title: Leaf_tZ-treatment_30min_replicate 2

source_name: Oryza sativa leaf, tZ-treated, 30 min

treatment_protocol: Third leaves, which were cut at the lamina joint with a razor blade in water, were excised from the two-week-old seedlings and immediately dipped in distilled water containing 5 µM trans-zeatin (tZ) and 0.1% dimethylsulfoxide (DMSO). The excised organ was incubated at 30°C for 30 min, harvested and stored at -80°C until the RNA was extracted.


title: Leaf_DMSO-treatment_30min_replicate 2

status: Public on Feb 15 2007

type: RNA

city: Yokohama

first: Hitoshi

last: Sakakibara

address: 1-7-22 Suehiro, Tsurumi

department: Plant Science Center

country: Japan

institute: RIKEN

description: Publication: Naoya Hirose, Nobue Makita, Mikiko Kojima, Tomoe Kamada-Nobusada and Hitoshi Sakakibara (2007) Over-expression of a Type-A Response Regulator Alters Rice Morphology and Cytokinin Metabolism. Plant Cell Physiology, 48: in press.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

label: biotin

molecule: total RNA

organism: Oryza sativa

source_name: Oryza sativa leaf, DMSO-control, 30 min

label_protocol: Approximately 10 µg of total RNA was processed to produce biotinylated cRNA targets.

growth_protocol: Rice (Oryza sativa L. cv Nipponbare) seeds were sterilized with 70 % ethanol for 1 min and then with 2 % (w/v) sodium hypochlorite for 15 min, soaked in distilled water at 30°C for 1 d and 30 germinated seeds were transferred to a nylon net floating on tap water that had been adjusted to pH 5.5. Seedlings were grown for 2-weeks in an environment-controlled greenhouse with a photoperiod of 12 h light (30°C)/12 h dark (25°C).

extract_protocol: Total RNA was prepared with the RNeasy plant Mini Kit (Qiagen).

treatment_protocol: Third leaves, which were cut at the lamina joint with a razor blade in water, were excised from the two-week-old seedlings and immediately dipped in distilled water containing 0.1% dimethylsulfoxide (DMSO). The excised organ was incubated at 30°C for 30 min, harvested and stored at -80°C until the RNA was extracted.

tag: Strain

value: Oryza sativa L. cv Nipponbare, Tissue:root, Age:two weeks after germination


title: Leaf_DMSO-treatment_30min_replicate 3


title: Leaf_tZ-treatment_30min_replicate 3


title: Leaf_tZ-treatment_30min_replicate 1


title: Leaf_DMSO-treatment_30min_replicate 1


title: Lovastatin treated mouse Smpl1

city: Ljubljana

first: Drago

last: Kuzman

address: Verovskova 57

country: Slovenia

institute: Lek pharmaceuticals d.d.

description: All treated samples were hybridized with the same non tretaed (reference) sample.

hyb_protocol: Agilent oligonucleotide microarray in situ Hybridization Plus kit

scan_protocol: The two fluorescent images (Cy3 and Cy5) were scanned separately by TECAN LS200 scanner (Tecan Group Ltd., Maennedorf, Switzerland). The image data were analyzed using ArrayPro4.5 software (Media Cybernetics).

data_processing: Adjustment local background subtraction and global background Normalization method : Linear&Lowess method. only features with a Signal-to-Noise Ratio (SNR) in at least one channel ≥ 2.6 were used for further analysis.

organism: Mus musculus

source_name: Lovastatin treated mouse

label_protocol: 0.5 ug of total RNA was used for labelling. Synthesis of Cyanine 5 -labeled cDNA was performed by Low RNA input fluorescence linear amplification kit (Agilent Technologies, CA, USA) according to the manufacturer's instructions.

extract_protocol: Liver samples were homogenized in TRI reagent (Sigma, Taufkirchen, Germany) and total RNA was isolated according to the manufacturer’s instructions. Total RNA was subjected to RNeasy Cleanup (Qiagen, Valencia, CA). RNA concentration and quality was determined by RNA 6000 Nano Assay with Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA).

treatment_protocol: A seven week old mouse C57BL/6 was fed on HFC diet (diet 2094, Provimi Kliba AG, Kaiseraugst, Switzerland) for 12 days. On day five HFC diet fed mouse was treated orally once daily with fenofibrate (100mg/kg). On day 12 liver was excised and immediately frozen in liquid nitrogen and stored at -80°C for the subsequent transriptome analyses

tag: Sample is obtained from individual C57BL/6 mouse

source_name: Non treated mice

label_protocol: 0.5 ug of total RNA was used for labelling. Synthesis of Cyanine 3-labeled cDNA was performed by Low RNA input fluorescence linear amplification kit (Agilent Technologies, CA, USA) according to the manufacturer's instructions.

extract_protocol: Liver samples from 6 mice were homogenized in TRI reagent (Sigma, Taufkirchen, Germany) and total RNA was isolated according to the manufacturer’s instructions. Total RNA was subjected to RNeasy Cleanup (Qiagen, Valencia, CA). RNA concentration and quality was determined by RNA 6000 Nano Assay with Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA).

treatment_protocol: Six seven week old C57BL/6 mice were fed on a standard chow diet (diet 3430, Provimi Kliba AG, Kaiseraugst, Switzerland) for 12 days. On day 12 liver was excised and immediately frozen in liquid nitrogen and stored at -80°C for the subsequent transriptome analyses.

tag: Sample is pooled from 6 mice.


title: Lovastatin treated mouse Smpl2


title: Root_tZ-treatment_120min_replicate 3

source_name: Oryza sativa root, tZ-treated, 120 min

treatment_protocol: Whole roots were excised from the two-week-old seedlings and immediately dipped in distilled water containing either 5 µM trans-zeatin (tZ) and 0.1% dimethylsulfoxide (DMSO). The excised organ was incubated at 30°C for 120 min, harvested and stored at -80°C until the RNA was extracted.


title: Leaf_DMSO-treatment_120min_replicate 2

source_name: Oryza sativa leaf, DMSO-control, 120 min

treatment_protocol: Third leaves, which were cut at the lamina joint with a razor blade in water, were excised from the two-week-old seedlings and immediately dipped in distilled water containing 0.1% dimethylsulfoxide (DMSO). The excised organ was incubated at 30°C for 120 min, harvested and stored at -80°C until the RNA was extracted.


title: Root_DMSO-treatment_120min_replicate 3

source_name: Oryza sativa root, DMSO-control, 120 min

treatment_protocol: Whole roots were excised from the two-week-old seedlings and immediately dipped in distilled water containing 0.1% dimethylsulfoxide (DMSO). The excised organ was incubated at 30°C for 120 min, harvested and stored at -80°C until the RNA was extracted.


title: Root_DMSO-treatment_120min_replicate 2


title: Leaf_OsRR6-overexpressor_replicate 2

source_name: Oryza sativa leaf, OsRR6 overexpression

growth_protocol: Transgenic plants of the T0 generation from callus grown on regeneration agar plates for 6 weeks were transferred to agar plates containing 1 X Murashige and Skoog salts, 3 % (w/v) sucrose, and 50 µg mL-1 hygromycin-B (MS-agar plate) for 7 d, and then hydroponically grown until heading in an environment-controlled greenhouse with a photoperiod of 12 h light (30°C)/12 h dark (25°C).

value: Oryza sativa L. cv Nipponbare transformed with pActnos/Hmz-OsRR6, T0 line, Tissue:leaf, Age:75 days after germination


title: High fat diet Smpl1

source_name: High fat diet

label_protocol: 0.5 ug of total RNA was used for labelling. Synthesis of  Cyanine 5-labeled cDNA was performed by Low RNA input fluorescence linear amplification kit (Agilent Technologies, CA, USA) according to the manufacturer's instructions.

treatment_protocol: A seven week old mouse C57BL/6 was fed on HFC diet (diet 2094, Provimi Kliba AG, Kaiseraugst, Switzerland)  for 12 days. On day 12 liver was excised and immediately frozen in liquid nitrogen and stored at -80°C for the subsequent transriptome analyses.

tag: Sample is obtained from individual C57BL/6 mouse.

label_protocol: 0.5 ug of total RNA was used for labelling. Synthesis of  Cyanine 3-labeled cDNA was performed by Low RNA input fluorescence linear amplification kit (Agilent Technologies, CA, USA) according to the manufacturer's instructions.

treatment_protocol: Six  seven week old C57BL/6 mice were fed on a standard chow diet (diet 3430, Provimi Kliba AG, Kaiseraugst, Switzerland)  for 12 days. On day 12 liver was excised and immediately frozen in liquid nitrogen and stored at -80°C for the subsequent transriptome analyses.

tag: Sample is pooled from mice.


title: High fat diet Smpl2


title: Root_tZ-treatment_120min_replicate 1


title: S2_Sham_wildtype_8

city: St. Louis

first: J

middle: Perren

last: Cobb

state: MO

address: Campus Box 8109, 660 South Euclid Avenue

country: USA

institute: Washington University in St. Louis

description: Gene expression data (Affy Chip MOE430a)

data_processing: The data were analyzed (including normalization and modelling) with dChip

tag: Tissue

value: Spleen

tag: Type

value: Sham

tag: Batch


title: Fenofibrate treated mouse Smpl2

source_name: Fenofibrate treated mouse

label_protocol: 0.5 ug of total RNA was used for labelling. Synthesis of Cyanine 3 -labeled cDNA was performed by Low RNA input fluorescence linear amplification kit (Agilent Technologies, CA, USA) according to the manufacturer's instructions.

label_protocol: 0.5 ug of total RNA was used for labelling. Synthesis of Cyanine 5-labeled cDNA was performed by Low RNA input fluorescence linear amplification kit (Agilent Technologies, CA, USA) according to the manufacturer's instructions.


title: Fenofibrate treated mouse Smpl1

treatment_protocol: A seven week old mouse C57BL/6 was fed on HFC diet (diet 2094, Provimi Kliba AG, Kaiseraugst, Switzerland) for 12 days. On day five HFC diet fed mouse was treated orally once daily with fenofibrate (100mg/kg). On day 12 liver was excised and immediately frozen in liquid nitrogen and stored at -80°C for the subsequent transriptome analyses.


title: S3star_Sham_wildtype_8


title: Root_DMSO-treatment_120min_replicate 1


title: Root_tZ-treatment_30min_replicate 2

source_name: Oryza sativa root, tZ-treated, 30 min

treatment_protocol: Whole roots were excised from the two-week-old seedlings and immediately dipped in distilled water containing either 5 µM trans-seatin (tZ) and 0.1% dimethylsulfoxide (DMSO). The excised organ was incubated at 30°C for 30 or 120 min, harvested and stored at -80°C until the RNA was extracted.


title: Root_tZ-treatment_30min_replicate 3

treatment_protocol: Whole roots were excised from the two-week-old seedlings and immediately dipped in distilled water containing either 5 µM trans-zeatin (tZ) and 0.1% dimethylsulfoxide (DMSO). The excised organ was incubated at 30°C for 30 or 120 min, harvested and stored at -80°C until the RNA was extracted.


title: Root_tZ-treatment_120min_replicate 2


title: S4_Sham_wildtype_8


title: S6_Sham_wildtype_8


title: C5star_CLP_wildtype_8

value: CLP


title: C1_CLP_wildtype_8


title: Root_tZ-treatment_30min_replicate 1

treatment_protocol: Whole roots were excised from the two-week-old seedlings and immediately dipped in distilled water containing either 5 µM tZ and 0.1% dimethylsulfoxide (DMSO). The excised organ was incubated at 30°C for 30 or 120 min, harvested and stored at -80°C until the RNA was extracted.


title: Root_DMSO-treatment_30min_replicate 2

source_name: Oryza sativa root, DMSO-control, 30 min

label_protocol: Total RNA was prepared with the RNeasy plant Mini Kit (Qiagen).

extract_protocol: Approximately 100 mg excised roots of the 2 week-old seedlings, which cut by a razor blade in water, were treated with 0.1% DMSO for 30 min.

treatment_protocol: Whole roots were excised from the two-week-old seedlings and immediately dipped in distilled water containing 0.1% dimethylsulfoxide (DMSO). The excised organ was incubated at 30°C for 30 min, harvested and stored at -80°C until the RNA was extracted.


title: C6star_CLP_wildtype_8


title: S5_sham_overexpressor_12


title: Root_DMSO-treatment_30min_replicate 1


title: C6_CLP_wildtype_12


title: S4_sham_overexpressor_12


title: S3_sham_overexpressor_12


title: C3_CLP_wildtype_8


title: C4_CLP_overexpressor_12


title: C1_CLP_overexpressor_12


title: S6_Sham_wildtype_12


title: S2_sham_overexpressor_12


title: C2_CLP_overexpressor_12


title: B5_Pseudomonas_overexpressor_48

value: Pseudomonas aeruginosa


title: R6_Pseudomonas_wildtype_48


title: S1_sham_overexpressor_12


title: Root_DMSO-treatment_30min_replicate 3


title: Leaf_tZ-treatment_120min_replicate 1

source_name: Oryza sativa leaf, tZ-treated, 120 min

treatment_protocol: Third leaves, which were cut at the lamina joint with a razor blade in water, were excised from the two-week-old seedlings and immediately dipped in distilled water containing 5 µM trans-zeatin (tZ) and 0.1% dimethylsulfoxide (DMSO). The excised organ was incubated at 30°C for 120 min, harvested and stored at -80°C until the RNA was extracted.

tag: Oryza sativa L. cv Nipponbare, Tissue

value: root, Age:two weeks after germination


title: R3_saline_wildtype_48

value: Saline


title: C4_CLP_wildtype_8


title: R7_Pseudomonas_wildtype_422


title: B6_Pseudomonas_overexpressor_48


title: R5_Pseudomonas_wildtype_48


title: C5_CLP_overexpressor_12


title: B3_saline_overexpressor_48


title: Brown Norway Rat Lung- HTV Ventilated_B40

city: Chicago

first: Ankit

middle: A

last: Desai

state: IL

address: 929 East 57th Street, Room W403R

department: Medicine

institute: The University of Chicago

description: Gene expression data from rat lungs exposed to room air (ventilation)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Rattus norvegicus

source_name: Rat Lung

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

growth_protocol: Not Applicable

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

treatment_protocol: At the termination of each experiment, all animals were euthanized by exsanguination under anesthesia in accordance with institutional guidelines. The pulmonary vasculature was perfused via the pulmonary artery with sterile phosphate-buffered saline (PBS) and the right lung was clamped at the level of the mainstem bronchus, excised, and snap frozen in liquid nitrogen for subsequent RNA analysis/expression profiling. Right lung mRNA was isolated from 3 samples per strain and condition (as an example, we analyzed 3 SS rat strains exposed to control, and 3 SS rat strains exposed to HTV for expression profiling).

tag: Genotype

value: HTV Ventilated Brown Norway Rats

tag: Weights


title: Brown Norway Rat Lung- HTV Ventilated_B36


title: R2_saline_wildtype_48


title: B2_saline_overexpressor_48


title: Brown Norway Rat Lung- HTV Ventilated_B37


title: R5_Pseudomonas_wildtype_422


title: Dahl Salt Sensitive Rat Lung- HTV Ventilation_A70

value: HTV Ventilated Dahl Salt Sensitive Rats


title: R6_Pseudomonas_wildtype_422


title: R1_saline_wildtype_422


title: C3_CLP_overexpressor_12


title: R4_saline_wildtype_422


title: Dahl Salt Sensitive Rat Lung- HTV Ventilation_A82


title: R2_saline_wildtype_422


title: Brown Norway Rat Lung- Control_B30

value: Control Brown Norway Rats


title: Brown Norway Rat Lung- Control_B31


title: B6_pseudomonas_overexpressor_422


title: B2_saline_overexpressor_422


title: Brown Norway Rat Lung- Control_B32


title: B1_saline_overexpressor_422


title: B5_pseudomonas_overexpressor_422


title: B4_pseudomonas_overexpressor_422


title: L. helveticus CNRZ32 MRS3.2

status: Public on Feb 14 2007

city: Madison

first: James

last: Steele

email: jlsteele@wisc.edu, vvsmeianov@wisc.edu

state: WI

address: 1605 Linden Dr.

department: Food Science

institute: UW-Madison

description:
References:
1. Ulijasz, A.T., D. R. Andes, J. D. Glasner, B. Weisblum. 2004. Regulation of iron transport in Streptococcus pneumoniae by RitR, an orphan response regulator. J. Bacteriol. 186:8123-8136.
2. Bolstad, B. M., R. A. Irizarry, M. Astrand, and T. P. Speed. 2003. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics. 19:185-193.

hyb_protocol: All hybridizations, staining and processing of arrays were performed essentially as described by Ulijasz et al., 2003 (44) by personnel at NimbleGen Systems. In brief: hybridizations were performed at 45oC for 16 hours on a rotisserie-like apparatus (HybriWheel) to enhance uniformity of hybridizations across the array surface. After hybridization, the arrays were washed in buffers of varying stringency, then streptavidin was conjugated to the end-labeled biotin, followed by biotin-anti-streptavidin in the presence of normal goat IgG, and finally conjugated to a Cy3-streptavidin.

scan_protocol: Arrays were scanned using an Axon model 4000 scanner (Molecular Devices Corporation, Union City, Calif.) and the data extracted using NimbleScan software.

data_processing: Array normalization was performed using a quantile normalization method of Bolstad et al., 2003

label: biotin-N6-ddATP; Cy-3 post-hybe

organism: Lactobacillus helveticus

source_name: L. helveticus was grown in MRS until mid-log phase, replicate 3/2

label_protocol: cDNA was synthesized from 12 μg of total RNA using random hexamer primers (Amersham Bioscience, Piscataway, N.J.) and SuperScript II reverse transcriptase (Invitrogen). After the synthesis, template RNA was digested with RNaseH (Promega) and RNaseA (Epicentre, Madison, Wisc.), and cDNA was purified using the QIAquick PCR purification kit (Qiagen), then fragmented to approx. 70-base fragments using appropriately diluted RQ1 DNaseI (Promega). Fragmentation efficiency was determined with Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, Calif.). Fragmented cDNA was end-labeled with biotin-N6-ddATP (NEN/Perkin-Elmer, Boston, Mass.) using terminal deoxynucleotidyl transferase (Promega) followed by concentration of labeled-sample on Microcon YM-10 columns (Millipore, Bedford, Mass.).

extract_protocol: Cultures were mixed by vortexing with two volumes of RNAprotect reagent (Qiagen Inc., Valencia, Calif.) containing 10 mg/ml of rifampicin (Sigma, St. Louis, Mo.) and incubated for 5 min at room temperature, followed by centrifugation at 5,500 x g, 15 min, 4oC. The cell pellets were resuspended in 5 ml of lysozyme solution (20 mg/ml) containing 0.1 mg/ml of rifampicin and incubated 25 min at 37oC. After repeated centrifugation, the pellets were resuspended by vortexing in 5 ml of TRIzol reagent (Invitrogen, Carlsbad, Calif.) and incubated 10 min at room temperature. Next, 1 ml of chloroform was added followed by vortexing for 15 sec and incubation for 10 min at room temperature. The mixtures were centrifuged at 16000 ґ g for 20 min at 4oC, then 2.5 ml of the upper aqueous phase were transferred into a fresh tube, mixed with 2.5 ml of isopropanol, incubated at room temperature for 10 min and RNA was pelleted at 16000 x g, 20 min, 4oC. After washing in 75% ethanol, the RNA pellet was dried and dissolved in 100 μl of water. The isolated total RNA was treated with 5 U of RQ1 DNAseI (Promega, Madison, Wis.), then purified using the RNeasy purification system (Qiagen).

tag: Strain CNRZ32


title: Dahl Salt Sensitive Rat Lung- HTV Ventilation_A69


title: B3_saline_overexpressor_422


title: S4

city: Laramie

first: Mark

last: Gomelsky

state: WY

department: Molecular Biology

institute: University of Wyoming

description: semiaerobically-grown R.sphaeroides 2.4.1 cells; used in 2 experimental series.

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: MAS 5.0 values are shown (for compartibility with other submissions). The context-dependent data processing (for every experimental series where this sample is used) were performed using Robust Multichip Analysis

label: dd-UTP

organism: Cereibacter sphaeroides

source_name: Total cell pellet, flash-frozen after fast sedimentation in presence of rifampicin

label_protocol: standard Affymetrix protocol

extract_protocol: RNA was isolated after disruption of cells with bead beater following RNesy (Quiagen) Midi kit. 2 x 10 min DNAse treatment. cDNA was synthesized according Affymetrix protocol.

tag: Cells were grown at semiaerobic conditions (3% oxygen).


title: Dahl Salt Sensitive Rat Lung- Control_A81

value: Control Dahl Salt Sensitive Rats


title: L. helveticus CNRZ32 MRS1.2

source_name: L. helveticus was grown in MRS until mid-log phase, replicate 1/2


title: Dahl Salt Sensitive Rat Lung- Control_A72


title: L. helveticus CNRZ32 MRS1.1

source_name: L. helveticus was grown in MRS until mid-log phase, replicate 1/1


title: L. helveticus CNRZ32 milk2.2

source_name: L. helveticus was grown in milk until mid-log phase, replicate 2/2


title: Dahl Salt Sensitive Rat Lung- Control_A73


title: L. helveticus CNRZ32 milk3.1

source_name: L. helveticus was grown in milk until mid-log phase, replicate 3/1


title: L. helveticus CNRZ32 MRS3.1

source_name: L. helveticus was grown in MRS until mid-log phase, replicate 3/1


title: L. helveticus CNRZ32 MRS2.1

source_name: L. helveticus was grown in MRS until mid-log phase, replicate 2/1


title: L. helveticus CNRZ32 milk3.2

source_name: L. helveticus was grown in milk until mid-log phase, replicate 3/2


title: L. helveticus CNRZ32 milk2.1

source_name: L. helveticus was grown in milk until mid-log phase, replicate2/1


title: L. helveticus CNRZ32 milk1.1

hyb_protocol: All hybridizations, staining and processing of arrays were performed essentially as described by Ulijasz et al., 2003 (44) by personnel at NimbleGen Systems.  In brief: hybridizations were performed at 45oC for 16 hours on a rotisserie-like apparatus (HybriWheel) to enhance uniformity of hybridizations across the array surface.  After hybridization, the arrays were washed in buffers of varying stringency, then streptavidin was conjugated to the end-labeled biotin, followed by biotin-anti-streptavidin in the presence of normal goat IgG, and finally conjugated to a Cy3-streptavidin.

scan_protocol: Arrays were scanned using an Axon model 4000 scanner (Molecular Devices Corporation, Union City,  Calif.) and the data extracted using NimbleScan software.

source_name: L. helveticus was grown in milk until mid-log phase, replicate 1/1

label_protocol: cDNA was synthesized from 12 μg of total RNA using random hexamer primers (Amersham Bioscience, Piscataway, N.J.) and SuperScript II reverse transcriptase (Invitrogen).  After the synthesis, template RNA was digested with RNaseH (Promega) and RNaseA (Epicentre, Madison, Wisc.), and cDNA was purified using the QIAquick PCR purification kit (Qiagen), then fragmented to approx. 70-base fragments using appropriately diluted RQ1 DNaseI (Promega).  Fragmentation efficiency was determined with Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, Calif.).  Fragmented cDNA was end-labeled with biotin-N6-ddATP (NEN/Perkin-Elmer, Boston, Mass.) using terminal deoxynucleotidyl transferase (Promega) followed by concentration of labeled-sample on Microcon YM-10 columns (Millipore, Bedford, Mass.).

extract_protocol: Cultures were mixed by vortexing with two volumes of RNAprotect reagent (Qiagen Inc., Valencia, Calif.) containing 10 mg/ml of rifampicin (Sigma, St. Louis, Mo.) and incubated for 5 min at room temperature, followed by centrifugation at 5,500 x g, 15 min, 4oC.  The cell pellets were resuspended in 5 ml of lysozyme solution (20 mg/ml) containing 0.1 mg/ml of rifampicin and incubated 25 min at 37oC.  After repeated centrifugation, the pellets were resuspended by vortexing in 5 ml of TRIzol reagent (Invitrogen, Carlsbad, Calif.) and incubated 10 min at room temperature.  Next, 1 ml of chloroform was added followed by vortexing for 15 sec and incubation for 10 min at room temperature. The mixtures were centrifuged at 16000 ґ g for 20 min at 4oC, then 2.5 ml of the upper aqueous phase were transferred into a fresh tube, mixed with 2.5 ml of isopropanol, incubated at room temperature for 10 min and RNA was pelleted at 16000 x g, 20 min, 4oC.  After washing in 75% ethanol, the RNA pellet was dried and dissolved in 100 μl of water. The isolated total RNA was treated with 5 U of RQ1 DNAseI (Promega, Madison, Wis.), then purified using the RNeasy purification system (Qiagen).


title: EWING175

city: Paris

first: Olivier

last: Delattre

address: 26 rue d'Ulm

department: Genetics

country: France

institute: Institut Curie

description: Ewing tumor

hyb_protocol: According to Affymetrix Gene-Chip expression analysis technical manual, Affymetrix, Santa Clara, Calif.

organism: Homo sapiens

source_name: Ewing tumor

extract_protocol: Total RNAs were isolated using the Trizol Reagent

tag: Ewing tumor


title: EWING172

description: Ewing tumor

scan_protocol: According to Affymetrix Gene-Chip expression analysis technical manual, Affymetrix, Santa Clara, Calif.


title: EWING182

description: Ewing tumor

label_protocol: According to Affymetrix Gene-Chip expression analysis technical manual, Affymetrix, Santa Clara, Calif.


title: EWING168

description: Ewing tumor


title: EWING158

description: Ewing tumor


title: EWING163

description: Ewing tumor


title: EWING143

description: Ewing tumor


title: EWING138

description: Ewing tumor


title: EWING118

description: Ewing tumor


title: EWING150

description: Ewing tumor


title: EWING82

description: Ewing tumor


title: EWING131

description: Ewing tumor


title: EWING137

description: Ewing tumor


title: EWING76

description: Ewing tumor


title: L. helveticus CNRZ32 MRS2.2

source_name: L. helveticus was grown in MRS until mid-log phase, replicate 2/2


title: EWING53

description: Ewing tumor


title: EWING110

description: Ewing tumor


title: EWING162

description: Ewing tumor


title: EWING89

description: Ewing tumor


title: EWING97

description: Ewing tumor


title: EWING94

description: Ewing tumor


title: EWING73

description: Ewing tumor


title: EWING79

description: Ewing tumor


title: 48 hour PEG treatment-library1-replicate2

city: Shanghai

first: Youxin

last: Jin

address: 320 Yueyang Road

country: China

institute: Institute of Biochemistry and Cell Biology,Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

description:
analysis of rice microRNAs expression under osmotic stress,
keyword=rice
keyword=microRNA
keyword=osmotic stress

scan_protocol: scaned by ScanArray5000

data_processing: Signal intensity (VALUE) for each spot was calculated by subtracting local background from total intensities.

source_name: rice seeding, PEG6000 treatment, 48 hour

label_protocol: labeled by PCR using a Cy5 labeled primer

growth_protocol:
Yoshida’s culture solution,
13-h light (26°C)/11-h dark (22°C) photoperiod

treatment_protocol: treated by 15% PEG6000

tag: Oryza sativa (japonica),

tag: 12 day seeding,

tag: PEG6000 treatment


title: 48 hour PEG treatment-library2-replicate1


title: 48 hour PEG treatment-library2-replicate2


title: EWING36

description: Ewing tumor


title: 48 hour PEG treatment-library1-replicate1


title: EWING20

description: Ewing tumor


title: EWING116

description: Ewing tumor


title: 24 hour PEG treatment-library2-replicate2

source_name: rice seeding, PEG6000 treatment, 24 hour


title: 24 hour PEG treatment-library2-replicate1

data_processing: Signal intensities (VALUE) for each spot were calculated by subtracting local background from total intensities.


title: 24 hour PEG treatment-library1-replicate2


title: Log 4.6 uM biological replicate #4

city: Durham

first: William

last: Ward

state: NC

address: 109 TW Alexander Dr

department: NHEERL

institute: United States EPA

description: Gene expression data from log phase Salmonella typhimurim TA100 treated with MX.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.  Details of hybridization protocol are found in S. Porwollik, J, Frye, L,D, Florea, F, Blackmer, M, McClelland, A non-redundant  microarray of  genes for two related bacteria, Nucleic Acids Res. 31 (2003) 1869-76.

scan_protocol: The slides were scanned on a GenePix 4000B Axon Scanner (Axon Instruments, Inc., Union City, CA), and signal intensities were quantified using the GenePix TM Pro 4.1 software package (Axon Instruments, Inc., Union City, CA).

data_processing: Spot intensities were quantified by scanner software, the local background intensities were subtracted, and the ratios of the contribution of each spot to total signal in each channel were calculated.  Because each gene was spotted three times per slide, the average of the three replicate set of genes/slide constituted the measure of expression of a gene for each experiment.

label: RNA dye was Cy3;DNA dye wasCy5

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: Salmonella typhimurium TA100 treated with 4.6 uM MX

label_protocol: On each slide, RNA isolated from treated and control cells were compared to genomic DNA from control TA100 cells.  All slides were hybridized reciprocally, such that the DNA was labeled with Cy3-labeled probes and the RNA with Cy5-labeled probes, and then vice versa.  Details of labelling protocol are found in S. Porwollik, J, Frye, L,D, Florea, F, Blackmer, M, McClelland, A non-redundant  microarray of  genes for two related bacteria, Nucleic Acids Res. 31 (2003) 1869-76.

growth_protocol: The base-substitution strain TA100 [hisG46 chl-1005 (bio uvrB gal) rfa-1001 pKM101+ Fels-1+ Fels-2+ Gifsy-1+ Gifsy-2+] [7] was grown overnight in Oxoid nutrient broth No. 2 to stationary phase (~109 cells/ml).  A sample of the overnight culture was diluted 1:50 in nutrient broth and grown ~2 h until the cell concentration was mid-log (~ 2 X 108 cells/ml).  These log-phase cells were then concentrated 50X in PBS to produce a suspension of ~1010 cells/ml.  Cell concentrations were determined by optical density

extract_protocol: RNA was extracted and purified using the Institute of Food Research Microarray Facility protocol (http://www.ifr.bbsrc.ac.uk/Safety/Microarrays/protocols.html).

treatment_protocol: Mutagenesis experiments were performed in 50-ml plastic flasks to which were added 2.9 ml of PBS, 1 ml of cell concentrate, and 100 µl of dimethyl sulfoxide (DMSO, Burdick and Jackson, Muskegan, MI) or MX (Sigma, St. Louis, MO) in DMSO.  Thus, mutagenesis experiments were performed with cells at a final concentration of ~2.5 X 109 per ml.  Suspensions were incubated with MX at 3 concentrations with shaking at 120 rpm for 30 min at 37oC and then sampled for survival, mutagenesis, and RNA extraction.


title: 24 hour PEG treatment-library1-replicate1


title: BT474_replicate1

type: genomic

city: Vancouver

first: Bradley

middle: P

last: Coe

state: BC

address: 675 West 10th Ave

department: Cancer Genetics and Developmental Biology

country: Canada

institute: BC Cancer Research Centre

description: Part of a two entry flip fluor record

hyb_protocol: Standard Agilent Protocols from http://www.opengenomics.com/oligoaCGHLiterature.aspx Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis, Version 4.0.  Part number is G4410-90010.

scan_protocol: Agilent DNA Microarray Scanner p/n G2565BA. Scan Region: 61x21.6 mm Scan Resolution 5 micron Dye Channel Red & Green Red and Green PMT 100%

data_processing: Value represent LOG10 Ratio (CH1/CH2) generated by Standard Agilent Protocols from http://www.opengenomics.com/oligoaCGHLiterature.aspx

molecule: genomic DNA

source_name: Promega Human Male DNA

extract_protocol: DNA provided by Promega Part Number G1471

tag: Normal Male DNA Promega

label_protocol:
0.5ug of DNA was labelled using standard agilent protocols from http://www.opengenomics.com/oligoaCGHLiterature.aspx (
Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis, Version 4.0.  Part number is G4410-90010)

extract_protocol: DNA provided by ATCC Part Number HTB-20D

tag: breast ductal carcinoma cell line


title: Log 4.6 uM biological replicate #3

tag: Salmonella typhimurium TA100 treated with 4.6 uM MX


title: 6 hour PEG treatment-library2-replicate2

source_name: rice seeding, PEG6000 treatment, 6 hour


title: Log 4.6 uM biological replicate #2


title: EWING17

description: Ewing tumor


title: 6 hour PEG treatment-library2-replicate1


title: Log 4.6 uM biological replicate #1


title: 6 hour PEG treatment-library1-replicate1

description:
analysis of rice microRNAs expression under osmotic stress,
keyword=rice
keyword=microRNA
keyword=ommotic stress


title: 6 hour PEG treatment-library1-replicate2


title: L. helveticus CNRZ32 milk1.2

source_name: L. helveticus was grown in milk until mid-log phase, replicate 1/2


title: BT474_replicate2

description:
Part of a two entry flip fluor record
This Entry (BT474/Male)
Other Entry (Male/BT474) GSM147888

hyb_protocol: Standard Agilent Protocols from http://www.opengenomics.com/oligoaCGHLiterature.aspx Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis, Version 4.0. Part number is G4410-90010.

label_protocol:
0.5ug of DNA was labelled using standard agilent protocols from http://www.opengenomics.com/oligoaCGHLiterature.aspx (
Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis, Version 4.0. Part number is G4410-90010)


title: Log 2.3 uM biological replicate #3

source_name: Salmonella typhimurium TA100 treated with 2.3 uM MX


title: Log 2.3 uM biological replicate #1

tag: Salmonella typhimurium TA100 treated with 2.3 uM MX


title: Log 2.3 uM biological replicate #4


title: 2 hour PEG treatment-library2-replicate2

source_name: rice seeding, PEG6000 treatment, 2 hour


title: 2 hour PEG treatment-library1-replicate2


title: 2 hour PEG treatment-library2-replicate1


title: EWING24

description: Ewing tumor


title: Log 2.3 uM biological replicate #2


title: Log 1.15 uM biological replicate #3

source_name: Salmonella typhimurium TA100 treated with 1.15 uM MX


title: 0.5 hour PEG treatment-library2-replicate2

source_name: rice seeding, PEG6000 treatment, 0.5 hour


title: Log 1.15 uM biological replicate #2

tag: Salmonella typhimurium TA100 treated with 1.15 uM MX


title: 0.5 hour PEG treatment-library2-replicate1

data_processing: Signal intensities for each spot were calculated by subtracting local background from total intensities.


title: Log 0 uM biological replicate #4

source_name: Salmonella typhimurium TA100 treated with 0 uM MX


title: 2 hour PEG treatment-library1-replicate1


title: 0.5 hour PEG treatment-library1-replicate1


title: Log 1.15 uM biological replicate #1


title: 0 hour PEG treatment-library2-replicate2

source_name: rice seeding, PEG6000 treatment, 0 hour


title: 0.5 hour PEG treatment-library1-replicate2


title: Log 0 uM biological replicate #3

tag: Salmonella typhimurium TA100 treated with 0 uM MX


title: EW24_shCTL_rep2

description: Ewing EW24 cell line treated with scramble (control) shRNA lentivirus for 3 days

source_name: Ewing Tumor

treatment_protocol: Treated with scramble (control) shRNA lentivirus for 3 days

tag: Ewing EW24 cell line


title: 0 hour PEG treatment-library2-replicate1

data_processing: Signal intensities for each spot were calculated by subtracting local background from total intensities. No further process was performed.


title: BMSC

description: Human BMSC from bone marrow aspirates

source_name: bone marrow aspirates (iliac crest)

tag: Tissue

value: bone marrow


title: Log 0 uM biological replicate #2


title: 0 hour PEG treatment-library1-replicate2


title: Log 0 uM biological replicate #1


title: BAF170 ChIP-ChIP from K562 cells applied to the NimbleGen ENCODE Array [unpublished] Sample 2

city: New Haven

first: Guoneng

last: Zhong

state: CT

address: 300 George St

institute: Yale Med

description: Red Channel: BAF170 ChIP DNA purified from K562 cells with polyclonal antibody; Green Channel: Normal rabbit IgG ChIP DNA purified from K562 cells.

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html).

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: value = log_2(Signal for Cy5 / Signal for Cy3)

source_name: BAF170 ChIP DNA from K562 cells

label_protocol: ChIP DNA prepared from 1 x 10^8 cells was directly labeled by Klenow (New England Biolabs), random priming with Cy5-coupled nonamers (for BAF170 ChIP DNA) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: K562 cells were grown in suspension in RPMI medium, supplemented with 10% FBS at 37C in 5% CO2, to a density of 5 to 6 x10^5 cells/ml. Cells (density at 1x 10^7 cells/ml) were fixed with 1% formaldehyde at room temperature for 12 min. Fixation was terminated with 125 mM glycine (2 M stock made in 1x PBS), and cells were washed twice in cold 1x Dulbeccos PBS (Invitrogen), and then swelled on ice for 10 min in 7 ml hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, and protease inhibitors). Cell lysates (1x 10^9 cells in 7 ml) were homogenized with 30 to 40 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 20 ml of 1x RIPA buffer (1x RIPA buffer: 10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, and protease inhibitors). Chromatin (density at 1x 10^9 cells in 20 ml) was sheared with a Branson Digital Sonifier (65% duty cycle; 17x 25-second pulses; cooled 5 min on ice between each 25 second round) to an average of 600 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with 20 ug of anti-BAF170 rabbit polyclonal antibody per 1x10^8 cells. Following this incubation Protein A agarose (Upstate) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with RNase A for 1 h at 37C, with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol, 2 volumes of 100% ethanol and 1.5 ul of pellet paint (Novagen).

tag: Polyclonal antibody

source_name: normal rabbit IgG ChIP DNA from K562 cells

label_protocol: ChIP DNA prepared from 1 x 10^8 cells was directly labeled by Klenow (New England Biolabs), random priming with Cy3-coupled nonamers (for normal rabbit IgG ChIP DNA) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: K562 cells were grown in suspension in RPMI medium, supplemented with 10% FBS at 37C in 5% CO2, to a density of 5 to 6 x10^5 cells/ml. Cells (density at 1x 10^7 cells/ml) were fixed with 1% formaldehyde at room temperature for 12 min. Fixation was terminated with 125 mM glycine (2 M stock made in 1x PBS), and cells were washed twice in cold 1x Dulbeccos PBS (Invitrogen), and then swelled on ice for 10 min in 7 ml hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, and protease inhibitors). Cell lysates (1x 10^9 cells in 7 ml) were homogenized with 30 to 40 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 20 ml of 1x RIPA buffer (1x RIPA buffer: 10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, and protease inhibitors). Chromatin (density at 1x 10^9 cells in 20 ml) was sheared with a Branson Digital Sonifier (65% duty cycle; 17x 25-second pulses; cooled 5 min on ice between each 25 second round) to an average of 600 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with 20 ug of normal rabbit IgG per 1x10^8 cells. Following this incubation Protein A agarose (Upstate) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with RNase A for 1 h at 37C, with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol, 2 volumes of 100% ethanol and 1.5 ul of pellet paint (Novagen).

tag: Normal rabbit IgG


title: 0 hour PEG treatment-library1-replicate1

source_name: rice seeding, PEG6000 treated, 0 hour

tag: 0 hour treatment


title: Short-chain fructooligosaccharides culture 3 vs glucose culture 2 FOS4_GLC2

status: Public on Feb 13 2007

city: Amsterdam

first: Douwe

last: Molenaar

address: De Boelelaan 1085

department: Systems Bioinformatics

country: Netherlands

institute: Vrije Universiteit Amsterdam

description: Hybridisation of Cy3 labeled Sample FOS4 and Cy5 labeled sample GLC2

data_processing: Normalization was performed by subtraction of background intensities and lowess normalization on M-A transformed data. The VALUE column holds the Log2 of the ratio of the normalized signals

organism: Lactiplantibacillus plantarum WCFS1

source_name: L. plantarum WCFS1 grown on chemically defined medium with 1% scFOS Actilight until OD600=1.5

tag: Culture#

tag: Carbon/energy source

value: scFOS Actilight

tag: Optical density

source_name: L. plantarum WCFS1 grown on chemically defined medium with 1% glucose until OD600=1

value: glucose


title: Ini1 ChIP-ChIP from K562 cells applied to the NimbleGen ENCODE Array Sample 1 [unpublished]

description: Red Channel: Ini1 ChIP DNA purified from K562 cells with polyclonal antibody; Green Channel: Normal rabbit IgG ChIP DNA purified from K562 cells.

source_name: Ini1 ChIP DNA from K562 cells

label_protocol: ChIP DNA prepared from 1 x 10^8 cells was directly labeled by Klenow (New England Biolabs), random priming with Cy5-coupled nonamers (for Ini1 ChIP DNA) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: K562 cells were grown in suspension in RPMI medium, supplemented with 10% FBS at 37C in 5% CO2, to a density of 5 to 6 x10^5 cells/ml. Cells (density at 1x 10^7 cells/ml) were fixed with 1% formaldehyde at room temperature for 12 min. Fixation was terminated with 125 mM glycine (2 M stock made in 1x PBS), and cells were washed twice in cold 1x Dulbeccos PBS (Invitrogen), and then swelled on ice for 10 min in 7 ml hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, and protease inhibitors). Cell lysates (1x 10^9 cells in 7 ml) were homogenized with 30 to 40 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 20 ml of 1x RIPA buffer (1x RIPA buffer: 10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, and protease inhibitors). Chromatin (density at 1x 10^9 cells in 20 ml) was sheared with a Branson Digital Sonifier (65% duty cycle; 17x 25-second pulses; cooled 5 min on ice between each 25 second round) to an average of 600 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with 20 ug of anti-Ini1 rabbit polyclonal antibody per 1x10^8 cells. Following this incubation Protein A agarose (Upstate) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with RNase A for 1 h at 37C, with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol, 2 volumes of 100% ethanol and 1.5 ul of pellet paint (Novagen).


title: Short-chain fructooligosaccharides culture 3 vs glucose culture 1 FOS1_GLC1

description: Hybridisation of Cy3 labeled Sample FOS1 and Cy5 labeled sample GLC1

source_name: L. plantarum WCFS1 grown on chemically defined medium with 1% scFOS Actilight until OD600=1


title: Ini1 ChIP-ChIP from K562 cells applied to the NimbleGen ENCODE Array Sample 2 [unpublished]


title: BAF155 ChIP-ChIP from K562 cells applied to the NimbleGen ENCODE Array [unpublished] Sample 1

description: Red Channel: BAF155 ChIP DNA purified from K562 cells with polyclonal antibody; Green Channel: Normal rabbit IgG ChIP DNA purified from K562 cells.

source_name: BAF155 ChIP DNA from K562 cells

label_protocol: ChIP DNA prepared from 1 x 10^8 cells was directly labeled by Klenow (New England Biolabs), random priming with Cy5-coupled nonamers (for BAF155 ChIP DNA) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: K562 cells were grown in suspension in RPMI medium, supplemented with 10% FBS at 37C in 5% CO2, to a density of 5 to 6 x10^5 cells/ml. Cells (density at 1x 10^7 cells/ml) were fixed with 1% formaldehyde at room temperature for 12 min. Fixation was terminated with 125 mM glycine (2 M stock made in 1x PBS), and cells were washed twice in cold 1x Dulbeccos PBS (Invitrogen), and then swelled on ice for 10 min in 7 ml hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, and protease inhibitors). Cell lysates (1x 10^9 cells in 7 ml) were homogenized with 30 to 40 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 20 ml of 1x RIPA buffer (1x RIPA buffer: 10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, and protease inhibitors). Chromatin (density at 1x 10^9 cells in 20 ml) was sheared with a Branson Digital Sonifier (65% duty cycle; 17x 25-second pulses; cooled 5 min on ice between each 25 second round) to an average of 600 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with 20 ug of anti-BAF155 rabbit polyclonal antibody per 1x10^8 cells. Following this incubation Protein A agarose (Upstate) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with RNase A for 1 h at 37C, with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol, 2 volumes of 100% ethanol and 1.5 ul of pellet paint (Novagen).


title: Short-chain fructooligosaccharides culture 3 vs 4 FOS4_FOS5

description: Hybridisation of Cy5 labeled Sample FOS4 and Cy3 labeled sample FOS5


title: Glucose culture 1 vs short-chain fructooligosaccharides culture 4 GLC2_FOS2

description: Hybridisation of Cy3 labeled Sample GLC2 and Cy5 labeled sample FOS2


title: p65 ChIP-chip on TNF-alpha-stimulated HeLaS3 cells using polyclonal antibody (N-) [unpublished] Sample 2

description: Rel A (p65) ChIP-chip in ENCODE region in TNF-alpha-stimulated HeLaS3 cells using anti-p65 (N-terminus) rabbit polyclonal antibody

source_name: p65 ChIP in TNF-alpha-stimulated HeLaS3 Cells

label_protocol: For NimbleGen arrays, ChIP DNA prepared from 1 x 10^8 was directly labeled by Klenow (New England Biolabs) random priming with Cy5 nonamers (ChIP DNA isolated from p65-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: HeLaS3 cells were grown in Minimum Essential Medium modified for Suspension (SMEM, Invitrogen), supplemented with glutamine, 10% FBS, and antibiotics (penicillin-streptomycin) at 37C in 5% CO2 to a density of 5 x10^5 cells/ml and were treated with 10 ng/ml TNF-alpha (Sigma) for 20 min. Cells were fixed with 1% formaldehyde at room temperature for 10 min. Fixation was terminated with 125 mM glycine, and cells were washed twice in cold 1x PBS, and then swelled on ice in hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, and protease inhibitors). Cell lysates were homogenized with 30 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 1x RIPA buffer (10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, and protease inhibitors). Chromatin was sheared with a Branson 250 Sonifier (output setting 2, 100% duty cycle, five 30-second pulses) to an average of 700 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with anti-p65 (N-terminus) rabbit polyclonal antibody (Santa Cruz). Following this incubation Protein A agarose (Upstate) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with RNase A for 1 h at 37C, with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol.

tag: Polyclonal antibody for p65 (N-terminus)

source_name: IgG control ChIP in TNF-alpha-stimulated HeLaS3 Cells

label_protocol: For NimbleGen arrays, ChIP DNA prepared from 1 x 10^8 was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: HeLaS3 cells were grown in Minimum Essential Medium modified for Suspension (SMEM, Invitrogen), supplemented with glutamine, 10% FBS, and antibiotics (penicillin-streptomycin) at 37C in 5% CO2 to a density of 5 x10^5 cells/ml and were treated with 10 ng/ml TNF-alpha (Sigma) for 20 min. Cells were fixed with 1% formaldehyde at room temperature for 10 min. Fixation was terminated with 125 mM glycine, and cells were washed twice in cold 1x PBS, and then swelled on ice in hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, and protease inhibitors). Cell lysates were homogenized with 30 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 1x RIPA buffer (10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, and protease inhibitors). Chromatin was sheared with a Branson 250 Sonifier (output setting 2, 100% duty cycle, five 30-second pulses) to an average of 700 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with normal rabbit IgG (Santa Cruz). Following this incubation Protein A agarose (Upstate) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with RNase A for 1 h at 37C, with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol.

tag: IgG reference


title: Ini1 ChIP-ChIP from HeLaS3 Cells applied to the NimbleGen ENCODE Array Sample 4 [unpublished]

description: Red Channel: Ini1 ChIP DNA purified from HeLaS3 cells with polyclonal antibody; Green Channel: Normal rabbit IgG ChIP DNA purified from HeLaS3 cells.

source_name: Ini1 ChIP DNA from HeLaS3 cells

extract_protocol: HeLaS3 cells were grown in suspension in Joklik's modified minimal essential medium (MEM), supplemented with 5% FBS at 37C in 5% CO2, to a density of 6 x10^5 cells/ml. Cells were fixed with 1% formaldehyde at room temperature for 10 min. Fixation was terminated with 125 mM glycine (2 M stock made in 1x PBS), and cells were washed twice in cold 1x Dulbeccos PBS (Invitrogen), and then swelled on ice in 10 ml hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, and protease inhibitors). Cell lysates were homogenized with 30 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 10 ml of 1x RIPA buffer per 3 x 10^8 cells (1x RIPA buffer: 10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, and protease inhibitors). Chromatin was sheared with a Branson 250 Sonifier (power setting 2, 100% duty cycle, six 30-second pulses) to an average of 700 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with 20 ug of anti-Ini1 rabbit polyclonal antibody per 1x10^8 cells. Following this incubation Protein A agarose (Upstate) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with RNase A for 1 h at 37C, with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol, 2 volumes of 100% ethanol and 1.5 ul of pellet paint (Novagen).

source_name: normal rabbit IgG ChIP DNA from HeLaS3 cells

extract_protocol: HeLaS3 cells were grown in suspension in Joklik's modified minimal essential medium (MEM), supplemented with 5% FBS at 37C in 5% CO2, to a density of 6 x10^5 cells/ml. Cells were fixed with 1% formaldehyde at room temperature for 10 min. Fixation was terminated with 125 mM glycine (2 M stock made in 1x PBS), and cells were washed twice in cold 1x Dulbeccos PBS (Invitrogen), and then swelled on ice in 10 ml hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, and protease inhibitors). Cell lysates were homogenized with 30 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 10 ml of 1x RIPA buffer per 3 x 10^8 cells (1x RIPA buffer: 10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, and protease inhibitors). Chromatin was sheared with a Branson 250 Sonifier (power setting 2, 100% duty cycle, six 30-second pulses) to an average of 700 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with 20 ug of normal rabbit IgG per 1x10^8 cells. Following this incubation Protein A agarose (Upstate) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with RNase A for 1 h at 37C, with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol, 2 volumes of 100% ethanol and 1.5 ul of pellet paint (Novagen).


title: p65 ChIP-chip on TNF-alpha-stimulated HeLaS3 cells using polyclonal antibody (N-) [unpublished] Sample 3


title: BAF155 ChIP-ChIP from K562 cells applied to the NimbleGen ENCODE Array [unpublished] Sample 3


title: Short-chain fructooligosaccharides culture 4 vs 5 FOS2_FOS1

description: Hybridisation of Cy3 labeled Sample FOS2 and Cy5 labeled sample FOS1


title: p65 ChIP-chip on TNF-alpha-stimulated HeLaS3 cells using polyclonal antibody (N-) [unpublished] Sample 1


title: BAF155 ChIP-ChIP from K562 cells applied to the NimbleGen ENCODE Array [unpublished] Sample 2


title: Ini1 ChIP-ChIP from HeLaS3 Cells applied to the NimbleGen ENCODE Array Sample 2 [unpublished]


title: Ini1 ChIP-ChIP from K562 cells applied to the NimbleGen ENCODE Array Sample 3 [unpublished]


title: BAF170 ChIP-ChIP from K562 cells applied to the NimbleGen ENCODE Array [unpublished] Sample 1


title: BAF170 ChIP-ChIP from K562 cells applied to the NimbleGen ENCODE Array [unpublished] Sample 3


title: S. aureus PVL-positive strain (LUG881)_stationary phase_replicate1

city: Houston

first: Gabriela

last: Bowden

state: TX

address: 2121 Holcombe Blvd

department: CEMB

institute: Texas A&M

description: stationary phase

hyb_protocol: Hybridization was performed by NimbleGen Systems, Inc. www.nimblegen.com

scan_protocol: Scan was performed by NimbleGen Systems, Inc. www.nimblegen.com

data_processing:
The data was normalized using quantile
normalization and gene calls generated using RMA (Robust Multichip Average), tools available through Bioconductor project (http://www.bioconductor.org).

organism: Staphylococcus aureus

label_protocol:
Samples were labeled by NimbleGen Systems, Inc.
www.nimblegen.com

growth_protocol: S. aureus strain were cultured at 37C to stationary phase OD600=2 (~7h) in tryptic soy broth

extract_protocol: Microarray analysis of S. aureus gene expression. Aliquots of cells harvested during exponential phase (3 x 108 CFU/ml) and stationary phase (4 x 109 CFU/ml) were pelleted by centrifugation at 8000 x g for 5 minutes at 4ºC. Each pellet was washed in an equal volume of TE buffer (10mM TrisHCl, 1mM EDTA [pH=8]), resuspended to 109 CFU/ml in TE buffer containing 100μg lysostaphin (Sigma-Aldrich, St. Louis, MO) and 250 μg lysozyme (Sigma-Aldrich, St. Louis, MO) and incubated at 37ºC for 15 minutes. Total bacterial RNA was isolated using the Qiagen RNeasy Mini Kit according to the manufacturer’s instructions (Qiagen Sciences, Maryland). Contaminating DNA was removed incubating the total bacterial RNA with RNase-free DNase I (Ambion Inc., Austin, USA) 30U/100μg of total RNA, for 1h at 37°C. RNA was then re-purified using RNeasy Mini columns (Qiagen Sciences). The amount of RNA recovered was determined using a NanoDrop Fluorospectometer (NanoDrop Technologies, Wilmington,DE) and the purity and quality of RNA were determined using a Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA). The microarray experiment was performed by NimbleGen Systems Inc., Madison, WI. RNA was converted to cDNA, labeled and hybridized to a 24 mer Staphylococcus aureus NCTC 8325 gene expression array (2641 genes; 190,000 probes).

treatment_protocol: no treatment


title: S. aureus PVL-positive strain (LUG881)_exponential phase_replicate1

description: exponential phase

growth_protocol: S. aureus strain were cultured at 37C to mid exponential phase OD600=1 (~2h) in tryptic soy broth


title: S. aureus PVL-positive strain (LUG881)_exponential phase_replicate2

description: exponential phase


title: Log 1.15 uM biological replicate #4

source_name: Salmonella typhimurium TA100 treated with 1.15 uM MX


title: S. aureus PVL-negative  strain (LUG776)_stationary phase_replicate2

description: stationary phase


title: S. aureus PVL-negative strain (LUG776)_stationary phase_replicate3

description: stationary phase


title: S. aureus PVL-negative strain (LUG776)_exponential phase_replicate1

description: exponential phase

hyb_protocol: Hibridization was performed by Nimblegen Systems, Inc. www.nimblegen.com

scan_protocol: Scan was performed by Nimblegen Systems, Inc. www.nimblegen.com

label_protocol:
The sample was labeled by Nimblegen Systems, Inc.
www.nimblegen.com

growth_protocol: S. aureus strain was cultured at 37C to mid exponential phase OD600=1(~2h) in tryptic soy broth.


title: S. aureus PVL-positive strain (LUG881)_exponential phase_replicate3

description: exponential phase


title: STAT1 (Interferon-alpha) ChIP-ChIP from HeLaS3 applied to the NimbleGen ENCODE Array Sample 3 [unpublished]

description: Red Channel: STAT1 ChIP DNA purified from HeLaS3 cells following Interferon-alpha stimulation for 30 min; Green Channel: STAT1 ChIP DNA purified from untreated HeLaS3 cells. Both samples were isolated using the polyclonal antibody sc-345.

source_name: STAT1 ChIP from IFN-alpha stimulated HeLaS3 cells

label_protocol: ChIP DNA prepared from 1 x 10^8 cells was directly labeled by Klenow (New England Biolabs), random priming with Cy5-coupled nonamers (for STAT1 ChIP DNA isolated from IFN-alpha stimulated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: HeLaS3 cells were grown in Minimum Essential Medium modified for Suspension (SMEM, Invitrogen), supplemented with glutamine, 10% FBS, and antibiotics (penicillin-streptomycin) at 37C in 5% CO2, to a density of 5 x10^5 cells/ml and then stimulated at these same growth conditions with 1000 U/ml (final) of Interferon alpha [PBL Biomedical Laboratories Product #11100-1, Recombinant human IFN alpha (Hu-IFN-alpha-A; Hu-IFN-alpha-2a)]. Cells were fixed with 1% formaldehyde at room temperature for 10 min. Fixation was terminated with 125 mM glycine, and cells were washed twice in cold 1x PBS, and then swelled on ice in hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, 0.1 mM sodium orthovanadate and protease inhibitors). Cell lysates were homogenized with 30 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 1x RIPA buffer (10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, 0.1 mM sodium orthovanadate and protease inhibitors). Chromatin was sheared with a Branson 250 Sonifier (output setting 2, 100% duty cycle, seven 30-second pulses) to an average of 700 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with anti-STAT1 rabbit polyclonal antibody (Santa Cruz sc-345). Following this incubation Protein A agarose beads (Upstate) were added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with RNase A for 1 h at 37C, with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, 2 volumes of 100% ethanol and 1.5 ul of pellet paint (Novagen).

source_name: STAT1 ChIP from unstimulated HeLaS3 cells

label_protocol: ChIP DNA prepared from 1 x 10^8 cells was directly labeled by Klenow (New England Biolabs), random priming with Cy3-coupled nonamers (for STAT1 ChIP DNA isolated from unstimulated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: HeLaS3 cells were grown in Minimum Essential Medium modified for Suspension (SMEM, Invitrogen), supplemented with glutamine, 10% FBS, and antibiotics (penicillin-streptomycin) at 37C in 5% CO2, to a density of 5 x10^5 cells/ml. Cells were fixed with 1% formaldehyde at room temperature for 10 min. Fixation was terminated with 125 mM glycine, and cells were washed twice in cold 1x PBS, and then swelled on ice in hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, 0.1 mM sodium orthovanadate and protease inhibitors). Cell lysates were homogenized with 30 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 1x RIPA buffer (10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, 0.1 mM sodium orthovanadate and protease inhibitors). Chromatin was sheared with a Branson 250 Sonifier (output setting 2, 100% duty cycle, seven 30-second pulses) to an average of 700 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with anti-STAT1 rabbit polyclonal antibody (Santa Cruz sc-345). Following this incubation Protein A agarose beads (Upstate) were added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with RNase A for 1 h at 37C, with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, 2 volumes of 100% ethanol and 1.5 ul of pellet paint (Novagen).


title: S. aureus PVL-negative strain (LUG776)_stationary phase_replicate1

description: stationary phase

data_processing:
The data was normalized using quantile
normalization and gene calls generated using RMA (Robust Multichip Average)
, tools available through Bioconductor project (http://www.bioconductor.org).

growth_protocol: S. aureus strain was cultured at 37C to stationary phase OD600=2 (~7h) in tryptic soy broth.


title: Short-chain fructooligosaccharides culture 4 vs glucose culture 1 FOS5_GLC1

description: Hybridisation of Cy5 labeled Sample FOS5 and Cy3 labeled sample GLC1


title: S. aureus PVL-negative strain (LUG776)_exponential phase_replicate3

description: exponential phase

hyb_protocol: Hybridization wasperformed by NimbleGen Systems, Inc. www.nimblegen.com

data_processing: The data was normalized using quantile normalization  and gene calls generated using RMA (Robust Multichip Average), tools available through Bioconductor project (http://www.bioconductor.org).

label_protocol:
Sample was labeled by NimbleGen Systems, Inc.
www.nimblegen.com

growth_protocol: S. aureus strains were cultured to mid exponential phase, OD600=1 (~2hrs) in tryptic soy broth.


title: Ini1 ChIP-ChIP from HeLaS3 Cells applied to the NimbleGen ENCODE Array Sample 3 [unpublished]


title: p65 ChIP-chip on TNF-alpha-stimulated HeLaS3 cells using polyclonal antibody (C-20) [unpublished] Sample 2

description: Rel A (p65) ChIP-chip in ENCODE region in TNF-alpha-stimulated HeLaS3 cells using anti-p65 (C-20) rabbit polyclonal antibody

extract_protocol: HeLaS3 cells were grown in Minimum Essential Medium modified for Suspension (SMEM, Invitrogen), supplemented with glutamine, 10% FBS, and antibiotics (penicillin-streptomycin) at 37C in 5% CO2 to a density of 5 x10^5 cells/ml and were treated with 10 ng/ml TNF-alpha (Sigma) for 20 min. Cells were fixed with 1% formaldehyde at room temperature for 10 min. Fixation was terminated with 125 mM glycine, and cells were washed twice in cold 1x PBS, and then swelled on ice in hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, and protease inhibitors). Cell lysates were homogenized with 30 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 1x RIPA buffer (10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, and protease inhibitors). Chromatin was sheared with a Branson 250 Sonifier (output setting 2, 100% duty cycle, five 30-second pulses) to an average of 700 bp as verified on a 1.5% agarose gel. Clarified lysates were agitated overnight at 4C with anti-p65 (C-20) rabbit polyclonal antibody (Santa Cruz). Following this incubation Protein A agarose (Upstate) was added and allowed to bind for 60 min at 4C. Immunoprecipitates were washed three times in 1x RIPA, once in 1x PBS, and then eluted in 1xTE/1%SDS. Crosslinks were reversed overnight at 65C. ChIP DNA was purified by incubation with RNase A for 1 h at 37C, with 200 ug/ml Proteinase K for 2 h at 45C, phenol:chloroform:isoamyl alcohol extraction, and precipitation with 0.1 volumes of 3M sodium acetate, and 2 volumes of 100% ethanol.

tag: Polyclonal antibody for p65 (C-20)


title: S. aureus PVL-positive strain (LUG881)_stationary phase_replicate2

description: stationary phase


title: S. aureus PVL-negative strain (LUG776)_exponential phase_replicate2

description: exponential phase

scan_protocol: Scan was performed by Nimblegen Systems, Inc.

label_protocol:
Samples were labeled by Nimblegen Systems, Inc.
www.nimblegen.com

growth_protocol: S. aureus strains were cultured at 37C to mid exponential phase OD600=1 (~2 hrs) in tryptic soy broth.


title: STAT1 (Interferon-alpha) ChIP-ChIP from HeLaS3 applied to the NimbleGen ENCODE Array Sample 1 [unpublished]


title: p65 ChIP-chip on TNF-alpha-stimulated HeLaS3 cells using polyclonal antibody (C-20) [unpublished] Sample 1


title: Mit1_2_WT

status: Public on Feb 12 2007

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

description: Schizosaccharomyces pombe cells,Mit1 ChIP(chromatin immunoprecipitation)-on-chip, wild type replicate 2

hyb_protocol: 500 ng of Cy3 labeled WCE DNA was mixed with 500 ng of Cy5 labeled ChIP DNA plus 50 ul Agilent 10X control targets and 250 ul of 2X Agilent Hybridization buffer

scan_protocol: Slides were scanned using Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software version 8.5

data_processing: Log ratios of ChIP over WCE were obtained by dividing normalized median Cy5 value over its corrresponding Cy3 value

organism: Schizosaccharomyces pombe

source_name: Schizosaccharomyces pombe whole cell extract (WCE) genomic DNA

label_protocol: WCE DNA after amplified by random priming PCR incorporating amino-allyl dUTP was covalently coupled with Cy3 mono NHS ester in 100 mM sodium bicarbonate for 1 hr at room temperature. Labeled DNA was recovered by Qiagen QIAquick PCR column

growth_protocol: Asynchronous growing fission yeast cells at 30 C and cross-linked with paraformadehyde at 18C for 30 minutes, followed by dimethyl adipimidate crosslinking at room temperature for 45 min.

extract_protocol: Chromatin was extracted from cross-linked cells following lysis with bead beater and sonication.  After reverse cross-linked and digested with Rnase A and proteinase K, DNA was recovered by phenol/chloroform extraction and ethanol precipitation

treatment_protocol: Schizosaccharomyces pombe cells crosslinked with paraformadehyde/dimethyl adipimidate

source_name: Schizosaccharomyces pombe chromatin immunoprecipitated DNA

label_protocol: ChIP DNA after amplified by random priming PCR incorporating amino-allyl dUTP was covalently coupled with Cy5 mono  NHS ester in 100 mM sodium bicarbonate for 1 hr at room temperature. Labeled DNA was recovered by Qiagen QIAquick PCR column

tag: Chromatin DNA isolated from paraformaldehyde cross-linked wild type Schizosaccharomyces pombe cells and enriched for Mit1-Myc chromatin with anti-Myc antibody.


title: STAT1 (Interferon-alpha) ChIP-ChIP from HeLaS3 applied to the NimbleGen ENCODE Array Sample 2 [unpublished]


title: Destruxin vs PBS #1

status: Public on Feb 10 2007

city: College Park

first: Subhamoy

last: Pal

address: 5126 Plant Sciences Building

department: Center for Biosystems Research

institute: University of Maryland

description: The experiment is meant to determine the effect of sublethal Destruxin A injection on Drosophila gene expression.

hyb_protocol: Detailed protocols can be downloaded from the GE/Amersham website (Amersham CyScribe First-Strand cDNA Labeling Kit)

scan_protocol: scan

data_processing: Spot intensities generated using TIGR Spotfinder, Data normalized using TIGR MIDAS-- Lowess and Standard deviation Normalization. Dividing IB by IA gives foldchange.

organism: Drosophila melanogaster

source_name: OR wt flies injected with PBS

label_protocol: Direct Labelling using Amersham Biosciences' Cyscribe First Strand Labelling Kit.

growth_protocol: Using standard protocol, larvae were kept in Fly vials with fly food consisting of mollasses, yeast, and agar.

extract_protocol: RNA was extracted from a pooled sample of 20 adult flies with STAT-60 Buffer, according to the manufacturer's protocols (Isotex Diagnostics).

treatment_protocol: Approximately 0.5 microliter of PBS or 86 micromolar solution of Destruxin suspended in PBS, was injected into the abdomen of the fly.  RNA was extracted 4 hours after injection.

tag: Wildtype adult Oregon R flies that are greater than 5 days old are used for this experiment.

source_name: OR wt flies injected with Destruxin


title: Destruxin vs PBS #3


title: Mit1_1_WT

description: Schizosaccharomyces pombe cells,Mit1 ChIP(chromatin immunoprecipitation)-on-chip, wild type replicate 1

tag: Chromatin DNA isolated from paraformaldehyde cross-linked wild type Schizosaccharomyces pombe cells


title: Clr3_2_WT

description: Schizosaccharomyces pombe cells,Clr3 ChIP(chromatin immunoprecipitation)-on-chip, wild type replicate 2

tag: Chromatin DNA isolated from paraformaldehyde cross-linked wild type Schizosaccharomyces pombe cells and enriched for Clr3-FLAG chromatin with anti-Myc antibody.


title: Clr2_2_WT

description: Schizosaccharomyces pombe cells,Clr2 ChIP(chromatin immunoprecipitation)-on-chip, wild type replicate 2

tag: Chromatin DNA isolated from paraformaldehyde cross-linked wild type Schizosaccharomyces pombe cells and enriched for V5-Clr2 chromatin with anti-Myc antibody.


title: Clr3_1_WT

description: Schizosaccharomyces pombe cells,Clr3 ChIP(chromatin immunoprecipitation)-on-chip, wild type replicate 1


title: Ccq1_1_WT

description: Schizosaccharomyces pombe cells, Ccq1 ChIP(chromatin immunoprecipitation)-on-chip, wild type replicate 1

tag: Chromatin DNA isolated from paraformaldehyde cross-linked wild type Schizosaccharomyces pombe cells and enriched for Ccq1-GFP chromatin with anti-Myc antibody.


title: Clr1_2_WT

description: Schizosaccharomyces pombe cells,Clr1 ChIP(chromatin immunoprecipitation)-on-chip, wild type replicate 2

tag: Chromatin DNA isolated from paraformaldehyde cross-linked wild type Schizosaccharomyces pombe cells and enriched for Clr1-Myc chromatin with anti-Myc antibody.


title: Clr2_1_WT

description: Schizosaccharomyces pombe cells,Clr2 ChIP(chromatin immunoprecipitation)-on-chip, wild type replicate 1


title: Ccq1_2_WT

description: Schizosaccharomyces pombe cells, Ccq1 ChIP(chromatin immunoprecipitation)-on-chip, wild type replicate 2


title: Destruxin vs PBS #2


title: A3-1 Aberration (1200kb)

type: mixed

first: Juan Lucas

last: Argueso

state: SP

address: 371 CARL Building, Box 3054

department: Molecular Genetics and Microbiology

institute: Duke University Medical Center

description: This array represents the hybridization of total genomic (Cy3) and DNA present in a specific region of a CHEF gel which was linearly amplified and labelled with Cy5.

hyb_protocol: DNA was hybridized according to Lemoine et al 2005, Cell 120:587.

scan_protocol: Arrays were scanned with a GenePix 4000B scanner. Red and Green PMT gain were manually adjusted to about equal brightness in each channel. Pixel size was 10um and 2 lines were averaged.

data_processing: The data in the VALUE column was obtained by analyzing the data deposited at the University of North Carolina Microarray database (genome.unc.edu). The data from repeated spots in the array were collapsed to a single value per spot and centered according to the median.  The VALUE corresponds to the Log2 RED/GREEN Normalized ratio based on the Median.

organism: Saccharomyces cerevisiae

source_name: Reference strain genomic DNA

label_protocol: DNA was labelled according to Lemoine et al 2005, Cell 120:587.

extract_protocol: DNA was prepared according to Lemoine et al 2005, Cell 120:587.

tag: Reference strain genomic DNA

molecule: other

source_name: A3 1200kb band DNA

extract_protocol: Agarose in CHEF gel slices was digested with beta-agarase I (New England Bioloabs) according to manufacturer recommendations. The DNA was then linearly amplified using the GenomiPhi DNA Amplification Kit (Amersham Biosciences) according to manufacturer recommendations. The DNA was then fragmented with a sonicator, concentrated with DNA Clean and Concentrator System (Zymo Research) and quantified in a spectrophotometer. Around 3ug of band-specific DNA were obtained using this protocol.

tag: DNA excised from CHEF gel.


title: JW13-2 Aberration (898kb)

source_name: JW13 898kb band DNA


title: A3-2 Aberration (599kb)

source_name: A3 599kb band DNA


title: A2 Aberrations (A2-3, 751kb; A2-4, 679kb; A2-5, 656kb)

source_name: A2 656, 679 and 701kb bands DNA


title: M1655 wild type at t10, rep2

city: Amherst

first: Jeffrey

middle: L

last: Blanchard

state: MA

address: 203 Morrill Science Center IVN

department: Biology

institute: University of Massachusetts Amherst

description: Gene expression data from growing Escherichia coli cells 10 minutes paraquat treatment

hyb_protocol: The cDNA samples were hybridized with Affymetrix GeneChip E. coli genome 2.0 Arrays according to Affymetrix guidelines

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000

data_processing: The data were analyzed using Robust Multi-Array average as implemented in Bioconductor

organism: Escherichia coli

source_name: Escherichia coli MG1655 10 minutes paraquat treatment

label_protocol: The total RNA from each sample was used as template to synthesize labeled cDNAs using Affymetrix GeneChip DNA Labeling Reagent Kits.

growth_protocol: Overnight cultures were inoculated 1:100 into 20ml of EZ Rich Defined Medium (Neidhardt et al., 1974) in 125 ml Erlenmeyer flasks and grown at 37oC and 250 rpm in a reciprocating water bath.

extract_protocol: Total RNA was isolated using Qiagen RNeasy Mini Kit and treated with DNase I

treatment_protocol: Paraquat was added to growing cultures at a final concentration of 250 ?M. Samples (1.4ml) were taken every 2 minutes following paraquat treatment for the length of the time course, and flash-frozen by immersion of the tubes in liquid nitrogen.  The cells were collected by centrifugation for 1 minute at 13,000 rpm,


title: M1655 wild type at t8, rep2

description: Gene expression data from growing Escherichia coli cells 8 minutes paraquat treatment

source_name: Escherichia coli MG1655 8 minutes paraquat treatment


title: Clr1_1_WT

description: Schizosaccharomyces pombe cells,Clr1 ChIP(chromatin immunoprecipitation)-on-chip, wild type replicate 1


title: Ini1 ChIP-ChIP from HeLaS3 Cells applied to the NimbleGen ENCODE Array Sample 1 [unpublished]

description: Red Channel: Ini1 ChIP DNA purified from HeLaS3 cells with polyclonal antibody; Green Channel: Normal rabbit IgG ChIP DNA purified from HeLaS3 cells.

tag: Polyclonal antibody

tag: Normal rabbit IgG


title: JW13-1 Aberration (1296kb)

source_name: JW13 1296kb band DNA


title: JW12-1 Aberration (645kb)

source_name: JW12 645kb band DNA


title: M1655 wild type at t4, rep2

description: Gene expression data from growing Escherichia coli cells 4 minutes paraquat treatment

source_name: Escherichia coli MG1655 4 minutes paraquat treatment


title: p65 ChIP-chip on TNF-alpha-stimulated HeLaS3 cells using polyclonal antibody (C-20) [unpublished] Sample 3

description: Rel A (p65) ChIP-chip in ENCODE region in TNF-alpha-stimulated HeLaS3 cells using anti-p65 (C-20) rabbit polyclonal antibody

source_name: p65 ChIP in TNF-alpha-stimulated HeLaS3 Cells

source_name: IgG control ChIP in TNF-alpha-stimulated HeLaS3 Cells


title: JW12-2 Aberration (460kb)

source_name: JW12 460kb band DNA


title: M1655 wild type at t2, rep2

description: Gene expression data from growing Escherichia coli cells 2 minutes paraquat treatment

source_name: Escherichia coli MG1655 2 minutes paraquat treatment


title: M1655 wild type at t0, rep2

description: Gene expression data from growing Escherichia coli cells before paraquat treatment

source_name: Escherichia coli MG1655 before paraquat treatment


title: M1655 wild type at t6, rep2

description: Gene expression data from growing Escherichia coli cells 6 minutes paraquat treatment

source_name: Escherichia coli MG1655 6 minutes paraquat treatment


title: M1655 wild type at t10, rep1

tag: Escherichia coli MG1655 10 minutes paraquat treatment


title: JW9-4 Aberration (378kb)

source_name: JW9 378kb band DNA


title: A2-2 Aberration (751kb)

source_name: Reference strain genomic DNA

source_name: A2 751kb band DNA


title: JW6-3 Aberration (210kb)

source_name: JW6 210kb band DNA


title: JW6-2 Aberration (459kb)

source_name: JW6 459kb band DNA


title: JW9-5 Aberration (297kb)

source_name: JW9 297kb band DNA


title: M1655 wild type at t8, rep1

tag: Escherichia coli MG1655 8 minutes paraquat treatment


title: JW9-2 and JW9-3 Aberrations (527kb)

source_name: JW9 527kb band DNA


title: JW5-1 Aberration (183kb)

source_name: JW5 183kb band DNA (circle stuck at loading well)


title: S. aureus PVL-positive strain (LUG881)_stationary phase_replicate3

description: stationary phase


title: JW6-1 Aberration (941kb)

source_name: JW6 941kb band DNA


title: M1655 wild type at t6, rep1

tag: Escherichia coli MG1655 6 minutes paraquat treatment


title: M1655 wild type at t4, rep1

tag: Escherichia coli MG1655 4 minutes paraquat treatment


title: JW5-2 Aberration (1432kb)

source_name: JW5 1432b band DNA


title: M1655 wild type at t2, rep1

tag: Escherichia coli MG1655 2 minutes paraquat treatment


title: M1655 with deletion in soxR at t10, rep1

source_name: Escherichia coli MG1655 with a precise deletion in soxR and 10 minutes paraquat treatment


title: M1655 wild type at t0, rep1

tag: Escherichia coli MG1655 before paraquat treatment


title: JW8-2 Aberration (471kb)

source_name: JW8 471kb band DNA


title: JW2-4 Aberration (486kb)

source_name: JW2 486kb band DNA


title: Control 3 band-array

description: This REFxREF array was used to provide a control for the CGH Miner analysis.


title: Control 2 band-array

growth_protocol: DNA was labelled according to Lemoine et al 2005, Cell 120:587.


title: Control 1 band-array


title: Control 4 band-array


title: M1655 with deletion in soxR at t0, rep1

source_name: Escherichia coli MG1655 with a precise deletion in soxR before paraquat treatment


title: M1655 with deletion in soxR at t4, rep1

source_name: Escherichia coli MG1655 with a precise deletion in soxR and 4 minutes paraquat treatment


title: M1655 with deletion in soxR at t2, rep1

source_name: Escherichia coli MG1655 with a precise deletion in soxR and 2 minutes paraquat treatment


title: JW1-2 Aberration (486kb)

source_name: JW1 486kb band DNA


title: M1655 with deletion in soxR at t6, rep1

source_name: Escherichia coli MG1655 with a precise deletion in soxR and 6 minutes paraquat treatment


title: M1655 with deletion in soxR at t8, rep1

source_name: Escherichia coli MG1655 with a precise deletion in soxR and 8 minutes paraquat treatment


title: JW2-2 Aberration (729kb)

source_name: Reference strain genomic DNA

source_name: JW2 729kb band DNA


title: JW2-3 Aberration (672kb)

source_name: JW2 672kb band DNA


title: 12 Hour Spleen Cell Envelope replicate 4

status: Public on Feb 09 2007

city: Guelph

first: Shayan

last: Sharif

state: Ontario

address: Ontario Veterinary College

department: Department of Pathobiology

institute: University of Guelph

description: Four replicates of cells from cecal tonsil or spleen mononuclear cells were stimulated with either DNA, Peptidoglycan, Cell Envelope or were left unstimulated for 3, 6, and 12 hours.

hyb_protocol: The labeled probes were hybridized to the microarrays for 16 hours at 65C

scan_protocol: Scanned on ScanArray Express instrument and analyzed with the ScanArray Express software,

data_processing: log (base 2) transform of the ratio of the medians

organism: Gallus gallus

source_name: Total RNA from Cell Envelope stimulated Spleencells labelled with Cy5

label_protocol: Samples were concentrated to approximately 5 ul with Microcon YM-30 filters (Millipore), labeled with the Cy5 monofunctional dye and the unincorporated dye was removed with the QIA-quick PCR Purification kit

extract_protocol: TriZol procedure

tag: Spleen mononuclear cells

tag: 12 Hour

tag: 10 ug Cell Envelope from Lactobacillus acidophilus

tag: Replicate 4

source_name: Total RNA from control unstimulated Spleen cells labelled with Cy3

label_protocol: Samples were concentrated to approximately 5 ul with Microcon YM-30 filters (Millipore), labeled with the Cy3 monofunctional dye and the unincorporated dye was removed with the QIA-quick PCR Purification kit

tag: unstimulated


title: 12 Hour Spleen Cell Envelope replicate 3

source_name: Total RNA from unstimulated control Spleen cells labelled with Cy5

tag: Unstimulated

tag: Replicate 3

source_name: Total RNA from Cell Envelope stimulated Spleen cells labelled with Cy3

tag: 10ug Cell Envelope from lactobacillus acidophilus


title: 6 Hour Spleen Cell Envelope replicate 4

source_name: Total RNA from Cell Envelope stimulated Spleen cells labelled with Cy5

tag: 6 Hour


title: 12 Hour Spleen Cell Envelope replicate 2

tag: 10 ug Cell Envelope from lactobacillus acidophilus

tag: Replicate 2

tag: control unstimulated


title: 3 Hour Spleen Cell Envelope replicate 3

tag: 3 Hour


title: 6 Hour Spleen Cell Envelope replicate 3


title: 12 Hour Spleen Peptidoglycan replicate 4

source_name: Total RNA from Peptidoglycan stimulated Spleen cells labelled with Cy5

tag: 10 ug Peptidoglycan from Lactobacillus acidophilus


title: 3 Hour Spleen Cell Envelope replicate 2


title: 3 Hour Spleen Cell Envelope replicate 1

tag: Replicate 1

source_name: Total RNA from Cell Envelope stimulated Spleen labelled with Cy3

tag: 10ug Cell Envelope from Lactobacillus acidophilus


title: 6 Hour Spleen Cell Envelope replicate 2


title: 6 Hour Spleen Cell Envelope replicate 1


title: JW2-1 Aberration (897kb)

tag: Reference strain genomic DNA

source_name: JW2 897kb band DNA

tag: DNA excised from CHEF gel.


title: 12 Hour Spleen Cell Envelope replicate 1

tag: Spleen mononuclear cells

tag: 12 Hour

source_name: Total RNA from Cell Envelope stimulated cecal Spleen labelled with Cy3


title: 12 Hour Spleen Peptidoglycan replicate 3

source_name: Total RNA from Peptidoglycan stimulated Spleen cells labelled with Cy3

tag: 10ug Peptidoglycan from lactobacillus acidophilus


title: 12 Hour Spleen Peptidoglycan replicate 1

tag: 10ug Peptidoglycan from Lactobacillus acidophilus


title: 12 Hour Spleen Peptidoglycan replicate 2

tag: 10 ug Peptidoglycan from lactobacillus acidophilus


title: 12 Hour Spleen DNA replicate 4

source_name: Total RNA from DNA stimulated Spleen cells labelled with Cy5

tag: 10 ug DNA from Lactobacillus acidophilus

tag: Replicate 4

tag: unstimulated


title: 12 Hour Spleen DNA replicate 2

tag: 10 ug DNA from lactobacillus acidophilus


title: 6 Hour Spleen Peptidoglycan replicate 4

tag: 6 Hour


title: 6 Hour Spleen Peptidoglycan replicate 1

tag: Unstimulated


title: 3 Hour Spleen Peptidoglycan replicate 4

tag: 3 Hour


title: 6 Hour Spleen Peptidoglycan replicate 2

tag: Replicate 2

tag: control unstimulated


title: 6 Hour Spleen Peptidoglycan replicate 3

tag: Replicate 3


title: 12 Hour Spleen DNA replicate 3

source_name: Total RNA from DNA stimulated Spleen cells labelled with Cy3

tag: 10ug DNA from lactobacillus acidophilus


title: 12 Hour Spleen DNA replicate 1

tag: Replicate 1

tag: 10ug DNA from Lactobacillus acidophilus


title: 3 Hour Spleen Cell Envelope replicate 4

tag: Spleen mononuclear cells

tag: 10 ug Cell Envelope from Lactobacillus acidophilus


title: 6 Hour Spleen DNA replicate 4


title: 3 Hour Spleen DNA replicate 4


title: 6 Hour Spleen DNA replicate 2

source_name: Total RNA from control unstimulated cecal tonsil cells labelled with Cy3

tag: Cecal Tonsil mononuclear cells


title: 3 Hour Spleen DNA replicate 3


title: 6 Hour Spleen DNA replicate 1


title: 3 Hour Spleen DNA replicate 1


title: 12 Hour Cecal Tonsil Cell Envelope replicate 4

source_name: Total RNA from Cell Envelope stimulated cecal tonsil cells labelled with Cy5

tag: 12 Hour


title: 3 Hour Spleen DNA replicate 2


title: 12 Hour Cecal Tonsil Cell Envelope replicate 3

source_name: Total RNA from unstimulated control cecal tonsil cells labelled with Cy5

source_name: Total RNA from Cell Envelope stimulated cecal tonsil cells labelled with Cy3

tag: 10ug Cell Envelope from lactobacillus acidophilus


title: 12 Hour Cecal Tonsil Cell Envelope replicate 2

tag: 10 ug Cell Envelope from lactobacillus acidophilus


title: 6 Hour Spleen DNA replicate 3


title: 3 Hour Spleen Peptidoglycan replicate 3

tag: 10ug Peptidoglycan from lactobacillus acidophilus


title: 3 Hour Spleen Peptidoglycan replicate 2

tag: 10 ug Peptidoglycan from lactobacillus acidophilus


title: 12 Hour Cecal Tonsil Cell Envelope replicate 1

tag: 10ug Cell Envelope from Lactobacillus acidophilus


title: 3 Hour Spleen Peptidoglycan replicate 1

tag: Unstimulated

tag: 10ug Peptidoglycan from Lactobacillus acidophilus


title: 6 Hour Cecal Tonsil Cell Envelope replicate 4

tag: 6 Hour

tag: Replicate 4

tag: unstimulated


title: JW5-3 Aberration (651kb)

source_name: Reference strain genomic DNA

tag: Reference strain genomic DNA

source_name: JW5 651kb band DNA

tag: DNA excised from CHEF gel.


title: 6 Hour Cecal Tonsil Cell Envelope replicate 3

tag: Replicate 3


title: 3 Hour Cecal Tonsil Cell Envelope replicate 4

tag: 3 Hour


title: 12 Hour Cecal Tonsil Peptidoglycan replicate 2

source_name: Total RNA from Peptidoglycan stimulated cecal tonsil cells labelled with Cy5

tag: Replicate 2

tag: control unstimulated


title: 12 Hour Cecal Tonsil Peptidoglycan replicate 3

tag: Cecal Tonsil mononuclear cells

tag: 12 Hour

source_name: Total RNA from Peptidoglycan stimulated cecal tonsil cells labelled with Cy3


title: 6 Hour Cecal Tonsil Cell Envelope replicate 1

tag: Replicate 1


title: 3 Hour Cecal Tonsil Cell Envelope replicate 2

tag: 10 ug Cell Envelope from lactobacillus acidophilus


title: 6 Hour Cecal Tonsil Peptidoglycan replicate 4

tag: 10 ug Peptidoglycan from Lactobacillus acidophilus


title: 12 Hour Cecal Tonsil Peptidoglycan replicate 4


title: 3 Hour Cecal Tonsil Cell Envelope replicate 1

tag: 10ug Cell Envelope from Lactobacillus acidophilus


title: 6 Hour Cecal Tonsil Peptidoglycan replicate 3

tag: Unstimulated

tag: 10ug Peptidoglycan from lactobacillus acidophilus


title: 6 Hour Cecal Tonsil Peptidoglycan replicate 2

tag: 6 Hour

tag: 10 ug Peptidoglycan from lactobacillus acidophilus


title: 3 Hour Cecal Tonsil Peptidoglycan replicate 4

tag: Replicate 4

tag: unstimulated


title: 6 Hour Cecal Tonsil Peptidoglycan replicate 1

tag: 10ug Peptidoglycan from Lactobacillus acidophilus


title: 3 Hour Cecal Tonsil Peptidoglycan replicate 3

tag: Replicate 3


title: 6 Hour Cecal Tonsil Cell Envelope replicate 2


title: 12 Hour Cecal Tonsil DNA replicate 3

source_name: Total RNA from DNA stimulated cecal tonsil cells labelled with Cy3

tag: 10ug DNA from lactobacillus acidophilus


title: 3 Hour Cecal Tonsil Cell Envelope replicate 3

tag: 3 Hour

tag: 10ug Cell Envelope from lactobacillus acidophilus


title: 3 Hour Cecal Tonsil Peptidoglycan replicate 2

tag: Cecal Tonsil mononuclear cells

tag: Replicate 2

tag: control unstimulated


title: 3 Hour Cecal Tonsil Peptidoglycan replicate 1

tag: Replicate 1


title: 12 Hour Cecal Tonsil Peptidoglycan replicate 1

tag: 12 Hour


title: 6 Hour Cecal Tonsil DNA replicate 4

source_name: Total RNA from DNA stimulated cecal tonsil cells labelled with Cy5

tag: 10 ug DNA from Lactobacillus acidophilus


title: 12 Hour Cecal Tonsil DNA replicate 2

tag: 10 ug DNA from lactobacillus acidophilus


title: 6 Hour Cecal Tonsil DNA replicate 3

tag: Unstimulated


title: 12 Hour Cecal Tonsil DNA replicate 1

tag: 10ug DNA from Lactobacillus acidophilus


title: 12 Hour Cecal Tonsil DNA replicate 4


title: 6 Hour Cecal Tonsil DNA replicate 2

tag: 6 Hour


title: 3 Hour Cecal Tonsil DNA replicate 1


title: 6 Hour Cecal Tonsil DNA replicate 1


title: 3 Hour Cecal Tonsil DNA replicate 3


title: 3 Hour Cecal Tonsil DNA replicate 4

tag: Replicate 4


title: 3 Hour Cecal Tonsil DNA replicate 2


title: S70, 48h, 2.5 uM Al, rep4

status: Public on Feb 08 2007

city: St Paul

first: Kathryn

last: VandenBosch

state: MN

address: Room 250 BioSci 6022 1445 Gortner Ave

department: Plant Biology

institute: University of Minnesota

description: Medicago truncatula 48 hours after Al treatment rep4

hyb_protocol: Microarrays for each time point were hybridized to cDNAs from both Al- treated and control roots, with cDNAs from the two different treatments labeled with Cy5 and Cy3 dyes. Each hybridization was repeated at least six times to account for technical variability, with triplicates of each dye combination to control for dye effects. A modified two-step hybridization reaction was performed as described in the 3DNA Array 900 Expression Array Detection Kit (Genisphere).

scan_protocol: Microarray slides were scanned using an GenePix4000B (Axon) two-laser scanner and image analysis was performed using GenePix 5.0 (Axon) software

data_processing: Background-subtracted mean intensities for both tissues were log2 transformed and normalized using lowess and ANOVA

organism: Medicago truncatula

source_name: Medicago truncatula 48 hours after control (-Al) treatment

label_protocol: 11 ug RNA from each of 3 biological replicates was pooled to make a total of 33 ug for cDNA synthesis with a RT Primer for labeling with either Cy3 or Cy5 dye molecules using a 3DNA Array 900 Expression Array Detection Kit for cDNA Microarrays (Genisphere, Inc., Hatfield, PA). cDNA was synthesized following instructions from 3DNA Array 900 Expression Array Detection Kit Appendix A (Genisphere Inc.).

growth_protocol: Medicago truncatula seeds from each line were germinated as previously described (Penmetsa and Cook, 2000). Seedlings with radicles of about 1 cm in length were sown through the mesh bottoms of polypropylene cups. The cups were placed in precut holes of a plastic insert placed over a plastic tub that held 7.3 L of aerated nutrient solution. The nutrient solution contained: 1.2 mM KNO3, 0.8 mM Ca(NO3)2, 0.1 mM NH4H2PO4, 0.2 mM MgSO4, 10 uM FeNaEDTA, 50 uM KCl, 12.5 uM H3BO3, 1 uM MnSO4, 1 uM ZnSO4, 0.5 uM CuSO4, 0.1 uM Na2MoO4, and 0.1 uM NiCl2 (Pence et al., 2000). The pH of the nutrient solution was adjusted to 4.5 using 1 N HCl. Seedlings were grown for 72 h in a growth chamber (light/dark, 14/10 h) under a light intensity of 440 µmol photons m-2 s-1. Al treatment was initiated after 72 h by replacing the control growth solution with an identical solution that contained either 0 uM (control) or 2.5 uM Al added as AlK(SO4)3. The control and treatment solutions were adjusted to pH 4.5. Root tips (approximately 0.5 cm in length) from control and 2.5 uM Al treated seedlings were harvested at 12 and 48 h after Al treatment immediately frozen in liquid nitrogen.

extract_protocol: Root tip samples from 3 independent experimental replicates were collected for the experiment. RNA from frozen root tip samples was isolated using the RNeasy Plant Mini Kit (Qiagen, Valencia, CA) following the manufacturer's instructions.

tag: Medicago truncatula; lines - S70; tissue-root tips; age - 4 days; treatment - 48 hours after control (-Al) treatment

source_name: Medicago truncatula 48 hours after 2.5 uM Al treatment

tag: Medicago truncatula; lines - S70; tissue-root tips; age - 4 days; treatment - 48 hours after Al treatment


title: T32, 48h, 2.5 uM Al, rep4

description: Medicago truncatula (T32) 48 hours after Al treatment rep4

source_name: Medicago truncatula (T32) 48 hours after control (-Al) treatment

growth_protocol: Medicago truncatula seeds from each line were germinated as previously described (Penmetsa and Cook, 2000). Seedlings with radicles of about 1 cm in length were sown through the mesh bottoms of polypropylene cups. The cups were placed in precut holes of a plastic insert placed over a plastic tub that held 7.3 L of aerated nutrient solution. The nutrient solution contained: 1.2 mM KNO3, 0.8 mM Ca(NO3)2, 0.1 mM NH4H2PO4, 0.2 mM MgSO4, 10 uM FeNaEDTA, 50 uM KCl, 12.5 uM H3BO3, 1 uM MnSO4, 1 uM ZnSO4, 0.5 uM CuSO4, 0.1 uM Na2MoO4, and 0.1 uM NiCl2 (Pence et al., 2000). The pH of the nutrient solution was adjusted to 4.5 using 1 N HCl. Seedlings were grown for 72 h in a growth chamber (light/dark, 14/10 h) under a light intensity of 440 umol photons m-2 s-1. Al treatment was initiated after 72 h by replacing the control growth solution with an identical solution that contained either 0 uM (control) or 2.5 uM Al added as AlK(SO4)3. The control and treatment solutions were adjusted to pH 4.5.  Root tips (approximately 0.5 cm in length) from control and 2.5 uM Al treated seedlings were harvested at 12 and 48 h after Al treatment immediately frozen in liquid nitrogen.

tag: Medicago truncatula; lines - T32; tissue-root tips; age - 4 days; treatment -  48 hours after control (-Al) treatment

source_name: Medicago truncatula (T32) 48 hours after 2.5 uM Al treatment

tag: Medicago truncatula; lines - T32; tissue-root tips; age - 4 days; treatment -  48 hours after Al treatment


title: S70, 48h, 2.5 uM Al, rep1

description: Medicago truncatula 48 hours after Al treatment rep1


title: T32, 48h, 2.5 uM Al, rep5

description: Medicago truncatula (T32) 48 hours after Al treatment rep5


title: S70, 12h, 2.5 uM Al, rep4

description: Medicago truncatula (S70) 12 hours after Al treatment rep4

source_name: Medicago truncatula (S70) 12 hours after control (-Al) treatment

tag: Medicago truncatula; lines - S70; tissue-root tips; age - 4 days; treatment -  12 hours after control (-Al) treatment

source_name: Medicago truncatula (S70) 12 hours after 2.5 uM Al treatment

tag: Medicago truncatula; lines - S70; tissue-root tips; age - 4 days; treatment -  12 hours after Al treatment


title: S70, 48h, 2.5 uM Al, rep6

description: Medicago truncatula 48 hours after Al treatment rep6


title: S70, 12h, 2.5 uM Al, rep5

description: Medicago truncatula (S70) 12 hours after Al treatment rep5


title: T32, 48h, 2.5 uM Al, rep6

description: Medicago truncatula (T32) 48 hours after Al treatment rep6


title: T32, 12h, 2.5 uM Al, rep6

description: Medicago truncatula (T32) 12 hours after Al treatment rep6

source_name: Medicago truncatula (T32) 12 hours after control (-Al) treatment

tag: Medicago truncatula; lines - T32; tissue-root tips; age - 4 days; treatment -  12 hours after control (-Al) treatment

source_name: Medicago truncatula (T32) 12 hours after 2.5 uM Al treatment

tag: Medicago truncatula; lines - T32; tissue-root tips; age - 4 days; treatment -  12 hours after Al treatment


title: T32, 48h, 2.5 uM Al, rep3

description: Medicago truncatula (T32) 48 hours after Al treatment rep3


title: T32, 12h, 2.5 uM Al, rep3

description: Medicago truncatula (T32) 12 hours after Al treatment rep3