title: LDO_extract3_rep2

city: Tjele

first: Jakob

last: Hedegaard

address: PO-box 50

department: Department of Genetics and Biotechnology

country: Denmark

institute: Aarhus University, Faculty of Agricultural Sciences

description: Statistical analysis was carried out in the R computing environment (version 2.4.1 for Linux) using the package Linear Models for Microarray Analysis (Limma, version 2.9.16) which is part of the Bioconductor project. The log2-transformed ratios of Alexa-647 to Alexa-555 were normalized within-slide using the printtip-loess method with default parameters as implemented in Limma. The set of normalized log-ratios were then analyzed in Limma to identify genes being significantly differentially expressed between tissues.

hyb_protocol: The slides were hybridized in a Discovery XT hybridization station (Ventana Discovery Systems, Tucson, AZ, USA). Transfer Chip Prep-2 from 4 ºC to room temperature 1 hour before use. Prepare ChipSpread by mixing equal volumes of ChipSpread A (20 mg/mL BSA, 4x SSC, 0.5 mg/mL sodium azide) and B (formamide; 2 mg/mL SDS) and incubate at room temperature for 1 hour before use. A total of 2.5 mL is needed per slide. Print labels, trim them and place them on the slides. Mix the Chip Map reagents (Chip Prep-1, -2 and - 3) by inversion, remove the cap and place the reagents in the Discovery. Place the slides in the machine and initiate the run. Cover slide with 2.5 mL ChipSpread when the message appears (after few minutes). The machine now runs for app. 1.5 hours to pre-hybridize the slides. Heat a waterbath to 90°C or use a PCR machine. Mix the Chiphybe80, add 200 µL to the sample (<20 µL) and mix carefully. Heat the sample mixture at 90°C for 3 minutes and mix carefully by pipetting. Press ""button"" on the machine which then prepares the slides for hybridization. When the message appears apply the samples onto the slides and press ""button"" and the machine hybridizes at 48 ºC for 6 hours. Wipe oil from backside of slides using a clean-room napkin and place slides in the slide-holder from the High Throughput Wash Station (Telechem, cat.no. HTW) placed in a mTub filled with RiboWash. If processing more than 20 slides, place equal number of slides in two slide-holders and continue in parallel. Transfer the slide-holder to a HTW filled with RiboWash and wash for 2 min with magnetic stirring at 700 rpm. Refill the HTW with RiboWash and repeat the wash. Dip the slide-holder in 2x SSC filled in a mTub (200 mL 20x SSC, Elga H2O + 1800 mL water). Transfer the slide-holder to a HTW filled with 2x SSC and wash for 2 min with magnetic stirring at 700 rpm. Refill the HTW with 2x SSC and repeat the wash. Dip the slide-holder 10 times in 0.1x SSC filled in a mTub (5 mL 20x SSC, Elga H2O + 995 mL water) and leave the holder submerged in 0.1x SSC. Transfer the slides to a mBox slide holder placed in a mTub filled with Elga H2O. Dry arrays by centrifugation (at 300 x g for 4 min placed in a mBox)

scan_protocol: Scanner: ScanArray Express HT system (Perkin Elmer), 5 µm resolution, 100 % laser power and PMT adjusted individually for each channel. Image analysis software: GenePix Pro (version 6.0.1.22, Molecular Devices) using FeatureType = Irregular Filled and BackgroundSubtraction = MorphologicalClosingFollowedByOpening

data_processing: Tissue samples of heart (HEA) and Longissimus dorsi (LDO) were prepared by pooling from five healthy Hampshire gilts at age four to six months and division into six sub-samples, three for each tissue named HEA1, HEA2, HEA3, LDO1, LDO2 and LDO3. The exact same six tissue samples were used for subsequent expression profiling with cDNA microarray, 454-sequencing and iTRAQ-based proteomics. A reference sample for the cDNA microarray experiment and iTRAQ-based proteomics was constructed by combining the six samples. In the microarray experiment, three cDNA microarray slides were used per sample.

organism: Sus scrofa

label_protocol: 20 µg total RNA was labelled with Alexa 647 using the Superscript Plus Direct cDNA Labeling System (Invitrogen) following the enclosed protocol. Spike-in RNA (“red”) from the Lucidea Universal ScoreCard (Amersham Biosciences) was added to the cDNA reactions.

extract_protocol: RNeasy Maxi Kit with DNase treatment following the enclosed protocol (Qiagen)

tag: Breed

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:longissimus dorsi, RNA extraction 3

source_name: reference: pool of all extractions

label_protocol: 20 µg total RNA was labelled with Alexa-555 using the Superscript Plus Direct cDNA Labeling System (Invitrogen) following the enclosed protocol. Spike-in RNA (""green"") from the Lucidea Universal ScoreCard (Amersham Biosciences) was added to the cDNA reactions.

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:pool of heart and longissimus dorsi RNA extractions


title: PBMC_Common_ref_vs_Boran130_pre-T._congolense_infection

status: Public on Jan 22 2009

type: RNA

city: Dublin

first: David

middle: E

last: MacHugh

address: University College Dublin, Belfield

department: College of Agriculture, Food Science and Veterinary Medicine

country: Ireland

institute: University College Dublin

description: No additional information.

hyb_protocol: Labelled samples were purified using the purification module included with the SuperScript™ Plus Direct cDNA labelling System, combined and supplemented with approximately 60-70 µl SlideHyb Glass Hybridization Buffer #3 (Ambion Inc., www.ambion.com) to a final probe volume of 100 µl. Probes were hybridized to bovine long oligonucleotide (BLO) microarrays, using an automated HS400 hybridization station (Tecan UK Ltd., www.tecan.com) with the following optimized protocol; WASH: 75°C, Runs 1, Wash 10 s, Soak 20 s; PROBE INJECTION: 85°C; Denaturation: 95°C, 2 mins; HYBRIDISATION: 42°C – 4 hrs; 35°C – 4 hrs; 30°C – 4 hrs; agitation frequency medium, WASH: 37°C, Runs 2, Wash 10 s, Soak 20 s; 25°C, Runs 2, Wash 15 s, Soak 30 s; 25°C, Runs 2, Wash 20 s, Soak 40 s and SLIDE DRYING: 25°C for 2 mins.

scan_protocol: Microarrays were scanned using a GenePix® 4000B scanner (Molecular Devices Corp., www.moleculardevices.com). Scans were performed at medium and high photomultipler tube (PMT) gain settings.

data_processing: Where appropriate, data from medium and high PMT gain scans were combined and corrected for saturation using the method described by Lyng et al., BMC Genomics. 2004 Feb 3;5(1):10. Spots classed by Genepix software as 'bad', 'absent' or 'not found' were flagged and downweighted in subsequent analysis. The Robust Multichip Average (RMA) expression measure (Irizarry et al., Biostatistics 2003, 4(2):249-264) was calculated. An intensity-based normalization method was employed: within microarray print-tip dependent locally weighted scatterplot smoothing (LOWESS) normalization, followed by quantile normalization between microarrays. Normalised data submitted here was combined across duplicate spots using the limma package of Bioconductor.

molecule: total RNA

organism:
Bos taurus
Bos indicus

source_name: African Bos taurus and Bos indicus pooled PBMC from a Trypanosoma congolense infection time course.

label_protocol: Labelled cDNA was generated using the SuperScript™ Plus Direct cDNA labelling System (Invitrogen Corp., www.invitrogen.com) according to the manufacturers’ instructions. 10 µg of common reference RNA (CRR) was labelled with Alexa Fluor® 647.

extract_protocol: PBMC were isolated using Percoll™ gradients (GE Healthcare, www.gehealthcare.com) and as described in Ulmer et al., Immunobiology 1984, 166(3):238-250. The isolated PBMC were washed with sterile PBS and stored immediately at -80°C in Tri-reagent (Molecular Research Center, Inc, www.mrcgene.com) for further processing. Total RNA was extracted with chloroform and precipitated with isopropanol. Each sample was further DNase-treated with RQ1 RNase-free DNase (Promega Corp., www.promega.com) and purified using the RNeasy® mini kit (Qiagen, www.qiagen.com). A common reference RNA pool was generated by combining equal quantities of all samples in the study.

treatment_protocol: Peripheral blood (200 ml) was collected in heparanized syringes

tag: Source

value: Pooled peripheral blood mononuclear cells from eight Boran (B. indicus, trypanosusceptible) and eight N’Dama (B. taurus, trypanotolerant) female cattle aged between 19-28 months, raised together at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The cattle were each experimentally infected with the T. congolense clone IL1180, which was delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected before infection and at 14, 21, 25, 29 and 34 days post infection.

organism: Bos indicus

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran130, pre-infection

label_protocol: Labelled cDNA was generated using the SuperScript™ Plus Direct cDNA labelling System (Invitrogen Corp., www.invitrogen.com) according to the manufacturers’ instructions. 8 µg of sample RNA was labelled with Alexa Fluor® 555.

extract_protocol: PBMC were isolated using Percoll™ gradients (GE Healthcare, www.gehealthcare.com) and as described in Ulmer et al. Immunobiology 1984, 166(3):238-250. The isolated PBMC were washed with sterile PBS and stored immediately at -80°C in Tri-reagent (Molecular Research Center, Inc, www.mrcgene.com) for further processing. Total RNA was extracted with chloroform and precipitated with isopropanol. Each sample was further DNase-treated with RQ1 RNase-free DNase (Promega Corp., www.promega.com) and purified using the RNeasy® mini kit (Qiagen, www.qiagen.com).

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran130) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected prior to infection


title: PBMC_Common_ref_vs_Boran130_T._congolense_infected_21_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran130, 21dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran130) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 21 days post-infection


title: PBMC_Common_ref_vs_Boran130_T._congolense_infected_25_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran130, 25dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran130) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 25 days post-infection


title: PBMC_Common_ref_vs_Boran130_T._congolense_infected_14_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran130, 14dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran130) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 14 days post-infection


title: PBMC_Common_ref_vs_Boran86_T._congolense_infected_14_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran86, 14dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran86) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 14 days post-infection


title: LDO_extract1_rep1

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:longissimus dorsi, RNA extraction 1


title: LDO_extract1_rep2


title: LDO_extract1_rep3


title: HEA_extract2_rep3

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:heart, RNA extraction 2


title: PBMC_Common_ref_vs_Boran100_pre-T._congolense_infection

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran100, pre-infection

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran100) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected prior to infection


title: LDO_extract2_rep2

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:longissimus dorsi, RNA extraction 2


title: HEA_extract1_rep1

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:heart, RNA extraction 1


title: PBMC_Common_ref_vs_Boran100_T._congolense_infected_34_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran100, 34dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran100) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 34 days post-infection


title: HEA_extract3_rep3

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:heart, RNA extraction 3


title: LDO_extract3_rep1


title: LDO_extract3_rep3


title: HEA_extract2_rep1


title: PBMC_Common_ref_vs_Boran100_T._congolense_infected_29_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran100, 29dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran100) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 29 days post-infection


title: PBMC_Common_ref_vs_Boran100_T._congolense_infected_14_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran100, 14dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran100) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 14 days post-infection


title: PBMC_Common_ref_vs_Boran100_T._congolense_infected_21_dpi

description: No additional information.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran100, 21dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran100) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 21 days post-infection


title: HEA_extract1_rep2

value: Hampshire, gender:gilt, status:healthy, age:4 to 6 months, tissue:pool of heart and longissimus dorsi RNA extractions


title: PBMC_Common_ref_vs_Boran100_T._congolense_infected_25_dpi

description: No additional information.

value: Pooled peripheral blood mononuclear cells from eight Boran (B. indicus, trypanosusceptible) and eight N’Dama (B. taurus, trypanotolerant) female cattle aged between 19-28 months, raised together at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The cattle were each experimentally infected with the T. congolense clone IL1180, which was delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected before infection and at 14, 21, 25, 29 and 34 days post infection.

source_name: PBMC from Trypanosoma congolense infection time course : African bos indicus animal Boran100, 25dpi

value: Peripheral blood mononuclear cells (PBMC) from a female trypanosusceptible African Bos indicus Boran cow (individual ID Boran100) aged between 19-28 months, raised at the International Livestock Research Institute (ILRI) farm at Kapiti Plains Estate, Kenya in an area free from trypanosomiasis. The animal was experimentally infected with the T. congolense clone IL1180, delivered via the bites of eight infected tsetse flies [Glossina morsitans morsitans]. Peripheral blood (200 ml) was collected 25 days post-infection


title: LDO_extract2_rep3


title: HEA_extract1_rep3


title: HEA_extract3_rep2


title: HEA_extract3_rep1


title: CEBPAmutantAML_#4

status: Public on Jan 21 2009

city: Rotterdam

first: Bas

last: Wouters

address: P.O. Box 2040, room Ee1330B

department: Hematology

country: Netherlands

institute: Erasmus University Medical Center

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: RMA, log2 transformation

label: biotin

organism: Homo sapiens

source_name: AML blasts, CEBPA mutant

label_protocol: Affymetrix protocol

extract_protocol: Total RNA was extracted by lysis with guanidium isothiocyanate followed by cesium chloride gradient purification.

tag: Female, 54 years, FAB M1, Cytogenetics

value: del9q, CEBPA mut +


title: CEBPAmutantAML_#2

tag: Male, 45 years, FAB M1, Normal cytogenetics, CEBPA mut +


title: CEBPAmutantAML_#8

tag: Female, 59 years, FAB M1, Normal cytogenetics, CEBPA mut +


title: CEBPAsilencedAML_#8

source_name: AML blasts, CEBPA silenced

tag: Female, 40 years, FAB M0, CEBPA silenced,  46,XX,del(6)(q13q23)[16];46,XX[4].nuc ish(MLLx2)[200]


title: HEA_extract2_rep2


title: LDO_extract2_rep1


title: CEBPAmutantAML_#7

tag: Male 34 years, FAB M1, Cytogenetics


title: volunteer7-oral_intake_dead_bacteria

city: Wageningen

first: Peter

last: van Baarlen

address: De Elst 1

department: Animal Sciences

institute: Wageningen University

description: mucosal response of healthy adult humans to lactic acid bacteria

hyb_protocol: The labelled RNA was hybridised to a GeneChip Hu133 Plus2 array (Affymetrix, Santa Clara, CA), washed, and stained. Detailed methods for the labelling and subsequent hybridisations to the arrays are described in the eukaryotic section of the GeneChip Expression Analysis Technical Manual, Revision 3, from Affymetrix.

scan_protocol: The GeneChip Hu133 Plus2 array was scanned on an Affymetrix GeneChip 3000 7G scanner. Detailed methods are described in the eukaryotic section of the GeneChip Expression Analysis Technical Manual, Revision 3, from Affymetrix

data_processing: Packages from the Bioconductor project, integrated in an in-house developed on-line management and analysis database for multiplatform microarray experiments, were used for analysing the scanned Affymetrix arrays (Gentleman et al., 2004; Gavai et al, submitted).

source_name: biopsy from proximal duodenum, 10-15 cm after pylorus, taken after 6 hrs of oral intake of dead (heat-killed at stationary phase) Lactobacillus plantarum (each half-hour)

label_protocol: Total RNA (500 ng) extracted from biopsies was labelled using the Ambion MessageAmp II biotin enhanced single-round amplification kit (cat. no. 1791).

extract_protocol: Total RNA was extracted from biopsies with TRIzol reagent, purified and DNAse treated using the SV Total RNA Isolation System (Promega, Leiden, The Netherlands). RNA integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies, Amsterdam, the Netherlands) with 6000 Nano Chips according to the manufacturer’s instructions. RNA was judged as suitable for array hybridization only if samples showed intact bands corresponding to the 18S and 28S ribosomal RNA subunits, displayed no chromosomal peaks or RNA degradation products, and had a RIN (RNA integrity number) above 8.0.

tag: biopsies were taken after 6 hrs of oral intake and immediately snap-frozen in liquid nitrogen until RNA extraction


title: CEBPAmutantAML_#6

tag: Male, 24 years, FAB M1, Normal cytogenetics, CEBPA mut +


title: CEBPAmutantAML_#1

tag: Male, 19 years, FAB M1, CEBPA mut +, normal cytogenetics


title: CEBPAmutantAML_#3

tag: Male, 40 years, FAB M1, Normal cytogenetic, CEBPA mut +


title: volunteer5-oral_intake_dead_bacteria


title: CEBPAmutantAML_#5

tag: Male, 16 years, FAB M1, Normal cytogenetics, CEBPA mut +


title: CEBPAsilencedAML_#4

tag: Male, 31 years, Complex karyotype, CEBPA silenced


title: CEBPAsilencedAML_#2

tag: Female, 41 years, CEBPA silenced, FAB M0, Complex karyotype


title: volunteer6-oral_intake_dead_bacteria


title: volunteer8-oral_intake_dead_bacteria


title: CEBPAsilencedAML_#5

tag: Male, 45 years, FAB M1, 46,XY,add(2)(q35)[13]/46,XY[19], CEBPA silenced


title: volunteer4-oral_intake_dead_bacteria


title: CEBPAsilencedAML_#7

tag: Male, 21 years, FAB M1, CEBPA silenced, 47,XY,+19[22]


title: wingless pathway activation - replicate 2

city: Barcelona

first: Stephanie

last: Boue

address: Dr Aiguader 88

country: Spain

institute: CMRB

description: Global analysis of alternative splicing regulation by wingless signalling in Drosophila cells

hyb_protocol: cDNA was hybridized to custom 44k Agilent oligonucleotide arrays.

scan_protocol: After hybridization, arrays were washed, scanned and images analyzed following the manufacturers’ recommendations.

data_processing: Agilent Feature Extraction software

organism: Drosophila melanogaster

source_name: wingless activated S2 cells

label_protocol: cDNA was generated from 15µg of total RNA with the incorporation of aminoallyl-dUTP (Sigma). cDNA was then conjugated with Cy5 mono-functional dye (Amersham)

growth_protocol: S2 cells were grown to exponential phase

extract_protocol: Total RNA was isolated from cells following the RNeasy Miniprep protocol (QIAGEN) including DNase treatment. The integrity of the RNA was controlled using a Bioanalyzer and only RNA preparations with undetectable degradation of ribosomal RNA peaks were utilized for further analyses.

treatment_protocol: 1.5 x 106 S2 cells with 15 µg of axin dsRNA for 4 days (see Clemens JC, Worby CA, Simonson-Leff N, Muda M, Maehama T, Hemmings BA, Dixon JE: Use of double-stranded RNA interference in Drosophila cell lines to dissect signal transduction pathways. Proc Natl Acad Sci U S A 2000, 97(12):6499-6503.)

source_name: control S2 cells

label_protocol: cDNA was generated from 15µg of total RNA with the incorporation of aminoallyl-dUTP (Sigma). cDNA was then conjugated with Cy3 mono-functional dye (Amersham)

tag: control


title: wingless pathway activation - replicate 3

tag: S2 cells with 15 µg of axin dsRNA for 4 days

tag: control S2 cells


title: CEBPAsilencedAML_#3

tag: Female, 31 years, FAB M1, Normal cytogenetics


title: CEBPAsilencedAML_#6

tag: Male, 72 years, FAB M1, CEBPA silenced, Normal cytogenetics


title: volunteer3-oral_intake_dead_bacteria


title: volunteer1-oral_intake_dead_bacteria


title: volunteer7-oral_intake_midlog_bacteria

source_name: biopsy from proximal duodenum, 10-15 cm after pylorus, taken after 6 hrs of oral intake of midlog-phase-grown Lactobacillus plantarum (each half-hour)


title: volunteer6-oral_intake_midlog_bacteria


title: Insulin pathway activation - replicate 3

description: Global analysis of alternative splicing regulation by insulin signalling in Drosophila cells

source_name: insulin treated cells

treatment_protocol: 30µg/ml human insulin (Actrapid 100 Ul/ml, Novo Nordisk) was added to the cell medium.

tag: Drosophila S2 cells were treated with 30µg/ml human insulin

source_name: control

tag: Drosophila control S2 cells


title: volunteer2-oral_intake_dead_bacteria


title: Insulin pathway activation - replicate 2


title: volunteer5-oral_intake_midlog_bacteria


title: volunteer4-oral_intake_midlog_bacteria


title: volunteer8-oral_intake_midlog_bacteria


title: wingless pathway activation - replicate 1


title: volunteer3-oral_intake_midlog_bacteria


title: volunteer2-oral_intake_midlog_bacteria


title: H.influenzae 10810 110-3

city: Oklahoma City

first: Timothy

middle: M

last: VanWagoner

state: OK

address: 940 SL Young Blvd, BMS340

department: Pediatrics

country: USA

institute: University of Oklahoma Health Sciences Center

description: Biological replicate 3, 90 minutes in FeHm Deplete BHI, followed by supplementation with Fe and Heme and growth for 20 minutes

hyb_protocol: Arrays were pre-hybridized in NimbleGen hybridization chamber at 45°C for two hours with gentle rotation using a buffer containing 100mg/ml herring sperm DNA (Promega Corporation, Madison, WI) 50mM MES, 1M NaCl, 10mM EDTA, 0.005% Tween-20 for fifteen minutes. The prehybe solution was replaced with a 350ml volume of the same composition as the pre-hybridization buffer but supplemented with 4mg of labeled prokaryotic cDNA and 1nM labeled control oligonucleotide. The array was hybridized overnight at 45°C with gentle rotation. Following hybridization, the arrays were removed from the hybridization and washed three times, at room temperature, in a buffer containing 6X SSPE, 0.01% (v/v) Tween-20 and then six times in a buffer containing 100mM MES, 26mM NaCl, 0.01% (v/v) Tween-20 at 45°C. Arrays were stained) in a buffer containing 50mM MES, pH 6.6, 1M NaCl, 0.005% Tween-20, and 1:1000 dilution of Streptavidin-Cy3 (GE Healthcare) for ten minutes with gentle agitation, then washed twice in 6X SSPE, 0.01% (v/v) Tween-20 at room temperature, dried under argon and stored desiccated.

scan_protocol: Not provided

data_processing: RMA normalized using quantile normalization and gene calls generated using the RMA algorithm. On chip replicates were averaged and log (base 2) transformed prior to statistical analysis.

organism: Haemophilus influenzae

source_name: H. influenzae 10810 grown in iron and heme deplete media for 90 minutes, then supplemented with Fe and Heme, replicate 3

label_protocol: Total prokaryotic RNA is converted to cDNA by random primed reverse transcription with SuperScript II (Invitrogen Corporation, Carlsbad, CA) in a reaction containing 10mg RNA, 1mg random hexamer, 1200U SuperScript II, 1X SuperScript first strand buffer, 20mM DTT, 500mM dNTPs in a total volume of 60ml. Following incubation, residual RNA was enzymatically degraded with the addition of 1U RNase H and 1mg RNase A. Reactions were purified by extraction with phenol:chloroform:isoamyl alcohol (25:24:1) followed by ethanol precipitation.in the presence of 1ml of Pellet Paint Co-Precipitant (EMD Biosciences, Madison WI). cDNA was enzymatically fragmented with 0.2U Dnase I in a 40ml reaction volume for 15 minutes at 37°C. Dnase I was inactivated by incubation at 99°C for ten minutes. Fragmented cDNA was end-labeled by the catalytic addition of 3’ biotin-N6-ddATP (Perkin-Elmer, Boston, MA) with terminal deoxynucleotidyl transferase (Promega Corporation, Madison, WI). The biotin-labeled reaction products were purified by centrifugal concentration through a Centricon YM-10 Concentrator (Millipore Corporation, Billerica, MA).

growth_protocol: H. influenzae 10810 was used to inoculate 5 ml of brain heart infusion broth (BHI) containing 10ug/ml NAD and 0.1ug/ml hemin. These cultures were grown at 37C for 3 hours, collected by centrifugation, washed once in PBS with 0.1% gelatin, and resuspended in PBS-gelatin. The cultures were adjusted to an OD(605)=0.5. 5 ml of the cultures were inoculated into 120 ml of BHI broth containing NAD and 150uM deferoxamine to a final concentration of ~2x10^7 cfu/ml. 60 ml samples were taken after 90 minutes growth and transferred into an equal volume of RNAProtect reagent. Iron (500 uM FeCl3) and hemin (10ug/ml) were added to the remaining 60 ml and the cultures allowed to continue incubation at 37C for an additional 20 minutes post supplementation and 60 ml samples collected as above.

extract_protocol: RNA was prepared using Trizol (as described by the manufacturer). Residual genomic DNA was removed by treatment with RNase-free DNase (Invitrogen) as directed by the manufacturer and confirmed by q-rt-PCR analysis. RNA samples were then precipitated using LiCl and samples resolved by PAGE to ensure sample integrity.

tag: Strain 10810


title: Insulin pathway activation - replicate 1


title: volunteer8-oral_intake_stationary_bacteria

source_name: biopsy from proximal duodenum, 10-15 cm after pylorus, taken after 6 hrs of oral intake of stationary-phase-grown Lactobacillus plantarum (each half-hour)

tag: biopsies were taken after 6 hrs of oral intake and immediately snap-frozen in liquid nitrogen until RNA extraction


title: volunteer1-oral_intake_midlog_bacteria


title: H.influenzae 10810 110-1

description: Biological replicate 1, 90 minutes in FeHm Deplete BHI, followed by supplementation with Fe and Heme and growth for 20 minutes

source_name: H. influenzae 10810 grown in iron and heme deplete media for 90 minutes, then supplemented with Fe and Heme, replicate 1


title: H.influenzae 10810 110-2

description: Biological replicate 2, 90 minutes in FeHm Deplete BHI, followed by supplementation with Fe and Heme and growth for 20 minutes

source_name: H. influenzae 10810 grown in iron and heme deplete media for 90 minutes, then supplemented with Fe and Heme, replicate 2


title: H.influenzae 10810 90-1

description: Biological replicate 1, 90 minutes in FeHm deplete BHI

source_name: H. influenzae 10810 grown in iron and heme deplete media for 90 minutes, replicate 1


title: H.influenzae 10810 90-3

description: Biological replicate 3, 90 minutes in FeHm deplete BHI

source_name: H. influenzae 10810 grown in iron and heme deplete media for 90 minutes, replicate 3


title: volunteer6-oral_intake_stationary_bacteria


title: volunteer7-oral_intake_stationary_bacteria


title: volunteer5-oral_intake_stationary_bacteria


title: H.influenzae R2866 110-3

scan_protocol: not provided

organism: Haemophilus influenzae R2866

source_name: H. influenzae R2866 grown in iron and heme deplete media for 90 minutes, then supplemented with Fe and Heme, replicate 3

growth_protocol: H. influenzae R2866 was used to inoculate 5 ml of brain heart infusion broth (BHI) containing 10ug/ml NAD and 0.1ug/ml hemin. These cultures were grown at 37C for 3 hours, collected by centrifugation, washed once in PBS with 0.1% gelatin, and resuspended in PBS-gelatin. The cultures were adjusted to an OD(605)=0.5. 5 ml of the cultures were inoculated into 120 ml of BHI broth containing NAD and 150uM deferoxamine to a final concentration of ~2x10^7 cfu/ml. 60 ml samples were taken after 90 minutes growth and transferred into an equal volume of RNAProtect reagent. Iron (500 uM FeCl3) and hemin (10ug/ml) were added to the remaining 60 ml and the cultures allowed to continue incubation at 37C for an additional 20 minutes post supplementation and 60 ml samples collected as above.

tag: Strain R2866


title: H.influenzae R2866 110-2

source_name: H. influenzae R2866 grown in iron and heme deplete media for 90 minutes, then supplemented with Fe and Heme, replicate 2


title: volunteer4-oral_intake_stationary_bacteria


title: broccoli sprouts 10uM 18h

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/37133.gif
Measurement: time(change) 18 h
Compound Based Treatment: broccoli, 10 uM

hyb_protocol: not provided

scan_protocol: GenePix 4000B

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: cells treated with DMSO

label_protocol: not provided

extract_protocol: not provided

tag: cells treated with DMSO

source_name: 10uM broccoli sprouts 18h

tag: 10uM broccoli sprouts 18h


title: lncap 4hr 10uM sulforaphane

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35785.gif
Measurement: time(change) 4 h
Compound Based Treatment: sulforaphane, 10 uM

source_name: 80ug total RNA 10uM sulforaphane treated


title: 0.3uM egcg

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/48926.gif
Measurement: time(change) 0 h
Compound Based Treatment: DMSO

source_name: 0hr self

tag: 0hr self


title: H.influenzae R2866 90-3

source_name: H. influenzae R2866 grown in iron and heme deplete media for 90 minutes, replicate 3


title: H.influenzae R2866 90-2

description: Biological replicate 2, 90 minutes in FeHm deplete BHI

source_name: H. influenzae R2866 grown in iron and heme deplete media for 90 minutes, replicate 2


title: volunteer2-oral_intake_stationary_bacteria


title: lncap 18hr 10uM sulforaphane

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35789.gif
Measurement: time(change) 18 h
Compound Based Treatment: sulforaphane, 10 uM

tag: 80ug total RNA 10uM sulforaphane treated


title: H.influenzae R2866 90-1

source_name: H. influenzae R2866 grown in iron and heme deplete media for 90 minutes, replicate 1


title: volunteer3-oral_intake_stationary_bacteria


title: H.influenzae R2866 110-1

source_name: H. influenzae R2866 grown in iron and heme deplete media for 90 minutes, then supplemented with Fe and Heme, replicate 1


title: lncap 0hr sulforaphane

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35784.gif
Measurement: time(change) 0 h
Compound Based Treatment: DMSO

source_name: 80ug total RNA  untreated

tag: 80ug total RNA  untreated


title: 0h Sulf

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30470.gif
Measurement: time(change) 0 h
Compound Based Treatment: DMSO

source_name: 0h exp

tag: 0h exp


title: H.influenzae 10810 90-2

source_name: H. influenzae 10810 grown in iron and heme deplete media for 90 minutes, replicate 2


title: volunteer1-oral_intake_stationary_bacteria

source_name: biopsy from proximal duodenum, 10-15 cm after pylorus, taken after 6 hrs of oral intake of stationary-phase-grown Lactobacillus plantarum (each half-hour)


title: broccoli sprouts 10uM 24h

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/37134.gif
Measurement: time(change) 24 h
Compound Based Treatment: broccoli, 10 uM

source_name: 10uM broccoli sprouts 24h

tag: 10uM broccoli sprouts 24h


title: lncap24hrsulforaphane

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34311.gif
Measurement: time(change) 24 h
Compound Based Treatment: sulforaphane, 25 uM

source_name: 80ug total RNA 25uM sulforaphane

tag: 80ug total RNA 25uM sulforaphane


title: lncap genistein 0hr

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46713.gif
Measurement: time(change) 0 h
Compound Based Treatment: DMSO

source_name: DMSO 0hr

tag: DMSO 0hr


title: broccoli sprouts 10 uM 4h

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/37136.gif
Measurement: time(change) 4 h
Compound Based Treatment: broccoli, 10 uM

source_name: 10 uM broccoli sprouts

tag: 10 uM broccoli sprouts


title: lncap 12hr 10uM sulforaphane

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35788.gif
Measurement: time(change) 12 h
Compound Based Treatment: sulforaphane, 10 uM


title: lncap 6hr 10uM sulforaphane

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35786.gif
Measurement: time(change) 6 h
Compound Based Treatment: sulforaphane, 10 uM


title: volunteer8-placebo_control

description: mucosal response of healthy adult humans to lactic acid bacteria

source_name: biopsy from proximal duodenum, 10-15 cm after pylorus, taken after 6 hrs of oral intake of placebo control (each half-hour)


title: volunteer6-placebo_control


title: volunteer5-placebo_control


title: lncap 8hr 10uM sulforaphane

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35787.gif
Measurement: time(change) 8 h
Compound Based Treatment: sulforaphane, 10 uM

source_name: cells treated with DMSO


title: volunteer4-placebo_control


title: volunteer7-placebo_control


title: volunteer2-placebo_control


title: volunteer1-placebo_control


title: volunteer3-placebo_control


title: lncap 36hr 10uM sulforaphane

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35791.gif
Measurement: time(change) 36 h
Compound Based Treatment: sulforaphane, 10 uM


title: T1 0h 75uM Resv LN

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28904.gif
Measurement: time(change) 0 h
Compound Based Treatment: DMSO

source_name: 0h 75uM Resveratrol

tag: 0h 75uM Resveratrol


title: Huh7_IFNA2+OSM_Rep3

city: Pamplona

first: Iranzu

last: Gonzalez

state: Navarra

address: Avda. Pio XII nº 55

department: Hepathology and Gene Therapy

institute: Center for applied medical research

description: Expression analysis of Huh7 cells treated with both IFNA2 and OSM.

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133A 2.0 chip according to the protocols provided by the manufacturer.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 from Affymetrix.

data_processing: RMA

source_name: Hepatoma cell line, treated with IFNA2 and OSM

label_protocol: The cDNA was prepared from 5 microg total RNA using the One –Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthesizing the cRNA using the IVT labeling kit (Affimetrix). The synthesized cRNA was purified with the GeneChip Sample Cleanup Module (Affimetrix).

growth_protocol: Huh7 cells were seeded at 1x106 cells/plate in DMEM plus 10% FBS. Treatment was performed in DMEM supplemented with 2% FBS.

extract_protocol: The cells were harvested with TRIzol Reagent (Invitrogen)  and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

treatment_protocol: IFNa2 (50IU/mL) or OSM (20ng/mL) or IFNa2 (50IU/mL) combined with OSM (20ng/mL) for 72 hours.

tag: Huh7 cell line

value: Differentiated hepatoma from a male, 57 years old, Japanese.


title: Huh7_IFNA2+OSM_Rep1


title: Huh7_IFNA2+OSM_Rep4


title: shdb084_25uM_4hr_sulf

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35876.gif
Measurement: time(change) 4 h
Compound Based Treatment: sulforaphane, 25 uM


title: Huh7_OSM_Rep3

description: Expression analysis of Huh7 cells treated with OSM.

source_name: Hepatoma cell line, treated with OSM


title: Huh7_OSM_Rep2


title: Huh7_OSM_Rep4


title: Huh7_OSM_Rep1


title: sulforaphane 8h

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34156.gif
Measurement: time(change) 8 h
Compound Based Treatment: sulforaphane, 25 uM

source_name: dmso

tag: dmso


title: Huh7_IFNA2+OSM_Rep2


title: AKI 7h vcb1076b  wt AKI experiment

description:
Simple annotation: Pathogen, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28546.gif
Measurement: time(change) 7 h

organism: Vibrio cholerae

source_name: wt  mid log ref for AKI ( combined from several experiments)  2 ug

source_name: 7h AKI   (2 ug)

tag: 7h AKI   (2 ug)


title: Huh7_IFNA2_Rep4

description: Expression analysis of Huh7 cells treated with IFNA2.

source_name: Hepatoma cell line, treated with IFNA2


title: AKI 4h vcb1098a  wt AKI experiment

description:
Simple annotation: Pathogen, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28543.gif
Measurement: time(change) 4 h

tag: wt  mid log ref for AKI ( combined from several experiments)  2 ug

source_name: 4h AKI   (2 ug)

tag: 4h AKI   (2 ug)


title: broccoli sprouts 10uM 12h

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/37304.gif
Measurement: time(change) 12 h
Compound Based Treatment: broccoli, 10 uM

source_name: 10uM broccoli sprouts

tag: 10uM broccoli sprouts


title: broccoli sprouts 10uM 33h

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/37135.gif
Measurement: time(change) 33 h
Compound Based Treatment: broccoli, 10 uM

tag: cells treated with DMSO

source_name: 10uM broccoli sprouts 33h

tag: 10uM broccoli sprouts 33h


title: Huh7_IFNA2_Rep3


title: LN_MSA_10uM_0h

description:
Simple annotation: prostate cancer, selenium
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28349.gif
Measurement: time(change) 0 h
Compound Based Treatment: MSA, 10 uM

source_name: 14.5 uM selenium LNCaP total RNA

tag: 14.5 uM selenium LNCaP total RNA

source_name: MSA 10 uM 0h LNCaP total RNA

tag: MSA 10 uM 0h LNCaP total RNA


title: AKI 8h vcb1107a  wt AKI experiment

description:
Simple annotation: Pathogen, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28547.gif
Measurement: time(change) 8 h

source_name: 8h AKI   (2 ug)

tag: 8h AKI   (2 ug)


title: broccoli sprouts 10uM

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/37132.gif
Measurement: time(change) 8 h
Compound Based Treatment: broccoli, 10 uM

source_name: 10uM broccoli sprouts 8h

tag: 10uM broccoli sprouts 8h


title: lncap 24hr 10uM sulforaphane

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35790.gif
Measurement: time(change) 24 h
Compound Based Treatment: sulforaphane, 10 uM

source_name: 80ug total RNA 10uM sulforaphane treated


title: LNCaP 25uM sulforaphane 18hr

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/36355.gif
Measurement: time(change) 18 h
Compound Based Treatment: sulforaphane, 25 uM

source_name: 25uM sulforaphane 18hrs

tag: 25uM sulforaphane 18hrs


title: 25uM sulforaphane treated LNCaP cells 36hr

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35900.gif
Measurement: time(change) 36 h
Compound Based Treatment: sulforaphane, 25 uM

source_name: cells treated with DMSO

source_name: 25uM sulforaphane

tag: 25uM sulforaphane


title: Huh7_IFNA2_Rep2


title: AKI 6h vcb1076a  wt AKI experiment

description:
Simple annotation: Pathogen, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28545.gif
Measurement: time(change) 6 h

source_name: 6h AKI   (2 ug)

tag: 6h AKI   (2 ug)


title: Huh7_Untreated_Rep2

description: Expression analysis of untreated Huh7 cells. Control.

source_name: Hepatoma cell line, untreated


title: Huh7_Untreated_Rep1


title: AKI 5h vcb1098b  wt AKI experiment

description:
Simple annotation: Pathogen, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28544.gif
Measurement: time(change) 5 h

source_name: 5h AKI   (2 ug)

tag: 5h AKI   (2 ug)


title: Huh7_Untreated_Rep3


title: AKI 1h vcb1031b  wt AKI experiment

description:
Simple annotation: Pathogen, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28540.gif
Measurement: time(change) 1 h

source_name: wt  mid log ref for AKI ( combined from several experiments)  2 ug

source_name: 1 h AKI   (2 ug)

tag: 1 h AKI   (2 ug)


title: exp.n 48 atra Y atorvastatin Y time 48 h

status: Public on Jan 20 2009

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

description:
BeadChip array data quality control was performed using Illumina BeadStudio software version 1.3.1.5. Probe average intensity signal was calculated with
BeadStudio without background correction. Raw data were analyzed with Bioconductor. To remove low quality signals two filters were applied sequentially to the 47293 reference sequences available in the Sentrix Human-6 Expression BeadChip: gene specific detection value should be >0.6 in at least 50% of the samples, gene specific interquantile range should be >0.2.  The statistical analysis of the time course experiments was performed using maSigPro Bioconductor library.

hyb_protocol: Sentrix Human-6 Expression BeadChip hybridization, washing and staining were also done as suggested by the manufacturer.

scan_protocol: Arrays were scanned on Illumina BeadStation 500

data_processing: Average probe intensities were log2 transformed and normalized by loess

label: Biotin

source_name: NB4 human APL cell line

label_protocol: cRNA was synthesized using Illumina RNA Amplification Kit Ambion (Austin, TX) starting from 500 ng of total RNA and following the procedure suggested by manufacturer.

growth_protocol: NB4 human APL cell line was grown in RPMI 1640 supplemented with 10% fetal bovine serum and antibiotics.

extract_protocol: Trizol extraction as recomanded by manufacturer

treatment_protocol: NB-4 cells were pretreated for one hour with ATRA, then treated with atorvastatin at times indicated in Title field

tag: NB4 human APL cell line


title: AKI 98 9h vcb1107b  wt AKI experiment

description:
Simple annotation: Pathogen, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28548.gif
Measurement: time(change) 9 h

source_name: 9h AKI   (2 ug)

tag: 9h AKI   (2 ug)


title: broccoli sprouts 10uM 6h

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/37303.gif
Measurement: time(change) 6 h
Compound Based Treatment: broccoli, 10 uM

source_name: 10uM broccoli sprouts


title: exp.n 46 atra Y atorvastatin N time 48 h


title: sulforaphane 6h

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/34158.gif
Measurement: time(change) 6 h
Compound Based Treatment: sulforaphane, 25 uM

source_name: dmso

tag: dmso


title: T1 0h Curcumin LNCaP

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26975.gif
Measurement: time(change) 0 h
Compound Based Treatment: DMSO

source_name: 10uM Curcumin

tag: 10uM Curcumin


title: exp.n 45 atra N atorvastatin N time 48 h


title: exp.n 40 atra Y atorvastatin Y time 8 h


title: Huh7_IFNA2_Rep1

description: Expression analysis of Huh7 cells treated with IFNA2.

source_name: Hepatoma cell line, treated with IFNA2

tag: Huh7 cell line


title: AKI 3h vcb1033b  wt AKI experiment

description:
Simple annotation: Pathogen, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28542.gif
Measurement: time(change) 3 h

tag: wt  mid log ref for AKI ( combined from several experiments)  2 ug

source_name: 3 h AKI   (2 ug)

tag: 3 h AKI   (2 ug)


title: AKI 2h vcb1033a  wt AKI experiment

description:
Simple annotation: Pathogen, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28541.gif
Measurement: time(change) 2 h

source_name: 2 h AKI   (2 ug)

tag: 2 h AKI   (2 ug)


title: Huh7_Untreated_Rep4


title: Kidney_transplanted_CO-treated_24h_donor8

city: Vienna

first: Florian

middle: Leopold

last: Klinglmueller

address: Spitalgasse 23

department: Medizinische Statistik und Informatik

country: Austria

institute: Medizinische Universitaet Wien

hyb_protocol: Affymetrix recommended procedure

scan_protocol: Affymetrix recommended procedure

data_processing:
RMA default procedure:
Bg - Corretion: Exponential-Normal Deconvolution
Normalization: Quantile
Summarization: RMA

software:
GNU R
Bioconductor - package:affy

source_name: Kidney, transplanted, treated with CO, 24h

label_protocol: Affymetrix recommended procedure

extract_protocol: Affymetrix recommended procedure

tag: Tissue

value: Kidney, Treatment:air, Transplant:yes, Time:24h, Donor:8


title: exp.n 38 atra Y atorvastatin N time 8 h


title: exp.n 44 atra Y atorvastatin Y time 24 h


title: exp.n 42 atra Y atorvastatin N time 24 h


title: exp.n 47 atra N atorvastatin Y time 48 h


title: exp.n 43 atra N atorvastatin Y time 24 h


title: shdb087

description:
Simple annotation: prostate cancer, Chemoprevention
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35899.gif
Measurement: time(change) 12 h
Compound Based Treatment: sulforaphane, 25 uM

tag: cells treated with DMSO


title: Kidney_transplanted_CO-treated_24h_donor7

value: Kidney, Treatment:air, Transplant:yes, Time:24h, Donor:7


title: AKI 99 10 h vcb1108a  wt AKI experiment

description:
Simple annotation: Pathogen, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28549.gif
Measurement: time(change) 10 h

source_name: 10h AKI   (2 ug)

tag: 10h AKI   (2 ug)


title: Kidney_transplanted_untreated_24h_donor7

source_name: Kidney, transplanted, untreated, 24h


title: exp.n 36 atra Y atorvastatin Y time 48 h


title: Kidney_transplanted_CO-treated_24h_donor6

value: Kidney, Treatment:air, Transplant:yes, Time:24h, Donor:6


title: exp.n 39 atra N atorvastatin Y time 8 h


title: Kidney_transplanted_CO-treated_24h_donor5

value: Kidney, Treatment:air, Transplant:yes, Time:24h, Donor:5


title: Kidney_transplanted_CO-treated_4h_donor2

source_name: Kidney, transplanted, treated with CO, 4h

value: Kidney, Treatment:air, Transplant:yes, Time:4h, Donor:2


title: Kidney_transplanted_CO-treated_4h_donor3

value: Kidney, Treatment:air, Transplant:yes, Time:4h, Donor:3


title: exp.n 41 atra N atorvastatin N time 24 h


title: Kidney_transplanted_untreated_4h_donor4

source_name: Kidney, transplanted, untreated, 4h

value: Kidney, Treatment:air, Transplant:yes, Time:4h, Donor:4


title: Kidney_transplanted_CO-treated_4h_donor4


title: Kidney_transplanted_untreated_24h_donor6


title: exp.n 31 atra N atorvastatin Y time 24 h

description:
BeadChip array data quality control was performed using Illumina BeadStudio software version 1.3.1.5. Probe average intensity signal was calculated with
BeadStudio without background correction. Raw data were analyzed with Bioconductor. To remove low quality signals two filters were applied sequentially to the 47293 reference sequences available in the Sentrix® Human-6 Expression BeadChip: gene specific detection value should be ≥0.6 in at least 50% of the samples, gene specific interquantile range should be ≥0.2.  The statistical analysis of the time course experiments was performed using maSigPro Bioconductor library.

hyb_protocol: Sentrix® Human-6 Expression BeadChip hybridization, washing and staining were also done as suggested by the manufacturer.

data_processing: Average probe intensities were log2 transformed and normalized by loess method.


title: Kidney_transplanted_untreated_24h_donor5


title: exp.n 37 atra N atorvastatin N time 8 h


title: exp.n 33 atra N atorvastatin N time 48 h


title: exp.n 34 atra Y atorvastatin N time 48 h


title: exp.n 26 atra Y atorvastatin N time 8 h


title: exp.n 30 atra Y atorvastatin N time 24 h


title: Kidney_transplanted_untreated_4h_donor2


title: exp.n 28 atra Y atorvastatin Y time 8 h


title: Kidney_transplanted_untreated_24h_donor8


title: exp.n 35 atra N atorvastatin Y time 48 h


title: exp.n 32 atra Y atorvastatin Y time 24 h


title: exp.n 29 atra N atorvastatin N time 24 h


title: exp.n 27 atra N atorvastatin Y time 8 h


title: Kidney_transplanted_CO-treated_4h_donor1

value: Kidney, Treatment:air, Transplant:yes, Time:4h, Donor:1


title: Kidney_naive_rep1

source_name: Kidney, untreated

value: Kidney, Treatment:naive, Transplant:no, Time:None, Donor:None


title: exp.n 20 atra Y atorvastatin Y time 24 h


title: exp.n 25 atra N atorvastatin N time 8 h


title: Kidney_naive_rep2


title: 500 ng total RNA, Prep. 2

description: MVs obtained from MSCs contained mRNA. To identify the mRNA species shuttled by the MVs we used microarray analysis. Specifically, microarrays were used not to define the amount of mRNA in the MVs but only to define which transcripts were present. Transcripts present in the MVs were defined as those characterized by a positive linear relation between the transcript signal detected by the microarray analysis and the amount of total RNA hybridized. This analysis was done hybridizing arrays with labelled-cRNA produced using three different concentrations of total RNA extracted from two independent preparations of MVs.

hyb_protocol: Hybridization, washing and staining were done as suggested by the manufacturer.

scan_protocol: Arrays were scanned on Illumina BeadStation 500 (Illumina, San Diego, CA, USA)

data_processing: BeadChip array data quality control was performed using Illumina BeadStudio software version 1.3.1.5. Transcript average intensity signals were calculated with BeadStudio without background correction. Raw data were analyzed using Bioconductor. Average transcript intensities were log2 transformed and normalized by loess method.

source_name: Microvesicles (MV) from Mesenchymal Stem Cells (MSC)

label_protocol: cRNA synthesis and labeling was done using Illumina RNA Amplification Kit (Ambion) following the procedure suggested by manufacturer.

extract_protocol: RNA was extracted from MVs using TRIZOL reagent (Invitrogen) following the procedure suggested by the manufacturer.

tag: MVs were obtained from supernatants of MSCs cultured in RPMI deprived of FCS and supplemented with 0.5% of BSA (Sigma).


title: 1000 ng total RNA, Prep. 2


title: 250 ng total RNA, Prep. 2


title: Kidney_transplanted_untreated_4h_donor1


title: exp.n 18 atra Y atorvastatin N time 24 h


title: exp.n 22 atra Y atorvastatin N time 48 h


title: exp.n 16 atra Y atorvastatin Y time 8 h


title: Kidney_transplanted_untreated_4h_donor3


title: exp.n 24 atra Y atorvastatin Y time 48 h


title: exp.n 14 atra Y atorvastatin N time 8 h


title: 500 ng total RNA, Prep. 1


title: exp.n 19 atra N atorvastatin Y time 24 h


title: exp.n 21 atra N atorvastatin N time 48 h


title: colorectal cancer DNA hypermethylome: DAC vs mock in HCT 116

city: Ghent

first: Leander

last: Van Neste

address: Coupure Links 653

department: Molecular Biotechnology

country: Belgium

institute: Ghent University

description: Identification of the colorectal cancer DNA hypermethylome revealed by gene expression profiling: DAC vs mock in HCT 116

hyb_protocol: Agilent Gene Expression Hybridization Kit using manufacturer's protocol (G4140-90050)

scan_protocol: Microarrays are scanned with Agilent G2565BA microarray scanner under default settings recommended by Agilent Technologies for expression microarrays. with 100% PMT and 10 micrometer resolutions. Data are extracted using Feature Extraction Software v8.1 (Agilent Technologies) under default settings for expression microarrays.

data_processing: Log ratio of red signal to green signal was calculated after loess normalization as implemented in the Limma package from Bioconductor

source_name: Mock treated HCT 116 cells

label_protocol: Agilent low RNA input linear amplification kit

growth_protocol: McCoy's 5A medium with 10% BCS and 1x P/S

extract_protocol: TriZol extraction followed by RNeasy kit (Qiagen) clean-up with on-column DNase treatment

treatment_protocol: 1x PBS for 96 hours

source_name: 5-AZA treated HCT 116 cells

treatment_protocol: 5 micromolar 5-AZA for 96 hours

tag: HCT 116 human colorectal cancer cell line treated with 5-AZA


title: 1000 ng total RNA, Prep. 1


title: Colorectal cancer DNA hypermethylome: DKO of HCT116

scan_protocol: Microarrays are scanned with Agilent G2565BA microarray scanner under default settings recommended by Agilent Technologies for expression microarrays with 100% PMT and 10 micrometer resolutions. Data are extracted using Feature Extraction Software v8.1 (Agilent Technologies) under default settings for expression microarrays.

source_name: Wild type HCT116

source_name: DKO of HCT116

tag: DNMT1 and DNMT3b deficient HCT116 human colorectal cancer cell line


title: exp.n 23 atra N atorvastatin Y time 48 h

source_name: NB4 human APL cell line


title: colorectal cancer DNA hypermethylome: TSA vs mock in HCT 116

description: Identification of the colorectal cancer DNA hypermethylome revealed by gene expression profiling: TSA vs mock in HCT 116

source_name: TSA treated HCT 116 cells

treatment_protocol: 300 nanomolar TSA for 18 hours

tag: HCT 116 human colorectal cancer cell line treated with TSA


title: 250 ng total RNA, Prep. 1


title: H3K4me2 patterns in DKO

type: genomic

hyb_protocol: Labeled DNA was mixed (5 – 6 µg each of immunoenriched and whole cell extract DNA) and hybridized to arrays in Agilent hybridization chambers for 20 hours at 40°C.

scan_protocol: Hybridized microarrays were scanned using an Agilent G2565BA microarray scanner.

data_processing: Median blanks subtraction followed by an inter-array median normalization and a dye-bias median normalization. Downstream analysis in R.

molecule: genomic DNA

source_name: DKO Immunoprecipitated DNA

label_protocol: Bioprime random primer labeling kits

growth_protocol: McCoy’s 5A modified medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin

extract_protocol: Multiple phenol:chloroform:isoamyl alcohol extractions

treatment_protocol: ChIP DNA using a H3K4me2 specific antibody

tag: Immunoprecipitation using a specific antibody for H3K4me2 of the DKO human colorectal cancer cell line

source_name: DKO WCE

treatment_protocol: Whole cell extract

tag: Whole cell extract of the DKO human colorectal cancer cell line


title: Mycobacterium bovis BCG_hydrogen peroxide_60min_replicate2

city: ft. meade

first: Hyeung-Jin

last: Jang

state: MD

address: 701 Mapes Road

department: OPP/BEAD

institute: USEPA

description: Hydrogen peroxide treatment for 60 min.

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures (target signal value was 500)

data_processing: Affymetrix GeneChip Opererating Software (GCOS) version 1.2

organism: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2

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

growth_protocol: (i) we initiated M. bovis cultures at 37°C with shaking at 250 rpm using sterilized Middlebrook 7H9 broth for 5days, (ii) Mycobacteria were harvested, washed and resuspended in sterilized Lurria-Bertani (LB) broth with 0.1% (v/v) Tween 80. Then the cultures were incubated for further 24 hours shaking at 37°C. To see the efficacy of an antimicrobial against mycobacteria, several concentrations of sodium hypochlorite were added to the cells.

extract_protocol: Total RNA was isolated after 10 and 60 min incubation with and without (control) hydrogen peroxide using the RiboPure – Bacteria kit (Ambion, Inc., Austin, TX)[16]. The mycobacterial cells treated with hydrogen peroxide and untreated cells as controls were harvested and resuspended in PBS buffer. For stabilize of RNA, we used for breaking the micobaterium cell, we used bead beater, 5 times for 1min beating and 2min on ice.

treatment_protocol: 2.5mM hydrogen peroxide

tag: strain Pasteur 1173P2 Wild type


title: Mycobacterium bovis BCG_hydrogen peroxide_60min_replicate3

description: Hydrogen peroxide treatment for 60 min.


title: exp.n 13 atra N atorvastatin N time 8 h

tag: NB4 human APL cell line


title: H3K27me3 patterns in DKO

treatment_protocol: ChIP DNA using a H3K27me3 specific antibody

tag: Immunoprecipitation using a specific antibody for H3K27me3 of the DKO human colorectal cancer cell line


title: exp.n 15 atra N atorvastatin Y time 8 h


title: Mycobacterium bovis BCG_hydrogen peroxide_10min_replicate3

description: Hydrogen peroxide treatment for 10 min.


title: Mycobacterium bovis BCG_hydrogen peroxide_60min_replicate1

description: Hydrogen peroxide treatment for 60 min.


title: Mycobacterium bovis BCG_hydrogen peroxide_10min_replicate2

description: Hydrogen peroxide treatment for 10 min.


title: Mycobacterium bovis BCG_hydrogen peroxide_10min_replicate1

description: Hydrogen peroxide treatment for 10 min.


title: H3K27me3 patterns in HCT116

source_name: HCT116 Immunoprecipitated DNA

tag: Immunoprecipitation using a specific antibody for H3K27me3 of the HCT116 human colorectal cancer cell line

source_name: HCT116 WCE

tag: Whole cell extract of the HCT116 human colorectal cancer cell line


title: ProstateCancer_140

status: Public on Jan 19 2009

city: Oslo

first: Gard

middle: Olav

last: Thomassen

address: Radiumhospitalet, Rikshospitalet HF

department: Institute for Cancer Research

country: Norway

institute: Rikshospitalet

hyb_protocol: According to Nimblegen service standard

scan_protocol: According to Nimblegen service standard

data_processing: Each oligo intensity (log2) from each chip has been divided by the median value of the three leukemia cell lines (log2).

source_name: Human prostate

label_protocol: According to Nimblegen service standard

growth_protocol: See materials and methods in the original paper.

extract_protocol: TRIzol

tag: Prostate cancer

tag: Total RNA depleated for ribosomal RNA


title: CellLine_REH_rep_c

source_name: Human leukaemia REH cell line

tag: Leukaemia, cell line


title: ProstateCancer_139


title: exp.n 17 atra N atorvastatin N time 24 h


title: CellLine_RCHACV_rep_c

source_name: Human leukaemia RCHACV cell line


title: CellLine_TOM1_rep_c

source_name: Human leukaemia TOM1 cell line


title: ProstateCancer_40


title: H3R2me1_wild-type yeast_complete medium

city: Cambridge

first: Antonis

last: Kirmizis

state: England

address: Gurdon institute, Tennis Court Rd

country: United Kingdom

institute: Antonis Kirmizis

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

hyb_protocol: NimbleGen

scan_protocol: NimbleGen

data_processing: NimbleGen

organism: Saccharomyces cerevisiae

source_name: Chromatin Immunoprecipitated DNA from S.cerevisiae using H3R2me1 antibody

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

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

tag: BY4741 strain

source_name: Input chromatin DNA control

tag: BY4741 Strain


title: H3K4me2 patterns in HCT116

tag: Immunoprecipitation using a specific antibody for H3K4me2 of the HCT116 human colorectal cancer cell line


title: H3K36me3_wild-type yeast_complete medium

source_name: Chromatin Immunoprecipitated DNA from S.cerevisiae using H3K36me3 antibody


title: CellLine_TOM1_rep_a


title: ProstateCancer_114


title: CellLine_TOM1_rep_b


title: H3K79me3_wild-type yeast_complete medium

source_name: Chromatin Immunoprecipitated DNA from S.cerevisiae using H3K79me3 antibody


title: CellLine_RCHACV_rep_a


title: Vegetative shoot apical meristem, replicate B

status: Public on Jan 17 2009

city: Parkville

first: Chui

last: WONG

state: Victoria

address: University of Melbourne

department: Land and Food

country: Australia

institute: University of Melbourne

description: This experiment consists of 5 samples with two biological replicates ( a total of 10 arrays)

hyb_protocol: cDNA labelling and Affymetrix Soybean GeneChip hybridization was carried out by AGRF (Australian Genome Research Facility, Melbourne, Australia) according to protocol provided by Affymetrix using 3 µg of total RNA.

scan_protocol: Scanning of the arrays was carried out by AGRF (Australian Genome Research Facility, Melbourne, Australia) according to protocol provided by Affymetrix.

data_processing: Expression levels were estimated from Affymetrix hybridization intensity data using MicroArray Suite 5.0 (Affymetrix 2001). Raw numeric values representing the signal of each feature were filtered so that genes with expression levels that were called as “Marginal” or “Absence” in all 10 arrays according to the Affymetrix Statistical Algorithms were excluded from further analysis. The resulting data were then normalized using Robust Multiarray Averaging (RMA) implemented in AffylmGUI (Wettenhall and Smyth, 2004) and then imported into maSigPro, a statistical method employing a two-step regression approach (Conesa et al., 2006). For the first regression model, the p value is set at <0.05 while in the second regression step, a backward method was selected. A combination of quadratic and cubic model was used to evaluate significantly differential expression profiles in the process.

organism: Glycine max

source_name: soybean shoot apical meristem, vegetative

growth_protocol: Soybean plants [Glycine max. (L) Merr. Cv. Bragg] were grown from seeds in a greenhouse located at the University of Melbourne, Victoria, Australia for 10 days.

extract_protocol: Total RNA was extracted from dissected SAMs using Qiagen RNeasy Mini Kit with on-column DNAse digestion (Qiagen Pty Ltd, Victoria, Australia).

treatment_protocol: Soybean plants [Glycine max. (L) Merr. Cv. Bragg] were grown from seeds in a greenhouse located at the University of Melbourne, Victoria, Australia for 10 days before being shifted to growth chamber (short-day treatment) under a 10-hour light regime (100 µmol m-2 s-1) maintained at a constant temperature of 24°C.

tag: Vegetative shoot apical meristem micro-dissected from 10-day-old soybean plants under the dissecting microscope at 40x magnification


title: Soybean shoot apical meristem, 2 short-day replicate B

source_name: shoot apical meristems from 2 short-day treated soybean

label_protocol: cDNA labelling and Affymetrix Soybean GeneChip hybridization was carried out by AGRF (Australian Genome Research Facility, Melbourne, Australia) according to protocol provided by Affymetrix using 3 µg of total RNA.

tag: shoot apical meristem micro-dissected from soybeans treated with 2 complete short-day cycles


title: Soybean shoot apical meristem, 4 short-day replicate B

source_name: shoot apical meristem from soybean subjected to 4 complete short-day cycles

tag: soybean shoot apical meristems micro-dissected from soybean subjected to 4 complete short-day cycles


title: Soybean shoot apical meristem, 6 short-day treatment

source_name: shoot apical meristem micro-dissected from soybean plants after 6 short-day treatment

growth_protocol: Soybean plants [Glycine max. (L) Merr. Cv. Bragg] were grown from seeds in a greenhouse located at the University of Melbourne, Victoria, Australia for 10 days and then shifted to short-day growth chamber for short-day treatment.

tag: hoot apical meristem micro-dissected from 10-day-old soybean plants that has been subjected to 6 complete short-day cycle


title: Soybean shoot apical meristem, 1 short-day treatment replicate B

source_name: shoot apical meristem micro-dissected from soybean treated with 1 short-day

tag: Shoot apical meristem micro-dissected from 10-day-old soybean plants that has been subjected to 1 complete short-day cycle


title: Soybean shoot apical meristem, 6 short-day replicate B

source_name: soybean shoot apical meristem subjected to 6 complete short-day cycles

tag: Shoot apical meristem micro-dissected from 10-day-old soybean plants that has been subjected to 6 complete short-day cycle


title: Soybean shoot apical meristem, 2 short-day treatment

source_name: shoot apical meristem micro-dissected from 2 short-day treated soybean plants

tag: hoot apical meristem micro-dissected from 10-day-old soybean plants that has been subjected to 2 complete short-day cycles.


title: Soybean shoot apical meristem, 4 short-day treatment

source_name: shoot apical meristem from soybean under 4 complete short-day treatment

tag: Shoot apical meristem micro-dissected from 10-day-old soybean plants that has been subjected to 4 complete short-day cycle


title: HCT116

status: Public on Jan 18 2009

city: Baltimore

first: Andrew

middle: P.

last: Feinberg

address: 855 N. Wolfe Street

department: Center for Epigenetics and Department of Medicine

institute: Johns Hopkins University

hyb_protocol: Performed by NimbleGen using standard protocol

data_processing: Briefly, we first quantile normalized Cy3 (Input) intensities from all arrays to a common target. We used a smoothing procedure to improve the signal to noise ratio of the M (log2 ratio Cy5/Cy3) values and fitted a function of M values to the chromosomal location using loess. We then picked the genomic regions with the lowest 20% fitted values as the reference region. The Cy5 intensities in the reference regions should have similar distributions in each sample. We therefore quantile normalized them to the same distribution target. The quantile procedure was used to construct a function to map pre-normalization Cy5 intensities to post-normalization Cy5 intensities. This map was then applied to all the Cy5 intensities. This procedure made the M values comparable from array to array.

source_name: Chromatin immunoprecipitated DNA from HCT116 cells using H3K9Me2 antibody

source_name: Input DNA


title: Soybean Shoot Apical Meristem, 1 short-day treatment

source_name: Shoot apical meristem after one short-day treatment

growth_protocol: Soybean plants [Glycine max. (L) Merr. Cv. Bragg] were grown from seeds in a greenhouse located at the University of Melbourne, Victoria, Australia for 10 days and then shifted to short-day growth chamber for one complete short-day treatment.


title: sample13793A_SASG511_ID219

city: Bonn

last: Sass

state: NRW

address: Sigmund-Freud-Straße 25

department: Institute for Microbiology (IMMIP)

country: Germany

institute: University of Bonn

hyb_protocol: Microarray transcriptional profiling by competitive hybridization of fluorescence-labeled DNA was performed using the custom PCR product full-genome chip sciTracer (Scienion, Berlin, Germany) containing 2338 unique open reading frames representing 90% of the S. aureus N315 genome (NC_002745). Additional information on the microarray platform is described elsewhere. The experiment was performed 2 times including a dye swap resulting in two chips per competitive comparison with the incorporated dye reversed on two separate arrays. All hybridizations were done with equal amounts of fluorescence-labeled DNA probes or picomols of dye. Fluorescence-labeled DNA probes were mixed in hybridization buffer (Scienion) in a total volume of 55 µl and denatured at 95°C for 2 min and subsequently applied to the microarray slide following incubation at 42°C for 72 hours under humidified conditions according to the manufacturer’s instructions. Hybridized microarrays were washed at room temperature in SSC buffer with decreasing salt concentrations (1 x SSC/0.3% SDS for 5 min, 0.2 x SSC for 5 min, 0.06 x SSC for 30s).

scan_protocol: The intensity of fluorescence of the microarray was scanned with a GenePix 4000B scanner (Axon Instruments/Distribution by Biozyme Scientific GmbH, Hessisch Oldendorf, Germany). TIFF images were captured and analysed with GenePixPro4.1 software (Axon Instruments). The actual signal intensity was calculated by substracting the mean value of the local background intensity from the mean value of the signal intensity of the individual spot.

data_processing: The data sets were then normalized by using Acuity 3.1 software (Axon Instruments) and by applying the LOWESS algorithm.

organism: Staphylococcus aureus

source_name: Staphylococcus aureus SG511

label_protocol: Fluorescence-labeled DNA was obtained by reverse transcription of total RNA. Therefore, total RNA preparations (3 µg) were transcribed into cDNA using BioScript reverse transcriptase (Bioline, Luckenwalde, Germany) and pd(N)6 random hexamers (GE Healthcare - Amersham, NJ, USA) following the manufacturers’ instructions. For fluorescence-labeling, three different aliquots of cDNA preparations from separate cultures of the respective experiment were pooled to a total amount of 300 ng (100 ng each) and were subsequently employed in the labeling reaction using the BioPrime(R) DNA Labeling System (Invitrogen, Karlsruhe, Germany) according to the instruction manual using pd(N)6 random hexamers (Invitrogen), 0.1 mM CyDye3- or CyDye5-dCTPs aside from 0.2 mM dCTP, 0.5 mM dATP, 0.5 mM dTTP, 0.5 mM dGTP (GE Healthcare - Amersham).

growth_protocol: 10 ml S. aureus cultures for RNA preparations were diluted 200-fold from fresh BHI broth overnight cultures and further incubated until they reached an OD600 ~ 1.0.

extract_protocol: Exponential-phase cultures of 10 ml for total RNA preparations were grown as aforementioned and fixed by incubation with two volumes of prewarmed RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany) for 5 min at 37°C. The cells were subsequently harvested by 20 min of centrifugation at 4000 rpm and 37°C, and the pellets were shock-frozen in liquid nitrogen and kept at -70°C. The cells were lysed in the presence of 400 µg/ml lysostaphin (Genmedics, Reutlingen, Germany) and total RNA was extracted using the PrestoSpin R bug kit including DNase I treatment (Molzym, Bremen, Germany) following the manufacturer’s instructions. Quality and quantity of total RNA were confirmed by agarose gel electrophoresis and measured using the Nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, USA).

tag: Staphylococcus aureus SG511 is a sensitive control strain (methicillin susceptible) from the strain collection of the Robert Koch-Institute, Berlin, Germany.

source_name: Staphylococcus aureus 137/93A

tag: Methicillin-resistant S. aureus (MRSA) SA137/93A, isolated from a tracheal secretion and displays heterogeneous intermediate vancomycin resistance (hVISA strain, MIC

value: 8 mg/L in BHI). Source:Reipert, A., K. Ehlert, T. Kast, and G. Bierbaum. 2003. Morphological and genetic differences in two isogenic Staphylococcus aureus strains with decreased susceptibilities to vancomycin. Antimicrob.Agents Chemother. 47:568-576.


title: sample13793A_SASG511_ID216

hyb_protocol: Microarray transcriptional profiling by competitive hybridization of fluorescence-labeled DNA was performed using the custom PCR product full-genome chip sciTracer (Scienion, Berlin, Germany) containing 2338 unique open reading frames representing 90% of the S. aureus N315 genome (NC_002745). Additional information on the microarray platform is described elsewhere. The experiment was performed 2 times including a dye swap resulting in two chips per competitive comparison with the incorporated dye reversed on two separate arrays. All hybridizations were done with equal amounts of fluorescence-labeled DNA probes or picomols of dye. Fluorescence-labeled DNA probes were mixed in hybridization buffer (Scienion) in a total volume of 55 µl and denatured at 95°C for 2 min and subsequently applied to the microarray slide following incubation at 42°C for 72 hours under humidified conditions according to the manufacturer’s  instructions. Hybridized microarrays were washed at room temperature in SSC buffer with decreasing salt concentrations (1 x SSC/0.3% SDS for 5 min, 0.2 x SSC for 5 min, 0.06 x SSC for 30s).


title: differentiated mES cells WT

description: differentiated mES cells WT

scan_protocol: Performed by NimbleGen using standard protocol

organism: Mus musculus

source_name: Chromatin immunoprecipitated DNA from differentiated mES cells WT cells using H3K9Me2 antibody

tag: differentiated mES cells WT


title: Placenta

description: Placenta

source_name: Chromatin immunoprecipitated DNA from Placenta cells using H3K9Me2 antibody

label_protocol: Performed by NimbleGen using standard protocol

tag: Placenta


title: Placenta

description: Placenta

extract_protocol: Performed by NimbleGen using standard protocol


title: GM06993

source_name: Chromatin immunoprecipitated DNA from GM06993 cells using H3K9Me2 antibody


title: Differentiated ES G9a-/-

description: Differentiated ES G9a-/-

source_name: Chromatin immunoprecipitated DNA from Differentiated ES G9a-/- cells using H3K9Me2 antibody

tag: Differentiated ES G9a-/-


title: U2OS_PRC_shRNA1_pLenti_2_2007

status: Public on Jan 16 2009

city: Chicago

first: Richard

middle: C

last: Scarpulla

state: IL

address: 303 East Chicago Ave.

department: CMB

institute: Northwestern Medical School

description: Total RNA was isolated from U2OS PRC shRNA1 transductants using TRIzol (Invitrogen) and DNase treated with the TURBO DNA-free kit (Ambion). RNA samples were further purified using the RNeasy MinElute Cleanup kit (Qiagen). Integrity of the RNA was evaluated using the Agilent 2100 BioAnalyzer. 500 ng of RNA was used to perform in vitro transcription in the presence of biotin UTP with the Illumina TotalPrep RNA amplification kit (Ambion). The amplified, labeled RNA (1.5 _g) was then hybridized in triplicate to an Illumina Whole-Genome Sentrix Human-6 v2 Expression BeadChip, and detected according to the Illumina user manual.

hyb_protocol: standard as recommended by the Illumina user manual

scan_protocol: standard as recommended by Illumina

data_processing: The data was preprocessed by Bioconductor lumi package (version 1.7.18). It was vst transformed and quantile normalized.

source_name: U2OS PRC shRNA1_pLenti_2007

label_protocol: Illumina TotalPrep RNA amplification kit (Ambion) per manufacturer's instructions

extract_protocol: Total RNA was extracted from U2OS PRC shRNA1 cells using TRIzol reagent (Invitrogen) and purified further using the RNeasy MinElute Cleanup kit (Qiagen).

tag: Cells

value: U2OS, Treatment:infected with PRC shRNA1_pLenti, blasticidin selection


title: Hela

description: Hela

source_name: Chromatin immunoprecipitated DNA from Hela cells using H3K9Me2 antibody

tag: Hela


title: U2OS_PRC_shRNA1_pLenti_3_2007


title: Vegetative soybean shoot apical meristem

source_name: Vegetative shoot apical meristem


title: U2OS_control_shRNA_pLenti_2_2007

description: Total RNA was isolated from U2OS control shRNA transductants using TRIzol (Invitrogen) and DNase treated with the TURBO DNA-free kit (Ambion). RNA samples were further purified using the RNeasy MinElute Cleanup kit (Qiagen). Integrity of the RNA was evaluated using the Agilent 2100 BioAnalyzer. 500 ng of RNA was used to perform in vitro transcription in the presence of biotin UTP with the Illumina TotalPrep RNA amplification kit (Ambion). The amplified, labeled RNA (1.5 _g) was then hybridized in triplicate to an Illumina Whole-Genome Sentrix Human-6 v2 Expression BeadChip, and detected according to the Illumina user manual.

source_name: U2OS control shRNA_pLenti_2007

extract_protocol: Total RNA was extracted from U2OS control shRNA cells using TRIzol reagent (Invitrogen) and purified further using the RNeasy MinElute Cleanup kit (Qiagen).

value: U2OS, Treatment:infected with control shRNA_pLenti, blasticidin selection


title: U2OS_control_shRNA_pLenti_3_2007


title: Liver

description: Liver

source_name: Chromatin immunoprecipitated DNA from liver cells using H3K9Me2 antibody

tag: Liver


title: U2OS_PRC_shRNA1_pLenti_1_2007


title: U2OS_control_shRNA_pLenti_1_2007


title: U2OS_PRC_shRNA4_pLenti_3

description: Total RNA was isolated from U2OS PRC shRNA4 transductants using TRIzol (Invitrogen) and DNase treated with the TURBO DNA-free kit (Ambion). RNA samples were further purified using the RNeasy MinElute Cleanup kit (Qiagen). Integrity of the RNA was evaluated using the Agilent 2100 BioAnalyzer. 500 ng of RNA was used to perform in vitro transcription in the presence of biotin UTP with the Illumina TotalPrep RNA amplification kit (Ambion). The amplified, labeled RNA (1.5 _g) was then hybridized in triplicate to an Illumina Whole-Genome Sentrix Human-6 v2 Expression BeadChip, and detected according to the Illumina user manual.

source_name: U2OS PRC shRNA4_pLenti

extract_protocol: Total RNA was extracted from U2OS PRC shRNA4 cells using TRIzol reagent (Invitrogen) and purified further using the RNeasy MinElute Cleanup kit (Qiagen).

value: U2OS, Treatment:infected with PRC shRNA4_pLenti, blasticidin selection


title: Undifferentiated ES

description: Undifferentiated ES

source_name: Chromatin immunoprecipitated DNA from Undifferentiated ES cells using H3K9Me2 antibody

tag: Undifferentiated ES


title: HeLa_siAgo2_48_rep2

city: Seoul

first: Jinju

last: Han

address: 599 Gwanangno, Gwanak-gu

country: South Korea

institute: Seoul National University

description: Expression changes of HeLa mRNA after Ago2 knockdown for 48hrs

hyb_protocol: Following fragmentation, 2.3 ug of cDNA were hybridized for 17 hr at 45C on GeneChip Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.  Hybridization cocktails containing 5 to 5.5 µg of fragmented, end-labeled single-stranded cDNA were prepared and hybridized to GeneChip Human gene 1.0 ST arrays

scan_protocol: GeneChips were scanned using the  GeneChip Scanner 3000 7G.

data_processing: All gene array data was analyzed using tools in Expression consol software (Affymetrix). The Robust Multi-array Analysis (RMA) (Irizarry, Hobbs, Collin, Beazer-Barclay, Antonellis, Scherf, and Speed 2003) algorithm was used for probeset (gene-level) intensity analysis.

source_name: HeLa total RNA, 48hrs after transfection of siRNA against Ago2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Wt_sensetarget_label_manual(updated manual)_1, 2007, Affymetrix).

growth_protocol: HeLa cells were cultured in DMEM supplemented with 10% FBS.

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

treatment_protocol: 32nM of siRNAs (Samchully Phamaceuticals) were transfected into HeLa cells with lipofectamine 2000 (InvitroGen).

tag: Cervical cancer cell line


title: HeLa_siDicer_48_rep2

description: Expression changes of HeLa mRNA after Dicer knockdown for 48hrs

source_name: HeLa total RNA, 48hrs after transfection of siRNA against Dicer


title: HeLa_siDicer_48_rep1


title: U2OS_PRC_shRNA4_pLenti_2


title: HeLa_siGFP_48_rep1

description: Expression changes of HeLa mRNA after GFP knockdown for 48hrs

source_name: HeLa total RNA, 48hrs after transfection of siRNA against GFP


title: HeLa_siGFP_48_rep2


title: HeLa_siAgo2_48_rep1


title: U2OS_control_shRNA_pLenti_3

source_name: U2OS control shRNA_pLenti


title: HeLa_siDicer_24_rep2

description: Expression changes of HeLa mRNA after Dicer knockdown for 24hrs

source_name: HeLa total RNA, 24hrs after transfection of siRNA against Dicer


title: U2OS_control_shRNA_pLenti_1


title: U2OS_PRC_shRNA4_pLenti_1


title: HeLa_siGFP_24_rep2

description: Expression changes of HeLa mRNA after GFP knockdown for 24hrs

source_name: HeLa total RNA, 24hrs after transfection of siRNA against GFP


title: HeLa_siAgo2_24_rep1

description: Expression changes of HeLa mRNA after Ago2 knockdown for 24hrs

source_name: HeLa total RNA, 24hrs after transfection of siRNA against Ago2


title: HeLa_siAgo2_24_rep2


title: HeLa_siDicer_24_rep1


title: U2OS_control_shRNA_pLenti_2


title: Differentiated ES

description: Differentiated ES

source_name: Chromatin immunoprecipitated DNA from Differentiated ES cells using H3K9Me2 antibody

tag: Differentiated ES

source_name: Input DNA


title: Brain

description: Brain

source_name: Chromatin immunoprecipitated DNA from Brain cells using H3K9Me2 antibody

tag: Brain


title: NIH3T3 unstimulated

status: Public on Jan 15 2009

first: Martin

last: Bilban

institute: Medical University of Vienna

description: Affymetrix

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: RMA normalization

source_name: NIH3T3 cell line

label_protocol: Affymetrix WT labeling kit

extract_protocol: RNeasy Mini kit, Qiagen

tag: NIH3T3 cells unstimulated (control)


title: L929 + IFN-beta (4hrs)

description: Affymetrix

source_name: L929 cell line

tag: L929 cells treated with Interferon-beta for 4 hrs


title: L929 unstimulated

description: Affymetrix

tag: L929 cells unstimulated (control)


title: Liver

description: Liver

source_name: Chromatin immunoprecipitated DNA from Liver cells using H3K9Me2 antibody


title: Undifferentiated ES

description: Undifferentiated ES


title: HeLa_siGFP_24_rep1


title: RAW 264.7 unstimulated

description: Affymetrix

source_name: RAW 264.7 macrophage cell line

tag: control (untreated) RAW 264.7 cells


title: RAW264.7 IFN-beta (4hrs)

description: Affymetrix

source_name: RAW264.7 macrophage cell line

tag: RAW264.7 cells treated with Interferon-beta for 4 hrs


title: heart_KO_rep2

city: San Francisco

first: Masaki

last: Ieda

address: 1650 Owens street,

institute: Gladstone Institute

description: Heart, KO2

hyb_protocol: Performed according to the manufacturer's (Affymetrix) recommendations

data_processing: Raw intensities from the CEL files were analyzed using Affymetrix Power Tool (APT, version 1.8.5) to generate robust multi-array average intensity in log2 scale for each probe set. The perfect match intensities for each probe set were corrected for background and quantile-normalized using a robust fit of linear models.

source_name: Heart, KO2

label_protocol: Ambion MessageAmp II-biotin enhanced kit (manufacturer's recommendations)

extract_protocol: Trizol extraction

tag: Heart RNA


title: heart_KO_rep3

description: Heart, KO3

scan_protocol: Performed according to the manufacturer's (Affymetrix) recommendations

source_name: Heart, KO3


title: embryo cardiac fibroblast_rep3

description: mouse embryo cardiac fibroblast

source_name: embryo cardiac fibroblast

tag: cardiac fibroblast RNA


title: embryo cardiac fibroblast_rep2

description: mouse embryo cardiac fibroblast


title: NIH3T3 + IFN-beta (4hr)

description: Affymetrix

tag: NIH3T3 cells treated with Interferon-beta for 4hrs


title: embryo cardiomyocyte_rep2

description: mouse embryo cardiomyocyte

source_name: embryo cardiomyocyte

tag: cardiomyocyte RNA


title: adult cardiac fibroblast_rep1

description: mouse adult cardiac fibroblast

source_name: adult cardiac fibroblast


title: embryo cardiomyocyte_rep3

description: mouse embryo cardiomyocyte


title: embryo cardiac fibroblast_rep1

description: mouse embryo cardiac fibroblast


title: embryo cardiomyocyte_rep1

description: mouse embryo cardiomyocyte


title: adult cardiac fibroblast_rep3

description: mouse adult cardiac fibroblast


title: adult cardiac fibroblast_rep2

description: mouse adult cardiac fibroblast


title: heart_KO_rep1

description: Heart, KO1

source_name: Heart, KO1


title: heart_WT_rep2

description: Heart, wild type2

source_name: Heart, wild type2


title: Juvenile vs Adult Regenerate 2

description:
Simple annotation: Development, adult
Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69100.gif
Measurement: time(change) Calvarial regeneration in 6 day old  vs 60 day old mice d

hyb_protocol: not provided

scan_protocol: GenePix 4000B

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: Adult  regenerate

label_protocol: TRIZOL method

extract_protocol:
Type of amplification = Ambion's MessageAmp aRNA Kit.
Parameter Amount of extract labeled = 2 ug; Parameter Type of label = Cy3-dUTP

tag: Parameter Age = 60 day old; Parameter Species = CD-1 mice; Parameter Developmental Stage = skeletally mature 60-day-old adult

source_name: Juvenile regenerate

label_protocol: Parameter Amount of extract labeled = 2 ug; Parameter Type of label = Cy5-dUTP

extract_protocol:
TRIZOL method
Type of amplification = Ambion's MessageAmp aRNA Kit

tag: Parameter Age = 6 day old; Parameter Species = CD-1 mice; Parameter Developmental Stage = skeletally immature 6-day-old juvenile


title: Differentiated ES

description: Differentiated ES

source_name: Chromatin immunoprecipitated DNA from Differentiated ES cells using H3K9Me2 antibody


title: Undifferentiated ES

description: Undifferentiated ES

source_name: Chromatin immunoprecipitated DNA from Undifferentiated ES cells using H3K9Me2 antibody

source_name: Input DNA


title: heart_WT_rep3

description: Heart, wild type3

source_name: Heart, wild type3


title: heart_WT_rep1

description: Heart, wild type1

source_name: Heart, wild type1


title: LWset3_Col-0_mock_3h

city: St Paul

first: lin

last: wang

state: MN

address: 350 Cargill building, 1500 Gortner Ave

department: Plant Biology

institute: University of Minnesota

description: Col-0 infiltrated with water, harvested 3h after infiltration in setLWset3 experiment.

hyb_protocol: Labeled RNA was suspended in hybridization buffer (50% Formamide, 5xSSC, 0.1% SDS, 10 ug Sheared Salmon Sperm DNA (Eppendorf), 50pg calbation oligo)

scan_protocol: Slide was scanned using Genepix4000B with low and high voltages of photomultiplier at 532nm and constant voltage at 635nm.

data_processing:
Note that each Sample corresponds to two GPR files (we use low PMT and high PMT, then combine them).

The median of ratios for each spot was processed by the following linear model: Sij = mu + Ai + Bj + Eij where Sij denotes the log2-transformed, median of ratios for the spot, mu denotes a constant, Ai and Bj denote the effects of i-th gene and j-th subarray. The residual Eij is assumed to be independent and normally distributed. Stable genes-based quantile normalization was applied for slide-to-slide comparisons. KTset1_Col-0_hrcC_03h, KTset1_Col-0_hrcC_09h, KTset1_coi1_hrcC_03h, KTset1_coi1_hrcC_09h, KTset1_dde2_hrcC_03h, KTset1_dde2_hrcC_09h, KTset1_ein2_hrcC_03h, KTset1_ein2_hrcC_09h, KTset1_Col-0_mock_03h, KTset1_Col-0_mock_09h, KTset1_mpk3_hrcC_03h, KTset1_mpk3_hrcC_09h, KTset1_pad4_hrcC_03h, KTset1_pad4_hrcC_09h, KTset1_sid2_hrcC_03h, KTset1_sid2_hrcC_09h, KTset2_Col-0_hrcC_03h, KTset2_Col-0_hrcC_09h, KTset2_coi1_hrcC_03h, KTset2_coi1_hrcC_09h, KTset2_dde2_hrcC_03h, KTset2_dde2_hrcC_09h, KTset2_ein2_hrcC_03h, KTset2_ein2_hrcC_09h, KTset2_Col-0_mock_03h, KTset2_Col-0_mock_09h, KTset2_mpk3_hrcC_03h, KTset2_mpk3_hrcC_09h, KTset2_pad4_hrcC_03h, KTset2_pad4_hrcC_09h, KTset2_sid2_hrcC_03h, KTset2_sid2_hrcC_09h, KTset3_Col-0_hrcC_03h, KTset3_Col-0_hrcC_09h, KTset3_coi1_hrcC_03h, KTset3_coi1_hrcC_09h, KTset3_dde2_hrcC_03h, KTset3_dde2_hrcC_09h, KTset3_ein2_hrcC_03h, KTset3_ein2_hrcC_09h, KTset3_Col-0_mock_03h, KTset3_Col-0_mock_09h, KTset3_mpk3_hrcC_03h, KTset3_mpk3_hrcC_09h, KTset3_pad4_hrcC_03h, KTset3_pad4_hrcC_09h, KTset3_sid2_hrcC_03h, KTset3_sid2_hrcC_09h, LWset1_SALK-023199_hrcC_09h, LWset1_Col-0_hrcC_09h, LWset1_Col-0_mock_09h, LWset2_SALK-023199_hrcC_09h, LWset2_Col-0_hrcC_09h, LWset2_Col-0_mock_09h, LWset3_SALK-023199_hrcC_09h, LWset3_Col-0_hrcC_09h, LWset3_Col-0_mock_09h, LWset1_Col-0_mock_03h, LWset1_Col-0_hrcC_03h, LWset1_SALK-023199_hrcC_03h, LWset2_Col-0_mock_03h, LWset2_Col-0_hrcC_03h, LWset2_SALK-023199_hrcC_03h, LWset3_SALK-023199_hrcC_03h, LWset3_Col-0_mock_03h, and LWset3_Col-0_hrcC_03h were normalized together. Perl scripts for the linear model and the normalization are available for non-commercial research conducted upon request (Fumiaki Katagiri, katagiri@umn.edu). Spots with bad quality (missing, lints, and high background) were flagged as indicated in Flag in the attached .gpr file for this sample.

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana Col-0, leaves, water-infiltrated, 3h

label_protocol: Following procedure was performed with Amino Allyl MessageAmp aRNA Amplification Kit II (Ambion).First, cDNA was synthesized from 1ug of total RNA.  Next, RNA was in vitro transcribed.  The RNA was then labeled with Alexa555 in coupling reaction.

growth_protocol: Plants were grown in pots with BM-2 soil (Berger Peat Moss Ltd, Quebec, Canada) at a density of 9 plants per pot and kept at 22 degrees Celsius and 75% humidity with a 12 hour day length.

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

treatment_protocol: Individual leaves were infiltrated in the morning using a needle-less syringe with water and harvested 3h later.

tag: Genotype

tag: Tissue

value: leaves

tag: Age

value: 4 week-old

tag: Treatment

value: water

tag: Time point


title: Juvenile vs Adult Regenerate 1

description:
Simple annotation: Development, adult
Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69101.gif
Measurement: time(change) Calvarial regeneration in 6 day old  vs 60 day old mice d

tag: Parameter Age = 6 day old; Parameter Species = CD- 1 mice; Parameter Developmental Stage = skeletally immature 6-day-old juvenile


title: LWset3_Col-0_hrcC_9h

description: Col-0 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in setLWset3 experiment.

source_name: Arabidopsis thaliana Col-0, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 9h

treatment_protocol: Individual leaves were infiltrated in the morning using a needle-less syringe with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC and harvested 9h later.


title: LWset3_Col-0_mock_9h

description: Col-0 infiltrated with water, harvested 9h after infiltration in setLWset3 experiment.

source_name: Arabidopsis thaliana Col-0, leaves, water-infiltrated, 9h

treatment_protocol: Individual leaves were infiltrated in the morning using a needle-less syringe with water and harvested 9h later.


title: LWset3_Col-0_hrcC_3h

description: Col-0 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 3h after infiltration in setLWset3 experiment.

source_name: Arabidopsis thaliana Col-0, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 3h

treatment_protocol: Individual leaves were infiltrated in the morning using a needle-less syringe with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC and harvested 3h later.


title: LWset2_SALK_023199_hrcC_9h

description: SALK_023199 infiltrated with 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC, harvested 9h after infiltration in setLWset2 experiment.

source_name: Arabidopsis thaliana SALK_023199, leaves, 1x10E8 Pseudomonas syringae pv. tomato DC3000 hrcC-infiltrated, 9h