title: S. Typhimurium relAspoT LB high salt low oxygen rep 2

description: Intensity ratios of RNA (channel 1) divided by DNA (channel 2) signals minus respective background signals. Total array is 16 blocks arranged in 4X4 configuration.

label_protocol: Labelling protocol at http://www.ifr.ac.uk/safety/Microarrays/protocols.html

growth_protocol: S. Typhimurium SL1344 deleted for relAspoT genes and grown to OD600 = 0.348 in Lennox Broth containing 0.3M NaCl in low-oxygen conditions.

extract_protocol: Total RNA isolation protocol at http://www.ifr.ac.uk/safety/Microarrays/protocols.html

treatment_protocol: RNA labelled during reverse transcription into cDNA with Cy5-dCTP according to protocol at http://www.ifr.ac.uk/safety/Microarrays/protocols.html

tag: RNA labelled with Cy5-dCTP and laser scanned at 635nm with background subtracted from feature signal

growth_protocol: S. Typhimurium grown to stationary phase

treatment_protocol: Genomic DNA labelled with Cy3-dCTP according to protocol at http://www.ifr.ac.uk/safety/Microarrays/protocols.html

tag: Genomic DNA labelled with Cy3-dCTP and laser scanned at 532nm with background subtracted from feature signal


title: S. Typhimurium relAspoT LB high salt low oxygen rep 1

status: Public on May 30 2006

type: mixed

city: Norwich

first: Arthur

last: Thompson

state: Norfolk

address: Colney Lane

department: Food Safety Science

country: United Kingdom

institute: Institute of Food Research

hyb_protocol: Slides blocked with DCE according to protocol at PMID 11266573. For hybridisation and washing protocols see http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

scan_protocol: Axon GenePix4000A, 10nm resolution scan & see http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

data_processing: Data centring was performed by bringing the median ratio (Cy5/Cy3) for each of the 16 blocks to one using the following equation: (Ti) = (Cy5i/Cy3i) - c, where T is the centred ratio, i is the gene index, Cy5 and Cy3 are the red and green intensities and c is the 50th percentile of all Cy5/Cy3 ratios. Flagged features are omitted from the data centring process.

molecule: total RNA

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: F635 Median-B635

molecule: genomic DNA

source_name: F532 Median-B532

label_protocol: Channel Label Protocol: Labelling protocol at http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

extract_protocol: Genomic DNA isolated using the Qiagen 'Genomic DNA' Kit (Cat. No.: 19060 for the buffer kit; 10243 for the columns)


title: S. Typhimurium relAspoT LB low oxygen rep 2

description: Intensity ratios of RNA (channel 1) divided by DNA (channel 2) signals minus respective local background signals. Total array is 16 blocks arranged in 4X4 configuration

label_protocol: Labelling protocol at http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

growth_protocol: S. Typhimurium SL1344 relAspoT mutant grown to OD600 = 0.328 in Lennox Broth in low-oxygen conditions

extract_protocol: Total RNA isolation protocol at http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

treatment_protocol: RNA labelled during reverse transcription into cDNA with Cy5-dCTP according to protocol at http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

tag: RNA labelled with Cy5-dCTP and laser scanned at 635nm with local background subtracted from feature signal

growth_protocol: S. Typhimurium SL1344 grown to stationary phase

treatment_protocol: Genomic DNA labelled with Cy3-dCTP according to protocol at http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

tag: Genomic DNA labelled with Cy3-dCTP and laser scanned at 532nm with local background subtracted from feature signal


title: S. Typhimurium relAspoT LB low oxygen rep 3


title: S. Typhimurium wild-type aerated LB high salt rep 1

growth_protocol: S. Typhimurium SL1344 wild-type grown to OD600 = 1.412 in aerated Lennox Broth containing 0.3M NaCl


title: ESC Nanog_shRNAi d5 post transduction MOE430A

status: Public on May 31 2006

type: RNA

city: Princeton

first: Ihor

last: Lemischka

state: NJ

address: Washington Rd

country: USA

institute: Princeton University

description: Gene expression data from ES cells transduced with Nanog shRNAi d5 post transduction.

hyb_protocol: 15 micrograms of biotin-labeled cRNA was fragmented for 35min. at 94C in fragmentation buffer (Affymetrix; Santa Clara, CA), and hybridized to Affymetrix MOE 430 A and B oligonucleotide microarrays.

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.

label: biotin

organism: Mus musculus

source_name: ES cells (CCE cell line) d5 post Nanog_shRNAi transduction.

label_protocol: Biotinylated cRNA probes were synthesized using the BioArray High-Yield Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY).

growth_protocol: Cells were maintained in the presence of LIF 1000 unit/ml.

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

treatment_protocol: 48 hours after transduction cells were re-plated at the density 0.3x10^6 cells per 10 cm dish. Simultaneously, GFP+ cells were FACS purified and used as day 0 time point. Re-plated cells were maintained in the presence of LIF. GFP+ cells from each culture were FACS purified every day for 7 consecutive days to obtain 8 day time course (d0-d7).

tag: Mouse embrionic stem cells

tag: Gender

value: male

tag: Strain


title: S. Typhimurium wild-type aerated LB high salt rep 3


title: S. Typhimurium relAspoT LB low oxygen rep 4


title: S. Typhimurium relAspoT LB low oxygen rep 1


title: S. Typhimurium wild-type LB low oxygen rep 4

growth_protocol: S. Typhimurium SL133 wild-type grown to OD600 = 0.353 in Lennox Broth in low-oxygen conditions


title: S. Typhimurium wild-type LB low oxygen rep 1


title: S. Typhimurium wild-type LB low oxygen rep 3


title: S. Typhimurium wild-type LB low oxygen rep 2


title: ESC Tbx3_shRNAi d4 post transduction MOE430A

description: Gene expression data from ES cells transduced with Tbx3 shRNAi d4 post transduction.

source_name: ES cells (CCE cell line) d4 post Tbx3_shRNAi transduction.


title: S. Typhimurium relAspoT LB aerated rep 1

growth_protocol: S. Typhimurium SL133 relAspoT deletion mutant grown to OD600 = 1.294 in aerated Lennox Broth


title: S. Typhimurium wild-type aerated LB high salt rep 4


title: NAB3 wild type control 37C

city: Baltimore

first: Jeff

middle: L

last: Corden

state: MD

address: 725 N. Wolfe St.

department: Molecular Biology and Genetics

institute: Johns Hopkins School of Medicine

description: yeast (nab3-11) total RNA from a 2 hour temperature shift at 25C. (the permissive temperature)

hyb_protocol: Hybridization protocol: 16hrs at 45 C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual, 2004.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual, 2004.

data_processing: Image analysis using GCOS 1.1.1, using MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 150.

organism: Saccharomyces cerevisiae

source_name: yeast 37C 2 hours

label_protocol: One round amplification protocol for total RNA following Affymetrix’ specifications using T7 promoter oligo dT primer for cDNA synthesis, and ENZO IVT kit (www.affymetrix.com, GeneChip Expression Analysis, Technical Manual, 2003).

growth_protocol:
YPD
temperature shift to 37C for 2 hours

extract_protocol:
Hot Acid Phenol
RNeasy clean up kit

treatment_protocol: temperature shift to 37C for 2 hours

tag: strain

value: 1415 wildtype

tag: media

value: YPD

tag: temp


title: S. Typhimurium relAspoT LB aerated rep 4


title: NAB3 WT strain 25C

source_name: yeast 25C 2 hours

growth_protocol: YPD

treatment_protocol: temperature shift to 25C for 2 hours


title: Small bowel_Adhesion_14Day_rep2

status: Public on May 24 2006

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

description: Preparation of cDNA probes: Total RNA of the livers was extracted using Trizol (GIBCO-BRL; Gaithersburg, MD). The mRNA was purified from total RNA using an mRNA Isolation Kit (Qiagen, Germany), following the manufacturers’ protocol, and five micrograms of mRNAs were used for preparation of the cDNA probe. The labeling reactions were performed during reverse transcription in the presence of 6 mM random primers; 0.5 mM each dATP, dCTP, and dGTP; 40 mM dTTP; 40 mM biotin-16-dUTP (Roche Molecular Biochemicals; Mannheim, Germany); 1X reaction buffer; 10 mM DTT; 0.5 unit/ml Ribonuclease inhibitor (GIBCO-BRL; Gaithersburg, MD); and 200 units of MMLV reverse transcriptase (GIBCO-BRL; Gaithersburg, MD) in a 50-ml solution. The reaction mixture was incubated at room temperature for 10 minutes, then transferred to 42 °C for 90 minutes, and was stopped by heating the reaction mixture to 99 °C for 5 minutes.  The RNA was degraded by adding of 5.5 ml of 3 M NaOH followed by a 30-min incubation at 50 °C.  The labeled samples were neutralized by the addition of 5.5 ml of 3 M acetic acid, and then precipitated by adding 50 ml of 7.5 M ammonium acetate, 20 mg of linear polyacrylamide as a carrier, 375 ml of absolute alcohol, and water, to make a total of 525 ml. The solution was mixed evenly and stood at –80 °C for 30 min, then was centrifuged at 14,000 rpm for 20 min to precipitate a single stranded DNA probe. The pellet was washed with 1 ml of 70% of ethanol and dried by speed vacuum, then dissolved in 5 ml of de-ionized water. Microarray hybridization and Colorimetric detection: The membrane carrying the double-stranded cDNA targets was pre-hybridized in 3 ml of hybridization buffer (5× SSC, 0.1% N-lauroylsarcosine, 0.1% SDS, 1% blocking reagent made by Roche Molecular Biochemicals, and 50 mg/ml salmon sperm DNA) at 68°C for 1 hour before hybridization was carried out. cDNA probes were resuspended in 100 ml hybridization buffer containing 200 mg/ml d(A)10 and  400 mg/ml human COT-1 DNA (GIBCO-BRL; Gaithersburg, MD) to prevent non-specific binding, and were hybridized to the cDNA fragments on the membrane by a Southern hybridization procedure. The 100 ml reaction mixture was sealed with the microarray membrane in a hybridization assembly (SureSeal, Hybaid, Middlesex, UK) at 68°C for 12 hours. The membrane was then washed with 2× SSC containing 0.1% SDS for 5 min at room temperature followed by three washes with 0.1× SSC containing 0.1% SDS at 65 °C for 15 min each. After hybridization, the membrane was blocked by 1 ml of 1% blocking reagent (Roche Molecular Biochemicals; Mannheim, Germany) containing 2% dextran sulphate at room temperature for 1 hour, and then was rinsed with 1 X TBS buffer solution (10 mM Tris-HCl, pH 7.4, 150 mM NaCl, 0.3% BSA). To detect the spots on the membrane in a single-color mode, b-galactosidase-conjugated streptavidin (GIBCO-BRL; Gaithersburg, MD) was employed. The membrane was incubated with a 3-ml mixture containing 700 X diluted Strep-Gal (1.38 units/ml, enzyme activity), 4% polyethylene glycol 8000 (Sigma, St. Louis, MO), and 0.3% BSA in 1 X TBS buffer for 2 hours. The membrane was then washed with 1 X TBS buffer three times, for 10 min each. The chromogen was generated by treating the membrane with X-gal substrate containing 1.2 mM X-gal, 1 mM MgCl2, 3 mM K3Fe(CN)6, and 3 mM K4Fe(CN)6 in 1 X TBS buffer for 1 hour at 37 °C for the beta-galactosidase reaction. The color development reactions were stopped by 1 X PBS containing 20 mM EDTA. After color development, the cDNA molecules labeled with biotin yield a blue chromogen. To measure the expression levels of the genes, the microarray was scanned using a flatbed scanner (PowerLook 3000, UMAX, Taipei, Taiwan). The images captured by a scanner were converted from true color to a gray scale, and digitized by analysis software GenePix 3.0 (Axon, Union City, CA).

data_processing: Only the signal values of spots above 3,000 were considered meaningful in the membrane format microarray system (i.e. the intensity of a spot less than 3,000 was hardly distinguished from the background, so an intensity value below 3,000 was given the value of 3,000). To reduce the variation arising between microarray experiments, the intensity value of spots from each microarray were normalized by a mean center to render the mean value equal to zero and the magnitude equal to one (sum of the squares of the values) using GeneSpring 7.3 (Silicon Genetics, Redwood City, CA). To focus on genes that were significantly regulated under studied conditions, those genes with greater than 1.5 fold change across all study-included time points were filtered and clustered into 9 groups by self organizing maps (SOMs). The resultant pattern featuring either an ascending or a descending trend, as a response to the progression of adhesion formation, was identified. The biological process annotation and pathway analysis of the selected genes were analyzed by GeneSpring 7.3 (Silicon Genetics, Redwood City, CA) and a web-based PANTHER classification system (http://www.pantherdb.org/). Some genes with multiple roles were included in more than one category.

molecule: polyA RNA

source_name: Small bowel, laparotomy with small bowel-scraping, 14 day after surgical intervention

extract_protocol: Total RNA of the small bowel was extracted using Trizol (GIBCO-BRL; Gaithersburg, MD). The mRNA was purified from total RNA using an mRNA Isolation Kit (Qiagen, Germany)

treatment_protocol: Subsequent to anesthesia and the mid-line laparotomy, the small bowel of BALB/c mouse was abraded at three sites (1 cm in length/per site) until a punctuate hemorrhage had arisen. Six scraped mice were sacrificed at day 3 after surgical intervention.

tag: Age

value: 56 days

tag: Tissue

value: small bowel

tag: Treatment


title: S. Typhimurium wild-type LB aerated rep 3

growth_protocol: S. Typhimurium SL133 wild-type grown to OD600 = 1.359 in aerated Lennox Broth


title: S. Typhimurium wild-type LB aerated rep 4


title: S. Typhimurium relAspoT LB aerated rep 3


title: S. Typhimurium wild-type LB aerated rep 2


title: Small bowel_Adhesion_14Day_rep1


title: nab3 ts mutant at 37C

description: yeast (nab3-11) total RNA from a 2 hour temperature shift at 37C.


title: S. Typhimurium wild-type LB aerated rep 1


title: nab3 ts mutant at 25C

growth_protocol:
YPD
temperature shift to 25C for 2 hours


title: S. Typhimurium relAspoT LB aerated rep 2


title: Small bowel_Adhesion_3Day_rep1

source_name: Small bowel, laparotomy with small bowel-scraping, 3 day after surgical intervention


title: Small bowel_Adhesion_1Day_rep2

source_name: Small bowel, laparotomy with small bowel-scraping, 1 day after surgical intervention

treatment_protocol: Subsequent to anesthesia and the mid-line laparotomy, the small bowel of BALB/c mouse was abraded at three sites (1 cm in length/per site) until a punctuate hemorrhage had arisen. Six scraped mice were sacrificed at day 1 after surgical intervention.


title: Small bowel_Adhesion_3Day_rep2


title: Small bowel_Adhesion_7Day_rep2

source_name: Small bowel, laparotomy with small bowel-scraping, 7 day after surgical intervention


title: Small bowel_Adhesion_1Day_rep1


title: Small bowel_Sham_rep2

source_name: Small bowel, laparotomy only without small bowel-scraping

treatment_protocol: Subsequent to anesthesia and the mid-line laparotomy, six mice were sacrificed at day 1, 3, 7 and 14 after surgical intervention. The small bowel of four groups was pooled to serve as sham control.


title: Small bowel_Adhesion_7Day_rep1


title: xcaf21(1)

status: Public on May 17 2006

city: Austin

first: Matthew

middle: Wayne

last: Vaughn

state: TX

address: 10100 Burnet Rd

department: Texas Advanced Computing Center

institute: University of Texas at Austin

organism: Arabidopsis thaliana

source_name: seedling

label_protocol: biotin cRNA

tag: Background

tag: Time (days)


title: xcaf21(4)


title: xWT21(3)

value: Ler (2)


title: xWT21(2)


title: xcaf21(2)


title: xWT21(1)


title: Small bowel_Sham_rep1

description:
Preparation of cDNA probes:
Total RNA of the livers was extracted using Trizol (GIBCO-BRL; Gaithersburg, MD). The mRNA was purified from total RNA using an mRNA Isolation Kit (Qiagen, Germany), following the manufacturers’ protocol, and five micrograms of mRNAs were used for preparation of the cDNA probe. The labeling reactions were performed during reverse transcription in the presence of 6 mM random primers; 0.5 mM each dATP, dCTP, and dGTP; 40 mM dTTP; 40 mM biotin-16-dUTP (Roche Molecular Biochemicals; Mannheim, Germany); 1X reaction buffer; 10 mM DTT; 0.5 unit/ml Ribonuclease inhibitor (GIBCO-BRL; Gaithersburg, MD); and 200 units of MMLV reverse transcriptase (GIBCO-BRL; Gaithersburg, MD) in a 50-ml solution. The reaction mixture was incubated at room temperature for 10 minutes, then transferred to 42 °C for 90 minutes, and was stopped by heating the reaction mixture to 99 °C for 5 minutes.  The RNA was degraded by adding of 5.5 ml of 3 M NaOH followed by a 30-min incubation at 50 °C.  The labeled samples were neutralized by the addition of 5.5 ml of 3 M acetic acid, and then precipitated by adding 50 ml of 7.5 M ammonium acetate, 20 mg of linear polyacrylamide as a carrier, 375 ml of absolute alcohol, and water, to make a total of 525 ml. The solution was mixed evenly and stood at –80 °C for 30 min, then was centrifuged at 14,000 rpm for 20 min to precipitate a single stranded DNA probe. The pellet was washed with 1 ml of 70% of ethanol and dried by speed vacuum, then dissolved in 5 ml of de-ionized water.
Microarray hybridization and Colorimetric detection:
 The membrane carrying the double-stranded cDNA targets was pre-hybridized in 3 ml of hybridization buffer (5× SSC, 0.1% N-lauroylsarcosine, 0.1% SDS, 1% blocking reagent made by Roche Molecular Biochemicals, and 50 mg/ml salmon sperm DNA) at 68°C for 1 hour before hybridization was carried out. cDNA probes were resuspended in 100 ml hybridization buffer containing 200 mg/ml d(A)10 and  400 mg/ml human COT-1 DNA (GIBCO-BRL; Gaithersburg, MD) to prevent non-specific binding, and were hybridized to the cDNA fragments on the membrane by a Southern hybridization procedure. The 100 ml reaction mixture was sealed with the microarray membrane in a hybridization assembly (SureSeal, Hybaid, Middlesex, UK) at 68°C for 12 hours. The membrane was then washed with 2× SSC containing 0.1% SDS for 5 min at room temperature followed by three washes with 0.1× SSC containing 0.1% SDS at 65 °C for 15 min each.
After hybridization, the membrane was blocked by 1 ml of 1% blocking reagent (Roche Molecular Biochemicals; Mannheim, Germany) containing 2% dextran sulphate at room temperature for 1 hour, and then was rinsed with 1 X TBS buffer solution (10 mM Tris-HCl, pH 7.4, 150 mM NaCl, 0.3% BSA). To detect the spots on the membrane in a single-color mode, b-galactosidase-conjugated streptavidin (GIBCO-BRL; Gaithersburg, MD) was employed. The membrane was incubated with a 3-ml mixture containing 700 X diluted Strep-Gal (1.38 units/ml, enzyme activity), 4% polyethylene glycol 8000 (Sigma, St. Louis, MO), and 0.3% BSA in 1 X TBS buffer for 2 hours. The membrane was then washed with 1 X TBS buffer three times, for 10 min each. The chromogen was generated by treating the membrane with X-gal substrate containing 1.2 mM X-gal, 1 mM MgCl2, 3 mM K3Fe(CN)6, and 3 mM K4Fe(CN)6 in 1 X TBS buffer for 1 hour at 37 °C for the beta-galactosidase reaction. The color development reactions were stopped by 1 X PBS containing 20 mM EDTA. After color development, the cDNA molecules labeled with biotin yield a blue chromogen. To measure the expression levels of the genes, the microarray was scanned using a flatbed scanner (PowerLook 3000, UMAX, Taipei, Taiwan). The images captured by a scanner were converted from true color to a gray scale, and digitized by analysis software GenePix 3.0 (Axon, Union City, CA).


title: xLer21(1)


title: xcaf21(3)


title: x49-3A


title: x51-1A


title: x57-2B


title: x53-1A


title: x57-1A


title: x49-3B


title: x54-1A2


title: x57-2C


title: x49-1A


title: x44-3B


title: x49-2A


title: x57-2A


title: x44-2A


title: x44-2C


title: x44-1C


title: x38-2A

value: Col


title: x38-2C


title: x44-1A2


title: x44-1B


title: x37-2C

value: Ler (1)


title: x38-1A


title: x38-1C


title: x38-1B2


title: x37-2D


title: x37-2E


title: x37-1C

value: Ler


title: x37-1D


status: Public on May 15 2006

city: Philadelphia

first: Norman

middle: B

last: Hecht

state: PA

address: 421 Curie Blvd

institute: University of Pennsylvania

description: RNP fraction from adult mouse testes, biological rep3

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip MOE 430A Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GCS3000 scanner.

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 100.

source_name: adult mouse, strain CD1

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

treatment_protocol: cytoplasmic extract of mouse testes were subjected to 10-30% sucrose gradient centrifugation.Total RNAs were extracted from fractions 2-8 from total 17 as RNP-associated fraction by Trizol.

tag: RNP fraction fromadult mouse testes, biological rep3,  adult mouse, strain CD1	!Sample_characteristics_ch1=,


title: x37-1A


treatment_protocol: cytoplasmic extract of mouse testes were subjected to 10-30% sucrose gradient centrifugation.Total RNAs were extracted from fractions 11-17 from total 17 as polysome-associated fraction by Trizol.

tag: Polysome fraction from adult mouse testes, biological rep1,  adult mouse, strain CD1	!Sample_characteristics_ch1=,


description: RNP fraction from adult mouse testes, biological rep1

tag: RNP fraction fromadult mouse testes, biological rep1,  adult mouse, strain CD1	!Sample_characteristics_ch1=,


description: Polysome fraction from 22day-old mouse testes, biological rep3

source_name: 22d mouse, strain CD1

tag: Polysome fraction from 22 day-old mouse testes, biological rep3,  22d mouse, strain CD1


tag: Polysome fraction from adult mouse testes, biological rep2,  adult mouse, strain CD1	!Sample_characteristics_ch1=,


tag: RNP fraction from 22day-old mouse testes, biological rep3,  22d mouse, strain CD1


description: RNP fraction from adult mouse testes, biological rep2

tag: RNP fraction fromadult mouse testes, biological rep2,  adult mouse, strain CD1	!Sample_characteristics_ch1=,


title: x38-2B


description: Polysome fraction from 22day-old mouse testes, biological rep1

tag: Polysome fraction from 22 day-old mouse testes, biological rep1,  22d mouse, strain CD1


description: Polysome fraction from 22day-old mouse testes, biological rep2

tag: Polysome fraction from 22 day-old mouse testes, biological rep2,  22d mouse, strain CD1


tag: RNP fraction from 22day-old mouse testes, biological rep1,  22d mouse, strain CD1


tag: RNP fraction from 22day-old mouse testes, biological rep2,  22d mouse, strain CD1


source_name: 17d mouse, strain CD1

tag: RNP fraction from 17day-old mouse testes, biological rep3,  17d mouse, strain CD1


tag: RNP fraction from 17day-old mouse testes, biological rep2,  17d mouse, strain CD1


tag: Polysome fraction from adult mouse testes, biological rep3,  adult mouse, strain CD1	!Sample_characteristics_ch1=,


tag: RNP fraction from 17day-old mouse testes, biological rep1,  17d mouse, strain CD1


title: ESC Mm343880_shRNAi d2 post transduction MOE430A

description: Gene expression data from ES cells transduced with Mm343880 shRNAi d2 post transduction.

source_name: ES cells (CCE cell line) d2 post Mm343880_shRNAi transduction.

tag: Mouse embrionic stem cells

tag: Gender

tag: Strain


tag: Polysome fraction from 17day-old mouse testes, biological rep1,  17d mouse, strain CD1


tag: Polysome fraction from 17day-old mouse testes, biological rep3,  17d mouse, strain CD1


title: ESC Nanog_shRNAi d1 post transduction MOE430A

description: Gene expression data from ES cells transduced with Nanog shRNAi d1 post transduction.

source_name: ES cells (CCE cell line) d1 post Nanog_shRNAi transduction.


tag: Polysome fraction from 17day-old mouse testes, biological rep2,  17d mouse, strain CD1


title: Semeralul_PFC_Development_Week10_Batch1_Animal_6

city: Toronto

first: Paul

middle: C

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description: Prefrontal Cortex

data_processing: GCRMA Normalization

label: Affymetrix

source_name: Prefrontal Cortex, Week 10 Postnatal

growth_protocol: Adult, wild-type C57BL/6 breeder mice were purchased at five weeks of age from Charles River Laboratories (Wilmington, MA). After seven days of acclimatization, timed matings were set up to generate offspring within our colony. Four to six male C57BL/6 mice were sacrificed on weeks 1-10, inclusive. Mice were killed by cervical dislocation, decapitated and the whole brain was removed from the skull. The PFC was dissected with a coronal cut approximately 3 mm caudal of the frontal pole (Franklin and Paxinos, 1997), and snap-frozen on dry ice, labeled and stored at -80oC.

extract_protocol: RNA was prepared using a combination of two common protocols, with slight modifications. TRIZOL Reagent was used for isolation of RNA (Invitrogen Life Technologies Corp., Carlsbad, CA) (Chomczynski, 1993) followed by purification using the Absolutely RNeasy RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) (Dolter, 2000). Approximately, 20-35 mg of PFC tissue was homogenized and completely lysed in 600 uL Trizol, followed by centrifugation at 14,000 rpm for 10 minutes at 4oC. The pellet was discarded; 120 uL of chloroform was added to the supernatant, vigorously shaken, incubated for 2-3 minutes at 20 C and centrifuged at 14,000 rpm for 10 minutes at 4 C. The aqueous phase containing RNA was transferred to a fresh 1.5 mL microcentrifuge tube and washed with an equal volume of pre-chilled 70% ethanol. RNA was then purified using Stratagene’s Absolutely RNeasy RT-PCR Miniprep kit. After estimating the yield of total RNA, the solution was concentrated to 1.2 ug/uL RNA using Microcron YM-10 centrifugal filter devices (Millipore Corp., Bedford, MA). RNA integrity was verified by visualization of the 18S and 28S ribosomal RNA bands using the Agilent bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Extracts with evidence of RNA degradation - as indicated by smearing of 28S and 18S ribosomal RNA on agarose/formaldehyde gel electrophoresis - were discarded.

tag: 'Strain

value: C57BL/6', 'Gender:male', 'Age:10 weeks', 'Tissue:prefrontal cortex', 'Batch:1'


title: Semeralul_PFC_Development_Week5_Batch1_Animal_7

description: Prefrontal Cortex

source_name: Prefrontal Cortex, Week 5 Postnatal

value: C57BL/6', 'Gender:male', 'Age:5 weeks', 'Tissue:prefrontal cortex', 'Batch:1'


title: Semeralul_PFC_Development_Week5_Batch1_Animal_8

description: Prefrontal Cortex


title: Semeralul_PFC_Development_Week5_Batch2_Animal_4

description: Prefrontal Cortex

value: C57BL/6', 'Gender:male', 'Age:5 weeks', 'Tissue:prefrontal cortex', 'Batch:2'


title: Semeralul_PFC_Development_Week10_Batch1_Animal_8

description: Prefrontal Cortex


title: Semeralul_PFC_Development_Week10_Batch1_Animal_7

description: Prefrontal Cortex


title: Semeralul_PFC_Development_Week10_Batch1_Animal_1

description: Prefrontal Cortex


title: Semeralul_PFC_Development_Week5_Batch2_Animal_2

description: Prefrontal Cortex


title: Semeralul_PFC_Development_Week4_Batch1_Animal_6

description: Prefrontal Cortex

source_name: Prefrontal Cortex, Week 4 Postnatal

value: C57BL/6', 'Gender:male', 'Age:4 weeks', 'Tissue:prefrontal cortex', 'Batch:1'


title: Semeralul_PFC_Development_Week4_Batch1_Animal_3

description: Prefrontal Cortex


title: Semeralul_PFC_Development_Week5_Batch1_Animal_2

description: Prefrontal Cortex


title: Semeralul_PFC_Development_Week3_Batch1_Animal_6

description: Prefrontal Cortex

source_name: Prefrontal Cortex, Week 3 Postnatal

extract_protocol: RNA was prepared using a combination of two common protocols, with slight modifications. TRIZOL® Reagent was used for isolation of RNA (Invitrogen Life Technologies Corp., Carlsbad, CA) (Chomczynski, 1993) followed by purification using the Absolutely RNeasy RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) (Dolter, 2000). Approximately, 20-35 mg of PFC tissue was homogenized and completely lysed in 600 uL Trizol, followed by centrifugation at 14,000 rpm for 10 minutes at 4oC. The pellet was discarded; 120 uL of chloroform was added to the supernatant, vigorously shaken, incubated for 2-3 minutes at 20 C and centrifuged at 14,000 rpm for 10 minutes at 4 C. The aqueous phase containing RNA was transferred to a fresh 1.5 mL microcentrifuge tube and washed with an equal volume of pre-chilled 70% ethanol. RNA was then purified using Stratagene’s Absolutely RNeasy RT-PCR Miniprep kit. After estimating the yield of total RNA, the solution was concentrated to 1.2 ug/uL RNA using Microcron YM-10 centrifugal filter devices (Millipore Corp., Bedford, MA). RNA integrity was verified by visualization of the 18S and 28S ribosomal RNA bands using the Agilent bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Extracts with evidence of RNA degradation - as indicated by smearing of 28S and 18S ribosomal RNA on agarose/formaldehyde gel electrophoresis - were discarded.

value: C57BL/6', 'Gender:male', 'Age:3 weeks', 'Tissue:prefrontal cortex', 'Batch:1'


title: - Azithromycin Chip 1

status: Public on May 10 2006

city: Braunschweig

first: Yusuf

last: Nalca

state: Niedersachsen

address: Mascheroder Weg 1

department: ZIB

country: Germany

institute: GBF Braunschweig

description:
Samples used, extract preparation and labeling:

Bio-source properties:
Pseudomonas aeruginosa PAO1 (DSM 1707).

Biomaterial manipulations:
P. aeruginosa was grown in Brain-Heart-Infusion (BHI) medium at 37°C with shaking with or without the addition of 2 µg/ml AZM (Pfizer, Germany).

RNA extraction, cDNA synthesis and labeling:
Total RNA was extracted from 10 ml samples of eight 150-ml cultures (4 containing 2 µg/ml AZM and 4 without AZM). In brief, bacteria were lysed in the presence of 10 ml killing buffer (Tris/HCL, 5 mM MgCl2, 2 mM NaN3, pH 7.5) and centrifuged at 4°C for 10 min. The aqueous phase was mixed carefully with 125 µl Saccharose/Na-Acetate (300 mM Saccharose, 10 mM NaAc, pH 4.5) and 125 µl SDS/ Na-Acetate (83 mM SDS, 10 mM NaAc, pH 4.5) was added. The suspension was heated to 65°C and 400 µl hot phenol was added. After 3 min of incubation at 65°C, the suspension was quickly cooled in liquid nitrogen and centrifuged for 10 min. The phenol extraction was repeated twice before the nucleic acids were pelleted with 40 µl 3M NaAc (pH 5.2) and 1 ml 90% ethanol at -20°C overnight, washed with 70% ethanol and treated with 40 U of DNaseI (Roche) in DNaseI buffer (20 mM NaAc, 10 mM MgCl2, 10 mM NaCl, pH 4.5) for 30 min at 37°C. After purification with RNeasy columns (Qiagen) the yield of total cellular RNA was determined by UV absorption.
cDNA was synthesized from RNA pooled from two independent cultures and subsequently two GeneChips were hybridized for each culture condition (4 independent GeneChips in total).
cDNA synthesis and biotin-ddUTP terminal labeling were performed in compliance with the manufacturer’s instructions for the P. aeruginosa GeneChip:
Ten micrograms of total RNA were mixed with random primers (Invitrogen) and incubated for 10 min at 70°C. Then a cDNA reaction mix was added, containing 10 µl of 5 x first strand buffer, 0,1 µmol dithiothreitol, deoxynucleotide triphosphate (3 µl of a dNTP-mix, 10 mM each) and 50 U of SuperScript II (Reverse Transcriptase). This was followed by an incubation step for 10 min at 25°C, 60 min at 37°C, 60 min at 42°C, and 15 min at 72°C. RNA was degradated by the addition of 1 N NaOH (20 µl) and an incubation for 30 min at 65°C. Subsequently the reaction mix was neutralized by addition of 1 N HCl (20 µl).
The cDNA was purified with QIAquick columns (Amersham Biosciences), quantified by UV absorption, fragmentized in one-for-all buffer with 0.5 U of DNase I (Amersham Pharmacia Biotech) per µg of cDNA for 10 min at 37°C and subsequently inactivated for 10 min at 98°C. The fragmentation of the cDNA (50-200-bp range) was checked by agarose gel electrophoresis. The fragmentized cDNA was labeled with the Enzo BioArray terminal labeling kit with biotin-ddUTP (Affymetrix).
Keywords = aeruginosa
Keywords = Azithromycin
Keywords = quorum sensing
Keywords = macrolide antibiotics
Keywords = cystic fibrosis

organism: Pseudomonas aeruginosa

source_name: P. aeruginosa PAO1, untreated, early stationary phase


title: Semeralul_PFC_Development_Week2_Batch1_Animal_4

description: Prefrontal Cortex

source_name: Prefrontal Cortex, Week 2 Postnatal

extract_protocol: RNA was prepared using a combination of two common protocols, with slight modifications. TRIZOL® Reagent was used for isolation of RNA (Invitrogen Life Technologies Corp., Carlsbad, CA) (Chomczynski, 1993) followed by purification using the Absolutely RNeasy RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) (Dolter, 2000). Approximately, 20-35 mg of PFC tissue was homogenized and completely lysed in 600 L Trizol, followed by centrifugation at 14,000 rpm for 10 minutes at 4oC. The pellet was discarded; 120 L of chloroform was added to the supernatant, vigorously shaken, incubated for 2-3 minutes at 20oC and centrifuged at 14,000 rpm for 10 minutes at 4oC. The aqueous phase containing RNA was transferred to a fresh 1.5 mL microcentrifuge tube and washed with an equal volume of pre-chilled 70% ethanol. RNA was then purified using Stratagene’s Absolutely RNeasy RT-PCR Miniprep kit. After estimating the yield of total RNA, the solution was concentrated to 1.2 g/L RNA using Microcron YM-10 centrifugal filter devices (Millipore Corp., Bedford, MA). RNA integrity was verified by visualization of the 18S and 28S ribosomal RNA bands using the Agilent bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Extracts with evidence of RNA degradation - as indicated by smearing of 28S and 18S ribosomal RNA on agarose/formaldehyde gel electrophoresis - were discarded.

value: C57BL/6', 'Gender:male', 'Age:2 weeks', 'Tissue:prefrontal cortex', 'Batch:1'


title: Semeralul_PFC_Development_Week3_Batch1_Animal_3

description: Prefrontal Cortex


title: Semeralul_PFC_Development_Week2_Batch2_Animal_1

description: Prefrontal Cortex

value: C57BL/6', 'Gender:male', 'Age:2 weeks', 'Tissue:prefrontal cortex', 'Batch:2'


title: Semeralul_PFC_Development_Week3_Batch1_Animal_2

description: Prefrontal Cortex

extract_protocol: RNA was prepared using a combination of two common protocols, with slight modifications. TRIZOL Reagent was used for isolation of RNA (Invitrogen Life Technologies Corp., Carlsbad, CA) (Chomczynski, 1993) followed by purification using the Absolutely RNeasy RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) (Dolter, 2000). Approximately, 20-35 mg of PFC tissue was homogenized and completely lysed in 600 uL Trizol, followed by centrifugation at 14,000 rpm for 10 minutes at 4 C. The pellet was discarded; 120 uL of chloroform was added to the supernatant, vigorously shaken, incubated for 2-3 minutes at 20 C and centrifuged at 14,000 rpm for 10 minutes at 4oC. The aqueous phase containing RNA was transferred to a fresh 1.5 mL microcentrifuge tube and washed with an equal volume of pre-chilled 70% ethanol. RNA was then purified using Stratagene’s Absolutely RNeasy RT-PCR Miniprep kit. After estimating the yield of total RNA, the solution was concentrated to 1.2 ug/uL RNA using Microcron YM-10 centrifugal filter devices (Millipore Corp., Bedford, MA). RNA integrity was verified by visualization of the 18S and 28S ribosomal RNA bands using the Agilent bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Extracts with evidence of RNA degradation - as indicated by smearing of 28S and 18S ribosomal RNA on agarose/formaldehyde gel electrophoresis - were discarded.


title: Semeralul_PFC_Development_Week3_Batch1_Animal_5

description: Prefrontal Cortex


title: Semeralul_PFC_Development_Week4_Batch1_Animal_2

description: Prefrontal Cortex


title: Semeralul_PFC_Development_Week4_Batch1_Animal_1

description: Prefrontal Cortex


title: Semeralul_PFC_Development_Week2_Batch1_Animal_6

description: Prefrontal Cortex

extract_protocol: RNA was prepared using a combination of two common protocols, with slight modifications. TRIZOL Reagent was used for isolation of RNA (Invitrogen Life Technologies Corp., Carlsbad, CA) (Chomczynski, 1993) followed by purification using the Absolutely RNeasy RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) (Dolter, 2000). Approximately, 20-35 mg of PFC tissue was homogenized and completely lysed in 600 uL Trizol, followed by centrifugation at 14,000 rpm for 10 minutes at 4 C. The pellet was discarded; 120 uL of chloroform was added to the supernatant, vigorously shaken, incubated for 2-3 minutes at 20 C and centrifuged at 14,000 rpm for 10 minutes at 4 C. The aqueous phase containing RNA was transferred to a fresh 1.5 mL microcentrifuge tube and washed with an equal volume of pre-chilled 70% ethanol. RNA was then purified using Stratagene’s Absolutely RNeasy RT-PCR Miniprep kit. After estimating the yield of total RNA, the solution was concentrated to 1.2 ug/uL RNA using Microcron YM-10 centrifugal filter devices (Millipore Corp., Bedford, MA). RNA integrity was verified by visualization of the 18S and 28S ribosomal RNA bands using the Agilent bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Extracts with evidence of RNA degradation - as indicated by smearing of 28S and 18S ribosomal RNA on agarose/formaldehyde gel electrophoresis - were discarded.


title: Semeralul_PFC_Development_Week2_Batch1_Animal_5

description: Week 2 Batch 2 Animal 2


title: Semeralul_PFC_Development_Week2_Batch2_Animal_2

description: Prefrontal Cortex


title: + Azithromycin Chip 3

description:
Samples used, extract preparation and labeling:

Bio-source properties:
Pseudomonas aeruginosa PAO1 (DSM 1707).

Biomaterial manipulations:
P. aeruginosa was grown in Brain-Heart-Infusion (BHI) medium at 37°C with shaking with or without the addition of 2 µg/ml AZM (Pfizer, Germany).

RNA extraction, cDNA synthesis and labeling:
Total RNA was extracted from 10 ml samples of eight 150-ml cultures (4 containing 2 µg/ml AZM and 4 without AZM). In brief, bacteria were lysed in the presence of 10 ml killing buffer (Tris/HCL, 5 mM MgCl2, 2 mM NaN3, pH 7.5) and centrifuged at 4°C for 10 min. The aqueous phase was mixed carefully with 125 µl Saccharose/Na-Acetate (300 mM Saccharose, 10 mM NaAc, pH 4.5) and 125 µl SDS/ Na-Acetate (83 mM SDS, 10 mM NaAc, pH 4.5) was added. The suspension was heated to 65°C and 400 µl hot phenol was added. After 3 min of incubation at 65°C, the suspension was quickly cooled in liquid nitrogen and centrifuged for 10 min. The phenol extraction was repeated twice before the nucleic acids were pelleted with 40 µl 3M NaAc (pH 5.2) and 1 ml 90% ethanol at -20°C overnight, washed with 70% ethanol and treated with 40 U of DNaseI (Roche) in DNaseI buffer (20 mM NaAc, 10 mM MgCl2, 10 mM NaCl, pH 4.5) for 30 min at 37°C. After purification with RNeasy columns (Qiagen) the yield of total cellular RNA was determined by UV absorption.
cDNA was synthesized from RNA pooled from two independent cultures and subsequently two GeneChips were hybridized for each culture condition (4 independent GeneChips in total).
cDNA synthesis and biotin-ddUTP terminal labeling were performed in compliance with the manufacturer’s instructions for the P. aeruginosa GeneChip:
Ten micrograms of total RNA were mixed with random primers (Invitrogen) and incubated for 10 min at 70°C. Then a cDNA reaction mix was added, containing 10 µl of 5 x first strand buffer, 0,1 µmol dithiothreitol, deoxynucleotide triphosphate (3 µl of a dNTP-mix, 10 mM each) and 50 U of SuperScript II (Reverse Transcriptase). This was followed by an incubation step for 10 min at 25°C, 60 min at 37°C, 60 min at 42°C, and 15 min at 72°C. RNA was degradated by the addition of 1 N NaOH (20 µl) and an incubation for 30 min at 65°C. Subsequently the reaction mix was neutralized by addition of 1 N HCl (20 µl).
The cDNA was purified with QIAquick columns (Amersham Biosciences), quantified by UV absorption, fragmentized in one-for-all buffer with 0.5 U of DNase I (Amersham Pharmacia Biotech) per µg of cDNA for 10 min at 37°C and subsequently inactivated for 10 min at 98°C. The fragmentation of the cDNA (50-200-bp range) was checked by agarose gel electrophoresis. The fragmentized cDNA was labeled with the Enzo BioArray terminal labeling kit with biotin-ddUTP (Affymetrix).
Keywords = aeruginosa
Keywords = Azithromycin
Keywords = macrolide antibiotics
Keywords = quorum sensing
Keywords = cystic fibrosis

source_name: P. aeruginosa PAO1, Azithromycin-treated (2µg/mL), early stationary phase


title: miRNA expression in newborn Dkk1-expressing transgenic skin sample TG2 versus control littermate skin sample C4

status: Public on May 04 2006

type: other

city: New York

first: Sarah

middle: E

last: Millar

state: NY

address: Icahn Building, Floor 13 Room 020C, 1425 Madison Ave

department: Developmental, Cell and Regenerative Biology

institute: Icahn School of Medicine at Mount Sinai

description:
miRNA expression was compared in skin from control newborn mice and littermate mice ectopically expressing the potent secreted WNT inhibitor Dickkopf 1 (DKK1) in the epidermis, which completely lack hair follicle development. Low molecular weight RNA was isolated using the mirVana RNA extraction kit (Ambion) from full thickness dorsal skin of K5-rtTA; tetO-Dkk1 newborn mice and control littermates following doxycycline treatment from E0.5 to induce expression of Dkk1 in double transgenic epidermis [1]. Control and Dkk1–expressing transgenic samples were tagged for labeling with Cy3 and Cy5 dyes respectively using the Ncode miRNA Labeling System (Invitrogen), mixed by equal mass, and co-hybridized to miRNA arrays that have been described previously [2]. Background-corrected median signals for pixels from each probe spot in both the Cy3 and Cy5 channels were used for analysis. Cy3 (control samples C2, C4, C5) were detected at 532nm and Cy5 (Dkk1–expressing transgenic samples TG1, TG2, TG4) at 635 nm.

References:
[1]
Wysolmerski, J.J., and Millar, S.E. (2004). Canonical WNT signaling promotes
mammary placode development and is essential for initiation of mammary gland
morphogenesis. Development 131, 4819-4829.

[2]
Mourelatos, Z. (2004). Microarray-based, high-throughput gene expression profiling of
microRNAs. Nat Methods 1, 155-161.

data_processing: The log (base 2) transform of the ratio of the background-subtracted medians (635/532) was calculated for each spot.

molecule: other

source_name: Dorsal skin dissected from newborn double transgenic K5-rtTA;tetO-Dkk1 mouse TG2

label_protocol: Samples were tagged for labeling using the Ncode miRNA Labeling System (Invitrogen)

growth_protocol: Treated with doxycycline from day 0.5 of gestation by maintaining the mother on doxycycline-containing chow.

extract_protocol: Low molecular weight RNA was isolated using the mirVana RNA extraction kit (Ambion).

value: K5-rtTA; tetO-Dkk1 treated with doxycycline from day 0.5 of gestation to induce epidermal expression of Dkk1.

tag: Strain background

value: mixed FVB/N, C57BL/6, SJ/L.

tag: Age

value: Newborn.

tag: Tissue

value: Full thickness dorsal skin.

source_name: Dorsal skin dissected from control newborn mouse C4

value: control littermate treated with doxycycline from day 0.5 of gestation to induce epidermal expression of Dkk1.


title: - Azithromycin Chip 2


title: Semeralul_PFC_Development_Week2_Batch1_Animal_3

description: Prefrontal Cortex


title: miRNA expression in newborn Dkk1-expressing transgenic skin sample TG4 versus control littermate skin sample C5

source_name: Dorsal skin dissected from newborn double transgenic K5-rtTA;tetO-Dkk1 mouse TG4

source_name: Dorsal skin dissected from control newborn mouse C5

value: Control littermate treated with doxycycline from day 0.5 of gestation to induce epidermal expression of Dkk1.


title: + Azithromycin Chip 4

description:
Samples used, extract preparation and labeling:

Bio-source properties:
Pseudomonas aeruginosa PAO1 (DSM 1707).

Biomaterial manipulations:
P. aeruginosa was grown in Brain-Heart-Infusion (BHI) medium at 37°C with shaking with or without the addition of 2 µg/ml AZM (Pfizer, Germany).

RNA extraction, cDNA synthesis and labeling:
Total RNA was extracted from 10 ml samples of eight 150-ml cultures (4 containing 2 µg/ml AZM and 4 without AZM). In brief, bacteria were lysed in the presence of 10 ml killing buffer (Tris/HCL, 5 mM MgCl2, 2 mM NaN3, pH 7.5) and centrifuged at 4°C for 10 min. The aqueous phase was mixed carefully with 125 µl Saccharose/Na-Acetate (300 mM Saccharose, 10 mM NaAc, pH 4.5) and 125 µl SDS/ Na-Acetate (83 mM SDS, 10 mM NaAc, pH 4.5) was added. The suspension was heated to 65°C and 400 µl hot phenol was added. After 3 min of incubation at 65°C, the suspension was quickly cooled in liquid nitrogen and centrifuged for 10 min. The phenol extraction was repeated twice before the nucleic acids were pelleted with 40 µl 3M NaAc (pH 5.2) and 1 ml 90% ethanol at -20°C overnight, washed with 70% ethanol and treated with 40 U of DNaseI (Roche) in DNaseI buffer (20 mM NaAc, 10 mM MgCl2, 10 mM NaCl, pH 4.5) for 30 min at 37°C. After purification with RNeasy columns (Qiagen) the yield of total cellular RNA was determined by UV absorption.
cDNA was synthesized from RNA pooled from two independent cultures and subsequently two GeneChips were hybridized for each culture condition (4 independent GeneChips in total).
cDNA synthesis and biotin-ddUTP terminal labeling were performed in compliance with the manufacturer’s instructions for the P. aeruginosa GeneChip:
Ten micrograms of total RNA were mixed with random primers (Invitrogen) and incubated for 10 min at 70°C. Then a cDNA reaction mix was added, containing 10 µl of 5 x first strand buffer, 0,1 µmol dithiothreitol, deoxynucleotide triphosphate (3 µl of a dNTP-mix, 10 mM each) and 50 U of SuperScript II (Reverse Transcriptase). This was followed by an incubation step for 10 min at 25°C, 60 min at 37°C, 60 min at 42°C, and 15 min at 72°C. RNA was degradated by the addition of 1 N NaOH (20 µl) and an incubation for 30 min at 65°C. Subsequently the reaction mix was neutralized by addition of 1 N HCl (20 µl).
The cDNA was purified with QIAquick columns (Amersham Biosciences), quantified by UV absorption, fragmentized in one-for-all buffer with 0.5 U of DNase I (Amersham Pharmacia Biotech) per µg of cDNA for 10 min at 37°C and subsequently inactivated for 10 min at 98°C. The fragmentation of the cDNA (50-200-bp range) was checked by agarose gel electrophoresis. The fragmentized cDNA was labeled with the Enzo BioArray terminal labeling kit with biotin-ddUTP (Affymetrix).


title: miRNA expression in newborn Dkk1-expressing transgenic skin sample TG1 versus control littermate skin sample C2

source_name: Dorsal skin dissected from newborn double transgenic K5-rtTA;tetO-Dkk1 mouse TG1

value: Mixed FVB/N, C57BL/6, SJ/L.

source_name: Dorsal skin dissected from control newborn mouse C2

value: Control littermate; treated with doxycycline from day 0.5 of gestation.


title: myotubes, differentiated C2C12, biological rep3

status: Public on Apr 30 2006

city: La Jolla

first: Ihsiung

middle: Brandon

last: Chen

state: CA

address: 10550 N. Torrey Pines Rd.

department: Cell Biology

institute: The Scripps Research Institute

description: Gene expression data from differentiated C2C12 cells on Day 6.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

source_name: C2C12 cells in 2% horse serum

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.

growth_protocol: 2% horse serum in MEM

treatment_protocol: cells were risned once with PBS and then directly lysed in TriZol (Invitrogen).

tag: Adult muscle myotubes

tag: Differentiated


title: CGH_replicate2

type: genomic

city: Brisbane

first: Karin

middle: Sonja

last: Kassahn

state: QLD

address: Queensland Bioscience Precinct

department: Institute for Molecular Bioscience

country: Australia

institute: University of Queensland

description: comparative genomic DNA hybridisation experiment comparing hybridisation of D. rerio and P. moluccensis gDNA on a D. rerio oligonucleotide microarray

hyb_protocol: mixed labelled gDNA with 50ug human Cot-1, dried under reduced pressure. hybridisation mix: 14ul formamide, 14ul 6.25*SSC, 0.6ul 10%SDS hybridisation overnight in humidified chamber (1*SSC) at 42C washing: 0.5*SSC/0.01% SDS, 0.5*SSC, 0.2*SSC

scan_protocol: Axon GenePix 4000B scanner

data_processing: SPOT software

organism: Danio rerio

source_name: genomic DNA, D. rerio

label_protocol: indirect dye coupling

extract_protocol: CTAB DNA extraction

tag: Organism

value: D. rerio

value: caudal fin

organism: Pomacentrus moluccensis

source_name: genomic DNA, P. moluccensis

value: P. moluccensis

tag: sample ID


title: liver_heat_stress_rep3

description: heat-stressed vs normal liver tissue extracted from individuals of a natural population of the coral reef fish Pomacentrus moluccensis

hyb_protocol: mixed labeled cDNA with 8ug poly-A and 5ug human Cot-1, dried under reduced pressure. hybridisation mix: 14ul formamide, 14ul 6.25*SSC, 0.6ul 10%SDS hybridisation overnight in humidified chamber (1*SSC) at 42C washing: 0.5*SSC/0.01% SDS, 0.5*SSC, 0.2*SSC

source_name: liver, 34C 3hrs heat stress

extract_protocol: TRIzol and RNeasy columns

treatment_protocol: short-term exposure (3hrs) to heat stress at 34C

value: Pomacentrus moluccensis

tag: Source

value: natural population, Lizard Island, northern Great Barrier Reef

value: adult

value: male

value: liver

tag: Treatment

value: 34C, 3hrs, heat stress

tag: Sample ID

source_name: liver, normal

treatment_protocol: fish remaining at the ambient temperature of 26C (controls)

value: ambient temperature, 3hrs

value: pooled control


title: CGH_replicate1

value: Danio rerio


title: CGH_replicate4

source_name: genomic DNA, D.rerio


title: myotubes, differentiated C2C12, biological rep2


title: Yeast ChIP-chip MycH4_Control_2

status: Public on Apr 28 2006

city: Chapel Hill

first: Jason

middle: D

last: Lieb

state: NC

address: 203 Fordham Hall

department: Department of Biology

institute: University of North Carolina at Chapel Hill

scan_protocol: Images were acquired using a GenePix 4000B scanner and Genepix software (Axon Instruments)

data_processing: We loaded data into the University of North Carolina (UNC) Microarray Database. We normalized the ratios and retrieved the following ratio for each spot: log2 (median of ChIP pixel intensities/ median reference pixel intensities). Only spots of high quality by visual inspection, with gel-verified PCR products and comprised of pixels with consistent ratio values (regression correlation >0.6), were used for analysis.

source_name: input

label_protocol: We amplified ChIP-enriched DNA and genomic DNA derived from input extract (used as reference) using a T7 RNA polymerase–based linear method (see Liu et al., 2003 BMC Genomics). We added T7 promoter sequences to genomic DNA fragments, which were then transcribed to produce RNA. We produced amino-allyl-dUMP-labeled cDNA from the synthesized RNA by reverse transcription using random primers and then conjugated it with either Cy5 (ChIP DNA) or Cy3 (input DNA) monofunctional ester. We mixed Cy5- and Cy3-labeled DNA samples and hybridized them to a DNA microarray.

tag: input


title: liver_heat_stress_rep4

tag: Gender


title: myotubes, differentiated C2C12, biological rep1


title: Yeast ChIP-chip Heat Shock_H3_IP_3

description: Heat Shock_H3_IP_3

source_name: anti H3 ChIP after heat shock

tag: anti H3 ChIP after heat shock


title: Yeast ChIP-chip MycH4_Control_1


title: liver_heat_stress_rep2


title: myoblast undifferentiated C2C12, biological rep2

description: Gene expression data from undifferentiated C2C12 cells.

source_name: C2C12 cells in 20% serum

growth_protocol: 20% serum in MEM

tag: Adult muscle myoblast

tag: Undifferentiated


title: liver_heat_stress_rep1

hyb_protocol: mixed labelled cDNA with 8ug poly-A and 5ug human Cot-1, dried under reduced pressure. hybridisation mix: 14ul formamide, 14ul 6.25*SSC, 0.6ul 10%SDS hybridisation overnight in humidified chamber (1*SSC) at 42C washing: 0.5*SSC/0.01% SDS, 0.5*SSC, 0.2*SSC


title: CD31+ rep5

city: Seattle

first: Asa

last: Oudes

state: WA

address: 401 Terry Ave. N

institute: Rosetta Biosoftware

description: endothelial cells

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: RMA of .cel files with Genespring 7.2

organism: Homo sapiens

source_name: normal prostate

label_protocol: Approximately 200 ng of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Prostate tissue was MACS sorted for positive cells. Total RNA was extracted from the cell lysate using an RNeasy kit (Qiagen).

tag: CD31+ MACS sorted cells


title: CD31+ rep2

description: endothelial cells


title: CD31+ rep3

description: endothelial cells


title: CD26a+ rep5

description: Prostate luminal cells

tag: CD26+ MACS sorted cells


title: CD31+ rep4

description: endothelial cells


title: myoblast undifferentiated C2C12, biological rep1


title: Yeast ChIP-chip Heat Shock_H3_IP_2

description: Heat Shock_H3_IP_2


title: Yeast ChIP-chip Heat Shock_H3_IP_1

description: Heat Shock_H3_IP_1


title: myoblast undifferentiated C2C12, biological rep3


title: CD49a+ rep5

description: Prostate stromal fibromuscular cells

tag: CD49a+ MACS sorted cells


title: Yeast ChIP-chip H3_IP_1

source_name: anti H3 ChIP

tag: anti H3 ChIP


title: CD49a+ rep4

description: Prostate stromal fibromuscular cells


title: Yeast ChIP-chip H3_IP_4


title: CD104+ rep5

description: Prostate basal cells

tag: CD104+ MACS sorted cells


title: Yeast ChIP-chip H3_Control_3


title: Yeast ChIP-chip H3_IP_3


title: CD104+ rep4

description: Prostate basal cells


title: CD31+ rep1

description: endothelial cells


title: Yeast ChIP-chip MycH4_IP_7

source_name: anti myc H4 ChIP

tag: anti myc H4 ChIP


title: CD26a+ rep3

description: Prostate luminal cells


title: Yeast ChIP-chip H3_Control_2


title: CD26a+ rep4

description: Prostate luminal cells


title: CD104+ rep3

description: Prostate basal cells


title: Yeast ChIP-chip H3_Control_1


title: Yeast ChIP-chip MycH4_IP_5


title: CGH_replicate3

tag: Tissue


title: CD49a+ rep3

description: Prostate stromal fibromuscular cells


title: Yeast ChIP-chip MycH4_IP_4


title: Yeast ChIP-chip MycH4_IP_6


title: Yeast ChIP-chip MycH4_IP_2


title: Yeast ChIP-chip MycH4_IP_3


title: CD104+ rep2

description: Prostate basal cells


title: CD49a+ rep1

description: Prostate stromal fibromuscular cells


title: CD26+ rep2

description: Prostate luminal cells


title: Yeast ChIP-chip MycH4_Control_4


title: Yeast ChIP-chip MycH4_Control_5


title: CD26+ rep1

description: Prostate luminal cells


title: Yeast ChIP-chip MycH4_Control_3


title: Yeast ChIP-chip MycH4_Control_6


title: Yeast ChIP-chip MycH4_IP_1


title: CD104+ rep1

description: Prostate basal cells


title: CD49a+ rep2

description: Prostate stromal fibromuscular cells


title: 500 hours 2

status: Public on Apr 26 2006

city: Dübendorf

first: Alessandro

middle: Guido

last: Franchini

address: Ueberlandstrasse 133

department: Environmental Microbiology

country: Switzerland

institute: EAWAG

description: see pubblication

data_processing: The data provided are the original data generated with the Jaguar software from the microarray images. The VALUEs reported represent log10 (Cy5/Cy3) ratios for this experiment/sample. They were not normalized across all samples in the study.

organism: Escherichia coli

source_name: Control

tag: Batch growth in mineral medium supplied with 4 g/l glucose as sole carbon source (optical density of 0.4 at 546 nm)

source_name: Sample

tag: 500 hours of cultivation in continuous colture (mineral medium with 100 mg/l glucose)


title: 500 hours 1

description: see pubblication


title: 500 hours 3

description: see pubblication


title: 40 hours 1

description: see pubblication

source_name: control

tag: Batch growth in mineral medium supplied with 4 g/l glucose as sole carbon source (optical density 0.4 at 546nm)

tag: 40 hours cultivation in continuous culture (mineral medium with 100 mg/l glucose)


title: 40 hours 2

description: see pubblication

tag: 40 hours of cultivation in continuous colture (mineral medium with 100 mg/l glucose)


title: fibroblast_G-positive_5aza_rep1

status: Public on Apr 27 2006

city: Chicago

first: Tammy

last: Vallender

state: IL

department: Human Genetics

institute: University of Chicago

description: X chromosome-linked GFP heterozygous female mice were used to derive dermal fibroblasts. Fibroblasts were sorted through FACS for GFP-nonexpressing cells. Cells were then untreated with 4uM 5A2dC for 48 hours followed by 24 hour recovery in normal medium. Cells were then sorted again by FACS to separate the GFP-activated (GFP-positive) and GFP-inactive (GFP-negative) cells.  This sample is GFP-positive.; biological replicate 1

hyb_protocol: standard Affymetrix hybridization protocol

scan_protocol: standard Affymetrix scan protocol

data_processing: MAS 5.0 data processing and normalization

label: biotin labeled with standard Affymetrix fluorescent stain cocktail

source_name: primary dermal fibroblasts 5aza-treated GFP-positive sorted

label_protocol: standard Affymetrix IVT labeling and staining protocols

growth_protocol: Cultures were maintained in Dulbecco’s modified Eagle’s medium (DMEM;Invitrogen; Carlsbad, CA, USA) with L-glutamine and high glucose plus 10% FBS (Invitrogen) and 100U/mL penicillin streptomycin (Invitrogen) at 37oC and 5% CO 2. Cells were passaged at confluence by 0.25% trypsin EDTA (Invitrogen).

extract_protocol: RNeasy total RNA extraction protocol (Qiagen)

treatment_protocol: Freshly prepared 5-aza-2'-deoxycytidine (5A2dC) (Sigma; Saint Louis, MO, USA) stock solution was diluted in growth medium to a concentration of 4 μM. A new preparation of the drug in growth medium was added every 24 hours for a total of 48-hour drug exposure. Cells were grown in normal medium following treatment for an additional 24 hours.

tag: strain

value: B6; gender:female; age:0-2d; tissue:dermis; passage #:4; treatment:4uM 5aza; biological replicate:1; sort:GFP-positive


title: fibroblast_G-negative_5aza_rep1

description: X chromosome-linked GFP heterozygous female mice were used to derive dermal fibroblasts. Fibroblasts were sorted through FACS for GFP-nonexpressing cells. Cells were then untreated with 4uM 5A2dC for 48 hours followed by 24 hour recovery in normal medium. Cells were then sorted again by FACS to separate the GFP-activated (GFP-positive) and GFP-inactive (GFP-negative) cells.  This sample is GFP-negative.; biological replicate 1

source_name: primary dermal fibroblasts 5aza-treated GFP-negative sorted

value: B6; gender:female; age:0-2d; tissue:dermis; passage #:4; treatment:4uM 5aza; biological replicate:1; sort:GFP-negative


title: 40 hours 3

description: see pubblication


title: fibroblast_G-negative_5aza_rep2

description: X chromosome-linked GFP heterozygous female mice were used to derive dermal fibroblasts. Fibroblasts were sorted through FACS for GFP-nonexpressing cells. Cells were then untreated with 4uM 5A2dC for 48 hours followed by 24 hour recovery in normal medium. Cells were then sorted again by FACS to separate the GFP-activated (GFP-positive) and GFP-inactive (GFP-negative) cells.  This sample is GFP-negative.; biological replicate 2

value: B6; gender:female; age:0-2d; tissue:dermis; passage #:4; treatment:4uM 5aza; biological replicate:2; sort:GFP-negative


title: JB1_WT_MMara_2h_1

status: Public on Apr 25 2006

city: Karlsruhe

first: Jörg

middle: Thomas

last: Kämper

address: Hertzstrasse 16, Geb. 06.40

department: Department for Applied Biosciences

institute: Karlsruhe Institute of Technology

description: Control experiment (base line) for measuring effects of genes expressed under the control of the arabinose inducable crg promoter

hyb_protocol: Affymetrix EukGE-WS2 on a GeneChip Fluidics Station 400

scan_protocol: Affymetrix GCS2500

label: biotin/phycoerythrin

organism: Mycosarcoma maydis

source_name: U. maydis strain JB1 (a1 delta b) grown for 2 h in ArrayMedium/Arabinose

label_protocol: Target preparation was performed according to the standard Affymetrix protocol using the Enzo BioArray RNA transcript labeling kit, except for a reaction temperature of 50°C for first-strand cDNA synthesis.

growth_protocol: JB1 was grown to an OD600 of 0.5 at 28°C in liquid array medium: 6.25 % (w/v) Holiday salt solution, 30 mM L-glutamine, 1 % (w/v) glucose, pH 7.0 (filter-sterilized). Subsequently, cells were shifted to liquid array medium containing 1 % (w/v) arabinose instead of glucose as a carbon source, and incubated for 2h.

extract_protocol: Total RNA was extracted using the TRIZOL-reagent (Invitrogen) according to the manufacturer’s instructions. RNA samples were further column purified (Qiagen RNeasy) and the quality checked using a Bioanalyzer with a RNA 6000 Nano LabChip kit (Agilent).

tag: Strain JB1 is a FB1 derivative with a deletion of the b-mating type (hygromycin replacement)


title: JB1_crgPclp1_MMara_2h_1

description: Experiment to measure the effects of induced expression of the U. maydis clp1 protein. Clp1 is required for the formation of clamp cells during the biotrophic phase of U. maydis.

source_name: U. maydis strain JB1-crgP::clp1 grown for 2 h in ArrayMedium/Arabinose

growth_protocol: JB1-crgP::clp1 was grown to an OD600 of 0.5 at 28°C in liquid array medium: 6.25 % (w/v) Holiday salt solution, 30 mM L-glutamine, 1 % (w/v) glucose, pH 7.0 (filter-sterilized). Subsequently, cells were shifted to liquid array medium containing 1 % (w/v) arabinose instead of glucose as a carbon source, and incubated for 2h.

tag: Strain JB1 is a FB1 derivative with a deletion of the b-mating type (hygromycin replacement). The clp1 gene under control of the arabinose inducable crg1 promoter was introduced in multiple copies into the cbx locus


title: JB1_crgPclp1_MMara_2h_2

source_name: Ustilago maydis


title: fibroblast_unsorted_control_rep1

description: X chromosome-linked GFP heterozygous female mice were used to derive dermal fibroblasts.  Fibroblasts were sorted through FACS for GFP-nonexpressing cells.  Cells were then untreated as a control for 48 hours followed by 24 hour recovery in normal medium.; biological replicate 1

source_name: primary dermal fibroblasts untreated unsorted

treatment_protocol: untreated

value: B6; gender:female; age:0-2d; tissue:dermis; passage #:4; treatment:untreated; biological replicate:1; sort:unsorted


title: JB1_WT_MMara_2h_2


title: fibroblast_unsorted_control_rep2

description: X chromosome-linked GFP heterozygous female mice were used to derive dermal fibroblasts.  Fibroblasts were sorted through FACS for GFP-nonexpressing cells.  Cells were then untreated as a control for 48 hours followed by 24 hour recovery in normal medium.; biological replicate 2

value: B6; gender:mix; age:0-2d; tissue:dermis; passage #:4; treatment:untreated; biological replicate:2


title: Yeast ChIP-chip H3_IP_2

tag: input


title: Yeast ChIP-chip Heat Shock_H3_IP_4

description: Heat Shock_H3_IP_4

tag: anti H3 ChIP after heat shock


title: fibroblast_5azacontrol_rep3

description: untreated control; biological replicate 3

source_name: primary dermal fibroblasts untreated

value: B6; gender:mix; age:0-2d; tissue:dermis; passage #:4; treatment:control; biological replicate:3


title: fibroblast_5azacontrol_rep1

description: untreated control; biological replicate 1

value: B6; gender:mix; age:0-2d; tissue:dermis; passage #:4; treatment:control; biological replicate:1


title: C57BL/6 heart left ventrical (LAD ligation 60 day)

status: Public on Apr 24 2006

city: Minneapolis

first: Daniel

middle: J

last: Garry

state: MN

department: Cancer & Cardiovascular Research Center

institute: LILLEHEI HEART INSTITUTE

description: Gene expression data from C57BL/6 strain mouse left ventrical with 60 day LAD ligated heart.

hyb_protocol: Following fragmentation, 20 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

source_name: 60 day LAD ligated heart from C57BL/6 strain

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

treatment_protocol: LAD ligation for 60 days

tag: Strain

tag: Gender

value: Male

tag: Age

value: 2 to 4 months

value: Heart, left ventrical


title: fibroblast_G-positive_5aza_rep2

description: X chromosome-linked GFP heterozygous female mice were used to derive dermal fibroblasts. Fibroblasts were sorted through FACS for GFP-nonexpressing cells. Cells were then untreated with 4uM 5A2dC for 48 hours followed by 24 hour recovery in normal medium. Cells were then sorted again by FACS to separate the GFP-activated (GFP-positive) and GFP-inactive (GFP-negative) cells.  This sample is GFP-positive.; biological replicate 2

value: B6; gender:female; age:0-2d; tissue:dermis; passage #:4; treatment:4uM 5aza; biological replicate:2; sort:GFP-positive


title: MRL/MpJ heart left ventrical (LAD ligation 60 day)

description: Gene expression data from MRL/MpJ strain mouse left ventrical with 60 day LAD ligated heart.

source_name: 60 day LAD ligated heart from MRL/MpJ strain

treatment_protocol: LAD ligation  for 60 days

value: MRL/MpJ


title: MRL/MpJ heart left ventrical (LAD ligation 30 day)

description: Gene expression data from MRL/MpJ strain mouse left ventrical with 30 day LAD ligated heart.

source_name: 30 day LAD ligated heart from MRL/MpJ strain

treatment_protocol: LAD ligation for 30 days


title: C57BL/6 heart left ventrical (LAD ligation 30 day)

description: Gene expression data from C57BL/6 strain mouse left ventrical with 30 day LAD ligated heart.

source_name: 30 day LAD ligated heart from C57BL/6 strain


title: MRL/MpJ heart left ventrical

description: Gene expression data from MRL/MpJ strain mouse heart left ventrical.

source_name: Normal heart from MRL/MpJ strain

treatment_protocol: Untreated


title: fibroblast_5azatreated_rep1

description: treated with 5-aza-2'-deoxycytidine for 96 hours plus 24 hours in normal medium; biological replicate 1

source_name: primary dermal fibroblasts treated

treatment_protocol: Freshly prepared 5A2dC (Sigma; Saint Louis, MO, USA) stock solution was diluted in growth medium to a concentration of 5 μM. A new preparation of the drug in growth medium was added every 24 hours for a total of 96-hour drug exposure. Cells were grown in normal medium following treatment for an additional 24 hours.

value: B6; gender:mix; age:0-2d; tissue:dermis; passage #:4; treatment:5-aza-2'-deoxycytidine; biological replicate:1


title: fibroblast_5azatreated_rep3

description: treated with 5-aza-2'-deoxycytidine for 96 hours plus 24 hours in normal medium; biological replicate 3

value: B6; gender:mix; age:0-2d; tissue:dermis; passage #:4; treatment:5-aza-2'-deoxycytidine; biological replicate:3


title: MRL/MpJ heart left ventrical (LAD ligation 3 day)

description: Gene expression data from MRL/MpJ strain mouse left ventrical with 3 day LAD ligated heart.

source_name: 3 day LAD ligated heart from MRL/MpJ strain

treatment_protocol: LAD ligation for 3 days


title: C57BL/6 heart left ventrical

description: Gene expression data from normal C57BL/6 strain mouse left ventrical.

source_name: Normal heart from C57BL/6 strain


title: fibroblast_5azatreated_rep2

description: treated with 5-aza-2'-deoxycytidine for 96 hours plus 24 hours in normal medium; biological replicate 2

value: B6; gender:mix; age:0-2d; tissue:dermis; passage #:4; treatment:5-aza-2'-deoxycytidine; biological replicate:2


title: fibroblast_5azacontrol_rep2

description: untreated control; biological replicate 2

value: B6; gender:mix; age:0-2d; tissue:dermis; passage #:4; treatment:control; biological replicate:2


title: Mdr2-KO homozygous mouse, 3 month old mouse 2

status: Public on Apr 23 2006

city: Ramat-Gan

first: Mark

last: Katzenellenbogen

address: Ramat-Gan 52900, Israel

department: THE FACULTY OF LIFE SCIENCE, BIOINFORMATICS AND MICROARRAY UNIT

country: Israel

institute: Bar Ilan University

description: According to paper: Multiple adaptive mechanisms to chronic liver disease revealed at early stages of liver carcinogenesis in the Mdr2-knockout mice.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

source_name: Mdr2-KO homozygous mouse, 3 month old mouse, liver sample

tag: Genotype

value: Mdr2-KO homozygous mouse

value: 3 month


title: Mdr2-KO homozygous mouse, 12 month old mouse 3

source_name: Mdr2-KO homozygous mouse, 12 month old mouse, liver sample

value: 12 month


title: Mdr2-KO homozygous mouse, 3 month old mouse 1


title: Mdr2-KO heterozygous mouse, 3 month old mouse 3

source_name: Mdr2-KO heterozygous mouse, 3 month old mouse, liver sample

value: Mdr2-KO heterozygous mouse


title: Mdr2-KO homozygous mouse, 3 month old mouse 3


title: Mdr2-KO homozygous mouse, 12 month old mouse 2


title: Mdr2-KO heterozygous mouse, 3 month old mouse 2


title: Mdr2-KO heterozygous mouse, 3 month old mouse 1

source_name: Mdr2-KO heterozygous mouse, 12 month old mouse, liver sample


title: Mdr2-KO heterozygous mouse, 12 month old mouse 2


title: Mdr2-KO heterozygous mouse, 12 month old mouse 1


title: 13130402

status: Public on Apr 20 2006

city: St-Hyacinthe

first: Vincent

last: Deslandes

state: Quebec

address: 3200 rue Sicotte

department: Groupe de Recherche sur les Maladies Infectieuses du Porc

institute: Université de Montréal - Faculté de Médecine Vétérinaire

description: Competitive hybridization of cDNA generated from A. pleuropneumoniae sero 1 strain s4074 RNA extracted in iron-rich or iron-restricted conditinos

data_processing: Image processing software: SpotFinder v.3.1.1.  Net median intensities were normalized using Lowess algorithm (MIDAS) and log2 ratios were generated

organism: Actinobacillus pleuropneumoniae

tag: serotype 1, strain s4074

tag: iron-rich medium

tag: iron-restricted medium


title: bHLHER

status: Public on Apr 22 2006

first: Tomokatsu

last: Ikawa

address: 9500 Gilman Drive

department: Biology

institute: UCSD

description: Amersham Codelink mouse 20k

data_processing: Median-Normalization method. The median was computationally calculated with the spot-based value.

source_name: E2A-deficient hematopoietic cells

tag: C57BL6 bone marrow progenitor cells infected by bHLHER


title: 12853107


title: E47ER

description: Codelink mouse 20k

source_name: E2A-deficient hematopoietic progenitor cells infected by E47ER

tag: C57BL6 bone marrow hematopoietic cells


title: 13130513


title: 13133765


title: 13130403


title: 13130357


title: 13130362


title: mur MZ B replicate 1

status: Public on Apr 21 2006

city: xi an

first: ping

last: zhang

state: shaanxi

address: changleroad 17

country: China

institute: fmmu

description: Wild type mur spleen Marginal zone B cells

data_processing: Affymetrix Microarray Suite version 5.0

source_name: Marginal zone B cells

label_protocol: Approximately 100 ng of total RNA was processed to produce biotinylated cRNA targets,following a standard two cycle target labelling assay provided by affymetrix.

extract_protocol: Approximately 4 ¡Á 107 B cells were isolated from 3 wild-type female C57BL/6 spleen cells with magnetic beads conjugated with anti B220. Then purified B cells were stained with anti CD21 and anti CD23,and were subjected to FACS-sorting. MZ B cells, which is CD23int CD21hig,were then sorted and Pooled sorted cells were lysed in RLT buffer (Qiagen).Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).using an RNeasy kit (Qiagen).

tag: Wild type, spleen , Marginal zone B cells


title: 12853102

description:
Competitive hybridization of cDNA generated from A. pleuropneumoniae sero 1 strain s4074 RNA extracted in iron-rich or iron-restricted conditinos

Category: cDNA
Subcategory: Expression profile
Scanner: Perkin-Elmer ScanArray Express
Image processing software: SpotFinder v.3.1.1


title: mur FO B replicate 1

description: Wild type mur spleen follicular B cells

source_name: Follicular B cell

label_protocol: Following a standard two cycle target labelling assay provided by affymetrix,approximately 100 ng of total RNA was processed to produce biotinylated cRNA targets,

extract_protocol: Approximately 4 ¡Á 107 B cells were isolated from 3 wild-type female C57BL/6 spleen cells with magnetic beads conjugated with anti B220. Then purified B cells were stained with anti CD21 and anti CD23,and were subjected to FACS-sorting. FO B cells, which is CD23hig CD21int,were then sorted and Pooled sorted cells were lysed in RLT buffer (Qiagen).Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

tag: Wild type, spleen ,Follicular B cells


title: C57BL/6 heart left ventrical (LAD ligation 3 day)

description: Gene expression data from C57BL/6 strain mouse heart left ventrical with 3 day LAD ligation.

source_name: 3 day LAD ligated heart from C57BL/6 strain

tag: Tissue


title: H3K27me3 ChIP-chip, cDNA 12K array, Embryonic Drosophila Kc167 cells, replicate 3

city: Amsterdam

first: Maarten

last: van Lohuizen

address: Plesmanlaan 121

department: Molecular Genetics

country: Netherlands

institute: NKI-AVL

description: Embryonic Drosophila cells, Kc167 cells

data_processing: After removal of low quality, redundant or ambiguous proves, hybridization data of 9,994 probes was used for analyses, all measured ratios were log base 2-transformed and normalized to the median value of the entire array

organism: Drosophila melanogaster

source_name: Embryonic Drosophila cells, Kc167 cells, ChIP histone H3K27me3

label_protocol: For the microarray analysis, immunoprecipitated DNA fragments were amplified using linker-modified PCR (LM-PCR). Randomly sheared DNA fragments were made blunt using T4 DNA polymerase for 15 min at 16�C in 10 mM Tris-HCl pH8.0, 50 mM NaCl, 10 mM MgCl2, 1 mM DTT, and 0.1 mM dNTPs. Adapter ligation, PCR amplification, labeling and hybridization were carried out according to the DamID protocol (Greil, F. et al. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev 17, 2825-38, 2003)

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23degC

extract_protocol:
The ChIP method was and adaptation of a previously published protocol (Rietveld, L.E., Caldenhoven, E. & Stunnenberg, H.G. In vivo repression of an erythroid-specific gene by distinct corepressor complexes. Embo J 21, 1389-97, 2002). Approximately 2x108 Kc cells were cross-linked by the addition of formaldehyde (1% final concentration). The reaction was quenched with 125 mM Glycine and the cells were washed twice with PBS. Subsequently, the cells were incubated 5� on ice in 1.5 ml lysis buffer (1% v/v SDS, 10 mM EDTA pH8.0, 50 mM Tris-HCl pH8.0, protease inhibitor cocktail - Roche). The cell lysates were sonicated and centrifuged to remove cell debris. We used the equivalent of 1 x 10E6 cells for one immunoprecipitation. Chromatin samples were diluted 10-fold in IP buffer (1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH8.0, 167 mM NaCl, protease inhibitor cocktail - Roche) and precleared with 10 ul 50% protein A Sepharose slurry containing 1mg/ml bovine serum albumine (BSA) for 1h agitation at 4degC. Precleared chromatin was incubated with 2 ug antibody overnight at 4degC. All subsequent ChIP steps were performed as described (Rietveld, L.E., Caldenhoven, E. & Stunnenberg, H.G. In vivo repression of an erythroid-specific gene by distinct corepressor complexes. Embo J 21, 1389-97, 2002). We used the following antibodies for ChIP analyses: anti-H3K27me3 - #07-449 from Upstate; anti-H3K4me3 - ab8580-50 from Abcam; and anti-IgG - 011-0000-003 from Jackson Immuno Research. The data were normalized to a parallel ChIP with anti-H3 antibody (ab1797-100 from Abcam), to correct for differences in nucleosome density.
The ChIP method was and adaptation of a previously published protocol (Rietveld, L.E., Caldenhoven, E. & Stunnenberg, H.G. In vivo repression of an erythroid-specific gene by distinct corepressor complexes. Embo J 21, 1389-97, 2002). Approximately 2x108 Kc cells were cross-linked by the addition of formaldehyde (1% final concentration). The reaction was quenched with 125 mM Glycine and the cells were washed twice with PBS. Subsequently, the cells were incubated 5� on ice in 1.5 ml lysis buffer (1% v/v SDS, 10 mM EDTA pH8.0, 50 mM Tris-HCl pH8.0, protease inhibitor cocktail - Roche). The cell lysates were sonicated and centrifuged to remove cell debris. We used the equivalent of 1 x 10E6 cells for one immunoprecipitation. Chromatin samples were diluted 10-fold in IP buffer (1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH8.0, 167 mM NaCl, protease inhibitor cocktail - Roche) and precleared with 10 ul 50% protein A Sepharose slurry containing 1mg/ml bovine serum albumine (BSA) for 1h agitation at 4degC. Precleared chromatin was incubated with 2 ug antibody overnight at 4degC. All subsequent ChIP steps were performed as described (Rietveld, L.E., Caldenhoven, E. & Stunnenberg, H.G. In vivo repression of an erythroid-specific gene by distinct corepressor complexes. Embo J 21, 1389-97, 2002). We used the following antibodies for ChIP analyses: anti-H3K27me3 - #07-449 from Upstate; anti-H3K4me3 - ab8580-50 from Abcam; and anti-IgG - 011-0000-003 from Jackson Immuno Research. The data were normalized to a parallel ChIP with anti-H3 antibody (ab1797-100 from Abcam), to correct for differences in nucleosome density.

tag: H3K27me3 ChIP-chip (EXPERIMENTAL)

source_name: Embryonic Drosophila cells, Kc167 cells, ChIP Histone H3

tag: H3 ChIP-chip (REFERENCE)


title: Rose bengal treated vs. untreated; slide 4

city: Berkeley

first: Heidi

middle: Kristine

last: Ledford

address: 111 Koshland Hall

department: Plant and Microbial Biology

institute: University of California, Berkeley

description: A comparison of rose bengal-treated and -untreated cells to find identify genes that may be regulated by singlet oxygen.

hyb_protocol: Slides were blocked in a succinic anhydride/sodium borate solution for 20 min, then rehydrated in a boiling water bath for 1 min. Slides were then rinsed in ethanol, and dried by brief centrifugation. Prehybridization was carried out for 20 min at 50 °C in a solution containing 3.5X SSC, 0.1% [w/v] SDS, 10 mg/ml BSA. After prehybridization, slides were rinsed in water followed by isopropanol, and dried. For hybridization, a 2X hybridization buffer containing 6X SSC, 0.2% [w/v] SDS, 0.1 mg/ml poly(dA), and 0.1 mg/ml yeast tRNA was prepared and mixed with an equal volume of labeled cDNA. Slides were hybridized overnight in a 50 °C water bath. The next day, slides were washed once in 2X SSC, 0.03% [w/v] SDS, once in 1X SSC, and once in 0.05X SSC, each for 5 min. Slides were then dried and stored until scanning.

scan_protocol: Slides were scanned on an ArrayWoRx Biochip Reader and quantitated using the SoftWoRx Tracker Microarray program, both from Applied Precision, LLC (Issaquah, WA). Each represented gene had to have a valid data point from each biological replicate to be considered further. Abnormal spots were flagged manually and excluded from further analysis, as was any spot in which the mean spot intensity did not exceed two times the median background intensity, or in which the signal to noise ratio value was less than 1. Spots which were >20% saturated were also excluded.

data_processing: p-values were generated using J/maanova

organism: Chlamydomonas reinhardtii

source_name: 4A+, treated

label_protocol: Reverse transcription of RNA samples was carried out at 42°C for 2 h in the presence of dNTPs containing a 1:1 ratio of amino-allyl dUTP to dTTP. Samples were treated with EDTA to stop the reaction and with NaOH to destroy RNA. After neutralizing the sample with HCl, cDNA was purified using a Microcon 30 column, dried and resuspended in 0.1 M Na2HCO3 buffer (pH 9.0). RNA samples were labeled using Post-Labelling Reactive Dye Packs from Amersham Biosciences (Amersham, Little Chalfont, Bucks., UK). Probes were purified individually using QiaQuick columns (Qiagen, Valencia, Calif.) and then combined.

growth_protocol: Cells were grown photoautotrophically in 100 mL high salt medium, under 50 umol photons m-2 s-1.

extract_protocol: Samples were harvested by centrifugation (3200 g, 4 °C, 3 min), then resuspended in 0.1 volume H2O at 4 °C. An equal volume of 2X lysis buffer (0.6 M NaCl, 10 mM EDTA, 100 mM Tris HCl (pH 8.0), 4% [w/v] SDS) was added to the cell suspension, which was subsequently incubated at 65°C for 5 min. 0.132 volumes of 2 M KCl were added, and the samples were incubated on ice for 15 min. Samples were then centrifuged at 12,000 g for 10 min at 4 °C. Supernatants were extracted twice with phenol/chloroform and once with chloroform before precipitating RNA overnight using 0.33 volumes of 8 M LiCl at 4 °C. This was followed by a final ethanol precipitation. RNA quality was assessed using the ratio of absorbance at 260 nm and 280 nm and by ethidium bromide staining following gel electrophoresis.

treatment_protocol: 100-ml cultures of 4A+ were grown photoautotrophically at 50 umol photons m-2 s-1 until they reached a density of 1.5 x 10^6 cells/ml. “Treated” samples were treated with 2 uM RB, whereas “untreated” cultures received a mock inoculation with an equal volume of water. Cells were incubated for 2 hours before RNA was harvested.

tag: Our lab's wild type strain of C. reinhardtii, described in

value: Dent, R.M., Haglund, C.M., Chin, B.L., Kobayashi, M.C., and Niyogi, K.K. (2005). Functional genomics of eukaryotic photosynthesis using insertional mutagenesis of Chlamydomonas reinhardtii. Plant Physiol. 137, 545-556.

source_name: 4A+, untreated

treatment_protocol: 100-ml cultures of 4A+ were grown photoautotrophically at 50 umol photons m-2 s-1 until they reached a density of 1.5 x 10^6 cells/ml. “Pretreated” samples were treated with 2 uM RB, whereas “unpretreated” cultures received a mock inoculation with an equal volume of water. Cells were incubated for 2 hours before RNA was harvested.


title: Rose bengal treated vs. untreated; slide 3

source_name: 4A+, treated with rose bengal


title: H3K27me3 ChIP-chip, cDNA 12K array, Embryonic Drosophila Kc167 cells, replicate 2

description: Embryonic Drosophila cells, Kc167 cells


title: H3K4me3 ChIP-chip, cDNA 12K array, Embryonic Drosophila Kc167 cells, replicate 2

description: Embryonic Drosophila cells, Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, ChIP histone H3K4me3

extract_protocol: The ChIP method was and adaptation of a previously published protocol (Rietveld, L.E., Caldenhoven, E. & Stunnenberg, H.G. In vivo repression of an erythroid-specific gene by distinct corepressor complexes. Embo J 21, 1389-97, 2002). Approximately 2x108 Kc cells were cross-linked by the addition of formaldehyde (1% final concentration). The reaction was quenched with 125 mM Glycine and the cells were washed twice with PBS. Subsequently, the cells were incubated 5� on ice in 1.5 ml lysis buffer (1% v/v SDS, 10 mM EDTA pH8.0, 50 mM Tris-HCl pH8.0, protease inhibitor cocktail - Roche). The cell lysates were sonicated and centrifuged to remove cell debris. We used the equivalent of 1 x 10E6 cells for one immunoprecipitation. Chromatin samples were diluted 10-fold in IP buffer (1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH8.0, 167 mM NaCl, protease inhibitor cocktail - Roche) and precleared with 10 ul 50% protein A Sepharose slurry containing 1mg/ml bovine serum albumine (BSA) for 1h agitation at 4degC. Precleared chromatin was incubated with 2 ug antibody overnight at 4degC. All subsequent ChIP steps were performed as described (Rietveld, L.E., Caldenhoven, E. & Stunnenberg, H.G. In vivo repression of an erythroid-specific gene by distinct corepressor complexes. Embo J 21, 1389-97, 2002). We used the following antibodies for ChIP analyses: anti-H3K27me3 - #07-449 from Upstate; anti-H3K4me3 - ab8580-50 from Abcam; and anti-IgG - 011-0000-003 from Jackson Immuno Research. The data were normalized to a parallel ChIP with anti-H3 antibody (ab1797-100 from Abcam), to correct for differences in nucleosome density.

tag: H3K4me3 ChIP-chip (EXPERIMENTAL)


title: IgG ChIP-chip, cDNA 12K array, Embryonic Drosophila Kc167 cells, replicate 2

description: Embryonic Drosophila cells, Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, ChIP IgG control

tag: IgG ChIP-chip (EXPERIMENTAL)


title: Rose bengal treated vs. untreated; slide 1

source_name: strain 4A+, treated


title: Rose bengal treated vs. untreated; slide 2


title: H3K27me3 ChIP-chip, cDNA 12K array, Embryonic Drosophila Kc167 cells, replicate 4

description: Embryonic Drosophila cells, Kc167 cells


title: H3K27me3 ChIP-chip, cDNA 12K array, Embryonic Drosophila Kc167 cells, replicate 1

description: Embryonic Drosophila cells, Kc167 cells

label_protocol:
For the microarray analysis, immunoprecipitated DNA fragments were amplified using linker-modified PCR (LM-PCR). Randomly sheared DNA fragments were made blunt using T4 DNA polymerase for 15 min at 16�C in 10 mM Tris-HCl pH8.0, 50 mM NaCl, 10 mM MgCl2, 1 mM DTT, and 0.1 mM dNTPs. Adapter ligation, PCR amplification, labeling and hybridization were carried out according to the DamID protocol (Greil, F. et al. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev 17, 2825-38, 2003)
For the microarray analysis, immunoprecipitated DNA fragments were amplified using linker-modified PCR (LM-PCR). Randomly sheared DNA fragments were made blunt using T4 DNA polymerase for 15 min at 16�C in 10 mM Tris-HCl pH8.0, 50 mM NaCl, 10 mM MgCl2, 1 mM DTT, and 0.1 mM dNTPs. Adapter ligation, PCR amplification, labeling and hybridization were carried out according to the DamID protocol (Greil, F. et al. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev 17, 2825-38, 2003)


title: Sce DamID, cDNA 12K array, Embryonic Drosophila Kc167 cells, replicate 4

description: Embryonic Drosophila cells, Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Sce-Dam

label_protocol: Sample labeling was performed as described (Greil, F. et al. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev 17, 2825-38, 2003)

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23�C. Full length Sce was cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) and plasmid was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

extract_protocol: Sample extraction was performed as described (Greil, F. et al. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev 17, 2825-38, 2003)

tag: Sce-Dam (EXPERIMENTAL)

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Dam

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23�C. pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) plasmid was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

tag: Dam (REFERENCE)


title: IgG ChIP-chip, cDNA 12K array, Embryonic Drosophila Kc167 cells, replicate 3

description: Embryonic Drosophila cells, Kc167 cells


title: Sce DamID, cDNA 12K array, Embryonic Drosophila Kc167 cells, replicate 1

description: Embryonic Drosophila cells, Kc167 cells


title: IgG ChIP-chip, cDNA 12K array, Embryonic Drosophila Kc167 cells, replicate 1

description: Embryonic Drosophila cells, Kc167 cells


title: Sce DamID, cDNA 12K array, Embryonic Drosophila Kc167 cells, replicate 3

description: Embryonic Drosophila cells, Kc167 cells


title: esc DamID, cDNA 12K array, Embryonic Drosophila Kc167 cells, replicate 3

description: Embryonic Drosophila cells, Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing esc-Dam

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23�C. Full length esc was cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) and plasmid was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

tag: esc-Dam (EXPERIMENTAL)


title: esc DamID, cDNA 12K array, Embryonic Drosophila Kc167 cells, replicate 2

description: Embryonic Drosophila cells, Kc167 cells

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23�C. Full length esc was  cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) and plasmid was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).


title: esc DamID, cDNA 12K array, Embryonic Drosophila Kc167 cells, replicate 1

description: Embryonic Drosophila cells, Kc167 cells

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23degC. Full length esc was cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) and plasmid was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).


title: Sce DamID, cDNA 12K array, Embryonic Drosophila Kc167 cells, replicate 2

description: Embryonic Drosophila cells, Kc167 cells


title: esc DamID, cDNA 12K array, Embryonic Drosophila Kc167 cells, replicate 4

description: Embryonic Drosophila cells, Kc167 cells


title: Pc DamID, cDNA 12K array, Embryonic Drosophila Kc167 cells, replicate 2

description: Embryonic Drosophila cells, Kc167 cells

source_name: Embryonic Drosophila cells, Kc167 cells, expressing Pc-Dam

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. Full length Pc were cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) and plasmid was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

tag: Pc-Dam (EXPERIMENTAL)

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23°C. pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) plasmid was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).


title: Pc DamID, cDNA 12K array, Embryonic Drosophila Kc167 cells, replicate 3

description: Embryonic Drosophila cells, Kc167 cells

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23degC. Full length Pc was cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) and plasmid was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23degC. pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) plasmid was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).


title: Pc DamID, cDNA 12K array, Embryonic Drosophila Kc167 cells, replicate 4

description: Embryonic Drosophila cells, Kc167 cells

growth_protocol: Drosophila Kc cells were grown in BPYE medium (Shields and Sang M3 Insect medium, Sigma, supplemented with 25% w/v bactopeptone, 20% w/v yeast extract, 5% heat inactivated fetal calf serum, all Gibco) at 23�C. Full length Pc were cloned into pNDamMyc (van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8, 2000) and plasmid was transfected into Kc cells as described  (Henikoff, S., Ahmad, K., Platero, J.S. & van Steensel, B. Heterochromatic deposition of centromeric histone H3-like proteins. Proc Natl Acad Sci U S A 97, 716-21, 2000).


title: WDG16-87 yneAB lexA HPUra repl 2

status: Public on Apr 18 2006

city: Cambridge

first: Alan

middle: D.

last: Grossman

email: clee2@mit.edu, adg@mit.edu

state: MA

address: 31 Ames Street, 68-530

institute: MIT

description: Hybridization of HPUra treated AIG266 and reference RNA

hyb_protocol: Goranov et al. A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.

data_processing: Ratio Cy5/Cy3 is normalized to total signal (log2 format, no background subtraction). Spots with >80% pixels above background were analyzed

organism: Bacillus subtilis

source_name: growing cells treated with HPUra

tag: AIG266 growing in minimal medium treated with HPUra for 60min. Replicate 2

source_name: reference RNA

tag: pooled RNA sample


title: WDG16-88 yneAB lexA HPUra repl 3

label_protocol: Goranov et al. A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.

tag: AIG266 growing in minimal medium treated with HPUra for 60min. replicate 3


title: WDG16-86 yneAB lexA HPUra repl 1

source_name: HPUra treated growing cells

growth_protocol: Goranov et al. A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA.

tag: AIG266 growing in minimal medium treated with HPUra (38ug/ml) for 60min. Replicate 1


title: Pc DamID, cDNA 12K array, Embryonic Drosophila Kc167 cells, replicate 1

description: Embryonic Drosophila cells, Kc167 cells