title: Soleus_HLS_24hr_rep4

source_name: Soleus muscle, muscle unloaded by hind-limb suspension, 24hr, animal #4


title: Soleus_Control_24hr_rep5

status: Public on Dec 01 2008

type: RNA

city: Sharnbrook

first: Fei Ling

last: Lim

state: Bedfordshire

address: Colworth Science Park

country: United Kingdom

institute: Unilever

hyb_protocol: The Agilent Hybridisation Kit (catalogue number 5188-5242) was used in conjunction with Agilent Mouse Oligo Arrays (catalogue number G4122F).  2μg of the labelled sample RNA were used for hybridisation according to the Agilent One-Color Microarray-Based Gene Expression Analysis Protocol The hybridisation was performed for 17 h at 65 ºC at 10 rpm. Slides were them washed for 1 min at 22 ºC in Wash Solution 1 (catalogue number 5188-5325) and 1 min at 22 ºC in Wash Solution 2, pre-warmed to 37 ºC (catalogue number 5188-5326). Slides were incubated for 30s in Agilent Stabilisation and Drying Solution (catalogue number 5185-5979).

scan_protocol: Microarrays were scanned using the Agilent Technologies Scanner G2505B US45102871 (ChipScan software version A.7.0.1), scan region 61 X 21.6mm, scan resolution 5 micron single pass, extended dynamic range selected (XDR Hi 100%; XDR Lo 10%).

data_processing: Data was extracted from the scanned image using the Agilent Feature Extraction Software version. 9.1.3.1 (protocol GE1-v5_91_0806). The VALUE column came from the gProcessedSignal column of the result table.

molecule: total RNA

organism: Mus musculus

source_name: Soleus muscle, freely ambulating control, 24hr, animal #5

label_protocol: 600 ng RNA and 3 µl Agilent One-Color RNA Spike-In RNA were labelled with the Agilent Low RNA Input Linear Amplification Kit PLUS, One-Color according to Manufacture’s instructions as follows:  1.2 µl T7 Promoter Primer was added to 600 ng RNA and 3 µl spike in control and denatured at 65 ºC. First Strand Buffer, DTT, dNTP MMLV and RNaseOut was added. The cDNA was synthesised during the following incubation step (2h at 40 ºC). After 10 min denaturation at 65 ºC and the addition of Cy-labelled CTP, Transcription Buffer, DTT, NTP, PEG, RNaseOUT, Inorganic Phosphatase, and T7 RNA Polymerase the synthesis of the fluorescent labelled cRNA was performed during the second incubation step (2 h at 40 ºC).  The labelled cRNA was purified with the Qiagen RNeasy Mini Kit according to Manufacturer’s protocol.

growth_protocol: Mice were maintained on a reversed 12:12-h light-dark cycle with controlled temperature (21 ± 1°C) and humidity. Food and water were provided ad libitum. At 1 wk after arrival, the animals were separated into individual cages for a 3-day acclimation period then were randomly assigned to either of two experimental groups: freely ambulating controls and hindlimb-unloaded animals.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy kit Qiagen.  The integrity of the RNA was confirmed with analysis by the Agilent 2100 bioanalyser using the RNA 6000 LabChip kit.

treatment_protocol: Hindlimb muscles were unloaded using methods described previously (Matuszczak, Arbogast, Reid 2004). Briefly, Elastoplast tape (Beiersdorf-Jobst, Rutherford College, NC) was used to wrap the tail of each animal. A metal clip on the tape was attached to a nylon monofilament line via a stainless steel swivel. The distal end of the nylon line was attached to an overhead support and shortened to suspend the animal in a 45° head-down tilt position. The swivel enabled the animal to explore the cage (360° range of motion) and obtain food and water freely. Animals were observed daily for changes in appearance and activity. Each animal was weighed and the angle of hindlimb suspension was adjusted if necessary. After 24hr, each animal was deeply anesthetized in the hindlimb-unloaded condition. The animal was removed from the unloading device, the soleus and gastrocnemius muscles were excised with the animal under surgical anesthesia, and the animal was euthanized.  Muscle was immediately placed in RNAlater (Ambion) and stored until RNA extraction.

tag: Strain

value: ICR

tag: Gender

value: Male

tag: Age

value: 6 months

tag: Body weight 27.1g

tag: Tissue

value: soleus muscle


title: Soleus_Control_24hr_rep1

source_name: Soleus muscle, freely ambulating control, 24hr, animal #1

tag: Body weight 26.85g


title: Gastrocnemius_HLS_24hr_rep2

source_name: Gastrocnemius muscle, muscle unloaded by hind-limb suspension, 24hr, animal #2

tag: Body weight 28.67g

value: gastrocnemius muscle


title: Gastrocnemius_HLS_24hr_rep5

source_name: Gastrocnemius muscle, muscle unloaded by hind-limb suspension, 24hr, animal #5

tag: Body weight 25.67g


title: Gastrocnemius_Control_24hr_rep5

source_name: Gastrocnemius muscle, freely ambulating control, 24hr, animal #5

extract_protocol: Total RNA was isolated using the Qiagen RNeasy kit.  The integrity of the RNA was confirmed with analysis by the Agilent 2100 bioanalyser using the RNA 6000 LabChip kit.


title: Gastrocnemius_HLS_24hr_rep3

source_name: Gastrocnemius muscle, muscle unloaded by hind-limb suspension, 24hr, animal #3

tag: Body weight 25.53g


title: Glucose-limited chemostat in absence of PAA strain DS17690 -2

city: Delft

first: Marco

middle: Alexander

last: van den Berg

address: PO Box 425

country: Netherlands

institute: DSM Anti Infectives

hyb_protocol: Probe preparation and Target hybridization Double stranded cDNA synthesis was carried out using 10 ug of total RNA and the components of the One Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, USA). The double-stranded cDNA was purified with the GeneChip® Sample Cleanup Module (Affymetrix/Qiagen) followed by in vitro transcription and labeling using the GeneChip® IVT labeling Kit (Affymetrix). Finally, labeled cRNA was purified (GeneChip® Sample Cleanup Module, Affymetrix/Qiagen) prior to fragmentation. 15 µg of fragmented, biotinylated cRNA was hybridized to the P. chrysogenum MicroArrays (a proprietary GeneChip®, DSM_PENa520255F) at 45 °C for 16 h as described in the Affymetrix users' manual. Washing and staining of arrays were performed using the GeneChip® Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner 3000.

data_processing: Data analysis Acquisition and quantification of array images were performed using Affymetrix GeneChip® Operating Software (GCOS version 1.2). CHP file targeted at 100.

label: Biotin

organism: Penicillium chrysogenum

source_name: Chemostat culture  steady state

growth_protocol:
Chemostat cultivation Aerobic glucose-limited chemostat cultivation was performed at 25 °C in 3 - L turbine stirred bioreactors (Applikon, Schiedam, The Netherlands) with a working volume of 1.8 L. The pH was maintained at 6.5 via automated addition of 2 M NaOH (ADI 1030 biocontroller, Applikon, Schiedam, The Netherlands). The fermenter was sparged with air at a flow rate of 0.9 L•min-1 using a Brooks mass-flow controller (Brooks Instruments, Hatfield, USA) and stirred at 750 rpm. The dissolved-oxygen concentration was continuously monitored with an oxygen electrode (Applisens, Schiedam, The Netherlands). Continuous cultivation was initiated after 50-60 hours of batch cultivation. The feed medium was supplied continuously by a peristaltic pump (Masterflex, Cole Parmer, USA) and the dilution rate was set at 0.03 h-1 for all chemostat experiments. Effluent was removed discontinuously by means of a special overflow device, which has been described previously (Harris, D.M., et al. Enzymic analysis of NADPH metabolism in Penicillium chrysogenum: presence of a mitochondrial NADPH dehydrogenase in beta-lactam-producing cultures. Metab. Eng. 8, 91-101 (2006)). The time interval between effluent removals was fixed in such a way that each time approximately 1 % of the culture volume was removed. To prevent excessive foaming, silicone antifoam (10 % vol/vol, BDH) was discontinuously added at timed intervals.
Media The mineral medium was set at pH 5.5 with KOH pellets and contained per liter of demineralised water 7.5 g glucose, 3.5 g (NH4)2SO4, 0.8 g KH2PO4, 0.5 g MgSO4•7H2O, 10 mL of a trace element solution. The trace element solution contained 15 g•L-1 Na2EDTA•2H2O, 0.5 g•L-1 Cu2SO4•5H2O, 2 g•L-1 ZnSO4•7H2O, 2 g•L-1 MnSO4•H2O, 4 g•L-1 FeSO4•7H2O, and 0.5 g•L-1 CaCl2•2H2O and was set at pH 6.0 by adding NaOH pellets. Glucose was heat-sterilized separately (110 °C) and added to the medium in a concentration of 7.5 g•L-1. After filter sterilization and during the chemostat experiments the medium vessel was mixed continuously by a magnetic stirrer.

extract_protocol: Sampling and RNA extraction procedures 60 mL of culture broth was sampled and rapidly filtered over a glass fiber filter (Type A/E, Pall Life Sciences, East Hills, USA). The filter with mycelium was wrapped in aluminum foil, quenched in liquid nitrogen and subsequently stored at -80 °C until further use. For total RNA extraction half of the pellet was grounded by mortar and pestle under constant cooling with liquid nitrogen. The powder was dissolved in 5 mL of Trizol reagent (Invitrogen) and 1 mL chloroform (Sigma) and mixed well. The two phases were separated by centrifugation (4600 g, 15 minutes). Total RNA was isolated using a phenol-chloroform extraction method, which consisted of two extraction steps in acid-phenol/chloroform/isoamyl alcohol (5:1, pH 4.8, Ambion), followed by a chloroform extraction step. Each time the phases were separated by centrifugation (4600 g, 15 minutes). Total RNA was precipitated for 30 minutes at -20°C in 96% ethanol and 0.3 M sodium acetate. The RNA was collected by centrifugation at 23000 g for 15 minutes and dissolved in RNAse free H2O.

treatment_protocol: Liquid nitrogen quenching

tag: Penicillium chrysogenum DS17690 Penicillin G high producing prototrophic strain (Harris, D.M., et al. Enzymic analysis of NADPH metabolism in Penicillium chrysogenum

value: presence of a mitochondrial NADPH dehydrogenase in beta-lactam-producing cultures. Metab. Eng. 8, 91-101 (2006). DS17690 is derived from the strain improvement program of DSM after several classical mutagenesis rounds and is an offspring of the sequenced Wisconsin 54-1255 strain.


title: Gastrocnemius_HLS_24hr_rep1

source_name: Gastrocnemius muscle, muscle unloaded by hind-limb suspension, 24hr, animal #1

tag: Body weight 27.15g


title: MRC-5 cells_replicate 1

city: Roma

first: Nathalie

last: Saulnier

address: Largo Francesco Vito,1

country: Italy

institute: Università Cattolica del Sacro Cuore di Roma

description:
Bone marrow (BM) has been considered so far the reference source for stromal cells (SC) originally called mesenchymal stem cells. Recently human adult adipose tissue (AT) has been reported as a valuable source for the isolation of cells exerting a mesenchymal-like phenotype. Though both BM- and AT- derived stromal cells (BMSC and ATSC) share similar immuno-phenotype and exhibit multi-lineage potential in vitro, a consensual panel of specific markers is still debated and the precise molecular mechanisms governing their differentiated fate are not fully understood.
The aim of this study was to compare the genome wide expression profiles of stromal cells isolated from AT and BM and to emphasize the core of MSC stemness properties. Moreover we focused on the molecular characteristics of ATSC, attempting to reveal their specific features.

hyb_protocol: Biotin-labeled cRNA was purified and chemically fragmented according to Affymetrix's protocol. Ten micrograms of fragmented and biotin-labeled cRNA were hybridized onto Human Focus array at 45°C for 16 hours in a rotisserie oven set at 60RPM. The following day, the chip was washed and labeled with streptavidin-phycoerythrin in a fluidic station using the EukGE-WS2v5 protocol according to Affymetrix' s recommendation.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were generated by using Affymetrix MAS 5.0 softwware. Briefly, the signal value was calculated from the combined background-adjusted, PerfectMatch and MisMatch values of the probe set using predefined algorithms of MAS 5.0 software. Data set was further exported to Genespring software for normalization and statistical analysis.

label: biotin

organism: Homo sapiens

source_name: MRC-5 cell line (diploid human embryonic lung fibroblasts)

label_protocol: Labeling protocol was accomplished according to Affymetrix recommended protocol. Briefly, following cDNA synthesis, the material was amplified and labeled with biotinylated dNTPs during an in vitro transcription (IVT) using the GeneChip Expression 3' Amplification One-Cycle target Labeling and Control Reagents (Affymetrix Inc.)

growth_protocol: Cells were grown in DMEM additioned with 10% fetal bovine serum (FBS) and 1% of antibiotics.

extract_protocol: Total RNA from 1 million of MRC-5 cells was isolated using the RNeasy Plus mini kit (Qiagen) according to the manufacturer's instructions. This kit allows the selective retrieval of RNA and the removal of double-stranded DNA during the extraction process. RNA was quantified by UV spectrophotometer and quality was assessed on agarose gel.

tag: Since Mesenchymal stem cells (MSC) are direct precursors of fibroblasts, we assumed that MRC-5 fibroblasts exhibit a large degree of similarity with MSC. Thus, by using MRC-5 cells as control in our study, we expected to rule out a large number of genes regulating cell homeostasis and select genes related to stemness.


title: Gastrocnemius_Control_24hr_rep4

source_name: Gastrocnemius muscle, freely ambulating control, 24hr, animal #4

tag: Body weight 28.89g


title: Gastrocnemius_Control_24hr_rep2

source_name: Gastrocnemius muscle, freely ambulating control, 24hr, animal #2

tag: Body weight 28.78g


title: Adipose tissue derived-MSC_patient 4

source_name: human sub-cutaneous adipose tissue

growth_protocol: Cells were grown in Mesenchymal Stem Cell medium (MSCGM) (Cambrex Inc.)

extract_protocol: Total RNA from 1 million of cultivated adipose tissue-derived mesenchymal stem cells was isolated using the RNeasy Plus mini kit (Qiagen) according to the manufacturer's instructions. This kit allows the selective retrieval of RNA and the removal of double-stranded DNA during the extraction process. RNA was quantified by UV spectrophotometer and quality was assessed on agarose gel.

tag: Cultivated mesenchymal stem cells (passage4) isolated from human adipose tissue extracted from a patient during surgical procedures.


title: Bone marrow derived-MSC_patient 4

source_name: human bone marrow

extract_protocol: Total RNA from 1 million of cultivated bone marrow-derived mesenchymal stem cells was isolated using the RNeasy Plus mini kit (Qiagen) according to the manufacturer's instructions. This kit allows the selective retrieval of RNA and the removal of double-stranded DNA during the extraction process. RNA was quantified by UV spectrophotometer and quality was assessed on agarose gel.

tag: Bone marrow aspirates were obtained from four long-term disease-free (more than five years after complete remission) Hodgkin lymphoma patients, during follow-up investigations. Patients were ruled out whenever leukemic progression at first diagnosis, neoplastic infiltration of bone marrow from other cancer sites or infectious diseases occurred. Bonw marrow mononuclear cells were separated by centrifugation in a Ficoll-Hypaque gradient (density = 1.077g/cm3) and resuspended in Mesenchymal Stem Cell Medium (MSCGM) to allow the selection of mesenchymal stem cells via their property of adherence to the plastic.


title: MRC-5 cells_replicate 3


title: Adipose tissue derived-MSC_patient 3

source_name: sub-cutaneous human adipose tissue


title: MRC-5 cells_replicate 2


title: Gastrocnemius_Control_24hr_rep1

source_name: Gastrocnemius muscle, freely ambulating control, 24hr, animal #1


title: Bone marrow derived-MSC_patient 3


title: Gastrocnemius_Control_24hr_rep3

source_name: Gastrocnemius muscle, freely ambulating control, 24hr, animal #3

tag: Body weight 31.3g


title: Adipose tissue derived-MSC_patient 2

source_name: sub-cutaneous adipose tissue

tag: Cultivated mesenchymal stem cells (passage ) isolated from human adipose tissue extracted from a patient during surgical procedures.


title: Slide 5, exponential type 4 Cy3 vs exponential type 5 Cy5

city: Toulouse

first: Julien

last: Storai

address: 135 avenue de Rangueil

country: France

institute: CNRS

description: For additional informations, see http://biopuce.insa-toulouse.fr/

hyb_protocol: Labeled cDNAs corresponding to reference and test conditions were pooled in presence of hybridization buffer ChipHybe (Discovery). Hybridizations were automatically performed using a Ventana apparatus (Discovery) using RNAs purified from independent cultures of pathogenic strains, in duplicate with dye swapping.

scan_protocol: Microarrays were scanned with an Axon 4000A scanner, and images were acquired with GenePixPro 3.0 software (Axon).

data_processing: Background correction and further analysis of raw data including statistical analysis (Log10 and total mean normalization, Student test selection) were made using Bioplot script, developed at the Biochips Platform of Toulouse (http://biopuce.insa-toulouse.fr/). Only genes with P values < 0.05 were considered statistically significant. Since this criterion is purely a statistical measure of differential gene expression and reproducibility across replicates, an additional ratio cut-off of < 0.7 or > 1.5 was applied for filtering differentially expressed genes.

organism: Streptococcus pneumoniae

source_name: Streptococcus pneumoniae type 4 exponential growth

label_protocol: For microarray cDNA synthesis, 15 µg of total RNA was mixed with Eurogentec S. pneumoniae TIGR4 open reading frame-specific primers (500 ng/µl), dithiothreitol (0.1 M, Invitrogen), dATP, dGTP, dTTP (5 mM each), dCTP (1mM), 5X first strand buffer (1X, Invitrogen) and sterile water to a final volume of 38.5 µl. The mixture was heated at 65°C for 5 min. Reverse transcription was performed for 1 h at 42°C after addition of 1.5 µl of Cy3-dCTP or Cy5-dCTP (1 mM, Perkin), with 1 µl of SuperscriptII reverse transcriptase (200 U/µl, Invitrogen) and 1 µl of RNAsin (Promega). After 1 h, 1 µl of SuperscriptII reverse transcriptase was added and the reaction performed for one more hour at 42°C. The reaction was stopped using 2 µl of stop solution (Promega). Before hybridization, labeled cDNA was purified using Qia-quick PCR purification kit (Qiagen) according to the manufacturer’s instructions.

extract_protocol: Total RNA was isolated from culture samples containing 10^9 cells. RNA was extracted from bacterial pellets using Ribopure Bacteria Kit (Ambion™), including a DNase treatment as described by the manufacturer. RNA concentration and quality were estimated using the Bioanalyzer Agilent technology.

tag: Streptococcus pneumoniae type 4 n°34348 Staten Serum Institute

source_name: Streptococcus pneumoniae type 5 exponential growth

tag: Streptococcus pneumoniae type 5 n°Pn5M, Collection of Dr Austrian, University of Pennsylvania, PA, USA


title: Bone marrow derived-MSC_patient 1

source_name: Human bone marrow

tag: Bone marrow aspirates were obtained from four long-term disease-free (more than five years after complete remission) Hodgkin lymphoma patients, during follow-up investigations. Patients were ruled out whenever leukemic progression at first diagnosis, neoplastic infiltration of bone marrow from other cancer sites or infectious diseases occurred. Bone marrow mononuclear cells were separated by centrifugation in a Ficoll-Hypaque gradient (density = 1.077g/cm3) and resuspended in Mesenchymal Stem Cell Medium (MSCGM) to allow the selection of mesenchymal stem cells via their property of adherence to the plastic.


title: Slide 4, type 5, exponential Cy5 vs stationary Cy3

source_name: Streptococcus pneumoniae type 5 stationnary growth


title: Slide 2, type 4, exponential Cy3 vs stationary Cy5

tag: Streptococcus pneumoniae type n°34348 Staten Serum Institute

source_name: Streptococcus pneumoniae type 4 stationary growth


title: Slide 1, type 4, exponential Cy5 vs stationary Cy3


title: Slide 3, type 5, exponential Cy3 vs stationary Cy5

source_name: Streptococcus pneumoniae type 5 stationary growth


title: Slide 6, exponential type 4 Cy5 vs exponential type 5 Cy3


title: Bone marrow derived-MSC_patient 2


title: Adipose tissue derived MSC_patient 1

tag: Cultivated mesenchymal stem cells (P4) isolated from adipose tissue. Adipose tissue specimens were acquired from exceeding tissues removed during partial abdominoplasty.


title: hcc17

city: Basel

first: Luigi

last: Terracciano

email: lterracciano@uhbs.ch, ccillo@uhbs.ch

state: Basel

address: Schönbeinstrasse 40

department: Molecular Pathology

country: Switzerland

institute: Pathology

description: Gene expression data from human liver tissue

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG 133A2. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: Gene Chips were scanned using the Affymetrix Gene Chip Scanner 3000 7G.

data_processing: The data were normalized using the vsn algorithm (PM-only, medianpolish summary)

source_name: Human liver

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3.1 microg total RNA

extract_protocol: Extraction of total RNA was performed using the Qiagen Rneasy Mini kit according to the manufacturer's instructions.

treatment_protocol: not applicable

tag: hcc17 (also described as PTL2) and ctrl13 (also described as PNL2) samples were obtained from the same patient

tag: Etiology

value: unknown


title: hcc03

tag: hcc03 (also described as PTL12) and ctrl01 (also described as PNL12) samples were obtained from the same patient

value: Alcohol


title: ctrl13

tag: ctrl13 (also described as PNL2) and hcc17 (also described as PTL2) samples were obtained from the same patient


title: ctrl07

tag: ctrl07 (also described as PNL1) and hcc09 (also described as PTL1) samples were obtained from the same patient


title: hcc09

tag: hcc09 (also described as PTL1) and ctrl07 (also described as PNL1) samples were obtained from the same patient


title: ctrl01

tag: ctrl01 (also described as PNL12) and hcc03 (also described as PTL12) samples were obtained from the same patient


title: cocultured 24h, biological rep4

status: Public on Nov 24 2008

city: Ashburn

first: Claire

last: McKellar

state: VA

address: 19700 Helix Drive

country: USA

institute: HHMI Janelia Farm Research Campus

description: Gene expression data from subplate neurons with induced synaptogenesis

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray 3000 Scanner 7G.

data_processing: Images of probe hybridization intensity on the scanned chips were quantified and scaled by Affymetrix Microarray Suite 5.0 software, using default settings.  Statistical methods are described in detail in the Affymetrix document: http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf.  The software uses normalized intensities from the 11 probe pairs per sequence to report a detection confidence score (Present, Absent or Marginal) and a signal intensity value representing expression level.  Data were then analyzed in GeneSpring software (Agilent Technologies), normalizing with an RMA file preprocessor and then by dividing each gene by the median of its measurements in all samples.

organism: Rattus norvegicus

source_name: 24h cocultured subplate neurons

label_protocol: RNA (100ng per condition) was amplified through two cycles of cDNA synthesis and in vitro transcription to give biotin-labeled cRNA, according to the Affymetrix GeneChip Expression Analysis Technical Manual protocol (www.affymetrix.com).

growth_protocol: The posterior third of the neocortex (primarily visual cortex) was harvested from E17 pups and digested with papain for one hour, then triturated to create a suspension of cells.  The cells were immunopanned on a petri dish that had been coated with goat anti-mouse followed by 1.13ug/cm2 of monoclonal mouse anti-rat p75 NTR, clone 192.1.  Non-adherent cells were washed off and saved to create cortical feeder layers.  Adherent cells (subplate neurons) were trypsinized off the panning plate, washed, and plated on 12mm glass coverslips in 24-well plates, at 22,100 cells/well.  Coverslips were coated with poly-ornithine and fibronectin.  Cultures were grown in serum-free conditions, in subplate medium: Neurobasal with B27 supplement plus 50ug/ml chondroitin sulfate A.

extract_protocol: RNA was isolated from the coverslips (generally six coverslips pooled per condition) using an RNAqueous Micro kit (Ambion).

treatment_protocol: Synaptogenesis was induced by coculturing coverslips of subplate neurons on top of dense feeder layers of cortical cells, plated in subplate medium at 650,000 cells/well in 24-well plates coated with poly-ornithine and fibronectin.  Wells contained ~2 mm2 spacer dots made with drops of melted paraffin wax to prevent direct contact between the feeder layer and the coverslip of subplate neurons above, in the manner of a Banker-style culture.  Control feeder wells contained wax dots and media, but no cells.  Feeder wells, with or without cells, were fed with fresh media at 4 days in vitro (d.i.v.).  24 hours later, coverslips of subplate neurons were added to feeder wells and cocultured for durations of 24h or 96h, without additional feeding.

tag: subplate neurons immunopurified from E17 rats

tag: cultured for 5d before treatment


title: cocultured 96h, biological rep5

source_name: 96h cocultured subplate neurons


title: control 96h, biological rep5

description: Gene expression data from subplate neurons with few synapses

source_name: 96h control subplate neurons


title: control 24h, biological rep4

source_name: 24h control subplate neurons


title: cocultured 96h, biological rep2


title: control 24h, biological rep3


title: cocultured 24h, biological rep5


title: control 96h, biological rep2


title: control 96h, biological rep3


title: cocultured 96h, biological rep3


title: control 24h, biological rep5


title: cocultured 96h, biological rep4


title: control 96h, biological rep4


title: cocultured 24h, biological rep2


title: cocultured 24h, biological rep1


title: control 96h, biological rep1


title: cocultured 24h, biological rep3


title: cocultured 96h, biological rep1


title: regenerating rib bone vs. BMD steady state (control rib bone)_HA74.136

status: Public on Nov 23 2008

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

description: Gene expression data from male red deer rib bones

hyb_protocol: Hybridization was performed at 50C and 35% formamide for 16 hours.

scan_protocol: Microarrays were scanned using the Agilent G2505B scanner.

data_processing: print tip loess normalization log2 ratio of Cy5/Cy3

organism: Cervus elaphus

source_name: regenerating rib bone

label_protocol: Direct incorporation of CyDye labeled dCTP by reverse transcription.

extract_protocol: Trizol

tag: rib bone (without bone marrow)

source_name: BMD steady state (control rib bone)


title: BMD steady state (control rib bone) vs. regenerating rib bone_HA74.138


title: regenerating rib bone vs. BMD steady state (control rib bone)_HB76.054


title: regenerating rib bone vs. BMD steady state (control rib bone)


title: osteoporotic rib bone vs. BMD steady state (control rib bone)_HB76.053

source_name: osteoporotic rib bone


title: control 24h, biological rep1


title: control 24h, biological rep2


title: regenerating rib bone vs. BMD steady state (control rib bone)_HB76.055


title: BMD steady state (control rib bone) vs. regenerating rib bone


title: BMD steady state (control rib bone) vs. osteoporotic rib bone_HA74.134


title: osteoporotic rib bone vs. regenerating rib bone_HA74.131


title: Glucose-limited chemostat in presence of PAA strain Wisconsin 14-1255 -2

scan_protocol: Probe preparation and Target hybridization Double stranded cDNA synthesis was carried out using 10 ug of total RNA and the components of the One Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, USA). The double-stranded cDNA was purified with the GeneChip® Sample Cleanup Module (Affymetrix/Qiagen) followed by in vitro transcription and labeling using the GeneChip® IVT labeling Kit (Affymetrix). Finally, labeled cRNA was purified (GeneChip® Sample Cleanup Module, Affymetrix/Qiagen) prior to fragmentation. 15 µg of fragmented, biotinylated cRNA was hybridized to the P. chrysogenum MicroArrays (a proprietary GeneChip®, DSM_PENa520255F) at 45 °C for 16 h as described in the Affymetrix users' manual. Washing and staining of arrays were performed using the GeneChip® Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner 3000.

source_name: Chemostat culture  steady state

tag: Penicillium chrysogenum Wisconsin 14-1255 Penicillin G low producing prototrophic strain (Elander, R. Strain improvement and preservation of beta-lactam producing microorganisms.. In A.L.Demain and N. Solomon (eds.). Antibiotics containing the beta-lactam structure I. Springer-Verlag, New York, N.Y., 97-146 (1983))


title: BMD steady state (control rib bone) vs. osteoporotic rib bone_HA74.133


title: osteoporotic rib bone vs. BMD steady state (control rib bone)_ HA74.135


title: BMD steady state (control rib bone) vs. osteoporotic rib bone_HB76.052


title: BMD steady state (control rib bone) vs. osteoporotic rib bone_HB76.051


title: osteoporotic rib bone vs. regenerating rib bone_HB76.048


title: regenerating rib bone vs. osteoporotic rib bone_HA74.132


title: Mixed infected tissue, biological rep3

status: Public on Nov 22 2008

city: Québec

first: Armand

last: Séguin

state: Québec

address: 1055 rue de PEPS

country: Canada

institute: Laurentian forestry Service

description: Gene expression data from infected tissues with both Melampsora larici poplulina and Melampsora medusae f.sp. deltoides

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Poplar Genome Array. GeneChips were washed and stained in the Fluidics protocol EukGE_WS2v5_450

scan_protocol: GeneChip scanner

data_processing: The data were analyzed with Robust Multichip Average (RMA)

organism: Populus maximowiczii x Populus nigra

source_name: poplar leaf tissues infected both with Mlp and Mmd

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Poplar clone NM6 was grown grown in Promix soil under controlled greenhouse conditions prior to inoculation. NM6 plants were kept under a 16-h photoperiod with weekly fertilizations (20:20:20 N: P: K). Melampsora larici-populina (Mlp) and Melampsora medusae f. sp. deltoidae (Mmd) were maintained on clone Jackii (Populus balsamifera L. x Populus deltoides Marsh.).

extract_protocol: Total RNA were extracted from frozen leaf tissues using the RNAeasy Plant Mini Kit (Qiagen, Mississauga, ON) according to the manufacturer’s instructions. Following a DNase I treatment (Qiagen), 10 μg of total RNA from each biological sample were used for each microarray experiment.

treatment_protocol: Poplar leaves were detached from trees and seperated to half-leaves. Half-leaves were kept on wet paper on their abaxial side inside Petri dishes prior to infection.

tag: Fully expanded leaves from leaf plastochron index (LPI) five and six were detached and infected with Mlp and Mmd at a density of 2,000 spores per cm2 each.


title: regenerating rib bone vs. osteoporotic rib bone_HB76.050


title: Mixed infected tissue, biological rep2


title: osteoporotic rib bone vs. regenerating rib bone_HB76.049


title: Mmd infected tissue, biological rep3

description: Gene expression data from infected tissues with Melampsora medusae f. s. deltoides

source_name: poplar leaf tissues infected with Mmd

tag: Fully expanded leaves from leaf plastochron index (LPI) five and six were detached and infected with Mmd at a density of 2,000 spores per cm2.


title: Mmd infected tissue, biological rep2


title: Mlp infected tissue, biological rep3

description: Gene expression data from infected tissues with Melampsora larici poplulina

source_name: poplar leaf tissues infected with Mlp

tag: Fully expanded leaves from leaf plastochron index (LPI) five and six were detached and infected with Mlp at a density of 2,000 spores per cm2.


title: Mmd infected tissue, biological rep1


title: Mlp infected tissue, biological rep2


title: non infected tissue, biological rep1

description: Gene expression data from non infected tissues

source_name: poplar leaf tissues mock-infected

tag: Fully expanded leaves from leaf plastochron index (LPI) five and six were detached and infected with tween 0.1%


title: osteoporotic rib bone vs. regenerating rib bone_HA74.130


title: Mixed infected tissue, biological rep1


title: non infected tissue, biological rep2


title: Mlp infected tissue, biological rep1


title: non infected tissue, biological rep3


title: pool 6b

status: Public on Nov 19 2008

city: Torino

first: Daniela

last: Cimino

state: Torino

address: Via Nizza 52

department: Oncological Science

institute: Molecular Biotechnology Center

description: Tumor samples of ductal invasive breast carcinoma from patients with relapse within 72 months from surgery

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: GCRMA Bioconductor

source_name: breast cancer patients with relapse

label_protocol: Approximately 2 microgram of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: RNA was isolated with Concert Cytoplasmic RNA Reagent (Invitrogen Corporation) from 20 to 50 mg tumor tissues, according to the manufacturer's guidelines. Frozen tumors were placed in this reagent and homogenized using a ball mill (MM200, Retsch, Düsseldorf, Germany). 10 µg aliquots of total RNA was treated with DNase I, using a commercially available kit (DNA free, Ambion, Inc., Austin, TX) to eliminate genomic DNA contamination. The quantity and quality of the RNA samples were determined using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano Assay kit (Agilent Technologies, Palo Alto, CA).

tag: Sample name

value: pool 6 replicate b


title: pool 12b

value: pool 12 replicate b


title: pool 6a

value: pool 6 replicate a


title: pool 8a

value: pool 8 replicate a


title: pool 9b

description: Tumor samples of ductal invasive breast carcinoma from patients without relapse within 72 months from surgery

source_name: breast cancer patients without relapse

value: pool 9 replicate b


title: pool 10b

value: pool 10 replicate b


title: pool 12a

value: pool 12 replicate a


title: AJ-vs-C57_gDNA_hyb-plus-dye-flip-repeat

status: Public on Nov 20 2008

type: genomic

city: Manchester

first: Catriona

last: Rennie

address: Oxford Rd

department: Faculty of Life Sciences

institute: The University of Manchester

description: Normalised log2 signal ratio for AJ (test) vs C57 (ref), average over hyb and  dye-flip hyb

hyb_protocol: Agilent standards as recommended in Oligonucleotide Array-Based CGH for Genomic DNA Analysis v.5.0

data_processing: Agilent standards as recommended in CGH Analytics v3.4 user guide (http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=47787)

molecule: genomic DNA

extract_protocol: None. Genomic DNA supplied by Jackson laboratories

tag: Strain

value: AJ and C57BL/6 (combined results from the original hybridization with AJ in this channel and C57BL/6 in channel 2 and a dye flip replicate with AJ in channel 2 and C57BL/6 in this channel).

tag: Sample material

value: genomic DNA

value: C57BL/6 and AJ (combined results from the original hybridization with C57BL/6 in this channel and AJ in channel 1 and a dye flip replicate with C57BL/6 in channel 1 and AJ in this channel).


title: pool 4b

value: pool 4 replicate b


title: pool 11a

value: pool 11 replicate a


title: pool 4a

value: pool 4 replicate a


title: pool 8b

value: pool 8 replicate b


title: Balb-vs-C57_gDNA_hyb-plus-dye-flip-repeat

description: Normalised log2 signal ratio for Balb (test) vs C57 (ref), average over hyb and  dye-flip hyb

scan_protocol: Agilent standards as recommended in Oligonucleotide Array-Based CGH for Genomic DNA Analysis v.5.0

value: Balb and C57BL/6 (combined results from the original hybridization with Balb in this channel and C57BL/6 in channel 2 and a dye flip replicate with Balb in channel 2 and C57BL/6 in this channel).

value: C57BL/6 and Balb (combined results from the original hybridization with C57BL/6 in this channel and Balb in channel 1 and a dye flip replicate with C57BL/6 in channel 1 and Balb in this channel).


title: pool 10a

value: pool 10 replicate a


title: Comparative genomic hybridization between Arabidopsis thaliana and Arabidopsis arenosa

city: Bethesda

first: Misook

last: Ha

state: MD

address: NIH

institute: National Heart Lung Blood Institute

description: 8 replicates with dye-swap experiments

hyb_protocol: Each lyophilized probe was re-suspended in 40 μL of hybridization solution (0.25 M Na2HPO4, 0.25 M NaH2PO4, pH 7.4, and 3.5% SDS, w/v). The solution was heated for 2 min at 95 °C, chilled immediately in ice, and applied directly to the array. After covering the array with a 24 × 40 mm coverslip (Sigma, St Louis, MO), the slide was placed in a microarray hybridization chamber (Corning Incorporated, Corning, NY). Hybridization was performed overnight (16 h) at 60 °C in a hybridization oven. After hybridization, the slides were washed for 2 min in 2× SSC, 0.03% (w/v) SDS, 2 min in 0.2× SSC, and 2 min in 0.05× SSC. Immediately after the last wash, the slides were dried by centrifugation (3 min at 500 r.p.m.).

scan_protocol: Slides were scanned using Genepix 4000B

data_processing:
The notation Xijkplm is used to denote the mth replicate spot of gene l with feature type p under target condition k labelled with dye j on slide i. After log transformation, Yijkplm = log(Xijkplm).
The anova model for this situation is given by:
Yijkplm = µ + Si + Dj + Tk + Fp + Gl + TFkp + SGil + DGjl + TGkl + FGpl + TFGkpl + ijkplm,where µ represents the overall mean effect, S, D, T, F and G represent main effects from the slide, dye, target (e.g. A.thaliana genome vs. A.arenosa genome), feature type (e.g. oligo vs. gene) and gene, respectively. The interaction terms TF, SG, DG, TG, FG and TFG represent target by feature type, array by gene, dye by gene, target by gene, feature type by gene, and target by feature type by gene interactions, and ijkplm denotes the random error and is used to test for significance of main and interaction effects in the model. Due to confounding and/or aliasing issues involving the slide, dye and target terms, not all two-way interactions are included in the model. The model residuals are assumed to be normally distributed with a common variance (i.e. ijkplm i.i.d. N(0, σ2)). Also, a per gene variance is assumed (i.e. ijkplm independent.
Hypothesis testing
The presence of differential expression in a microarray expression is represented by significant differences in T + TG terms for a particular gene. The following hypotheses are tested to determine whether a gene, g, has undergone differential expression between targets t and t' (e.g. A.thaliana RNA vs. A. arenosa RNA).
H0: Tt + TGtg = Tt' + TGt'g
A standard t-test statistic is used for this comparison, based on the normality assumption for the residuals. To control for multiple testing errors, both Holm's and the false discovery rate (FDR) were employed. Holm's sequential adjustment provides strong control of the family-wise error rate (FWER) below level α with greater power than the standard Bonferroni method (Hochberg and Tamhane, 1987). The false discovery rate (FDR) controlling method of Benjamini and Hochberg (Benjamini and Hochberg, 1995) provides weak control of the FWER, and controls the FDR below level α. The FDR is defined as the expected proportion of incorrect rejections of H0, relative to the total number of rejections. The significance level α= 0.05 was chosen for this study.

label: Cy3, Cy5 dye-swap

organism: Arabidopsis thaliana

source_name: Genomic DNA from Arabidopsis thaliana autotetraploid

label_protocol: DNA targets were prepared by the direct incorporation of fluorescently labelled deoxyribonucleotides (Cy3- and Cy5-dCTP) during one round of DNA synthesis. An aliquot of 1 µg of total genomic DNA was mixed with 2 µg of random nanomer primer. The mixture was incubated at 95 °C for 5 min, chilled on ice, and then added to a reaction mix (50 µL) with a final composition of 500 µm each of dATP and dGTP and 100 µm of dTTP and Cy3-dCTP or Cy5-dCTP and Klenow DNA polymerase. The reaction was incubated at 37 °C for 8 h.

growth_protocol: All plants were grown in a growth chamber at 22° and under 16 hr of light per day at the University of Washington with two biological replications. Leaves were collected from 20 plants in each biological replication prior to bolting (with seven to eight rosette leaves) in each line.

extract_protocol: Genomic DNA was isolated and sheared using a sonicator.

tag: A. thaliana isogenic autotetraploids (At4, accession no. CS3900)

label: Cy3, Cy5 dye swap

organism: Arabidopsis arenosa

source_name: Arabidopsis arenosa leaves

label_protocol: The same as Channel 1

growth_protocol: The same as Channel 1

extract_protocol: The same as Channel 1

treatment_protocol: The same as Channel 1

tag: A. arenosa (Aa, accession no. CS3901)


title: pool 9a

value: pool 9 replicate a


title: pool 2b

value: pool 2 replicate b


title: pool 7a

value: pool 7 replicate a


title: 129-vs-C57_gDNA_hyb-plus-dye-flip-repeat

description: Normalised log2 signal ratio for 129 (test) vs C57 (ref), average over hyb and  dye-flip hyb

label_protocol: Agilent standards as recommended in Oligonucleotide Array-Based CGH for Genomic DNA Analysis v.5.0

value: 129 and C57BL/6 (combined results from the original hybridization with 129 in this channel and C57BL/6 in channel 2 and a dye flip replicate with 129 in channel 2 and C57BL/6 in this channel).

value: C57BL/6 and 129 (combined results from the original hybridization with C57BL/6 in this channel and 129 in channel 1 and a dye flip replicate with C57BL/6 in channel 1 and 129 in this channel).


title: pool 5a

value: pool 5 replicate a


title: pool 5b

value: pool 5 replicate b


title: pool 7b

value: pool 7 replicate b


title: AJ-vs-C57_gDNA_hyb-plus-dye-flip-repeat

description: These data represent combined results from two hybridisations of AJ and C57BL/6 genomic DNA samples to the array, the second hybridisation being a dye-flip replicate of the first.

value: AJ and C57BL/6 (combined results from the original hybridization with AJ in this channel and C57BL/6 in channel 2 and a dye flip replicate with AJ in channel 2 and C57BL/6 in this channel).

value: genomic DNA

value: C57BL/6 and AJ  (combined results from the original hybridization with AJ in channel 1 and C57BL/6 in this channel and a dye flip replicate with AJ in this channel and C57BL/6 in channel 1).


title: BALB-vs-C57_gDNA_hyb-plus-dye-flip-repeat

description: These data represent combined results from two hybridisations of BALB/c and C57BL/6 genomic DNA samples to the array, the second hybridisation being a dye-flip replicate of the first.

value: BALB/c and C57BL/6 (combined results from the original hybridization with BALB/c in this channel and C57BL/6 in channel 2 and a dye flip replicate with BALB/c in channel 2 and C57BL/6 in this channel).

value: BALB/c and C57BL/6 (combined results from the original hybridization with BALB/c in channel 1 and C57BL/6 in this channel and a dye flip replicate with BALB/c in this channel and C57BL/6 in channel 1).


description: These data represent combined results from two hybridisations of 129 and C57BL/6 genomic DNA samples to the array, the second hybridisation being a dye-flip replicate of the first.

value: 129 and C57BL/6 (combined results from the original hybridization with 129 in channel 1 and C57BL/6 in this channel and a dye flip replicate with 129 in this channel and C57BL/6 in channel 1).


title: pool 1b

value: pool 1 replicate b


title: pool 3b

value: pool 3 replicate b


title: pool 1a

value: pool 1 replicate a


title: pool 3a

value: pool 3 replicate a


title: Pyr-TM4/8.2_2h_rep 4

status: Public on Nov 15 2008

city: Seattle

first: Pradipsinh

middle: K

last: Rathod

state: WA

address: Campus Box 351700

department: Chemistry

institute: University of Washington

description: Pyr-TM4/8.2_2h_rep 4

hyb_protocol: Purified labelled cDNAs were hybridized on microarray slides in hybridization solution containing 3X SSC, 0.2% SDS, 0.025 M HEPES and 0.75 µg/µl of poly A (Sigma) for 16 h at 63oC.

scan_protocol: Slides were scanned in an Axon GenePix 4000B microarray scanner and the intensity of spots was quantified using GenePix Pro 3.0 Software (Axon Instruments, Inc.).

data_processing: The ratio of intensity of the two channels was log2 transformed and normalized for print-tip variability and for slide to slide variability in order to correct the systematic biases in the data set using Aroma package version 0.89 [Bengtsson H: aroma – An R Object-oriented Microarray Analysis environment.], run in the R project environment.

organism: Plasmodium falciparum

source_name: Untreated TM4/8.2 strain parasites

label_protocol: 20 µg of total RNA was annealed with 10 µg of oligo-(dT)21 primer and reverse transcribed to produce aminoallyl-dUTP (Sigma)-labelled cDNA using StratascriptTM reverse transcriptase (Stratagene). cDNA samples were purified on Microcon YM-30 (Millipore) and labelled with either monoreactive-Cy3 or -Cy5 (Amersham Biosciences) in 0.05 M sodium bicarbonate buffer (pH 9.0) in dark at room temperature for 1 hour. Unincorporated dyes were removed using QIAquick PCR purification column (Qiagen).

growth_protocol: P. falciparum strain TM4/8.2 (the wild-type, Pyr-sensitive parasite) was maintained in continuous culture in vitro in human erythrocytes according to the candle-jar method of Trager and Jensen [Science 1976, 193(4254):673-675 and J Parasitol 1977, 63(5):883-886]. For experiments, parasite was synchronized at the ring stage by 5% sorbitol treatment [J Parasitol 1979, 65(3):418-420].

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: After synchronization, parasite culture was incubated at 37oC for a further 20 h to obtain early trophozoite stage parasites.  Pyr was then added to 10% parasitemia culture at a final IC50 concentration (0.5 µM). A culture containing 0.1% (v/v) DMSO lacking drug was used as control. After 2 h, 4 h,  and 8 h of drug exposure, parasites were collected and extracted from erythrocytes by saponin lysis.  Parasites were flash-frozen in liquid nitrogen and kept at -80oC until RNA samples were required.

tag: Strain TM4/8.2 synchronous parasites

tag: 2h untreated control

source_name: Pyr-treated TM4/8.2 strain parasites

tag: 2h Pyr treatment


title: Pyr-TM4/8.2_4h_rep 1

description: Pyr-TM4/8.2_4h_rep 1

tag: 4h Pyr treatment

tag: 4h untreated control


title: Pyr-TM4/8.2_4h_rep 3

description: Pyr-TM4/8.2_4h_rep 3


title: Pyr-TM4/8.2_8h_rep 6

description: Pyr-TM4/8.2_8h_rep 6

tag: 8h untreated control

tag: 8h Pyr treatment


title: Pyr-TM4/8.2_8h_rep 2

description: Pyr-TM4/8.2_8h_rep 2


title: Pyr-TM4/8.2_4h_rep 4

description: Pyr-TM4/8.2_4h_rep 4


title: Pyr-TM4/8.2_8h_rep 3

description: Pyr-TM4/8.2_8h_rep 3


title: Pyr-TM4/8.2_8h_rep 4

description: Pyr-TM4/8.2_8h_rep 4


title: Pyr-TM4/8.2_4h_rep 2

description: Pyr-TM4/8.2_4h_rep 2


title: Pyr-TM4/8.2_4h_rep 5

description: Pyr-TM4/8.2_4h_rep 5


title: Pyr-TM4/8.2_2h_rep 5

description: Pyr-TM4/8.2_2h_rep 5


title: Pyr-TM4/8.2_4h_rep 6

description: Pyr-TM4/8.2_4h_rep 6


title: Pyr-TM4/8.2_8h_rep 1

description: Pyr-TM4/8.2_8h_rep 1


title: Pyr-TM4/8.2_8h_rep 5

description: Pyr-TM4/8.2_8h_rep 5


title: Pyr-TM4/8.2_2h_rep 3

description: Pyr-TM4/8.2_2h_rep 3


title: Pyr-TM4/8.2_2h_rep 1

description: Pyr-TM4/8.2_2h_rep 1


title: Pyr-TM4/8.2_2h_rep 2

description: Pyr-TM4/8.2_2h_rep 2


title: DMSO-B1G9_18h_rep3

hyb_protocol: Purified labelled cDNAs were hybridized on microarray slides in hybridization solution containing 3X SSC, 0.2% SDS, 0.025 M HEPES and 0.75 µg/µl of poly A (Sigma) for 12-16 h at 63oC.

data_processing: The ratio of intensity of the two channels was log2 transformed and normalized for print-tip variability and for slide to slide variability in order to correct the systematic biases in the data set using Limma package [Smyth, G. K. (2005). Limma: linear models for microarray data. In: 'Bioinformatics and Computational Biology Solutions using R and Bioconductor'. R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (eds), Springer, New York, pages 397--420] run in R project environment (http://cran.r-project.org).

source_name: DMSO-treated P. falciparum B1G9 parasites

label_protocol: 10 µg of total RNA was annealed with 5 µg pd(N)6 random hexamer primers (Amersham Biosciences Corp.) and reverse transcribed to produce aminoallyl-dUTP (Sigma)-labelled cDNA using Stratascript reverse transcriptase (Stratagene). cDNA samples were purified on Microcon YM-30 (Millipore) and labelled with either monoreactive-Cy3 or -Cy5 (Amersham Biosciences) in 0.1 M sodium bicarbonate buffer (pH 9.0) in dark at room temperature for 1 hour. Unincorporated dyes were removed using QIAquick PCR purification column (Qiagen).

growth_protocol: P. falciparum clone Dd2 and a WR99210 resistant cell-line B1G9 were cultured by established method of Trager and Jensen [Science 1976, 193(4254):673-675].  For experiments, parasite was synchronized at the ring stage by 5% sorbitol treatment [J Parasitol 1979, 65(3):418-420].

extract_protocol: Total RNA extracted using Ambion RNAqueouse Kit following manufacturer's instructions

treatment_protocol: Dd2 and B1G9 trophozoites were treated with 10 nM WR99210 for 3 h, 6 h, 9 h, 15 h, 18 h, 21 h, and 24 h.

tag: B1G9 synchronous parasites

tag: 18h DMSO treatment

source_name: P. falciparum B1G9 total RNA reference pool

tag: pool of trophozoite total RNA


title: DMSO-B1G9_18h_rep2


title: DMSO-B1G9_21h_rep3

tag: 21h DMSO treatment


title: DMSO-B1G9_21h_rep2


title: DMSO-B1G9_21h_rep1


title: DMSO-B1G9_18h_rep1


title: DMSO-B1G9_9h_rep3

tag: 9h DMSO treatment


title: DMSO-B1G9_24h_rep2

tag: 24h DMSO treatment


title: DMSO-B1G9_24h_rep4


title: DMSO-B1G9_21h_rep4


title: DMSO-B1G9_24h_rep3


title: DMSO-B1G9_9h_rep2


title: DMSO-B1G9_24h_rep1


title: DMSO-B1G9_18h_rep4


title: DMSO-B1G9_9h_rep1


title: DMSO-B1G9_15h_rep2

tag: 15h DMSO treatment


title: DMSO-B1G9_15h_rep3


title: DMSO-B1G9_15h_rep1


title: DMSO-B1G9_15h_rep4


title: DMSO-B1G9_9h_rep4


title: DMSO-B1G9_6h_rep4

tag: 6h DMSO treatment


title: DMSO-B1G9_6h_rep3


title: pool 2a

tag: Sample name

value: pool 2 replicate a


title: UACC62 Nucleosome Sample 1

status: Public on Nov 16 2008

type: mixed

city: San Francisco

first: Jun

middle: S

last: Song

state: CA

address: 513 Parnassus Avenue, Box 0794

department: Institute for Human Genetics

institute: UCSF

description: Wavelet denoised data

hyb_protocol: Performed by NimbleGen Systems Inc.

scan_protocol: Performed by NimbleGen Systems Inc.

data_processing: The Cy5/Cy3 ratios were denoised using wavelets

source_name: UACC62 Genomic Input DNA

label_protocol: Random primer labeling

extract_protocol: Genomic DNA was isolated using the DNeasy Tissue Kit (Qiagen) and digested with hydroxyl radical-based cleavage in a sequence-independent manner

tag: Genomic Input DNA

molecule: other

source_name: UACC62 MNase digested and gel-extracted DNA

extract_protocol: DNA was treated with MNase, and the isolated DNA was run on a 1.5% agarose gel, and the band corresponding to mononucleosomes was gel-extracted using QiaQuick Gel Extraction Kit (Qiagen).

tag: MNase treated mononucleosomal DNA


title: pool 11b

value: pool 11 replicate b


title: MCF7 Nucleosome Sample 1

description: Wavelet denoised data

source_name: MCF7 Genomic Input DNA

source_name: MCF7 MNase digested and gel-extracted DNA


title: DMSO-Dd2_24h_rep3

source_name: P. falciparum Dd2 total RNA reference pool

tag: Dd2 synchronous parasites

source_name: DMSO-treated P. falciparum Dd2 parasites


title: DMSO-B1G9_3h_rep2

tag: 3h DMSO treatment


title: DMSO-Dd2_24h_rep2


title: DMSO-B1G9_3h_rep4


title: DMSO-Dd2_24h_rep4


title: DMSO-Dd2_21h_rep4


title: DMSO-Dd2_18h_rep4


title: DMSO-B1G9_3h_rep1


title: DMSO-Dd2_18h_rep3


title: DMSO-Dd2_21h_rep1


title: DMSO-Dd2_18h_rep2


title: DMSO-B1G9_6h_rep2


title: UACC62 Nucleosome Sample 2

description: Wavelet denoised data


title: MALME Nucleosome Sample 2

description: Wavelet denoised data

source_name: MALME Genomic Input DNA

source_name: MALME MNase digested and gel-extracted DNA


title: DMSO-Dd2_21h_rep3


title: DMSO-Dd2_15h_rep6


title: DMSO-B1G9_6h_rep1


title: DMSO-Dd2_24h_rep1


title: MCF7 Nucleosome Sample 2

description: Wavelet denoised data


title: DMSO-Dd2_21h_rep2


title: DMSO-Dd2_18h_rep1


title: DMSO-Dd2_24h_rep5


title: DMSO-Dd2_15h_rep5


title: DMSO-Dd2_15h_rep4


title: DMSO-Dd2_15h_rep3


title: MALME Nucleosome Sample 1

description: Wavelet denoised data


title: DMSO-Dd2_15h_rep2


title: DMSO-Dd2_15h_rep1


title: DMSO-Dd2_9h_rep4


title: DMSO-Dd2_9h_rep2


title: DMSO-Dd2_9h_rep3


title: DMSO-Dd2_6h_rep4


title: DMSO-Dd2_9h_rep1


title: DMSO-Dd2_6h_rep2


title: DMSO-Dd2_3h_rep4


title: DMSO-Dd2_6h_rep3


title: WR99210-B1G9_24h_rep4

source_name: WR99210-treated P. falciparum B1G9 parasites

tag: 24h WR99210 treatment


title: WR99210-B1G9_24h_rep2


title: WR99210-B1G9_21h_rep3

tag: 21h WR99210 treatment


title: WR99210-B1G9_21h_rep2


title: WR99210-B1G9_21h_rep5


title: WR99210-B1G9_24h_rep3


title: DMSO-Dd2_3h_rep1


title: WR99210-B1G9_21h_rep4


title: WR99210-B1G9_21h_rep1


title: DMSO-Dd2_3h_rep2


title: DMSO-Dd2_6h_rep1


title: DMSO-Dd2_3h_rep3


title: WR99210-B1G9_24h_rep1


title: WR99210-B1G9_18h_rep3

tag: 18h WR99210 treatment


title: WR99210-B1G9_18h_rep2


title: WR99210-B1G9_15h_rep4

tag: 15h WR99210 treatment


title: WR99210-B1G9_18h_rep4

tag: B1G9 synchronous parasites


title: WR99210-B1G9_15h_rep1


title: WR99210-B1G9_9h_rep4

tag: 9h WR99210 treatment


title: WR99210-B1G9_15h_rep3

tag: pool of trophozoite total RNA


title: WR99210-B1G9_18h_rep1


title: WR99210-B1G9_15h_rep2


title: WR99210-B1G9_3h_rep5

tag: 3h WR99210 treatment


title: WR99210-B1G9_9h_rep2


title: WR99210-B1G9_6h_rep5

tag: 6h WR99210 treatment


title: WR99210-B1G9_9h_rep1


title: WR99210-B1G9_6h_rep1


title: WR99210-B1G9_6h_rep3


title: WR99210-B1G9_6h_rep2


title: WR99210-B1G9_3h_rep1


title: WR99210-Dd2_24h_rep4

source_name: WR99210-treated P. falciparum Dd2 parasites


title: WR99210-Dd2_24h_rep2


title: WR99210-B1G9_3h_rep3


title: WR99210-Dd2_24h_rep3


title: WR99210-B1G9_3h_rep2


title: WR99210-B1G9_6h_rep4


title: WR99210-B1G9_3h_rep4


title: Root tips-Transgen. Line N7 rep.2

city: Raleigh

first: Mariya

last: Khodakovskaya

state: NC

address: 4218 Gardner Hall

department: Plant Biology

institute: North Carolina State University

description: Gene expression data from root tips of 10 days etiolated seedlings of tomato (cv. Micro-Tom)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Tomato Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400. Hybridization reactions to Affymetrix Maize GeneChip expression arrays were done using the services of Expression Analysis Inc. (http://www.expressionanalysis.com/).

scan_protocol: Scanning of the Affymetrix Tomato GeneChip expression arrays were done using the services of Expression Analysis Inc. (http://www.expressionanalysis.com/).

data_processing: Data extraction was also performed by Expression Analysis Inc.  Expression values were calculated using the Affymetrix GeneChip Operating System (GCOS) and were based on the difference of the PM (Perfect Match) signal and MM (Mismatch) signal at each of the probe pairs.  The fluorescent signal values from each array were normalized to achieve similar overall intensity between arrays.  The fluorescent signal values of any hybridization reaction were then multiplied by a scaling factor to make their (trimmed) mean intensity equal to 500.  The scaling factor is unique to each hybridization reaction and is in general below 10

organism: Solanum lycopersicum

source_name: 10 day old etiolated root apices of wilt type tomato

label_protocol: Complimentary RNA (cRNA) was produced according to Affymetrix Eukaryotic two-cycle target labeling assay as specified in the GeneChip Expression Analysis Technical Manual (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).

growth_protocol:
For fruits, tomato plants were grown in pots with growing medium containing 50% of sand and 50% of Sun Gro Redi-earth Plug and Seedling Mix  (Sun Gro Horticulture). All plants grown in growth chamber of Phytotron, NCSU  at day temperature 26 C, night temperature 22 C, humidity 45% and intensity of light  500 μmol.m-2.s-1. Plants were watered once at day to field capacity and fertilized on a weekly basis with fertilizer recipe as described at http://www.ncsu.edu/phytotron/manual.pdf. After  9 weeks in the growth chamber  transgenic and control ripe fruits of same age were harvested.
For leaves, tomato seeds were germinated on MS medium (agar Petri plates)  in light conditions. First two leaves of 10 days seedlings were harvested.
For roots, tomato seeds were germinated on MS medium (agar Petri plates)  in light conditions. First two leaves of 10 days seedlings were harvested.

extract_protocol:
Ripe fruits were immediately frozen in liquid nitrogen after harvesting in the greenhouses.  The harvested samples were then transferred to the laboratory and grinded to a fine powder in mortars and pestles using liquid nitrogen.  Total RNA was extracted using a RNeasy Plant Mini Kit (Qiagen).
Leaf tissue was immediately frozen in liquid nitrogen after harvesting in the sterile conditions.  The harvested leaf samples were then transferred to the laboratory and grinded to a fine powder in mortars and pestles using liquid nitrogen.  Total RNA was
Root tips were isolated from rootsand immediately frozen in liquid nitrogen after harvesting in the dark conditions.  The harvested root samples were then transferred to the laboratory and grinded to a fine powder in mortars and pestles using liquid nitro

treatment_protocol: No special treatments before harvesting were carried out.

tag: Root tips of 10 days etiolated seedlings of tomato -InsP 5-ptase LineN7


title: Root tips-Transgen. Line N7 rep.3

tag: Root tips of 10 days etiolated seedlings of tomato - InsP 5-ptase LineN7


title: WR99210-B1G9_9h_rep3


title: DMSO-B1G9_3h_rep3


title: WR99210-Dd2_24h_rep1


title: Root tips-Transgen. Line N7 rep.1


title: Root tips-Transgen. Line N6 rep.2

tag: Root tips of 10 days etiolated seedlings of tomato -InsP 5-ptase LineN6


title: Root tips-Transgen. Line N6 rep.3


title: Root tips-Transgen. Line N6 rep.1


title: Root tips-Vector control rep.3

tag: Root tips of 10 days etiolated seedlings of tomato - Vector Control


title: WR99210-Dd2_21h_rep4


title: WR99210-Dd2_21h_rep3


title: WR99210-Dd2_18h_rep6


title: WR99210-Dd2_18h_rep5


title: WR99210-Dd2_21h_rep2


title: WR99210-Dd2_18h_rep3


title: WR99210-Dd2_21h_rep1


title: Root tips-Vector control rep.1

tag: Root tips of 10 days etiolated seedlings of tomato - Vector control


title: WR99210-Dd2_18h_rep1


title: Root tips-Wild type rep.2

tag: Root tips of 10 days etiolated seedlings of tomato  - Wild type


title: WR99210-Dd2_18h_rep4

tag: Dd2 synchronous parasites


title: Root tips-Wild type rep.3


title: Leaves-Transgen. Line N7 rep.1

description: Gene expression data from first two leaves of tomato seedlings grown in vitro in light conditions

source_name: first two leaves of 10 day old light grown in vitro seedlings

tag: First two leaves of tomato seedlings grown  in light conditions -Trans. Line N7


title: Root tips-Wild type rep.1

tag: Root tips of 10 days etiolated seedlings of tomato - Wild type


title: WR99210-Dd2_18h_rep2


title: Leaves-Transgen. Line N7 rep.2

tag: First two leaves of tomato seedlings grown in vitro in light conditions -Trans. Line N7


title: WR99210-Dd2_15h_rep4


title: Leaves-Transgen. Line N6 rep.3

tag: First two leaves of tomato seedlings grown  in light conditions -Trans. LineN6


title: Root tips-Vector control rep.2


title: Leaves-Transgen. Line N6 rep.2


title: WR99210-Dd2_15h_rep3

tag: 15h WR99210 treatment


title: Leaves-Transgen. Line N7 rep.3

tag: First two leaves of tomato seedlings grown  in light conditions - Trans. Line N7


title: Leaves-Transgen. Line N6 rep.1

tag: First two leaves of tomato seedlings grown in vitro in light conditions - Trans. LineN6


title: WR99210-Dd2_15h_rep2

tag: pool of trophozoite total RNA


title: Leaves-Vector control rep.1

tag: First two leaves of tomato seedlings grown  in light conditions- Vector control


title: WR99210-Dd2_15h_rep1


title: Leaves-Wild type rep.3

tag: First two leaves of tomato seedlings grown  in light conditions -Wild type


title: WR99210-Dd2_9h_rep2

tag: 9h WR99210 treatment


title: WR99210-Dd2_9h_rep1


title: Leaves-Wild type rep.1


title: Leaves-Wild type rep.2


title: Leaves-Vector control rep.2

tag: First two leaves of tomato seedlings grown  in light conditions -Vector control


title: WR99210-Dd2_9h_rep4


title: WR99210-Dd2_3h_rep5

tag: 3h WR99210 treatment


title: WR99210-Dd2_6h_rep6

tag: 6h WR99210 treatment


title: Fruits-Transgen. Line N7 biological rep.4

description: Gene expression data from ripe (mature) fruits of tomato (cv. Micro-Tom)

source_name: ripe fruits

tag: Ripe (red) fruits of tomato - Trans.Line N7


title: WR99210-Dd2_9h_rep3


title: WR99210-Dd2_6h_rep5


title: WR99210-Dd2_6h_rep4


title: WR99210-Dd2_3h_rep4


title: Fruits-Transgen. Line N7 biological rep.2

tag: Ripe (red) fruits of tomato -Trans.Line N7


title: WR99210-Dd2_6h_rep1

tag: Dd2 synchronous parasites


title: WR99210-Dd2_6h_rep2


title: WR99210-Dd2_3h_rep3


title: Fruits-Transgen. Line N6 biological rep.1

tag: Ripe (red) fruits of tomato - Trans.Line N6


title: Fruits-Transgen. Line N7 biological rep.1


title: Leaves-Vector control rep.3


title: Fruits-Transgen. Line N6 biological rep.3


title: WR99210-Dd2_3h_rep2


title: Fruits-Transgen. Line N7 biological rep.3


title: WR99210-Dd2_3h_rep1


title: Fruits-Transgen. Line N6 biological rep.2


title: Fruits-Vector control biological rep.4

tag: Ripe (red) fruits of tomato - Verctor control


title: WR99210-Dd2_6h_rep3


title: Pyr-TM4/8.2_0h_rep 3

description: Pyr-TM4/8.2_0h_rep 3

data_processing: The ratio of intensity of the two channels was log2 transformed and normalized for print-tip variability and for slide to slide variability in order to correct the systematic biases in the data set using Aroma package version 0.89 [Bengtsson H: aroma – An R Object-oriented Microarray Analysis environment. [http://www.maths.lth.se/publications/]. 2004] run in R project environment (http://cran.r-project.org).

growth_protocol: P. falciparum strain TM4/8.2 (the wild-type, Pyr-sensitive parasite) was maintained in continuous culture in vitro in human erythrocytes according to the candle-jar method of Trager and Jensen [Science 1976, 193(4254):673-675 and J Parasitol 1977, 63(5):883-886].  For experiments, parasite was synchronized at the ring stage by 5% sorbitol treatment [J Parasitol 1979, 65(3):418-420].

treatment_protocol: After synchronization, parasite culture was incubated at 37oC for a further 20 h to obtain early trophozoite stage parasites.  Pyr was then added to 10% parasitemia culture at a final IC50 concentration (0.5 µM) A culture containing 0.1% (v/v) DMSO lacking drug was used as control. After 0 h and 24 h of drug exposure, parasites were collected and extracted from erythrocytes by saponin lysis.  Parasites were flash-frozen in liquid nitrogen and kept at -80oC until RNA samples were required.

tag: Strain TM4/8.2 synchronous parasites

tag: 0h Pyr treatment

source_name: Untreated TM4/8.2 strain parasites

tag: 0h untreated control


title: Pyr-TM4/8.2_0h_rep 4

description: Pyr-TM4/8.2_0h_rep 4

source_name: Pyr-treated TM4/8.2 strain parasites


title: Pyr-TM4/8.2_24h_rep 1

description: Pyr-TM4/8.2_24h_rep 1

tag: 24h untreated control

tag: 24h Pyr treatment


title: Pyr-TM4/8.2_24h_rep 3

description: Pyr-TM4/8.2_24h_rep 3


title: Fruits-Vector control biological rep.2

tag: Ripe (red) fruits of tomato - Vector vontrol


title: Fruits-Transgen. Line N6 biological rep.4

tag: Ripe (red) fruits of tomato -Trans.Line N6


title: Pyr-TM4/8.2_0h_rep 1

description: Pyr-TM4/8.2_0h_rep 1


title: Pyr-TM4/8.2_0h_rep 2

description: Pyr-TM4/8.2_0h_rep 2


title: Fruits-Wild type biological  rep.1

tag: Ripe (red) fruits of tomato - Wild type


title: Pyr-TM4/8.2_24h_rep 2

description: Pyr-TM4/8.2_24h_rep 2


title: Fruits-Wild type biological rep.2


title: Pyr-TM4/8.2_24h_rep 4

description: Pyr-TM4/8.2_24h_rep 4


title: Fruits-Vector control biological rep.1

tag: Ripe (red) fruits of tomato -Vector control


title: Fruits-Wild type biological rep.4

tag: Ripe (red) fruits of tomato -Wild type


title: Fruits-Vector control biological rep.3

tag: Ripe (red) fruits of tomato - Vector control


title: Fruits-Wild type biological rep.3


title: sp280202-9)803rb ORF expression wt

status: Public on Nov 14 2008

city: Stockholm

last: Ekwall

address: Alfred Nobels Alle 7

country: Sweden

institute: Karolinska Inst

description: Expression profile of wt

hyb_protocol: Xue Y. et al Yeast (2004)

scan_protocol: Chip Reader

data_processing: genespring

organism: Schizosaccharomyces pombe

source_name: wt

label_protocol: Xue Y. et al Yeast (2004)

extract_protocol: Xue Y. et al Yeast (2004)

tag: wt


title: sp280202-8)809ra ORF expression wt

description: Expression profile of wt


title: ORF wt expression 25)809

description: Expression profile of wt


title: ORF wt expression 16)804

description: Expression profile of wt


title: PA14 pyrF LB 37C 7h biofilms

status: Public on Nov 12 2008

city: College Station

first: Akihiro

last: Ueda

state: TX

address: 3122 TAMU

department: Chemical Engineering

institute: Texas A&M University

description:
RNA extracted from biofilm cells of P. aeruginosa PA14 pyrF mutant at 37C at 250 rpm after 7 hours of growth in LB with glass wool
Channel 2

hyb_protocol: Following affymetrix protocol. Prepared hybridization cocktail for Single Probe Array (49 Format) with total 200 ul volume including 1X hybrization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labelled cDNA. After loading of hybridization cocktail in Affymetrix E. coli Antisense Genome Array, the hybridization was performed at 50ºC, with 60 rpm for 16 hours.  After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS).

scan_protocol: Following affymetrix protocol. After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS).

data_processing: MAS 5.0 Expression Analysis Default Setting

organism: Pseudomonas aeruginosa

source_name: P. aeruginosa PA14, pyrF mutant

label_protocol: Following affymetrix protocol. cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).

extract_protocol: The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB medium with 10 g of submerged glass wool (Corning Glass Works, Corning, NY) for forming biofilm. After incubation for 7 h at 37°C with shaking (250 rpm), the glass wool was carefully and quickly removed and rinsed with 100 ml of sterile 0.85% NaCl solution at 0°C. Biofilm cells were removed by sonicating the glass wool in 200 ml of sterile 0.85% NaCl solution at 0°C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104).

tag: RNA extracted from biofilm cells of P. aeruginosa PA14 pyrF mutant strain at 37C at 250 rpm after 7 hours of growth in LB with glass wool


title: S. pombe ORF sp280202-6)803gB

description: Expression profile of wt


title: PA14 WT LB 37C 7h biofilms

description:
RNA extracted from biofilm cells of P. aeruginosa PA14 wild type strain at 37C at 250 rpm after 7 hours of growth in LB with glass wool
Channel 1

source_name: P. aeruginosa PA14, wild type


title: IGR I040F#16 pst3-GFP IP vs wt input

description: Chip on CHIP

hyb_protocol: Robyr et al Methods 31 (2003)

data_processing: GeneSpring

source_name: wt input

label_protocol: Robyr et al Methods 31 (2003)

extract_protocol: Chip on CHIP

tag: wt input

source_name: Pst3-GFP IP

extract_protocol: chip on CHIP

tag: Pst3-GFP IP


title: sp280202-7)806rb ORF expression

description: Expression profile of wt


title: Muscle PCOS case 251

status: Public on Nov 10 2008

city: Roskilde

first: Vibe

last: Skov

address: Koegevej 7-13

department: Hematology

country: Denmark

institute: Roskilde Hospital

description: Vastus lateralis muscle

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: The R statistical software was applied for data analysis. The RMA method was used for global background correction and constant normalization was used for normalization. Gene expression index calculation was done using model based index calculation (MBEI). Only perfect match probes were included in data analysis. Welch two sample t-test for paired data was used to calculate p-values

source_name: Vastus lateralis muscle

label_protocol: One µg purified total RNA was converted to biotin-labeled aRNA using the MessageAmpTM II-Biotin single round aRNA amplification kit.

extract_protocol: Frozen muscle tissue was homogenized in Trizol with a Polytron Homogenizer and total RNA was purified using TRIzol Reagent including an extra step after phase separation with chloroform. Briefly, 1 volume of phenol-chloroform-isoamylalcohol (25-24-1) was added to the aqueous phase and spun at 10.000 x g for 10 minutes at 4˚C. Then, 1 volume of chloroform was added to the aqueous phase and spun at 12.000 x g for 20 minutes at 4˚C before RNA precipitation.

tag: Vastus lateralis muscle


title: Muscle PCOS case 271

description: Vastus lateralis muscle


title: sp280202-10)804b ORF expression wt

description: Expression profile of wt


title: PA14 pyrF w/1 mM uracil LB 37C 7h biofilms

description:
RNA extracted from biofilm cells of P. aeruginosa PA14 pyrF mutant with 1 mM uracil supplement at 37C at 250 rpm after 7 hours of growth in LB with glass wool
Channel 3

source_name: P. aeruginosa PA14, pyrF mutant, 1mM uracil

tag: RNA extracted from biofilm cells of P. aeruginosa PA14 pyrF mutant strain with 1 mM uracil supplement at 37C at 250 rpm after 7 hours of growth in LB with glass wool


title: RL120502-Th2

status: Public on Nov 07 2008

city: Detroit

first: wenbo

last: xu

address: 3127 Scott Hall ,540 East Canfield

institute: wayne state university

description: Treated with cytokines typical of Th2 cells for 6 hours; recombinant rat IL-5, IL-10,  G-CSF and porcine TGF-b1, all at 10 ng/ml in defined medium with 2% fetal bovine serum.

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Rat RG-U34A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Agilent GeneArray Scanner.  Normalization Factor- 1.0, TGT=500 (all probe sets)

data_processing: All cel files were read and normalized by dChip v1.2, normalized data were analysed by GeneSpring software

source_name: brain; treated with cytokines typical of Th2 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mixed CNS glial cultures were prepared from neonatal rat brain using a modification of the shakeoff technique (McCarthy and deVellis, J. Cell. Biol. 85:890-902, 1980; Dyer and Benjamins, J. Neurosci. 8:4307-4318, 1988)

extract_protocol: Total RNA was isolated from cells 2-3 times for each time point. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were maintained in defined medium with 2% fetal bovine serum for 6-8 days, then treated with cytokine mixtures representative of Th1, Th2 or monocyte/macrophage cytokines for 6 hours (Lisak, et al., Mult. Scler. 12:149-168, 2006)

tag: CNS mixed glial cultures from 2-3 day old Sprague-Dawley rats


title: BB082802-control

description: Maintained in defined medium with 2% fetal bovine serum

source_name: brain; control


title: IGR I040F#15 pst3-GFP IP vs wt input

description: Chip on chip

source_name: Wt input

tag: wild type input


title: BB082802-Th1

description: Treated with cytokines typical of Th1 cells for 6 hours; recombinant rat IL-2, interferon-g, TNF-a, and g-CSF, all at 10 ng/ml in defined medium with 2% fetal bovine serum.

source_name: brain; treated with cytokines typical of Th1 cells


title: BB082802-mono macro

description: Treated with cytokines typical of monocyte/macrophages for 6 hours; recombinant rat IL1a, IL1b, IL-12p40, and TNF-a, all at 10 ng/ml in defined medium with 2% fetal bovine serum.

source_name: brain; treated with cytokines typical of monocyte/macrophages


title: RL120502-Th1


title: BB082802-Th2


title: Muscle PCOS pioglitazone 41

description: Vastus lateralis muscle


title: Muscle PCOS case 161

description: Vastus lateralis muscle


title: Muscle PCOS pioglitazone 81

description: Vastus lateralis muscle


title: Muscle PCOS case 101

description: Vastus lateralis muscle


title: Muscle PCOS case 31

description: Vastus lateralis muscle


title: Muscle PCOS pioglitazone 231

description: Vastus lateralis muscle


title: RL120502-control


title: RL120502-mono macro


title: Muscle PCOS pioglitazone 201

description: Vastus lateralis muscle


title: Muscle PCOS case 121

description: Vastus lateralis muscle


title: S. cerevisiae_Hg_EC10_rep1

status: Public on Nov 01 2008

city: RTP

first: Yohan

last: Jin

address: 111 TW Alexander Dr.

institute: NIEHS

description: Total RNA 100 ng) was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Cy3 or Cy5 labeled cRNA was produced according to manufacturer's protocol.  For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven using 11K features 60-mer oligo Yeast gene chip processing protocol.  Chips were scanned with an Agilent Scanner and processed with the Agilent Feature Extraction Software (version A.7.5.1).

hyb_protocol: Total RNA samples (100 ng) was labeled with Cy3 or Cy5 (PerkinElmer/NEN) using Low RNA Input Linear Amp Kit PLUS, Two-Color (Agilent Technologies).  Each Cy3 or Cy5 labeled cRNA (750 ng) from metal treated RNA was mixed with counter labeled cRNA from pooled RNA with non metal treatment control, and then hybridized with 11K features 60-mer oligo Yeast gene chip (Agilent Technologies).

data_processing: GeneSpring GX per spot and per chip: intensity dependent (Lowess) normalization, natural log ratio Treated/Control

organism: Saccharomyces cerevisiae

source_name: Control

label_protocol: Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Cy3 or Cy5 labeled cRNA was produced according to manufacturer's protocol.

extract_protocol: Total RNA was purified according to the hot phenol/chloroform method (Biochem Mol Biol Int, 1995, 37(2):339-344). Quality and quantity of total RNA purified were determined by using Bioanalyzer (Agilent).

treatment_protocol: Overnight culture of 3 ml of  BY4743 S. cerevisiae in YPD was added 7 ml of fresh YPD in the morning.  After 3 hours of incubation, cells were diluted into 50ml of YPD to have OD=0.1 (10E6 cell/ml).  Cells were incubated 2 hours more without any treatment.

tag: Control

treatment_protocol: Overnight culture of 3 ml of  BY4743 S. cerevisiae in YPD was added 7 ml of fresh YPD in the morning.  After 3 hours of incubation, cells were diluted into 50ml of YPD to have OD=0.1 (10E6 cell/ml).  Cells were treated with 18.8µM HgCl2 and incubated for 2 hours more.

tag: treated


title: S. cerevisiae_Cu_EC10_rep4

scan_protocol: Chips were scanned with an Agilent Scanner and processed with the Agilent Feature Extraction Software (version A.7.5.1).

treatment_protocol: Overnight culture of 3 ml of  BY4743 S. cerevisiae in YPD was added 7 ml of fresh YPD in the morning.  After 3 hours of incubation, cells were diluted into 50ml of YPD to have OD=0.1 (10E6 cell/ml).  Cells were treated with 5mM CuSO4 and incubated for 2 hours more.


title: S. cerevisiae_Cu_EC10_rep5


title: S. cerevisiae_Cu_EC10_rep6


title: S. cerevisiae_Cr_EC50_rep4

treatment_protocol: Overnight culture of 3 ml of  BY4743 S. cerevisiae in YPD was added 7 ml of fresh YPD in the morning.  After 3 hours of incubation, cells were diluted into 50ml of YPD to have OD=0.1 (10E6 cell/ml).  Cells were treated with 1.7mM CrO3 and incubated for 2 hours more.


title: S. cerevisiae_Cu_EC50_rep3

treatment_protocol: Overnight culture of 3 ml of  BY4743 S. cerevisiae in YPD was added 7 ml of fresh YPD in the morning.  After 3 hours of incubation, cells were diluted into 50ml of YPD to have OD=0.1 (10E6 cell/ml).  Cells were treated with 9mM CuSO4 and incubated for 2 hours more.


title: S. cerevisiae_Cu_EC10_rep1


title: S. cerevisiae_Cr_EC50_rep5


title: S. cerevisiae_Cu_EC50_rep2


title: S. cerevisiae_Cu_EC50_rep4


title: S. cerevisiae_Cr_EC10_rep5

treatment_protocol: Overnight culture of 3 ml of  BY4743 S. cerevisiae in YPD was added 7 ml of fresh YPD in the morning.  After 3 hours of incubation, cells were diluted into 50ml of YPD to have OD=0.1 (10E6 cell/ml).  Cells were treated with 0.4mM CrO3 and incubated for 2 hours more.


title: S. cerevisiae_Cu_EC10_rep2


title: S. cerevisiae_Cr_EC50_rep3


title: S. cerevisiae_Cr_EC10_rep6


title: S. cerevisiae_Cu_EC50_rep5


title: S. cerevisiae_Cu_EC10_rep3


title: S. cerevisiae_Cr_EC50_rep2


title: S. cerevisiae_Cr_EC50_rep1


title: S. cerevisiae_Cr_EC50_rep6


title: S. cerevisiae_Cr_EC10_rep4


title: S. cerevisiae_Cu_EC50_rep1


title: S. cerevisiae_Cu_EC50_rep6


title: S. cerevisiae_Cr_EC10_rep1


title: S. cerevisiae_Cr_EC10_rep2


title: S. cerevisiae_Cd_EC50_rep6

treatment_protocol: Overnight culture of 3 ml of  BY4743 S. cerevisiae in YPD was added 7 ml of fresh YPD in the morning.  After 3 hours of incubation, cells were diluted into 50ml of YPD to have OD=0.1 (10E6 cell/ml).  Cells were treated with 25µM CdCl2 and incubated for 2 hours more.


title: S. cerevisiae_Cd_EC50_rep4


title: S. cerevisiae_Cd_EC50_rep3


title: S. cerevisiae_Cd_EC50_rep5


title: S. cerevisiae_Cd_EC50_rep2


title: S. cerevisiae_Cd_EC50_rep1


title: S. cerevisiae_Cd_EC10_rep6

treatment_protocol: Overnight culture of 3 ml of  BY4743 S. cerevisiae in YPD was added 7 ml of fresh YPD in the morning.  After 3 hours of incubation, cells were diluted into 50ml of YPD to have OD=0.1 (10E6 cell/ml).  Cells were treated with 5µM CdCl2 and incubated for 2 hours more.


title: S. cerevisiae_As_EC50_rep4

treatment_protocol: Overnight culture of 3 ml of  BY4743 S. cerevisiae in YPD was added 7 ml of fresh YPD in the morning.  After 3 hours of incubation, cells were diluted into 50ml of YPD to have OD=0.1 (10E6 cell/ml).  Cells were treated with 1.25mM NaAsO2 and incubated for 2 hours more.


title: S. cerevisiae_Cd_EC10_rep3


title: S. cerevisiae_Cd_EC10_rep1


title: S. cerevisiae_As_EC50_rep1


title: S. cerevisiae_As_EC50_rep5


title: S. cerevisiae_As_EC50_rep3


title: S. cerevisiae_As_EC50_rep2


title: S. cerevisiae_As_EC10_rep6

treatment_protocol: Overnight culture of 3 ml of  BY4743 S. cerevisiae in YPD was added 7 ml of fresh YPD in the morning.  After 3 hours of incubation, cells were diluted into 50ml of YPD to have OD=0.1 (10E6 cell/ml).  Cells were treated with 0.4mM NaAsO2 and incubated for 2 hours more.


title: S. cerevisiae_Cd_EC10_rep4


title: S. cerevisiae_Ag_EC50_rep2

treatment_protocol: Overnight culture of 3 ml of  BY4743 S. cerevisiae in YPD was added 7 ml of fresh YPD in the morning.  After 3 hours of incubation, cells were diluted into 50ml of YPD to have OD=0.1 (10E6 cell/ml).  Cells were treated with 20µM AgNO3 and incubated for 2 hours more.


title: S. cerevisiae_Ag_EC50_rep4


title: S. cerevisiae_As_EC10_rep3


title: S. cerevisiae_As_EC50_rep6


title: S. cerevisiae_Cd_EC10_rep5


title: S. cerevisiae_Cd_EC10_rep2


title: S. cerevisiae_Ag_EC50_rep5


title: S. cerevisiae_Ag_EC50_rep1


title: S. cerevisiae_As_EC10_rep1


title: S. cerevisiae_Ag_EC50_rep6


title: S. cerevisiae_Ag_EC10_rep5

treatment_protocol: Overnight culture of 3 ml of  BY4743 S. cerevisiae in YPD was added 7 ml of fresh YPD in the morning.  After 3 hours of incubation, cells were diluted into 50ml of YPD to have OD=0.1 (10E6 cell/ml).  Cells were treated with 10µM AgNO3 and incubated for 2 hours more.


title: S. cerevisiae_Ag_EC10_rep6


title: S. cerevisiae_As_EC10_rep4


title: S. cerevisiae_As_EC10_rep2


title: S. cerevisiae_Ag_EC10_rep4


title: S. cerevisiae_As_EC10_rep5


title: S. cerevisiae_Ag_EC10_rep3


title: S. cerevisiae_Ag_EC50_rep3


title: S. cerevisiae_Ag_EC10_rep2


title: S. cerevisiae_Zn_EC50_rep5

treatment_protocol: Overnight culture of 3 ml of  BY4743 S. cerevisiae in YPD was added 7 ml of fresh YPD in the morning.  After 3 hours of incubation, cells were diluted into 50ml of YPD to have OD=0.1 (10E6 cell/ml).  Cells were treated with 2mM ZnSO4 and incubated for 2 hours more.


title: S. cerevisiae_Zn_EC50_rep3


title: S. cerevisiae_Zn_EC50_rep1


title: S. cerevisiae_Zn_EC10_rep3

treatment_protocol: Overnight culture of 3 ml of  BY4743 S. cerevisiae in YPD was added 7 ml of fresh YPD in the morning.  After 3 hours of incubation, cells were diluted into 50ml of YPD to have OD=0.1 (10E6 cell/ml).  Cells were treated with 1mM ZnSO4 and incubated for 2 hours more.


title: S. cerevisiae_Zn_EC10_rep5


title: S. cerevisiae_Zn_EC50_rep4


title: S. cerevisiae_Zn_EC10_rep6


title: S. cerevisiae_Zn_EC50_rep2


title: S. cerevisiae_Zn_EC10_rep4


title: S. cerevisiae_Hg_EC50_rep4

treatment_protocol: Overnight culture of 3 ml of  BY4743 S. cerevisiae in YPD was added 7 ml of fresh YPD in the morning.  After 3 hours of incubation, cells were diluted into 50ml of YPD to have OD=0.1 (10E6 cell/ml).  Cells were treated with 46.8µM HgCl2 and incubated for 2 hours more.


title: S. cerevisiae_Hg_EC50_rep6


title: S. cerevisiae_Hg_EC10_rep6


title: S. cerevisiae_Hg_EC50_rep1


title: S. cerevisiae_Zn_EC10_rep1


title: S. cerevisiae_Hg_EC10_rep4


title: S. cerevisiae_Hg_EC50_rep3


title: S. cerevisiae_Hg_EC10_rep5


title: S. cerevisiae_Hg_EC10_rep3


title: S. cerevisiae_Zn_EC50_rep6


title: S. cerevisiae_Hg_EC50_rep5


title: S. cerevisiae_Hg_EC10_rep2


title: S. cerevisiae_Hg_EC50_rep2


title: S. cerevisiae_Ag_EC10_rep1


title: LMPCR_B_REP3

city: Toronto

first: Paul

middle: C

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

hyb_protocol: The mixed DNA was resuspended in 5 μL of H2O and mixed with 85 μL hybridization mix (100 μL of DIG Easy Hyb solution (Roche 603 558), 5 μL of 10 mg/mL calf thymus DNA (Sigma D8661), 5 μL of 10 mg/mL yeast tRNA (Invitrogen 15401-029)). The resulting solution was incubated at 65 °C for 2 minutes, then cooled to room temperature and applied to a CpG island array slide (UHN Microarray Centre HCGI12K) and incubated overnight at 42 °C in a hybridization chamber.  After hybridization, the microarray slide was washed once with washing buffer 1 (1x SSC, 0.1% SDS) at 50°C for 5 minutes. This was followed by a wash with washing buffer 1 (room temperature for 5 minutes) and 2 washes with washing buffer 2 (0.2x SSC for 5 minutes) and one final wash with washing buffer 3 (0.1x SSC for 5 minutes at room temperature). The slide was then dried by spinning at 700 rpm for 15 minutes. To preserve the Cy5 dye from ozone-dependent degradation, which was observed during the summertime when the hybridization occurred, the slides were then dipped in DyeSaver 2 (Genisphere Q500600) and allowed to air dry.

scan_protocol: The microarray slides were scanned using a Gene Pix 4000B scanner (Axon Instruments) at multiple PMT voltages. Array images were first manually examined for image artifacts, and then quantitated using GenePix Pro (v6.0.1.27). A scan that maximized the dynamic range without saturating high-intensity signals was selected and carried forward for analysis. This scan was quantified using the “circular” segmentation algorithm.

data_processing: All data were pre-processed using the variance-stabilizing normalization algorithm (VSN). VSN was implemented in the R statistical environment (v2.4.1) in the BioConductor open-source project. Version 1.12.0 of the vsn package was employed, with print-tip groups used as strata, and default parameterization except for using 1000 iterations for fitting (increased from the default of 10).

source_name: Growing HL60 cells

label_protocol: A total of 3 μg of amplified DNA from the antibody sample, no antibody, or IgG sample were vacuum desiccated and resuspended in 2.5 μL of H2O (Sigma W4502). 4.5 μL of 0.1 M NaHCO3 at pH 9 was added. The DNA was resuspended by vortexing several times. 2 μL of Cy3 or Cy5 dye (Amersham, PA23001 and PA25001 respectively) were added to the sample. The mix was incubated for 1.5 hours at room temperature in the dark. After incubation, 35 μL of 100 mM Na-Acetate pH5.2 was added and topped with H2O (Sigma W4502) to a total volume of 100 μL for each sample. The fluorescent labeled probes were purified using QIAquick PCR Purification kit (Qiagen 28106). The DNA was eluted with 50 μL of EB buffer from the kit, heated to 65°C. The 100 μL combined ChIP and no antibody samples were vacuum desiccated using a SpeedVac for 60 minutes at maximum heat.

extract_protocol: Exponentially growing HL60 cells were cross-linked with 1% formaldehyde for 10 minutes at 37 °C. The crosslinking reaction was quenched by addition of glycine to a final concentration of 0.125 M for 5 minutes, followed by two washes with phosphatebuffered saline (PBS). Cells were resuspended in cell lysis buffer (5 mM PIPES pH 8, 85 mM KCl, 0.5% [v/v] NP40, 1 mM PMSF, 10 μg/mL aprotinin, 10 μg/mL leupeptin) for 10 minutes on ice and then pelleted (5000 rpm, 5 minutes, 4 °C). The pellet was resuspended in 1 mL of nuclei lysis buffer (50mM Tris-HCl pH 8.1, 10mM EDTA, 1% SDS, 1 mM PMSF, 10 μg/mL aprotinin, 10 μg/mL leupeptin) for 10 minutes on ice and then sonicated using 8 pulses (12-13 Watts, setting 10, 10 seconds per pulse, 45 seconds on ice between pulses) from a Model 60 Sonic Dismembrator (Fisher Scientific 15-338-53) to generate fragments between 600 bp and 1000 bp. Lysates were centrifuged for 10 minutes at 21,000 x g at 4 °C. Supernatants were diluted into an equal volume with IP dilution buffer (0.01% SDS, 1.1% Triton-X100, 1.2mN EDTA, 16.7mM Tris-HCl pH 8.1, 0.2% Sarkosyl, 1 mM PMSF, 10 μg/mL aprotinin, 10 μg/mL leupeptin) and precleared for 30 minutes at 4 °C with protein G-PLUS agarose beads (Santa Cruz Biotechnology  sc-2002). Prior to use, G-PLUS agarose beads were blocked with salmonsperm DNA at a final concentration of 50 μg/mL and rotated overnight at 4 °C. Diluted and cleared extracts corresponding to 10 x 106 HL60 cells were incubated and rotated at 4°C for approximately 12 to 16 hours. 50 μL of salmon sperm DNA pre-blocked Protein G-PLUS agarose beads were added to each sample, incubated on a rotating platform at 4 °C for 3 hours. Each pellet was washed once with 1.4 mL of sonication buffer and then twice with 1.4 mL of high salt buffer (0.1% [v/v] SDS, 1% [v/v] Triton X-100, 1 mM EDTA, 50 mM HEPES, 500 mM NaCl, 0.1% [w/v] sodium deoxycholate) and then once with 1.4 mL LiCl Buffer (250 mM LiCl, 1% [v/v] NP-40, 1% [w/v] sodium deoxycholate, 1 mM EDTA, 1 mM Tris pH 8) and finally twice with 1.4 mL TE pH 8 (10 mM Tris pH8, 1 mM EDTA). For each wash, the pellets were mixed for 5 minutes at room temperature then pelleted (3000 rpm, 30 seconds, room temperature). After the last wash, the pellets were eluted in 300 μL of Elution buffer (1% [w/v] SDS, 10 mM Tris pH 8, 5 mM EDTA), incubated at 65 °C for 15 minutes, and then pelleted (3000 rpm, 3 minutes, room temperature). Crosslinks were reversed in the presence of 200 mM NaCl at 65 °C over-night and samples were treated with RNase A (Sigma R5500). After ethanol precipitation, the samples were resuspended in 100 μL of TE (10 mM Tris, pH 7.5, 1 mM EDTA), 25 μL of 5x proteinase K buffer (1.25% SDS, 50 mM Tris, pH 7.5, 25 mM EDTA), and 1.5 μL of proteinase K (Roche 1413783) and incubated at 42 °C for 2 hours. DNA was extracted from each sample using phenol:chloroform:isoamyl alcohol (25:24:1), then precipitated with 1/10th volume of 3 M sodium acetate (pH 5.3), 5 μg of glycogen, and 2 volumes of ethanol at -20 °C overnight. Pellets were collected by microcentrifugation and resuspended in 60 μL of H2O.

tag: CellLine

tag: AmplificationStatus

value: LMPCR-B

value: Unamplified


title: S. cerevisiae_Zn_EC10_rep2


title: LMPCR_A_REP4

value: LMPCR-A


title: LMPCR_B_REP2


title: LMPCR_B_REP1


title: LMPCR_B_REP4


title: LMPCR_A_REP1


title: 5SC_New_Cy3

description: HybridizationDate: 14-Dec-04, ArrayBatch: New, Antibody: SC, SampleID: 5SC

source_name: Growing HL60 Cells

extract_protocol: Exponentially growing HL60 cells were cross-linked with 1% formaldehyde for 10 minutes at 37 °C. The crosslinking reaction was quenched by addition of glycine to a final concentration of 0.125 M for 5 minutes, followed by two washes with phosphatebuffered saline (PBS). Cells were resuspended in cell lysis buffer (5 mM PIPES pH 8, 85 mM KCl, 0.5% [v/v] NP40, 1 mM PMSF, 10 μg/mL aprotinin, 10 μg/mL leupeptin) for 10 minutes on ice and then pelleted (5000 rpm, 5 minutes, 4 °C). The pellet was resuspended in 1 mL of nuclei lysis buffer (50mM Tris-HCl pH 8.1, 10mM EDTA, 1% SDS, 1 mM PMSF, 10 μg/mL aprotinin, 10 μg/mL leupeptin) for 10 minutes on ice and then sonicated using 8 pulses (12-13 Watts, setting 10, 10 seconds per pulse, 45 seconds on ice between pulses) from a Model 60 Sonic Dismembrator (Fisher Scientific 15-338-53) to generate fragments between 600 bp and 1000 bp. Lysates were centrifuged for 10 minutes at 21,000 x g at 4 °C. Supernatants were diluted into an equal volume with IP dilution buffer (0.01% SDS, 1.1% Triton-X100, 1.2mN EDTA, 16.7mM Tris-HCl pH 8.1, 0.2% Sarkosyl, 1 mM PMSF, 10 μg/mL aprotinin, 10 μg/mL leupeptin) and precleared for 30 minutes at 4 °C with protein G-PLUS agarose beads (Santa Cruz Biotechnology  sc-2002). Prior to use, G-PLUS agarose beads were blocked with salmonsperm DNA at a final concentration of 50 μg/mL and rotated overnight at 4 °C. Diluted and cleared extracts corresponding to 10 x 106 HL60 cells were incubated and rotated at 4°C for approximately 12 to 16 hours with each of the following antibodies: no-antibody control, 0.7 μg normal rabbit IgG (Santa Cruz Biotechnology sc-2027), 0.7 μg N262 (Santa Cruz Biotechnology sc-764), for the N262 home-made unpurified and purified antibodies, we determined empirically, by serial dilutions, the amount of antibody to be used. 50 μL of salmon sperm DNA pre-blocked Protein G-PLUS agarose beads were added to each sample, incubated on a rotating platform at 4 °C for 3 hours. Each pellet was washed once with 1.4 mL of sonication buffer and then twice with 1.4 mL of high salt buffer (0.1% [v/v] SDS, 1% [v/v] Triton X-100, 1 mM EDTA, 50 mM HEPES, 500 mM NaCl, 0.1% [w/v] sodium deoxycholate) and then once with 1.4 mL LiCl Buffer (250 mM LiCl, 1% [v/v] NP-40, 1% [w/v] sodium deoxycholate, 1 mM EDTA, 1 mM Tris pH 8) and finally twice with 1.4 mL TE pH 8 (10 mM Tris pH8, 1 mM EDTA). For each wash, the pellets were mixed for 5 minutes at room temperature then pelleted (3000 rpm, 30 seconds, room temperature). After the last wash, the pellets were eluted in 300 μL of Elution buffer (1% [w/v] SDS, 10 mM Tris pH 8, 5 mM EDTA), incubated at 65 °C for 15 minutes, and then pelleted (3000 rpm, 3 minutes, room temperature). Crosslinks were reversed in the presence of 200 mM NaCl at 65 °C over-night and samples were treated with RNase A (Sigma R5500). After ethanol precipitation, the samples were resuspended in 100 μL of TE (10 mM Tris, pH 7.5, 1 mM EDTA), 25 μL of 5x proteinase K buffer (1.25% SDS, 50 mM Tris, pH 7.5, 25 mM EDTA), and 1.5 μL of proteinase K (Roche 1413783) and incubated at 42 °C for 2 hours. DNA was extracted from each sample using phenol:chloroform:isoamyl alcohol (25:24:1), then precipitated with 1/10th volume of 3 M sodium acetate (pH 5.3), 5 μg of glycogen, and 2 volumes of ethanol at -20 °C overnight. Pellets were collected by microcentrifugation and resuspended in 60 μL of H2O.

tag: SampleType

value: NoAntibody

value: Myc ChIP


title: RP_REP2

value: RandomPriming


title: LMPCR_A_REP2


title: LMPCR_A_REP3


title: RP_REP3


title: 5HM_New_Cy3

description: HybridizationDate: 14-Dec-04, ArrayBatch: New, Antibody: HM, SampleID: 5HM


title: 6SC_New_Cy5

description: HybridizationDate: 14-Dec-04, ArrayBatch: New, Antibody: SC, SampleID: 6SC


title: 6HM_New_Cy3

description: HybridizationDate: 14-Dec-04, ArrayBatch: New, Antibody: HM, SampleID: 6HM


title: RP_REP4


title: RP_REP1


title: TNBS day 14, replicate 2

city: Granada

first: Antonio

last: Suarez

state: Granada

address: Pharmacy Faculty, Campus Cartuja s/n

department: Biochemistry and Molecular Biology

country: Spain

institute: University of Granada

description: Affymetrix Technical Manual

hyb_protocol: Affymetrix Technical Manual

scan_protocol: Affymetrix Technical Manual

data_processing: Normalized with Bioconductor

source_name: Intestine from rats that received 10mg TNBS in 50% ethanol at day 0

label_protocol: Affymetrix Technical Manual

extract_protocol: Trizol reagent

tag: Sprague-Dawley female rat

tag: Tissue

value: full-thickness colon

tag: Rat received an enema of 10mg TNBS in 50% ethanol at day 0


title: 6HM_New_Cy5


title: TNBS day 14, replicate 3

description: Affymetrix Technical Manual


title: 5HM_New_Cy5


title: TNBS day 14, replicate 1

description: Affymetrix Technical Manual

data_processing: Normalized with bioconductor


title: TNBS day 7, replicate 2

description: Affymetrix Technical Manual


title: 6SC_Old_Cy5

description: HybridizationDate: 10-Dec-04, ArrayBatch: Old, Antibody: SC, SampleID: 6SC


title: 5SC_New_Cy5


title: TNBS day 5, replicate 2

description: Affymetrix Technical Manual


title: 6SC_New_Cy3


title: TNBS day 7, replicate 1

description: Affymetrix Technical Manual


title: 6SC_Old_Cy3


title: TNBS day 5, replicate 3

description: Affymetrix Technical Manual


title: TNBS day 5, replicate 1

description: Affymetrix Technical Manual


title: TNBS day 7, replicate 3

description: Affymetrix Technical Manual


title: 6HM_Old_Cy5

description: HybridizationDate: 10-Dec-04, ArrayBatch: Old, Antibody: HM, SampleID: 6HM


title: TNBS day 2, replicate 2

description: Affymetrix Technical Manual


title: DSS day 23, replicate 3

description: Affymetrix Technical Manual

data_processing: Affymetrix Technical Manual

label: Affymetrix Technical Manual

source_name: Intestine from rats that received 0% Dextran sodium sulphate (DSS)

extract_protocol: Affymetrix Technical Manual

tag: Rat received 0% Dextran sodium sulphate (DSS)


title: 6HM_Old_Cy3


title: S. cerevisiae_Cr_EC10_rep3


title: 5SC_Old_Cy5

description: HybridizationDate: 10-Dec-04, ArrayBatch: Old, Antibody: SC, SampleID: 5SC


title: 5HM_Old_Cy3

description: HybridizationDate: 10-Dec-04, ArrayBatch: Old, Antibody: HM, SampleID: 5HM


title: DSS day 23, replicate 1

description: Affymetrix Technical Manual


title: TNBS day 2, replicate 1

description: Affymetrix Technical Manual


title: DSS day 21, replicate 2

description: Affymetrix Technical Manual


title: 5SC_Old_Cy3


title: DSS day 23, replicate 2

description: Affymetrix Technical Manual


title: DSS day 21, replicate 1

description: Affymetrix Technical Manual


title: DSS day 19, replicate 1

description: Affymetrix Technical Manual


title: DSS day 17, replicate 3

description: Affymetrix Technical Manual


title: DSS day 17, replicate 2

description: Affymetrix Technical Manual


title: B10 TCR:HEL double positive rep 1

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

country: Australia

institute: University of Canberra

description: B10 pre-selection transgenic TCR:HEL thymocytes

data_processing: Affymetrix Microarray Suite version 5.0

source_name: double positive mouse thymocyte

label_protocol: Affymetrix GeneChip Eukaryotic Small Sample Target Labelling Assay Version II protocol was used on total RNA from 100000-1000000 cells

growth_protocol: Mice were 6-8 weeks old.

extract_protocol: Total RNA was extracted from sorted thymus using trizol and further purified using RNeasy spin columns.

treatment_protocol: The mice and cells were not treated.

tag: B10,TCR:HEL double transgenic 6-8 week old female mouse, double positive thymocytes


title: B10 TCR:HEL double positive rep 2


title: 4SC_New_Cy5

description: HybridizationDate: 7-Dec-04, ArrayBatch: New, Antibody: SC, SampleID: 4SC


title: DSS day 19, replicate 3

description: Affymetrix Technical Manual


title: 5HM_Old_Cy5


title: B10 TCR:HEL double positive rep 3


title: B10 TCR:HEL single positive rep 1

description: B10  CD4+ transgenic TCR:HEL thymocytes- negative selection thymocytes

source_name: CD4+ positive mouse thymocyte

tag: B10,TCR:HEL double transgenic 6-8 week old female mouse, CD4+ positive thymocytes


title: DSS day 21, replicate 3

description: Affymetrix Technical Manual