole of a 3’-biotin control oligonucleotide (oligo B2 probes) that hybridized to the border features on the array. Samples were heated to 100°C for 10 min., and then cooled on ice. Samples were hybridized for 16h at 42°C in a hybridization oven (GeneChip hybri oven 320, Affymetrix, CA). Washing and staining protocol (Mini_euk1 ver2) provided by Affymetrix was performed automatically on a fluidics station (GeneChip fluidics station 400, Affymetrix, CA).

scan_protocol: Each array was scanned by HP GeneArray Scanner (Affymetrix, CA) at an emission wavelength of 560nm at 7.5uM resolution. Grids were aligned to the scanned images using the know feature of the array. Primary data analyses were carried out using the Affymetrix Microarray Suite Ver.5.0 software to obtain hybridization intensity, fold change value, change p-value, and detection p-value for each locus.

data_processing: For the discrimination of positive and negative signals for the binding, we compared ChIP fraction with Sup (supernatant) fraction by using three criteria as follows. First, the reliability of strength of signal was judged by detection p-value of each locus (p-value lower than 0.025 was considered as significant). Secondly, reliability of binding ratio was judged by change p-value (p-value lower than 0.025 was considered as significant). Thirdly, clusters consisted of at least three contiguous loci which filled above two criteria were selected as significantly enriched locus, because it is apparent that a single site of protein-DNA interaction will result in immuno-precipitation of DNA fragments that hybridized not only to the locus of the actual binding site but also to its neighbors. This third criterion is very unique, make the data highly reliable and can be only applicable to the chip data obtained by our high-resolution tiling array.

organism: Saccharomyces cerevisiae

label_protocol: DNA was end-labelled with Biotin-N6ddATP by Terminal Transferase as previously described by Winzeler et al. (Science. 281, 1194-1197, 1998)

extract_protocol: 1.5X10^8 cells were disrupted by MULTI-BEADS SHOCKER (MB400U, YASUI KIKAI, Osaka), which was able to keep cells precisely at lower than 6°C during disruption by glass beads. This enabled us to retrieve more than 60% of tagged proteins to soluble fraction routinely. Chromosomal DNA was shared into the average size of 400-600bp by sonication. Anti-HA monoclonal antibody HA.11 (16B12) (CRP Inc., Denver, PA) and anti-FLAG monoclonal antibody M2 (Sigma-Aldrich Co., St Louis, MO) were used for chromatin immuno-precipitation. Immunoprecipitated chromosomal DNA was subsequently purified following the protocol of Young’s lab (http://inside.wi.mit.edu/young/pub/locationanalysis.html). Purified DNA was random primed and amplified by the protocol of Brown’s lab (http://www.microarrays.org). 2ug of amplified DNA was digested with DNaseI to a mean size of 100bp and used for labeling as previously described by Winzeler et al. (Science. 281, 1194-1197, 1998).

tag: Strain expressing 10XFLAG Top1 was used. All early origins were deleted in this strain.


title: 4 year old female with large cell/anaplastic medulloblastoma of Mstage 3, Philadelphia protocol (1M20)

value: 4 years old female patient with large cell/anaplastic medulloblastoma of Mstage 3 ,treated postoperatively with Philadelphia protocol


title: 4 year old female with large cell/anaplastic medulloblastoma of Mstage 0, Philadelphia protocol (1M19)

value: 4 years old female patient with large cell/anaplastic medulloblastoma of Mstage 0 ,treated postoperatively with Philadelphia protocol


title: Top1 distribution in HU(SUP fraction), on early origins deleted chromosome VI

description: This data was used for the normalization of GSM206231

source_name: Sup fraction after ChIP (equal to Whole cell extract DNA)

tag: Strain expressing 10XFLAG tagged was used. All eraly origins were deleted.


title: 16 year old male with classic medulloblastoma of Mstage 0, Philadelphia protocol (1M18)

value: 16 years old male patient with classic medulloblastoma of Mstage 0 ,treated postoperatively with Philadelphia protocol


title: Top1 distribution in HU(ChIP fraction) on Chromosome VI

description: Top1 distribution in HU.

tag: Strain expressing 10XFLAG Top1 was used.


title: Top1 distribution in HU(ChIP fraction) on ARS607 deleted Chromosome VI

description: Top1 distribution on ARS607 deleted chromosome VI.

tag: Strain expressing 10XFLAG Top1 was used. ARS607 was deleted in this strain.


title: Top1 distribution in G2(ChIP fraction)

description: Top1 binding profile in G2 phase.

tag: Strain expressing 10XFLAG tagged TOP1 was arrested by Nocodazole.


title: 13 year old male with classic medulloblastoma of Mstage 0, Philadelphia protocol (1M15)

value: 13 years old male patient with classic medulloblastoma of Mstage 0 ,treated postoperatively with Philadelphia protocol


title: Top1 distribution in HU(SUP fraction) on ARS607 deleted chromosome VI

description: This file was used for the normalization of GSM206229

tag: Strain expressing 10XFLAG tagged Top1 was used. ARS607 was deleted in this srain.


title: 10 year old female with classic medulloblastoma of Mstage 3, Philadelphia protocol (1M17)

value: 10 years old female patient with classic medulloblastoma of Mstage 3 ,treated postoperatively with Philadelphia protocol


title: 8 year old female with classic medulloblastoma of Mstage 0, Philadelphia protocol (1M13)

value: 8 years old female patient with classic medulloblastoma of Mstage 0 ,treated postoperatively with Philadelphia protocol


title: 26 year old male with nodular/desmoplastic medulloblastoma of Mstage 0, Philadelphia protocol (1M12)

value: 26 years old male patient with nodular/desmoplastic medulloblastoma of Mstage 0 ,treated postoperatively with Philadelphia protocol


title: RNA-tonsil_replicate

type: RNA

city: omaha

first: Javeed

last: Iqbal

state: NE

address: 40th street

department: Pathology and Microbiology

country: USA

institute: University of Nebraska Medical Center

description: To minimize biases in RNA amplification only one round amplification was performed and using similar incubations times and 200 ng of total RNA of good quality as template for the reverse transcription reaction.The quality and quantity of aRNA was monitored on agarose gel electrophoresis and by spectrophotometer. Typically, 10-20 ug of aRNA was generated from 200 ng of total RNA by one round of amplification and 10 ug of aRNA were employed for hybridization.

hyb_protocol: Labeled aRNA from NK cells and the lymphoid standard was combined in 6 ul of deionized water prior to the addition of poly (dA), human cot-1 DNA and yeast t-RNA at a final concentration of 10 ug each in a total volume of 45 ul containing 4.4 x SSC, 4.1 x Denharts and 50% formamide. Hybridisation and washing was described in following ref [Karen Dybkær, Guimei Zhou, Javeed Iqbal, David Kelly, Li Xiao, Simon Sherman, Francesco d’Amore and Wing C. Chan: Suitability of stratagene reference RNA for analysis of lymphoid tissues. Biotechniques. 2004;37:470-2, 474.]

scan_protocol: Arrays were scanned using an Axon 4000 scanner at 10 um resolution and images were analyzed using Genepix 5.0 software (Axon Instruments, Union City, CA).

data_processing: The fluorescent intensity levels corresponding to each hybridized DNA spot was analyzed with Genepix 5.0 software (Axon Instruments, Union City, CA), and hybridized spots having signal-to-noise ratios below 1.25 and spots with blemishes were flagged and removed prior to further analysis. Local background was subtracted from the individual spots and intensities for each channel were normalized with respect to median intensity from each channel for the entire array. The raw expression data from all the time series were uploaded in BRB-ArrayTools software (Biometric Research Branch-NCI, MA) and global normalization was used to median center the log-ratios on each array in order to adjust for differences in labeling intensities of the Cy3 and Cy5 dyes on different arrays. We excluded genes from the analysis showing minimal variation across time series experiments, and genes whose expression differed by at least 1.25 fold from the median in at least 20% of the arrays were retained. Adjusted data were further filtered to remove genes with opposite ratio values and genes differing more than 3 fold in duplicate analysis of the same NK sample

molecule: total RNA

source_name: Tonsil

label_protocol: aRNA was chemically labeled with a platinum-linked cyanine dye using the MicroMax ASAP RNA labeling kit (PerkinElmer, Boston, MA) as per the manufactures instruction. Briefly, 10 ug of aRNA was incubated at 85°C for 15 minutes with labeling buffer and either Cy5 in a total volume of 20 ul prior to termination of the reaction by cooling on ice and addition of 5 ul of stop buffer. Labeled aRNA was purified on MicroCon 50 columns before the final volume was reduced to 3 ul by vacuum centrifuge (Savant, Farmingdale, NY). aRNA from NK cells was labeled with Cy5

extract_protocol: Total RNA was extracted with Trizol and further purified with RNeasy Mini Columns (Qiagen, Valencia, CA) before aliquots were run in agarose gel electrophoresis and measured by spectrophotometer at 260 and 280 nm to assess the quality of the RNA. For each time point, equal amounts of RNA from at least 3 different healthy donors were pooled prior to one round of RNA amplification using MessageAMPTm aRNA kit (Ambion, Austin, TX) according to the manufacturer’s instruction

tag: RNA was extracted from tonsils of several healthy individuals

source_name: Lymphoid RNA reference standard

label_protocol: same as channel1

extract_protocol: same as for channe1 extract

tag: amplified lymphoid RNA reference standard, consisting of RNA from tonsil, thymus, spleen, and cell lines derived from malignant pre-B cells, plasma cells and NK cells


title: Top1 distribution in HU(SUP fraction), in HU for 2h

description: This data was used for the normalization of GSM206233.

tag: Strain expressing 10XFLAG tagged TOP1 was arrested by HU for 2h.


title: NK_timepoint24_replicate

source_name: NK cells isolated from healthy individuals

tag: Primary NK cells were isolated from seven healthy donors.The healthy donors provided peripheral blood mononuclear cells (PBMCs) with IRB approval. PBMCs were isolated by Ficoll-Hypaque density gradient centrifugation at room temperature. Non-adherent cells were collected after incubation in nylon wool for 1 hour at 37°C and were mixed with anti CD3, CD14, CD19, CD36 and IgE MicroBeads (MiltenyiBiotec, Auburn, CA) at temperatures between 4-10 ºC for the negative selection of NK cells. NK cells with the CD56+/CD16+ and CD3- phenotype were negatively selected at temperatures between 4-10 ºC. Purified NK cells were cultured in RPMI 1640 medium (Life Technologies, New York, NY) supplemented with 10% fetal bovine serum, 200 ug/ml streptomycin and 200 IU/ml penicillin, and IL2 (100 IU/ml) for 24 hours at 37ºC and 5% CO2, before harvest and storage in Trizol at -80°C till RNA isolation.

tag: Karen Dybkær, Guimei Zhou, Javeed Iqbal, David Kelly, Li Xiao, Simon Sherman, Francesco d’Amore and Wing C. Chan

value: Suitability of stratagene reference RNA for analysis of lymphoid tissues. Biotechniques. 2004;37:470-2, 474.


title: 30 year old female with nodular/desmoplastic medulloblastoma of Mstage 0, Philadelphia protocol (1M11)

value: 30 years old female patient with nodular/desmoplastic medulloblastoma of Mstage 0 ,treated postoperatively with Philadelphia protocol


title: Resting CD8_positive_ Tcell

hyb_protocol: Labeled aRNA from Tcells and the lymphoid standard was combined in 6 ul of deionized water prior to the addition of poly (dA), human cot-1 DNA and yeast t-RNA at a final concentration of 10 ug each in a total volume of 45 ul containing 4.4 x SSC, 4.1 x Denharts and 50% formamide. Hybridisation and washing was described in following ref [Karen Dybkær, Guimei Zhou, Javeed Iqbal, David Kelly, Li Xiao, Simon Sherman, Francesco d’Amore and Wing C. Chan: Suitability of stratagene reference RNA for analysis of lymphoid tissues. Biotechniques. 2004;37:470-2, 474.]

source_name: CD8 T cells

tag: Primary CD8+ T cells were isolated from several healthy indivduals


title: RNA-tonsil


title: NK_timepoint_8hr

tag: Primary NK cells were isolated from seven healthy donors.The healthy donors provided peripheral blood mononuclear cells (PBMCs) with IRB approval. PBMCs were isolated by Ficoll-Hypaque density gradient centrifugation at room temperature. Non-adherent cells were collected after incubation in nylon wool for 1 hour at 37°C and were mixed with anti CD3, CD14, CD19, CD36 and IgE MicroBeads (MiltenyiBiotec, Auburn, CA) at temperatures between 4-10 ºC for the negative selection of NK cells. NK cells with the CD56+/CD16+ and CD3- phenotype were negatively selected at temperatures between 4-10 ºC. Purified NK cells were cultured in RPMI 1640 medium (Life Technologies, New York, NY) supplemented with 10% fetal bovine serum, 200 ug/ml streptomycin and 200 IU/ml penicillin, and IL2 (100 IU/ml) for 8 hours at 37ºC and 5% CO2, before harvest and storage in Trizol


title: 11 year old male with classic medulloblastoma of Mstage 0, Philadelphia protocol (1M16)

value: 11 years old male patient with classic medulloblastoma of Mstage 0 ,treated postoperatively with Philadelphia protocol


title: NK_timepoint_8hr_replicate

tag: Primary NK cells were isolated from seven healthy donors.The healthy donors provided peripheral blood mononuclear cells (PBMCs) with IRB approval. PBMCs were isolated by Ficoll-Hypaque density gradient centrifugation at room temperature. Non-adherent cells were collected after incubation in nylon wool for 1 hour at 37°C and were mixed with anti CD3, CD14, CD19, CD36 and IgE MicroBeads (MiltenyiBiotec, Auburn, CA) at temperatures between 4-10 ºC for the negative selection of NK cells. NK cells with the CD56+/CD16+ and CD3- phenotype were negatively selected at temperatures between 4-10 ºC. Purified NK cells were cultured in RPMI 1640 medium (Life Technologies, New York, NY) supplemented with 10% fetal bovine serum, 200 ug/ml streptomycin and 200 IU/ml penicillin, and IL2 (100 IU/ml) for 8 hours at 37ºC and 5% CO2, before harvest and storage in Trizol at -80°C till RNA isolation.

source_name: lymphoid RNA reference standard


title: NK_timepoint_24hr


title: NK_timepoint_2hr_replicate

tag: Primary NK cells were isolated from seven healthy donors.The healthy donors provided peripheral blood mononuclear cells (PBMCs) with IRB approval. PBMCs were isolated by Ficoll-Hypaque density gradient centrifugation at room temperature. Non-adherent cells were collected after incubation in nylon wool for 1 hour at 37°C and were mixed with anti CD3, CD14, CD19, CD36 and IgE MicroBeads (MiltenyiBiotec, Auburn, CA) at temperatures between 4-10 ºC for the negative selection of NK cells. NK cells with the CD56+/CD16+ and CD3- phenotype were negatively selected at temperatures between 4-10 ºC. Purified NK cells were cultured in RPMI 1640 medium (Life Technologies, New York, NY) supplemented with 10% fetal bovine serum, 200 ug/ml streptomycin and 200 IU/ml penicillin, and IL2 (100 IU/ml) for 2 hours at 37ºC and 5% CO2, before harvest and storage in Trizol at -80°C till RNA isolation.


title: NK_timepoint_2hr_A

value: Suitability of stratagene reference RNA for analysis of lymphoid tissues. Biotechniques. 2004;37:470-2, 474]


title: 5 year old female with large cell/anaplastic medulloblastoma of Mstage 2, Philadelphia protocol (1M10)

value: 5 years old female patient with large cell/anaplastic medulloblastoma of Mstage 2 ,treated postoperatively with Philadelphia protocol


title: 33 year old male with classic medulloblastoma of Mstage 0, Philadelphia protocol (1M9)

value: 33 years old male patient with classic medulloblastoma of Mstage 0 ,treated postoperatively with Philadelphia protocol


title: NK_timepointO_replicate

tag: primary NK cells isolated from healthy individual

tag: [Karen Dybkær, Guimei Zhou, Javeed Iqbal, David Kelly, Li Xiao, Simon Sherman, Francesco d’Amore and Wing C. Chan

value: Suitability of stratagene reference RNA for analysis of lymphoid tissues. Biotechniques. 2004;37:470-2, 474.]


title: 18 year old male with nodular/desmoplastic medulloblastoma of Mstage 0, Philadelphia protocol (1M5)

tag: tissue

value: 18 years old male patient with nodular/desmoplastic medulloblastoma of Mstage 0 ,treated postoperatively with Philadelphia protocol


title: 2 year old male with large cell/anaplastic medulloblastoma of Mstage 0, Philadelphia protocol (1M3)

value: 2 years old male patient with large cell/anaplastic medulloblastoma of Mstage 0 ,treated postoperatively with Philadelphia protocol


title: 18 year old male with classic medulloblastoma of Mstage 0, Philadelphia protocol (1M2)

value: 18 years old male patient with classic medulloblastoma of Mstage 0 ,treated postoperatively with Philadelphia protocol

value: pooled DNA from peripheral blood mononuclear cells of ten healthy donors


title: 12 year old female with classic medulloblastoma of Mstage 1, Philadelphia protocol (1M4)

value: 12 years old female patient with classic medulloblastoma of Mstage 1 ,treated postoperatively with Philadelphia protocol


title: Resting_NK-timepoint0

hyb_protocol: Labeled aRNA from NK cells and the lymphoid standard  was combined in 6 ul of deionized water prior to the addition of poly (dA), human cot-1 DNA and yeast t-RNA at a final concentration of 10 ug each in a total volume of 45 ul containing 4.4 x SSC, 4.1 x Denharts and 50% formamide. Hybridisation and washing was described in following ref [Karen Dybkær, Guimei Zhou, Javeed Iqbal, David Kelly, Li Xiao, Simon Sherman, Francesco d’Amore and Wing C. Chan:  Suitability of stratagene reference RNA for analysis of lymphoid tissues. Biotechniques. 2004;37:470-2, 474.]

label_protocol: aRNA was chemically labeled with a platinum-linked cyanine dye using the MicroMax ASAP RNA labeling kit (PerkinElmer, Boston, MA) as per the manufactures instruction. Briefly, 10 ug of aRNA was incubated at 85°C for 15 minutes with labeling buffer and either Cy5 or Cy3 in a total volume of 20 ul prior to termination of the reaction by cooling on ice and addition of 5 ul of stop buffer. Labeled aRNA was purified on MicroCon 50 columns before the final volume was reduced to 3 ul by vacuum centrifuge (Savant, Farmingdale, NY). aRNA from NK cells was labeled with Cy5

extract_protocol: Total RNA was extracted with Trizol and further purified with RNeasy Mini Columns (Qiagen, Valencia, CA) before aliquots were run in agarose gel electrophoresis and measured by spectrophotometer at 260 and 280 nm to assess the quality of the RNA. For each time point, equal amounts of RNA from at least 3 different healthy donors were pooled prior to one round of RNA amplification using MessageAMPTm aRNA kit (Ambion, Austin, TX) according to the manufacturer’s instruction.

treatment_protocol: Primary NK cells were isolated from seven healthy donors.The healthy donors provided peripheral blood mononuclear cells (PBMCs) with IRB approval. PBMCs were isolated by Ficoll-Hypaque density gradient centrifugation at room temperature. Non-adherent cells were collected after incubation in nylon wool for 1 hour at 37°C and were mixed with anti CD3, CD14, CD19, CD36 and IgE MicroBeads (MiltenyiBiotec, Auburn, CA) at temperatures between 4-10 ºC for the negative selection of NK cells. NK cells with the CD56+/CD16+ and CD3- phenotype were negatively selected at temperatures between 4-10 ºC.Purified NK cells were treated immediately with Trizol.

tag: Primary NK cells


title: 1 year old male with classic medulloblastoma of Mstage 3, Philadelphia protocol (1M8)

value: 1 years old male patient with classic medulloblastoma of Mstage 3 ,treated postoperatively with Philadelphia protocol


title: Shifted_from_20%_oxygen_to_0.2%_and_grew_by_2_hours_rep5

city: Stanford

first: SMD

last: Staff

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description: Biological replicate 6 of 6. Control, strain H37Rv. Cell culture grew in 20% oxygen.

scan_protocol: Microarrays were scanned using a GenePix 4000 A (Axon Instruments). The intensities of the two dyes at each spot were quantified using SCANALYZE (M. Eisen; http://rana.lbl.gov/EisenSoftware.htm).

data_processing: The overall reproducibility of the microarray experiments was evaluated using the Signifi-cance Analysis of Microarrays (SAM) program.  The SAM algorithm was set for two-class unpaired analysis with 500 permutations and K-nearest imputer for missing data. Significantly regulated genes were selected by adjusting the delta value to give a false discovery rate below 1%. In each data set, all genes regulated 1.5-fold and greater were determined to be significant with a false discovery rate of less than 1%, indicating a high degree of reproducibility.

organism: Mycobacterium tuberculosis

source_name: Cell culture grew in 20% oxygen

label_protocol: All steps in the MTB DNA microarray gene expression analysis were performed as described (PMID: 10536008 and 11398407). Controls for array quality were printed onto each slide and included a dilution series of MTB genomic DNA (positive control) and salmon sperm DNA (negative control). Additionally, DNA prelabeled with the cyanine dyes Cy3 or Cy5 were printed to ascertain whether spot-to-spot carryover contamination had occurred during the printing step. The quality of cDNA labeling was monitored by quantitatively measuring the intensities of Cy3- and Cy5-labeled samples hybridized to the MTB genomic positive control spots.

growth_protocol: H37Rv (ATCC 27294) and Mycobacterium bovis bacillus Calmette–Gue´rin (BCG) Montreal (ATCC 35735) were maintained on Middlebrook 7H9 medium (Difco) with 0.05% Tween 80 and ADC supplement or on Middlebrook 7H10 plates at 37 C. Bacilli were grown in roller bottles unless otherwise noted. When needed, kanamycin was used at 30 ug/ml and hygromycin at 50 ug/ml. Defined hypoxic culture was as previously described. Gas flow was maintained at  aproximatly at 0.15 standard cubic feet (4.2 liters) per hour within each flask.

extract_protocol: Cells were disrupted by three 30-sec pulses in a BioSpec Products bead beater. After 5 min at room temperature, samples were centrifuged at 13,000 x g for 45 sec, and the supernatants were extracted with 300 ul of chloroformyisoamyl alcohol (24:1) and precipitated with isopropyl alcohol. Samples were incubated 10 min to overnight at 4 C and centrifuged for 10 min at 4 C. The RNA pellets were washed with 1 ml of 75% ethanol, centrifuged at 13,000 x g for 5 min, and air-dried. After suspension of the RNA pellets in 90 ul of water, 10 ul of DNase I 10x buffer and 4 units of DNase I (Ambion, Austin, TX) were added and the samples were incubated for 30 min. Final purification of RNA was by RNeasy column (Qiagen, Chatsworth, CA).

treatment_protocol: Frozen cell pellets were suspended in 1 ml of Trizol reagent (GIBCOy BRL) and transferred to 2-ml screw-cap tubes containing 0.4-ml of 0.1-mm diameter zirconiaysilica beads (BioSpec Products, Bartlesville, OK).

source_name: Cell culture shifted from 20% oxygen to 0.2% and grew by 2 hours


title: Shifted_from_20%_oxygen_to_0.2%_and_grew_by_2_hours_rep2

description: Biological replicate 3 of 6. Control, strain H37Rv. Cell culture grew in 20% oxygen.

hyb_protocol: All steps in the MTB DNA microarray gene expression analysis were performed as described (PMID: 10536008 and 11398407).


title: Shifted_from_20%_oxygen_to_0.2%_and_grew_by_2_hours_rep3

description: Biological replicate 4 of 6. Control, strain H37Rv. Cell culture grew in 20% oxygen.


title: Shifted_from_20%_oxygen_to_0.2%_and_grew_by_2_hours_rep4

description: Biological replicate 5 of 6. Control, strain H37Rv. Cell culture grew in 20% oxygen.


title: 23 year old male with classic medulloblastoma of Mstage 2, Philadelphia protocol (1M1)

value: 23 years old male patient with classic medulloblastoma of Mstage 2 ,treated postoperatively with Philadelphia protocol


title: Shifted_from_20%_oxygen_to_0.2%_and_grew_by_2_hours

description: Biological replicate 1 of 6. Control, strain H37Rv. Cell culture grew in 20% oxygen.


title: seminoma specimen, pT3, patient age: 49y; W01 134

status: Public on Jul 31 2007

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

institute: Institut fuer Zellbiologie

description: Analysis of gene expression in seminoma (pT1-pT3) vs. normal testis (NT)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U95Av2 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 2500

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 13.5 ug total RNA (Expression Analysis Technical Manual v1, Affymetrix).

extract_protocol: Tissues were lysed in TRIzol (Invitrogen, Karlsruhe, Germany) and total cellular RNA was prepared using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.

tag: seminoma specimen, pT3, patient age


title: Shifted_from_20%_oxygen_to_0.2%_and_grew_by_2_hours_rep1

description: Biological replicate 2 of 6. Control, strain H37Rv. Cell culture grew in 20% oxygen.


title: seminoma specimen, pT3, pN1, pM1, patient age: 23y; W00 011


title: seminoma specimen, pT3, patient age: 42y; W00 048


title: seminoma specimen, pT2, patient age: 31y; W03 033

tag: seminoma specimen, pT2, patient age


title: seminoma specimen, pT2, patient age: 27y; W03 021


title: seminoma specimen, pT3, patient age: 48y; W00 023


title: seminoma specimen, pT2, patient age: 30y; W03 036


title: SympatheticNeuron_WithMyocyteTarget

city: Waltham

first: Susan

middle: J

last: Birren

state: MA

address: 415 South st

department: Biology

institute: Brandeis University

description: Affymetrix Rat Expression Set 230A oligonucleotide arrays with 15,900 probe sets were screened with probes derived from neurons grown alone. Total RNA was extracted using the RNeasy mini kit (Qiagen). Eukaryotic probe preparation, hybridization, array washing, staining and scanning were performed according to Affymetrix manuals (Rev. 5).

hyb_protocol: Hybridization was done according to Affymetrix protocol for 16 hours. Staining and Washing was also done according to Affymetrix protocol (Fluidics Scripts: EukGE-WS2v4_450).

scan_protocol: Scan was done by Affymetrix GeneChip Scanner 3000 according to Affymetrix protocol

data_processing: Affymetrix MAS5.0 algorithm was used for data processing

organism: Rattus norvegicus

source_name: Sympathetic Neuron cultured with Myocyte Target

label_protocol: The synthesis of biotin-labeled cRNA was performed using the BioArray High-Yield Transcript Labeling Kit (Enzo Biochem, New York, NY).

extract_protocol: Neurons were isolated from cultures containing myocytes or other flat cells the culture dishes were washed with PBS and incubated with 1 mM EDTA in PBS for 2 min in 37°C.  The less adherent sympathetic neurons were then removed from the plate by pipetting 1 mM EDTA in PBS over the dish. Rinsed neurons were collected and centrifuged in a clinical centrifuge at 3,000 rpm for 10 min. Total RNA was extracted using the RNeasy mini kit (Qiagen) according to manufacture's protocol.

tag: Sympathetic neuron culture from neonatal superior cervical ganglia of Simonson Albino rat cultured with neonatal cardiac myocytes 2 days in vitro


title: seminoma specimen, pT2, patient age: 35y; W03 032


title: seminoma specimen, pT2, patient age: 40y; W03 025


title: seminoma specimen, pT2, patient age: 45y; W99 037


title: seminoma specimen, pT2, patient age: 34y; W03 031


title: seminoma specimen, pT2, patient age: 34y; W03 037


title: SympatheticNeuron_WithoutMyocyteTarget

source_name: Sympathetic Neuron cultured without Myocyte Target

tag: Sympathetic neuron culture from neonatal superior cervical ganglia of Simonson Albino rat cultured 2 days in vitro


title: seminoma specimen, pT2, patient age: 46y; W03 017


title: seminoma specimen, pT2, patient age: 34y; W03 013


title: seminoma specimen, pT2, patient age: 28y; W03 012


title: seminoma specimen, pT2, patient age: 37y; W00 025


title: seminoma specimen, pT2, pN1, patient age: 43y; W00 120


title: seminoma specimen, pT1, patient age: 37y; W03 023

tag: seminoma specimen, pT1, patient age


title: seminoma specimen, pT1, patient age: 38y; W97 082


title: seminoma specimen, pT1, pN1, patient age: 34y; W99 113


title: seminoma specimen, pT1, pN1, patient age: 42y; W95 194


title: seminoma specimen, pT1, patient age: 31y; W98 100


title: seminoma specimen, pT1, patient age: 38y; W99 063


title: seminoma specimen, pT1, patient age: 36y; W03 014


title: seminoma specimen, pT1, patient age: 56y; W02 151


title: seminoma specimen, pT1, patient age: 40y; W00 047


title: seminoma specimen, pT1, patient age: 35y; W00 222


title: seminoma specimen, pT1, patient age: 35y; W03 030


title: seminoma specimen, pT1, patient age: 55y; W03 011


title: seminoma specimen, pT1, patient age: 43y; W02 003


title: seminoma specimen, pT1, patient age: 39y; W02 102


title: seminoma specimen, pT1, patient age: 36y; W00 223


title: seminoma specimen, pT1, patient age: 33y; W03 015


title: testis with regular spermatogenesis from orchiectomy cases due to prostate carcinoma, patient age: 58y; W03 003


title: seminoma specimen, pT1, patient age: 39y; W03 035


title: testis with regular spermatogenesis with status after vasectomy, patient age: 34y; W03 020


title: seminoma specimen, pT1, patient age: 36y; W01 145


title: seminoma specimen, pT1, patient age: 25y; W01 075


title: seminoma specimen, pT1, patient age: 51y; W02 116


title: testis with regular spermatogenesis from orchiectomy cases due to prostate carcinoma, patient age: 67y; W03 002


title: seminoma specimen, pT1, patient age: 33y; W01 231


title: seminoma specimen, pT1, patient age: 29y; W03 022


title: Cervical carcinoma 97 Post-treatment

city: México

first: Carlos

last: Pérez-Plasencia

address: Av. San Fernando 22

department: BASIC RESEARCH

country: Mexico

institute: INSTITUTO NACIONAL DE CANCEROLOGIA

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 37C on Human Whole Genome CodeLink Bioarray. Stain and post-hybridization washes were performed according to the manufacturer's instructions.

scan_protocol: Bioarrays were scanned with a GenePix Personal 4100A scanner.

data_processing: Expression values were globally normalized to the median expression value of the whole array spots. To circumvent division by zero, values below three times background value were taken as 5.

label: Biotin

source_name: Cervical carcinoma Punch biopsy after hydralazine and magnesium valproate treatment

label_protocol: Biotinylated cRNA was prepared according to the standard CodeLink protocol from 2 ug total RNA

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

treatment_protocol: Patients received a single oral dose of 500 mg of sulphamethazine early in the morning, and urine was collected within the ensuing 6 h for phenotyping of acetylator status as reported. Afterward, patients began treatment (day –7) with a daily dose of a slow-release formulation of hydralazine tablets containing either 182 mg for rapid, or 83 mg for slow acetylators. Magnesium valproate tablets of 700 mg were also administered as a slow-release formulation at a dose of 30 mg/kg t.i.d. Both were administered until intracavitary therapy was completed. Punch biopsies were taken from primary cervical tumors at diagnosis and at day 8 of treatment with hydralazine and magnesium valproate prior to the first dose of cisplatin and external radiation. Part of the biopsy was sent to the Institution’s Pathology Department for routine hematoxilin and eosin evaluation. The remaining biopsy specimen was immediately frozen at –70°C for biological analyses.

tag: Gender

value: Female

tag: Tumor Stage

value: Cervical carcinoma IIIB (FIGO)


title: Sir2_wild-type H3_yeast complete medium

city: Cambridge

first: Antonis

last: Kirmizis

state: England

address: Gurdon institute, Tennis Court Rd

country: United Kingdom

institute: Antonis Kirmizis

description: Yeast grown to an A600 OD of ~0.9 in YPD containing 0.2% glucose

hyb_protocol: NimbleGen

scan_protocol: NimbleGen

data_processing: NimbleGen

source_name: Chromatin Immunoprecipitated DNA from S.cerevisiae using Sir2 antibody

label_protocol: One microgram (μg) of LM-PCR products were used for labeling and hybridization to each array. One microgram of immunoprecipitated or total genomic LM-PCR DNA was mixed with 40 μL of 1 μM Cy5 or Cy3 end labeled random prime nonamer oligonucleotides (TriLink Biotechnologies) respectively with the bacterial label control DNA in a total volume of 88 μL. The DNA and random primers were annealed by heating the sample to 98°C for 5 minutes and chilled quickly in ice water for 2-3 minutes. Two microliter of (100 units) of E. coli DNA polymerase Klenow fragment and 10 μL of 10 mM equimolar mixture of dATP, dTTP, dCTP, and dGTP were added to the annealed DNA sample and incubated at 37°C for 2 hours. The reaction was stopped by addition of 10 μL of 0.5 M EDTA. The labeled sample was ethanol precipitated by addition of 11μL 5 M NaCl and 110 μL isopropanol. The precipitate was collected by centrifugation and the resulting labeled DNA pellet was washed with 80% ethanol (V/V). The pellet was dried under vacuum for 5-15 minutes to remove any remaining liquid, and the resulting dry labeled DNA pellet was resuspended in 10 μL dH2O.

extract_protocol: Formaldehyde cross-linking and chromatin immunoprecipitations were performed as described previously with the following exceptions: the immunocomplexes were eluted from the Sepharose beads (17-5280-01, Amersham) using a total of 200 ul elution buffer (100 mM Sodium bicarbonate, 1% SDS) and RNAse (11119915001, Roche) treatment was performed during reversing of the cross-links at 65°C for 5 hours. After reversing the cross-links, each individual ChIP sample was purified using the Qiaquick PCR purification kit (QIAGEN) and DNA was eluted from the columns with 50 ul of EB buffer. The immunoprecipitated DNA was amplified using a ligation mediated PCR (LM-PCR). Additional PCR reactions were performed to generate 4 μg of ChIP DNA for hybridization.

tag: strain JHY6-H3WT

source_name: Input chromatin DNA control


title: seminoma specimen, pT2, pN2, pM1, patient age: 37y; W00 111


title: H3K4me3_wild-type yeast_complete medium

source_name: Chromatin Immunoprecipitated DNA from S.cerevisiae using H3K4me3 antibody

tag: strain BY4741


title: Cervical carcinoma 77 Pre-treatment

source_name: Cervical carcinoma Punch biopsy before hydralazine and magnesium valproate treatment


title: Sir2_mutant H3R2A_yeast complete medium

source_name: Chromatin Immunoprecipitated DNA from mutant H3R2A S.cerevisiae using Sir2 antibody

tag: strain JHY6-H3R2A


title: Rap1_wild-type H3_yeast complete medium

source_name: Chromatin Immunoprecipitated DNA from S.cerevisiae using Rap1 antibody


title: H3K4me2_wild-type yeast_complete medium

source_name: Chromatin Immunoprecipitated DNA from S.cerevisiae using H3K4me2 antibody


title: H3R2me2a_wild-type yeast_complete medium

source_name: Chromatin Immunoprecipitated DNA from S.cerevisiae using H3R2me2a antibody


title: Aerobic/hypoxic expression in hap1 deletion S.cerevisiae rep2

status: Public on Jul 28 2007

city: Princeton

first: Mark

last: Hickman

state: NJ

address: Washington Road

department: Lewis-Sigler Institute of Integrative Genomics

institute: Princeton University

description: Microarray spots were quantitated with GenePix 5.0  software (Axon Instrumentation), resulting in a GPR file. The GPR file is included as a supplementary file.

hyb_protocol: Hybridization contained labeled cDNA, yeast tRNA and salmon sperm DNA in DIG Easy Hyb solution (Roche).  Incubated on slide under Erie Scientific lifter slip overnight at 37C.  Rinsed slide in 1X SSC. Washed 3 times for 10 minues each in  1X SSC 0.1% SDS at 50C.  Then rinsed in 1X SSC followed by 0.1X SSC.  Slides were dried rapidly by centrifugation.

scan_protocol: Slides were scanned in a GenePix 4000B scanner and images were acquired and analyzed with GenePix 5.0  software (Axon Instrumentation).

data_processing: The GPR file was converted to MEV files using TIGR Express Converter.  The MEV data was total intensity and LOWESS normalized using TIGR MIDAS. These values are in the columns labeled WT_aerobic and WT_hypoxic. VALUE was obtained by taking the log base 10 of the WT_aerobic/WT_hypoxic ratio.

molecule: polyA RNA

source_name: hap1 deletion aerobic

label_protocol: Bioprime kit (Invitrogen)

extract_protocol: hot phenol RNA extraction, ethanol precipitation, RNeasy (Qiagen) purification, reverse transcribed with Superscript III (Invitrogen) and polyT primer

tag: strain yMH51 (S288C background, MATa ura3D0 his3D200 leu2D0 lys2-128d hap1D::KanMX), mid-log aerobic growth

source_name: hap1 deletion hypoxic

tag: strain yMH51 (S288C background, MATa ura3D0 his3D200 leu2D0 lys2-128d hap1D::KanMX), mid-log 8 hours hypoxic growth (N2 gas-sparged flasks)


title: Aerobic/hypoxic expression in hap1 deletion S.cerevisiae rep3


title: Rap1_mutant H3R2A_yeast complete medium

source_name: Chromatin Immunoprecipitated DNA from mutant H3R2A S.cerevisiae using Rap1 antibody


title: Cervical carcinoma 63 Post-treatment

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


title: Cervical carcinoma 69 Post-treatment


title: H3_wild-type yeast_complete medium

source_name: Chromatin Immunoprecipitated DNA from S.cerevisiae using H3 antibody


title: Aerobic/hypoxic expression in hap1 deletion S.cerevisiae rep1


title: Cervical carcinoma 77 Post-treatment


title: Cervical carcinoma 69 Pre-treatment


title: Aerobic/hypoxic expression in wild-type S.cerevisiae rep2

source_name: WT aerobic

tag: strain yMH36 (S288C with repaired HAP1 allele, MATa ura3D0 his3D200 leu2D0 lys2-128d), mid-log aerobic growth

source_name: WT hypoxic

tag: strain yMH36 (S288C with repaired HAP1 allele, MATa ura3D0 his3D200 leu2D0 lys2-128d), mid-log 8 hours hypoxic growth (N2 gas-sparged flasks)


title: Cervical carcinoma 49 Post-treatment


title: Cervical carcinoma 63 Pre-treatment


title: Cervical carcinoma 49 Pre-treatment


title: Cervical carcinoma 22 Post-treatment


title: Cervical carcinoma 24 Pre-treatment


title: Cervical carcinoma 33 Pre-treatment


title: Cervical carcinoma 26 Post-treatment


title: Lobular Carcinoma in situ (LCIS) Sample 22

status: Public on Jul 27 2007

first: Mitchell

last: Guttman

address: 7 Cambridge Center

institute: Broad Institute

description: We examined a set of human breast cancers that were laser-microdissected from archived formalin fixed paraffin embedded (FFPE) tissue. These samples represent an important resource; however, they also represent a challenging aCGH application, as they tend to have significant amounts of noise.

hyb_protocol: The arrays, in Corning Hybridization chambers were incubated at 37 °C for 72 h, then washed, dried, and scanned.

scan_protocol: The slides were scanned with the GenePix Microarrray Scanner (Axon Instruments, http://www.moleculardevices.com). Data was extracted using the GenePix Pro Software package.

data_processing: We observed an intensity dependent bias and performed print tip–specific loess normalization within each array.

source_name: Genomic DNA

label_protocol: Indirect DOP PCR amplified amina-allyl dUTP labelled

extract_protocol: Commercial human DNA obtained from female genomic DNA. A pool was used to reduce variation between arrays.

tag: We hybridized our samples to the array, where the reference channel consisted of a pool of degenerate oligonucleotide–primed PCR amplification products from a commercial DNA source. Aliquots of labeled target and reference DNA were cohybridized to each BAC microarray with 100 μg of human Cot-1 DNA (Invitrogen, http://www.invitrogen.com) to block repetitive sequences.

source_name: LCIS Cells

label_protocol: Indirect DOP PCR amplified amina-allyl dUTP labeled

extract_protocol: Extracted cells were digested with proteinase K and DOP amplified and labeled.

tag: A skilled histotechnologist cut and mounted single 10-μm thick paraffin sections of each target tissue onto PET-membrane slides used with the SL μCUT System (Molecular Machines & Industries, http://www.molecular-machines.com). We deparaffinized, rehydrated and stained the sections with hematoxylin. Within 1–2 h, we placed each section into a microdissection unit that sandwiches the tissue section between a clean glass slide and the membrane and microdissected it with the SL μCUT System (Molecular Machines & Industries).


title: Aerobic/hypoxic expression in wild-type S.cerevisiae rep3


title: Aerobic/hypoxic expression in wild-type S.cerevisiae rep1


title: Lobular Carcinoma in situ (LCIS) Sample 21


title: Lobular Carcinoma in situ (LCIS) Sample 8


title: Cervical carcinoma 16 Post-treatment

source_name: Cervical carcinoma Punch biopsy after hydralazine and magnesium valproate treatment


title: Cervical carcinoma 22 Pre-treatment


title: Lobular Carcinoma in situ (LCIS) Sample 10


title: Lobular Carcinoma in situ (LCIS) Sample 9


title: Lobular Carcinoma in situ (LCIS) Sample 13


title: Cervical carcinoma 16 Pre-treatment


title: Lobular Carcinoma in situ (LCIS) Sample 11


title: Lobular Carcinoma in situ (LCIS) Sample 20


title: Lobular Carcinoma in situ (LCIS) Sample 7


title: Lobular Carcinoma in situ (LCIS) Sample 4


title: Lobular Carcinoma in situ (LCIS) Sample 14


title: Lobular Carcinoma in situ (LCIS) Sample 15


title: Lobular Carcinoma in situ (LCIS) Sample 12


title: Lobular Carcinoma in situ (LCIS) Sample 5


title: Cervical carcinoma 2 Pre-treatment


title: Lobular Carcinoma in situ (LCIS) Sample 3


title: Cervical carcinoma 2 Post-treatment

tag: Punch biopsy were taken from primary cervical tumors at diagnosis and at day 8 of treatment with hydralazine and magnesium valproate


title: Lobular Carcinoma in situ (LCIS) Sample 2


title: Lobular Carcinoma in situ (LCIS) Sample 17


title: Lobular Carcinoma in situ (LCIS) Sample 18


title: Cervical carcinoma 33 Post-treatment


title: Ductal Carcinoma in situ (DCIS) Sample 10

source_name: DCIS Cells


title: Lobular Carcinoma in situ (LCIS) Sample 19


title: Ductal Carcinoma in situ (DCIS) Sample 6


title: Ductal Carcinoma in situ (DCIS) Sample 7


title: Lobular Carcinoma in situ (LCIS) Sample 6


title: Lobular Carcinoma in situ (LCIS) Sample 16


title: Lobular Carcinoma in situ (LCIS) Sample 1


title: Cervical carcinoma 97 Pre-treatment


title: Ductal Carcinoma in situ (DCIS) Sample 4


title: Cervical carcinoma 26 Pre-treatment


title: Ductal Carcinoma in situ (DCIS) Sample 5


title: Ductal Carcinoma in situ (DCIS) Sample 3


title: Ductal Carcinoma in situ (DCIS) Sample 9


title: Ductal Carcinoma in situ (DCIS) Sample 8


title: Cervical carcinoma 24  Post-treatment


title: H3K4me1_wild-type yeast_complete medium

source_name: Chromatin Immunoprecipitated DNA from S.cerevisiae using H3K4me1 antibody

source_name: Input chromatin DNA control


title: Ductal Carcinoma in situ (DCIS) Sample 2


title: Ductal Carcinoma in situ (DCIS) Sample 11

source_name: Ductal Carcinoma in situ Laser Captured Cells


title: Ductal Carcinoma in situ (DCIS) Sample 13

source_name: Human Genomic DNA


title: Ductal Carcinoma in situ (DCIS) Sample 1


title: Ductal Carcinoma in situ (DCIS) Sample 12


title: Ductal Carcinoma in situ (DCIS) Sample 14


title: Ductal Carcinoma in situ (DCIS) Sample 15


title: Ductal Carcinoma in situ (DCIS) Sample 19

tag: We hybridized our samples to the array, where the reference channel consisted of a pool of degenerate oligonucleotide–primed PCR amplification products from a commercial DNA source. Aliquots of labeled target and reference DNA were cohybridized to each BAC microarray with 100 μg of human Cot-1 DNA (Invitrogen, http://www.invitrogen.com) to block repetitive sequences

extract_protocol: Extracted cells were digested with proteinase K and DOP amplified and labelled.


title: Ductal Carcinoma in situ (DCIS) Sample 17


title: PCK_LB-GlC medium_D=0.1 h-1

status: Public on Jul 26 2007

city: Bucheon

first: Pil

last: Kim

state: Gyunggi

address: 43-1 Yokkok2-dong

country: South Korea

institute: Catholic Univ. of Korea

hyb_protocol: 1.	Dissolve the dried labeled sample in a reasonable volume of hybridization buffer depending on the area to be covered. (Typically, 22X22mm cover-slip requires 25 ㎕ of hybridization buffer.  22X60mm cover-slip requires 60 ㎕). 2.	Heat the labeled sample preparation for 5min at 95℃. 3.	Spin down for 30 sec.  Do not put on ice!!! 4.	Place slide in the hybridization chamber. Put 20㎕ of 3XSSC to the chamber at both ends of the slide. 5.	Pipette the labeled target onto the slide surface. 6.	Carefully place the cover-slip on top of the slide. Try to reduce the formation of air bubbles. 7.	Seal the hybridization chamber and incubate in 42℃. Water-bath or hybridization oven for more than 16 hr.

scan_protocol: DNA chips were scanned using an Axon GenePix 4000B Scanner(Axon Instruments, Union City, CA) with the laser set to 532 and 635 nm, the photomultiplier tube (PMT) voltage to 600 and the scan resolution to 10 µm.

data_processing: Scanned images were analyzed with GenePix Pro 3.0 software (Axon Instruments, Union City, CA) to obtain gene expression ratios. Logged gene expression ratios were normalized by LOWESS regression (Yang et al., 2002) using the GeneSpring GX 7.3 software (Agilent Technologies).

organism: Escherichia coli

label_protocol:
1.	To 20-50g of total RNA (or 2g poly(A) RNA), add necessary control RNA mixture and 2l of oligo(dT) primer (0.5g/l ).  Make the final volume up to 31L with RNase-free water.  For human and mouse RNA samples, 20g of total RNA is sufficient for hybridization in ASP.  For Drosophila RNA sample, 50 g of total RNA is needed for ASP.  For less amount of RNA, hybridization should be performed mannually in a smaller volume of hybridization buffer.
2.	Mix well and incubate at 70 C for 10 minutes.  Chill on ice for 1 min. Spin briefly.
3.	Add followings to the RNA solution:
5X First Strand buffer		10L
0.1 M DTT			5L
Rnasin				1L
50X aminoallyl-dNTP mix	1L
SuperScript II (200U/L)		2L
4.	Mix and incubate at 42 °C for 1 hr.  Add additional 1l of superscript II and incubate for another 1 hr.
5.	To hydrolyze RNA, add 16.5l of 1 M NaOH and 16.5l of 0.5 M EDTA.  Mix and incubate at 65 °C for 15 minutes.  Add 16.5L of 1 M HCl to neutralize pH.
6.	Clean-up the cDNA reaction with Microcon YM-30 (Cat No. 42409)
7.	Dry sample in a speed vac. Add D.W. and 1M sodium carbonate buffer to resuspend cDNA pellet in 9.0ul of 0.1M sodium carbonate buffer
8.	Add 2.0L of the appropriate NHS-ester Cy dye
9.	Incubate the reaction for 1 hour in the dark at room temperature.
10.	Clean up the coupling reaction with QIAquick PCR purification kit.  Repeat the elution step twice with 30L elution buffer to get 60L of elution volumn.
11.	Calculate the pmole nucleotide, pmole Cy3, Cy5, and nucleotide/dye ratio. (Determine O.D. at 260nm, 550nm, 650nm, and 700nm.)
12.	Dry the Cy3 and Cy5 sample in a speed vac. and proceed to hybridization step.

growth_protocol: The medium for continuous culture contained 20 g LB, 9 g glucose, 10 g NaHCO3, 50 mg ampicillin per liter and isopropyl--D-thiogalactopyranoside (IPTG) was supplemented to be 0.1 mM. The initial pH of the medium was set to be pH 7.3 by adding 1 N HCl solution. The inoculation culture was transferred into a 250 mL-fermentor containing 100 mL medium (Small scale multi-chemostat fermentor; Biotron Inc., Bucheon, Korea). The culture was performed at 37 C, 350 rpm with flushing CO2 gas at 20 mL/min. After 8 h inoculation, the feeding and outlet pumps were started at flow rate of 0.166 mL/h (dilution rate = 0.1 h-1).

extract_protocol: Transcriptome of cells was prepared using a RNA extraction kit (RNeasy mini kit;Qiagen, Hilden, Germany)

tag: E. coli W3110 grown at LB-glucose medium (IPTG induction) in chemostat (D=0.1 h-1)

source_name: E. coli W3110 expressing PCK

tag: E. coli W3110/pck grown at LB-glucose medium (IPTG induction) in chemostat (D=0.1 h-1)


title: PPC_glucose-minimal medium_early log phase

hyb_protocol: 1.	To 20-50g of total RNA (or 2g poly(A) RNA), add necessary control RNA mixture and 2l of oligo(dT) primer (0.5g/l ).  Make the final volume up to 31L with RNase-free water.  For human and mouse RNA samples, 20g of total RNA is sufficient for hybridization in ASP.  For Drosophila RNA sample, 50 g of total RNA is needed for ASP.  For less amount of RNA, hybridization should be performed mannually in a smaller volume of hybridization buffer. 2.	Mix well and incubate at 70 C for 10 minutes.  Chill on ice for 1 min. Spin briefly. 3.	Add followings to the RNA solution: 5X First Strand buffer		10L 0.1 M DTT			5L Rnasin				1L 50X aminoallyl-dNTP mix	1L SuperScript II (200U/L)		2L 4.	Mix and incubate at 42 °C for 1 hr.  Add additional 1l of superscript II and incubate for another 1 hr. 5.	To hydrolyze RNA, add 16.5l of 1 M NaOH and 16.5l of 0.5 M EDTA.  Mix and incubate at 65 °C for 15 minutes.  Add 16.5L of 1 M HCl to neutralize pH. 6.	Clean-up the cDNA reaction with Microcon YM-30 (Cat No. 42409) 7.	Dry sample in a speed vac. Add D.W. and 1M sodium carbonate buffer to resuspend cDNA pellet in 9.0ul of 0.1M sodium carbonate buffer 8.	Add 2.0L of the appropriate NHS-ester Cy dye 9.	Incubate the reaction for 1 hour in the dark at room temperature. 10.	Clean up the coupling reaction with QIAquick PCR purification kit.  Repeat the elution step twice with 30L elution buffer to get 60L of elution volumn. 11.	Calculate the pmole nucleotide, pmole Cy3, Cy5, and nucleotide/dye ratio. (Determine O.D. at 260nm, 550nm, 650nm, and 700nm.) 12.	Dry the Cy3 and Cy5 sample in a speed vac. and proceed to hybridization step.

label_protocol:
1.	To 20-50g of total RNA (or 2g poly(A) RNA), add necessary control RNA mixture and 2l of oligo(dT) primer (0.5g/l ).  Make the final volume up to 31L with RNase-free water.  For human and mouse RNA samples, 20g of total RNA is sufficient for hybridization in ASP.  For Drosophila RNA sample, 50 g of total RNA is needed for ASP.  For less amount of RNA, hybridization should be performed mannually in a smaller volume of hybridization buffer.
2.	Mix well and incubate at 70 C for 10 minutes.  Chill on ice for 1 min. Spin briefly.
3.	Add followings to the RNA solution:
5X First Strand buffer		10L
0.1 M DTT			5L
Rnasin				1L
50X aminoallyl-dNTP mix	1L
SuperScript II (200U/L)		2L
4.	Mix and incubate at 42 °C for 1 hr.  Add additional 1l of superscript II and incubate for another 1 hr.
5.	To hydrolyze RNA, add 16.5l of 1 M NaOH and 16.5l of 0.5 M EDTA.  Mix and incubate at 65 °C for 15 minutes.  Add 16.5L of 1 M HCl to neutralize pH.
6.	Clean-up the cDNA reaction with Microcon YM-30 (Cat No. 42409).
Add 400ul of D.W. (make up to 500ul).
Apply the mixture to Microcon YM-30 sample reservoir in an eppendrof tube.
Spin at 12,000rpm for 8-10 minutes (Spin times must be decided by retention volume after 1st centrifugation. 10-20ul of retention volume of sampe reservoir makes a good result.).
Discard flow through.
Repeat 3 times more this washing step.
Place the sample reservoir upside down in a new eppendrof tube.
Spin at 4000rmp for 3 minutes to transfer concentrate to tube. (Optimal collection volume is 20-30µL.)
7.	Dry sample in a speed vac. Add D.W. and 1M sodium carbonate buffer to resuspend cDNA pellet in 9.0ul of 0.1M sodium carbonate buffer.
8.	Add 2.0L of the appropriate NHS-ester Cy dye
9.	Incubate the reaction for 1 hour in the dark at room temperature.
10.	Clean up the coupling reaction with QIAquick PCR purification kit.  Repeat the elution step twice with 30L elution buffer to get 60L of elution volumn.
11.	Calculate the pmole nucleotide, pmole Cy3, Cy5, and nucleotide/dye ratio. (Determine O.D. at 260nm, 550nm, 650nm, and 700nm.)
12.	Dry the Cy3 and Cy5 sample in a speed vac. and proceed to hybridization step.

growth_protocol: The medium for batch culture was consisted of 11.3 g M9 medium, 0.2 g MgSO4•7H2O, 0.1 g CaCl2, 1 mg thiamine, 10 g NaHCO3 and 9 g glucose, 50 mg ampicillin and 0.1 mmole IPTG per liter.

tag: E. coli W3110 grown at glucose-minimal medium (IPTG induction) in early log phase (u=0.25 h-1)

source_name: E. coli W3110 expressing ppc

tag: E. coli W3110/ppc grown at glucose-minimal medium (IPTG induction) in early log phase (u=0.25 h-1)


title: M4 juvenile biol repl 2

city: Pittsburgh

first: Tunda

last: Hidvegi

state: PA

address: 3460 Fifth Ave

institute: University of Pittsburgh

description: no doxycycline, wt

hyb_protocol: Sample preparation and array hybridization was conducted by the Genomics and Proteomics Core Laboratories of the University of Pittsburgh.

data_processing: Probe level data (CEL files) were processed by S-PLUS 6.2 Array Analyzer Module (Insightful). Normalization to adjust for background noise, to correct for random and non-specific binding was done as follows: background control = RMA, normalization = quantiles. Then Differential Expression Analysis was performed applying Local Pooled Error (LPE) Test with Bonferroni adjustment (FWER/FDR control= 0.05).

organism: Mus musculus

source_name: liver from wild type mouse not receiving doxycycline

growth_protocol: Mice with hepatocyte-specific inducible expression of wild type AT (M mice), mutant ATZ (Z mice) human alpha1-antitrypsin were  were maintained with doxycycline (group1) or without doxycycline (group4)

extract_protocol: Curde RNA was prepared from liver samples by TRIZOL followed by RNEasy purification.

treatment_protocol: Group1 mice received 40 ug/mL doxycycline in drinking water from conception till they were sacrificed.

tag: 6 wk old male


title: Ductal Carcinoma in situ (DCIS) Sample 18


title: M4 juvenile biol repl 1

description: no doxycycline, wt

scan_protocol: Sample preparation and array hybridization was conducted by the Genomics and Proteomics Core Laboratories of the University of Pittsburgh.


title: M4 juvenile biol repl 3

description: no doxycycline, wt

label_protocol: Sample preparation and array hybridization was conducted by the Genomics and Proteomics Core Laboratories of the University of Pittsburgh.


title: Z4 biol repl 3

description: no doxycycline, mutant

data_processing: Probe level data (CEL files) were processed by S-PLUS 6.2 Array Analyzer Module (Insightful). Normalization to adjust for background noise, to correct for random and non-specific binding as  done as follows: background control = RMA, normalization = quantiles. Then Differential Expression Analysis was performed applying Local Pooled Error (LPE) Test with Bonferroni adjustment (FWER/FDR control= 0.05).

source_name: liver from mutant mouse not receiving doxycycline

growth_protocol: Mice with hepatocyte-specific inducible expression of wild type AT (M mice), mutant ATZ (Z mice) human alpha1-antitrypsin were maintained with doxycycline (group1) or without doxycycline (group4)

tag: 3 mo old male


title: Z1 juvenile biol repl 3

description: doxycycline, mutant

source_name: liver from mutant mouse receiving doxycycline


title: M1 juvenile biol repl 1

description: doxycycline, wt

source_name: liver from wild type mouse receiving doxycycline


title: WT biol repl2

description: no doxycycline, no AAT

source_name: liver from wild type littermates


title: Z4 juvenile biol repl 1

description: no doxycycline, mutant


title: M1 juvenile biol repl 3

description: doxycycline, wt


title: M4 biol repl 1

description: no doxycycline, wt


title: Ductal Carcinoma in situ (DCIS) Sample 20

tag: We hybridized our samples to the array, where the reference channel consisted of a pool of degenerate oligonucleotide–primed PCR amplification products from a commercial DNA source.  Aliquots of labeled target and reference DNA were cohybridized to each BAC microarray with 100 μg of human Cot-1 DNA (Invitrogen, http://www.invitrogen.com) to block repetitive sequences.


title: PPC_LB-GlC medium_D=0.1 h-1

source_name: E. coli W3110 (KCTC 2223) at LB-GlC medium, D=0.1 h-1

source_name: E. coli W3110 expressing ppc at LB-GlC medium, D=0.1 h-1

tag: E. coli W3110/ppc grown at LB-glucose medium (IPTG induction) in chemostat (D=0.1 h-1)


title: Ductal Carcinoma in situ (DCIS) Sample 16


title: WT biol repl3

description: no doxycycline, no AAT


title: M4 biol repl 3

description: no doxycycline, wt


title: PCK_glucose-minimal medium_early log phase

data_processing: Scanned images were analyzed with GenePix Pro 3.0 software (Axon Instruments, Union City, CA) to obtain gene expression ratios.

tag: E. coli W3110 with glucose-minimal medium (IPTG induced) at early log phase (u=0.25)

source_name: W3110 overexpressing pck

tag: E. coli W3110/PCK with glucose-minimal medium (IPTG induced) at early log phase (u=0.25)


title: M4 biol repl 2

description: no doxycycline, wt


title: Z4 biol repl 2

description: no doxycycline, mutant


title: Z1 juvenile biol repl 2

description: doxycycline, mutant


title: Z4 juvenile biol repl 3

description: no doxycycline, mutant


title: Z4 juvenile biol repl 2

description: no doxycycline, mutant


title: Z1 juvenile biol repl 1

description: doxycycline, mutant


title: Z4 biol repl 1

description: no doxycycline, mutant


title: Z1 biol repl 2

description: doxycycline, mutant


title: M1 juvenile biol repl 2

description: doxycycline, wt


title: WT biol repl1

description: no doxycycline, no AAT


title: Z1 biol repl 1

description: doxycycline, mutant


title: M1 biol repl 3

description: doxycycline, wt


title: M1 biol repl 2

description: doxycycline, wt


title: M1 biol repl 1

description: doxycycline, wt


title: treated group, sample 2

status: Public on Jul 25 2007

city: Barcelona

first: Xavier

last: Remesar

address: Av. Diagonal 645

department: Nutrició i Bromatologia

country: Spain

institute: Universitat de Barcelona

description: Array data analyses were conducted via a parametric comparison using all available error estimates as a filter based on variances calculated by the Cross-gene Error Model in GeneSpring 6.1 software (Silicon Genetics, Redwood City CA, USA). The Cross-gene Error Model performs a variance components analysis for the accurate comparison of mean expression levels between experimental conditions. In this model, separate estimates for two different kinds of random variation are used to estimate the variability in gene expression measurements: i) measurement variation: this comprises the lowest level of variation, corresponding to the variation of gene measurement of a single chip based on the actual value that would be obtained from a perfect measurement of the gene expression level for that sample, and ii) sample-to-sample variation: the variation between samples under the same condition reflecting biological or sampling variability.

hyb_protocol: Nylon membranes were pre-hybridized in ExpressHybTM (Clontech) with 100 µg/ml DNA salmon sperm for 30 min in an oven at 68ºC. Then, the 33P-labeled probe was added and hybridization continued overnight at the same conditions. Afterwards, membranes were washed lowering the astringency progressively to 0.1 X SSC, 0.5 % SDS at 68ºC and placed in contact with europium screens (Kodak, Rochester NY, USA) for 15 days.

scan_protocol: The screens were scanned with a Storm 840 phosphorimager (Molecular Dynamics, Sunnyvale CA, USA).

data_processing: Image analysis and quantification were carried out with Atlas Image 2.01 software (Clontech). After grid assignment, the adjusted intensity for each gene was calculated by subtracting the background. This value was used as the input for the GeneSpring 6.1 program (Agilent, Palo Alto CA, USA), that allows normalization of data analysis from different experiments, the generation of restriction lists, and the functional classification of the differentially expressed genes.

source_name: treated group, sample 2

label_protocol: Radiolabeled cDNA probes were prepared from 5 µg of total RNA. Briefly, the RNA was incubated for 2 min at 70ºC followed by 2 min at 50ºC with 1 µl  of the primer mix, containing the 1168 primers for the genes presented in the array. The RT reaction was carried out using 100U MMLV-RT, 40U RNAsin (Promega, Madison WI, USA) and 35 µCi [-33P] dATP (Amersham Biosciences, Piscataway NJ, UK) for 25 min at 50ºC. Labeled cDNA was purified from unincorporated nucleotide with Atlas NucleoSpin® Extraction Kit (Clontech).

extract_protocol: Total RNA was extracted from adipose mesenteric tissue using Tripure isolation kit (Roche). RNA concentration and quality were measured by spectrophotometric analysis at 260 nm and 280 nm using Nanodrop equipment (Wilmington DE, USA). RNA integrity was assessed by electrophoresis in agarose gel.

treatment_protocol:
Female Wistar rats (Harlan-Interfauna Ibérica, Sant Feliu de Codines, Spain) weighing initially 220-230 g were housed in individual cages under a light cycle (on from 08.00 to 20.00) and in a temperature-controlled environment (20-22ºC). Food (standard rat chow pellets, from Panlab, Barcelona, Spain) (available energy: 13.6 MJ/kg) and water were provided ad libitum.
The rats were given a daily oral gavage of 10 μmol/kg/day of oleoyl-estrone (OED, Barcelona, Spain) in 0.2 ml of sunflower oil during two days, by means of stomach cannulae. Controls received only the oil gavage.

tag: 48 hours

tag: Mesenteric adipose tissue of oleoyl-estrone treated rats (10 nmals/g/day).


title: treated group, sample 1

source_name: treated group, sample 1

tag: Mesenteric adipose tissue of Oleoyl-estrone treated rats (10 nmols/g/day).


title: Z1 biol repl 3

description: doxycycline, mutant


title: control group, sample 2

source_name: control group, sample 2

tag: Mesenteric adipose tissue. Control group (0.2 ml sunflower oil gavage).


title: wild type 90min growth vs. mutant (delta atmA) 90min growth dye swap

city: Ribeirão Preto

first: Gustavo

middle: Henrique

last: Goldman

state: São Paulo

address: Av do Café, s/n

country: Brazil

institute: Faculty of Pharmaceutical Sciences of Ribeirão Preto

description: Wild type and delta atmA strains were grown for 60, 90 and 120 mimutes in complete medium (YG) at 37°C, 250 rpm. Harvested conidia from each time point were DAPI stained and microscopically analyzed in terms of nucelar division kinetics  and polar growth before RNA extraction. This procedure validated the phenotipic traits of both wild type and mutant strains.

hyb_protocol: Labelled cDNAs were mixed with 8 µl Liquid block RPN3601 Batch 24 (GE Health Care), 5.5 µl SDS 2% and 19 µl SSC (20X) and the volume adjusted to 110 µl. Slides were hybridized overnight (42°C) in a Gene-Tac Hybridization Station (Genomic Solutions, Inc.) and washed in 2 X SSC 0,5% SDS, 0,5 X SSC and 0.05X SSC. All washing steps consisted of 1 min of flow, followed by 5 min of incubation.

scan_protocol: Slides were dried by centrifugation and subjected to fluorescent detection with a GMS 418 Array Scanner (Affymetrix Inc., Santa Clara, CA).

data_processing: TIFF images generated were analyzed using TIGR Spotfinder (http://www.tigr.org/software/) to obtain relative transcript levels. Spotfinder uses a dynamic thresholding algorithm to identify spots and calculate local background and integrated fluorescence intensity for each of the Cy3 and Cy5 channels. This software was also useful in eliminating questionable spots (those for which shape deviates significantly from that of a true circle, or those with a low signal-to-noise ratio). Spots with very low intensity in one channel (and thus aberrantly high or low expression ratios) were removed and eliminated from future analyses. Data was normalized using a local regression technique LOWESS (LOcally WEighted Scatterplot Smoothing) for hybridizations with RNA-based samples and SD regularization of the Cy5/Cy3 ratio across all sectors (blocks) of the array using a software tool MIDAS (http://www.tigr.org/softlab). Following normalization, the values for each gene's in-slide replicates were averaged (median variance <0.01), and corresponding flip-dye replicates were averaged to compensate for dye-specific effects. Differentially expressed genes at the 95% confidence level were determined using intensity-dependent Z-scores (with Z=1.96) as implemented in MIDAS and the union of all genes identified at each time point were considered significant in this experiment. The resulting data were organized and visualized based on similar expression vectors in genes using Euclidean distance and hierarchical clustering with average linkage clustering method to view the whole data set and k-means to group the genes in 60 clusters with TIGR MEV (multi experiment viewer), also available at http://www.tigr.org/software.

organism: Aspergillus nidulans

source_name: wild type conidia grown for 90 minutes

label_protocol: The RNA samples were extracted with Trizol and further purified with the RNA easy kit (Qiagen, Germany) and directly labelled by incorporation of Cy5-dUTP (GE Health Care). Briefly, 30 µg of total RNA were mixed with 20 µg of Randon Primer Hexamers (GE Health Care), 100 pmol of oligo dTV (Invitrogen) and 40 U of RNAse Out (Invitrogen) in a volume of 13 µl and heated to 70°C for 5 minutes. The tubes were briefly chilled to 4°C for 5 minutes and mixed with 5 µl of 5X first-strand buffer (Invitrogen), 2 µl DTT (Invitrogen), 2 µl dNTP (5 mM dATP, 5 mM dCTP, 5 mM dGTP, 2 mM dTTP), 2 µl of Suprescript II (Invitrogen) and 1 µl of Cy5-dUTP (25 nmol). The reaction was then incubated at 25°C for 5 minutes and at 42°C for 3 hours. The RNA was degraded by adding 2.5 µl EDTA (0.5 M, pH 8) and 5 µl NaOH (1M) following an incubation at 37°C for 40 minutes. The resulting first strand cDNA was purified and concentrated using a Microcon YM-50 cartridge.

extract_protocol: At each time point the germlings were harvested by centrifugation and quickly frozen in liquid nitrogen. For total RNA isolation, the germlings were disrupted by grinding in liquid nitrogen and total RNA was extracted with Trizol reagent (Invitrogen). Ten micrograms of RNA from each treatment were then fractionated in 2.2 M formaldehyde, 1.2% agarose gel, stained with ethidium bromide, and then visualized with UV-light. The presence of intact 25S and 17S ribosomal RNA bands was used as a criterion to assess the integrity of the RNA.

tag: For the time course microarray experiments, 1.0 x 1010 conidia/ml of A. nidulans wild type (GR5) and mutant strain (delta atmA, IM69) were used to inoculate 400 ml of pre-warmed liquid cultures (YG) in 1000-ml erlenmeyer flasks and allow to grow for  60, 90 and 120 minutes in a reciprocal shaker (250 rpm) at 37°C.  At each time point, germilings were harvested by centrifugation and total RNA was extracted. Hybridization experiments were competitive using probes derived from both wild type and delta atmA strain grown for 60, 90 and 120. Hybridizations were performed using the wild type RNA as reference in comparison to the mutant strain (test RNA) for the same time point. Normalized signal intensities were used to generate relative hybridization ratios (query/reference).

source_name: mutant (delta atmA) conidia grown for 90 minutes

label_protocol: The RNA samples were extracted with Trizol and further purified with the RNA easy kit (Qiagen, Germany) and directly labelled by incorporation of Cy3-dUTP (GE Health Care). Briefly, 30 µg of total RNA were mixed with 20 µg of Randon Primer Hexamers (GE Health Care), 100 pmol of oligo dTV (Invitrogen) and 40 U of RNAse Out (Invitrogen) in a volume of 13 µl and heated to 70°C for 5 minutes. The tubes were briefly chilled to 4°C for 5 minutes and mixed with 5 µl of 5X first-strand buffer (Invitrogen), 2 µl DTT (Invitrogen), 2 µl dNTP (5 mM dATP, 5 mM dCTP, 5 mM dGTP, 2 mM dTTP), 2 µl of Suprescript II (Invitrogen) and 1 µl of Cy3-dUTP (25 nmol). The reaction was then incubated at 25°C for 5 minutes and at 42°C for 3 hours. The RNA was degraded by adding 2.5 µl EDTA (0.5 M, pH 8) and 5 µl NaOH (1M) following an incubation at 37°C for 40 minutes. The resulting first strand cDNA was purified and concentrated using a Microcon YM-50 cartridge.


title: mutant (delta atmA) 0min after HU blockage vs. mutant (delta atmA) 120min after HU blockage dye swap

description: Mutant strain was incubated in 50mM of hydroxyrurea (HU) to cause transient S-phase arest and allowed to grow for additional 0, 60, 90 and 120 minutes after HU was withdrawn from the culture medium. Harvested conidia from each time point were DAPI stained and microscopically analyzed in terms of nucelar division kinetics  and polar growth before RNA extraction. This procedure validated the phenotipic traits of the delta atmA mutant strain.

hyb_protocol: Labelled cDNAs were mixed with 8 µl Liquid block RPN3601 Batch 24 (GE Health Care), 5.5 µl SDS 2% and 19 µl SSC (20X) and the volume adjusted to 110 µl. Slides were hybridized overnight (42°C) in a Gene-Tac Hybridization Station (Genomic Solutions, Inc.) and washed in 2 X SSC 0,5% SDS, 0,5 X SSC and 0.05X SSC. All washing steps consisted of 1 min of flow, followed by 5 min of incubation

source_name: mutant (delta atmA) conidia grown for 0 minutes after hydroxyurea blockage

tag: For the time course microarray experiments, 1.0 x 1010 conidia/ml of A. nidulans IM69 (delta atmA mutant) strain were used to inoculate 400 ml of pre-warmed liquid cultures (YG) in 1000-ml erlenmeyer flasks containing 50 mM of hydroxyurea (HU) and allow to grow for 5 hours in a reciprocal shaker (250 rpm) at 37°C to synchronize the germlings in the S-phase of cell cycle. After this time, the cultures were centrifuged, washed and pre-warmed drug-free fresh media was aseptically added to the cultures. They were allowed to grow for additional 60, 90 and 120 minutes after the HU-release. Hybridization experiments were competitive using probes derived from wild type and delta atmA strain grown for zero, 60, 90 and 120 minutes after HU blockage release using timepoint zero as the reference RNA for every hybridizantion. Normalized signal intensities were used to generate relative hybridization ratios (query/reference).

source_name: mutant (delta atmA) conidia grown for 120 minutes after hydroxyurea blockage


title: wild type 120min growth vs. mutant (delta atmA) 120min growth dye swap

source_name: wild type conidia grown for 120 minutes

source_name: mutant (delta atmA) conidia grown for 120 minutes


title: mutant (delta atmA) 0min after HU blockage vs. mutant (delta atmA) 90min after HU blockage dye swap

source_name: mutant (delta atmA) conidia grown for 90 minutes after hydroxyurea blockage


title: wild type 120min growth vs. mutant (delta atmA) 120min growth


title: wild type 60min growth vs. mutant (delta atmA) 60min growth dye swap

source_name: wild type conidia grown for 60 minutes

source_name: mutant (delta atmA) conidia grown for 60 minutes


title: wild type 0min after HU blockage vs. wild type 90min after HU blockage dye swap

description: Wild type strain was incubated in 50mM of hydroxyrurea (HU) to cause transient S-phase arest and allowed to grow for additional 0, 60, 90 and 120 minutes after HU was withdrawn from the culture medium. Harvested conidia from each time point were DAPI stained and microscopically analyzed in terms of nucelar division kinetics  and polar growth before RNA extraction. This procedure validated the phenotipic traits of the wild type strain.

source_name: wild type conidia grown for 0 minutes after hydroxyurea blockage

tag: For the time course microarray experiments, 1.0 x 1010 conidia/ml of A. nidulans wild type (GR5) strain were used to inoculate 400 ml of pre-warmed liquid cultures (YG) in 1000-ml erlenmeyer flasks containing 50 mM of hydroxyurea (HU) and allow to grow for 5 hours in a reciprocal shaker (250 rpm) at 37°C to synchronize the germlings in the S-phase of cell cycle. After this time, the cultures were centrifuged, washed and pre-warmed drug-free fresh media was aseptically added to the cultures. They were allowed to grow for additional 60, 90 and 120 minutes after the HU-release. Hybridization experiments were competitive using probes derived from wild type and delta atmA strain grown for zero, 60, 90 and 120 minutes after HU blockage release using timepoint zero as the reference RNA for every hybridizantion. Normalized signal intensities were used to generate relative hybridization ratios (query/reference).

source_name: wild type conidia grown for 90 minutes after hydroxyurea blockage


title: wild type 0min after HU blockage vs. wild type 120min after HU blockage dye swap

source_name: wild type conidia grown for 120 minutes after hydroxyurea blockage


title: wild type 0min after HU blockage vs. wild type 60min after HU blockage dye swap

source_name: wild type conidia grown for 60 minutes after hydroxyurea blockage


title: wild type 60min growth vs. mutant (delta atmA) 60min growth


title: mutant (delta atmA) 0min after HU blockage vs. mutant (delta atmA) 60min after HU blockage dye swap

source_name: mutant (delta atmA) conidia grown for 60 minutes after hydroxyurea blockage


title: liver_PPARa-knockout_WY14643_5d_pooled

status: Public on Jul 24 2007

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

description: liver, PPARa-null mice, treatment with WY14643 for 5 days

hyb_protocol: According to standard Affymetrix protocols.

data_processing: GCRMA version 2.20, emperical Bayes

extract_protocol: TRIzol (Invitrogen), according to manufacturer's instructions.

tag: Strain

value: 129S4/SvJae (PPARα-null)

tag: Gender

value: male

tag: Age

value: 12-20 weeks

tag: Tissue

value: liver


title: control group, sample 1

source_name: control group, sample 1


title: mutant (delta atmA) 0min after HU blockage vs. mutant (delta atmA) 60min after HU blockage

label_protocol: The RNA samples were extracted with Trizol and further purified with the RNA easy kit (Qiagen, Germany) and directly labelled by incorporation of Cy3-dUTP (GE Health Care). Briefly, 30 µg of total RNA were mixed with 20 µg of Randon Primer Hexamers (GE Health Care), 100 pmol of oligo dTV (Invitrogen) and 40 U of RNAse Out™ (Invitrogen) in a volume of 13 µl and heated to 70°C for 5 minutes. The tubes were briefly chilled to 4°C for 5 minutes and mixed with 5 µl of 5X first-strand buffer (Invitrogen), 2 µl DTT (Invitrogen), 2 µl dNTP (5 mM dATP, 5 mM dCTP, 5 mM dGTP, 2 mM dTTP), 2 µl of Suprescript II (Invitrogen) and 1 µl of Cy3-dUTP (25 nmol). The reaction was then incubated at 25°C for 5 minutes and at 42°C for 3 hours. The RNA was degraded by adding 2.5 µl EDTA (0.5 M, pH 8) and 5 µl NaOH (1M) following an incubation at 37°C for 40 minutes. The resulting first strand cDNA was purified and concentrated using a Microcon YM-50 cartridge.

label_protocol: The RNA samples were extracted with Trizol and further purified with the RNA easy kit (Qiagen, Germany) and directly labelled by incorporation of Cy5-dUTP (GE Health Care). Briefly, 30 µg of total RNA were mixed with 20 µg of Randon Primer Hexamers (GE Health Care), 100 pmol of oligo dTV (Invitrogen) and 40 U of RNAse Out™ (Invitrogen) in a volume of 13 µl and heated to 70°C for 5 minutes. The tubes were briefly chilled to 4°C for 5 minutes and mixed with 5 µl of 5X first-strand buffer (Invitrogen), 2 µl DTT (Invitrogen), 2 µl dNTP (5 mM dATP, 5 mM dCTP, 5 mM dGTP, 2 mM dTTP), 2 µl of Suprescript II (Invitrogen) and 1 µl of Cy5-dUTP (25 nmol). The reaction was then incubated at 25°C for 5 minutes and at 42°C for 3 hours. The RNA was degraded by adding 2.5 µl EDTA (0.5 M, pH 8) and 5 µl NaOH (1M) following an incubation at 37°C for 40 minutes. The resulting first strand cDNA was purified and concentrated using a Microcon YM-50 cartridge.


title: liver_wildtype_control_5d_pooled

description: liver, wild type mice, control conditions

scan_protocol: According to standard Affymetrix protocols.

extract_protocol: TRIzol reagent (Invitrogen), according to manufacturer's instructions.

value: 129S1/SvImJ (wildtype)


title: mutant (delta atmA) 0min after HU blockage vs. mutant (delta atmA) 90min after HU blockage


title: Gene expression profiling of Phgdh knockout embryo wild1

city: Fukuoka

first: Shigeki

last: Furuya

state: Fukuoka

address: 6-10-1 Hakozaki, Higashiku

department: Bio-Architecture Center

institute: Kyushu University

description: Affymetrix GeneChip® Mouse Genome 430 2.0 Array

hyb_protocol: Hybridization was carried out for 16 hr at 45 ºC according the Affymetrix GeneChip® Manual.

scan_protocol: Scanning was carried out using Affymetrix® GeneChip® Scanner with GCOS software according to manufactuer's protocol.

data_processing: Fluorescent data were processed using the Microarray Suite (MAS) 5.0 software (Affymetrix) and then were transferred to GeneSpring 7.0 software (Agilent).

source_name: Head RNA of littermate wild@E13.5 No.1

label_protocol: Labeling was carried out using Affymetrix GeneChip® One-Cycle Target Labeling kit, according to manufactuer's protocol.

extract_protocol: Total RNA from embryo heads was extracted and purified using RNeasy Lipid Tissue kit (Qiagen Inc) according to the manufacturer’s instructions.

treatment_protocol: Targeted disruption of D-3-Phosphoglycerate dehydrogenase (Phgdh; EC 1.1.1.95) in mice.

tag: ES cells

value: E14 (129P2/OlaHsd background),

tag: Genotype

value: Wild (Phgdh+/+), C57BL/6J background,

tag: Gestation

value: head


title: mutant (delta atmA) 0min after HU blockage vs. mutant (delta atmA) 120min after HU blockage


title: liver_PPARa-knockout_fasted24h_pooled

description: liver, PPARa-null mice, fasting conditions (24h)

data_processing: GCRMA version 2.20, empirical Bayes

label_protocol: According to standard Affymetrix protocols.


title: liver_PPARa-knockout_fed_pooled

description: Liver samples PPARa-null mice, control conditions

extract_protocol: TRIzol reagent (Invitrogen) according to manufacturer's instructions


title: ICC 3996 Salt shoots 48 h

city: Bundoora

first: Nitin

last: Mantri

state: Victoria

address: Bldg 223, Level 1, Plenty Road

department: Biotechnology & Environmental Biology

country: Australia

institute: RMIT University

description: The data submitted represents the mean data from three biological replications that inlcuded dye swaps between control and treatment samples

hyb_protocol: See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated during a resistance response to Ascochyta rabiei. Plant Biotechnology Journal. 4(6), 647–666

data_processing: Data transformations consisted of a local background correction (mean intensity of background was subtracted from mean signal intensity for each spot), omitting flagged spots, Lowess normalisation of the entire population, creating a Cy5/Cy3 mean signal ratio, taking a shifted log (base 2), and combination of duplicated spot data. To identify differentially expressed (DE) genes, expression ratio results were filtered to eliminate genes whose 95% confidence interval for mean fold change (FC) did not extend to 2-fold up or down, followed by Students t test with False Discovery Rate (FDR) multiple testing correction to retain only genes in which expression changes versus untreated control were significant at P < 0.05.

organism: Cicer arietinum

source_name: Treatment

growth_protocol: The treatment plants were cultivated in a hydroponic system using 50 L plastic crates. Forty holes (8 x 5 grid) of 5 cm diameter were drilled in the crates’ lid and rock wool plugs were placed in them. The germinated seeds were transplanted in alternate plugs within the crate. The seedlings were watered normally from above for four days. The following day, the crates were filled with 0.5 X modified Hoagland’s nutrient medium (pH 6.5; Taiz and Zeiger 2002). The medium was aerated using two aquarium pumps. The nutrient medium was subsequently replaced with 1.0 X Hoagland’s solution (pH 6.5) after a further seven days.

treatment_protocol: At day 18, the nutrient medium for the treatment plants was replaced with 1.0 X modified Hoagland’s with 150 mM Sodium Chloride (NaCl) (pH 6.5), which represented a salinity concentration known to be toxic to chickpea (unpublished data; Munns 2002). The shoot tissues were collected from five treatment plants at 48 h post-treatment (hpt).

value: 18 days (seedling)

value: Shoot (stem and leaf)

source_name: Control

growth_protocol: The control plants were cultivated in a hydroponic system using 50 L plastic crates. Forty holes (8 x 5 grid) of 5 cm diameter were drilled in the crates’ lid and rock wool plugs were placed in them. The germinated seeds were transplanted in alternate plugs within the crate. The seedlings were watered normally from above for four days. The following day, the crates were filled with 0.5 X modified Hoagland’s nutrient medium (pH 6.5; Taiz and Zeiger 2002). The medium was aerated using two aquarium pumps. The nutrient medium was subsequently replaced with 1.0 X Hoagland’s solution (pH 6.5) after a further seven days.

treatment_protocol: At day 18, the nutrient medium for the control plants was replaced with just 1.0 X modified Hoagland’s medium (pH 6.5). The shoot tissues were collected from five control plants at 48 h post medium change.


title: ICC 3996 Salt roots 24 h

scan_protocol: See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated during a resistance response to Ascochyta rabiei. Plant Biotechnology Journal. 4(6), 647–666

treatment_protocol: At day 18, the nutrient medium for the treatment plants was replaced with 1.0 X modified Hoagland’s with 150 mM Sodium Chloride (NaCl) (pH 6.5), which represented a salinity concentration known to be toxic to chickpea (unpublished data; Munns 2002). The root tissues were collected from five treatment plants at 24 h post-treatment (hpt).

value: Roots

treatment_protocol: At day 18, the nutrient medium for the control plants was replaced with just 1.0 X modified Hoagland’s medium (pH 6.5). The root tissues were collected from five control plants at 24 h post medium change.


title: ICC 3996 Salt roots 48 h

label_protocol: See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated during a resistance response to Ascochyta rabiei. Plant Biotechnology Journal. 4(6), 647–666

treatment_protocol: At day 18, the nutrient medium for the treatment plants was replaced with 1.0 X modified Hoagland’s with 150 mM Sodium Chloride (NaCl) (pH 6.5), which represented a salinity concentration known to be toxic to chickpea (unpublished data; Munns 2002). The root tissues were collected from five treatment plants at 48 h post-treatment (hpt).

treatment_protocol: At day 18, the nutrient medium for the control plants was replaced with just 1.0 X modified Hoagland’s medium (pH 6.5). The root tissues were collected from five control plants at 48 h post medium change.


title: ICC 3996 Salt shoots 24 h

extract_protocol: See Coram, TE. and Pang, ECK. 2006. Expression profiling of Chickpea genes differentially regulated during a resistance response to Ascochyta rabiei. Plant Biotechnology Journal. 4(6), 647–666

treatment_protocol: At day 18, the nutrient medium for the treatment plants was replaced with 1.0 X modified Hoagland’s with 150 mM Sodium Chloride (NaCl) (pH 6.5), which represented a salinity concentration known to be toxic to chickpea (unpublished data; Munns 2002). Leaf/shoot tissues were collected from five treatment plants at 24 h post-treatment (hpt).

treatment_protocol: At day 18, the nutrient medium for the control plants was replaced with just 1.0 X modified Hoagland’s medium (pH 6.5). Leaf/shoot tissues were collected from five control plants at 24 h post medium change.


title: wild type 90min growth vs. mutant (delta atmA) 90min growth

source_name: wild type conidia grown for 90 minutes

source_name: mutant (delta atmA) conidia grown for 90 minutes


title: liver_wildtype_WY14643_5d_pooled


title: liver_PPARa-knockout_control_5d_pooled

description: liver, PPARa-null mice, control conditions


title: liver_wildtype_fasted24h_pooled

description: Liver samples wild type mice, fasting conditions (24h)

value: 129Sv (wildtype)


title: ICC 3996 Cold flowers

growth_protocol: Five treatment plants were cultivated (one plant per 15 cm pot) in sterile potting mix in a glasshouse at 15-25oC. All plants were watered to keep the soil moist but excess watering was avoided. The plants were fertilized twice with urea during establishment and once with Nitrosol® (Amgrow, Australia) 10 days before flowering.

treatment_protocol: To simulate cold stress, the five treatment plants were exposed to a 12h day/12h night temperature cycle of 15-25oC and 5oC (Dr. H. Clarke, 2005, pers comm.; Croser et al. 2003; Clarke and Siddique 2004). The flower/early-pod tissues were harvested after the seventh night at 5oC.

value: 2 weeks after flowering

tag: Tissue type

value: flowers/early-pods

growth_protocol: Five control plants were cultivated (one plant per 15 cm pot) in sterile potting mix in a glasshouse at 15-25oC. All plants were watered to keep the soil moist but excess watering was avoided. The plants were fertilized twice with urea during establishment and once with Nitrosol® (Amgrow, Australia) 10 days before flowering.

treatment_protocol: The control plants were maintained in Glasshouse conditions at 15-25oC while the treatment plants were exposed to cold stress. The flower/early-pod tissues were harvested at the same time as treatment plants (after seventh night of cold stress to treatment plants)


title: ICC 3996 Drought leaves

treatment_protocol: The drought stress was imposed two weeks after flowering as follows: The pots were saturated with water late in the evening, and the following morning pots were bagged so that no water was allowed to evaporate. A 1.0 ml pipette tip was cut slightly at the tip and inserted in the pot to allow addition of water. The pots were then weighed and recorded as the initial pot weight. The amount of water (water content) in each pot was estimated to be 30% of the initial pot weight. From the subsequent day onwards, the pots were allowed to lose 5-10% of their water content per day and any extra water lost (>10%) was replenished. The leaf tissues were collected when the treatment pots reached 30% water content, indicative of a drought or high water deficit condition

value: leaves

treatment_protocol: Two weeks after flowering the pots were saturated with water late in the evening, and the following morning pots were bagged so that no water was allowed to evaporate. A 1.0 ml pipette tip was cut slightly at the tip and inserted in the pot to allow addition of water. The pots were then weighed and recorded as the initial pot weight. The amount of water (water content) in each pot was estimated to be 30% of the initial pot weight. From the subsequent day onwards, the control pots were maintained at 80% water content and any extra water lost was replenished. The leaf tissues were collected at the time when the treatment pots reached 30% water content


title: ICC 3996 Drought flowers

treatment_protocol: The drought stress was imposed two weeks after flowering as follows: The pots were saturated with water late in the evening, and the following morning pots were bagged so that no water was allowed to evaporate. A 1.0 ml pipette tip was cut slightly at the tip and inserted in the pot to allow addition of water. The pots were then weighed and recorded as the initial pot weight. The amount of water (water content) in each pot was estimated to be 30% of the initial pot weight. From the subsequent day onwards, the pots were allowed to lose 5-10% of their water content per day and any extra water lost (>10%) was replenished. The flower/early-pod tissues were collected when the treatment pots reached 30% water content, indicative of a drought or high water deficit condition

treatment_protocol: Two weeks after flowering the pots were saturated with water late in the evening, and the following morning pots were bagged so that no water was allowed to evaporate. A 1.0 ml pipette tip was cut slightly at the tip and inserted in the pot to allow addition of water. The pots were then weighed and recorded as the initial pot weight. The amount of water (water content) in each pot was estimated to be 30% of the initial pot weight. From the subsequent day onwards, the control pots were maintained at 80% water content and any extra water lost was replenished. The flower/early-pod tissues were collected at the time when the treatment pots reached 30% water content


title: ICC 3996 Cold leaves

treatment_protocol: To simulate cold stress, the treatment plants were exposed to a 12h day/12h night temperature cycle of 15-25oC and 5oC (Dr. H. Clarke, 2005, pers comm.; Croser et al. 2003; Clarke and Siddique 2004). The leaf tissues were harvested after the seventh night at 5oC.

value: Leaves

treatment_protocol: The control plants were maintained in Glasshouse conditions at 15-25oC while the treatment plants were exposed to cold stress. The leaf tissues were harvested at the same time as treatment plants (after seventh night of cold stress to treatment plants)


title: 13420180 - sdg26-2 vs wt-2

status: Public on Jul 20 2007

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Differential transcriptome in mutant plants

hyb_protocol: wt-2 Cy5 / sdg26-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 6.0, Cy3:pmt voltage 532nm,500V,laser power 30%, Cy5:635nm,pmt voltage 500V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 indirect, amplification=yes, DNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: whole plant - Media : MS 0255, 1% sucrose, 0,9% agar hygrometry : ? Temperature : 21degreeC/ 17degreeC Light : 16h

treatment_protocol: no treatment

tag: Arabidopsis thaliana (columbia)  - dev.stage (Boyes et al. Plant Cell 2001):boyes

tag: Arabidopsis thaliana (columbia) yes - dev.stage (Boyes et al. Plant Cell 2001):boyes


title: liver_wildtype_fed_pooled

description: Liver samples wild type mice, control conditions


title: 13420446 - sdg25-2 vs wt-2

hyb_protocol: wt-2 Cy5 / sdg25-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.