title: fetalliver-Rad23a-alpha-amanitin-A

scan_protocol: Details on the protocol can be found on http://www.nimblegen.com/technology/index.html

data_processing: Unprocessed (not normalized) hybridisation signals were used for analysis.

treatment_protocol: The cultured fetal liver cells were treated for 5 hours with 100 mg/ml alpha amanitin.


title: Soybean_Root

status: Public on Jan 15 2008

type: RNA

city: New Haven

first: Hang

last: He

state: CT

address: 165 Prospect St

department: MCDB

country: USA

institute: Yale University

description: Enriched for genomic DNA at all sequenced contexts

hyb_protocol: Sample Hybridization protocol provided and performed by NimbleGen.

scan_protocol: Nimblegen. Sample scan protocol provided and performed by NimbleGen.

data_processing: refer to "NMPP, A user-customized NimbleGen Microarray Processing Pipeline", By Xiangfeng Wang

molecule: total RNA

organism: Glycine max

source_name: Soybean root

label_protocol: The aa-dUTP decorated cDNA was fluorescent labeled by conjugating the monofunctional Cy3 dye (GE Healthcare, Piscataway, NJ) to the amino-allyl functional groups in the cDNA. Two μg dye-labeled targets were used for hybridization.

extract_protocol: Total RNA and mRNA were sequentially isolated using the RNeasy Plant Mini kit (Qiagen, Valencia, CA) and the Oligotex mRNA kit (Qiagen) according to the manufacturer’s recommendations, respectively. mRNA from different organ types was reverse transcribed using a mixture of oligo(dT)18 and random nonamer primers, during which amino-allyl-modified dUTP (aa-dUTP) was incoporated.


title: Soybean_Leaf

source_name: Soybean leaf

tag: Enriched for genomic DNA at all sequenced contexts


title: Soybean_Nodule

source_name: Soybean nodule


title: Medicago_Stem

organism: Medicago truncatula

source_name: Medicago stem


title: fetalliver-Rad23a-alpha-amanitin-B

type: genomic

city: Rotterdam

first: Wouter

last: de Laat

address: Dr. Molewaterplein 50

department: Cell Biology

country: Netherlands

institute: Erasmus MC

description: Unprocessed (not normalized) hybridisation signals were used for analysis. These signals showed clusters of 20-50 positive 4C-signals along the chromosome template. To define the clusters, a running mean or running median was applied, using a window size of 29 probes (on average 60 kb). Obtained values were compared to the running mean/median performed across randomised data. This was done for each array separately. Consequently, all measurements were appreciated relative to the amplitude and noise of that specific array. The False Discovery Rate (FDR), defined as (no. false positives) / (no. of false positives + no. of true positives), was determined as follows: (number of positives in the randomised set) / (number of positives in the data). The threshold level was determined using a top down approach to establish the minimal value for which: FDR<0.05.

hyb_protocol: Details on the protocol can be found on http://www.nimblegen.com/technology/index.html

molecule: genomic DNA

organism: Mus musculus

source_name: 4C sample obtained from cultured 14.5 dpc fetal liver cells, digested with HindIII and Sau3A

extract_protocol: 4C was performed as described before in Simonis et al. 2006 Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet. 38(11):1348-54

tag: 4C sample containing DNA amplified by inverse PCR using primers specific for a HindIII restriction fragment encompassing the murine Rad23a gene.


title: WT Rice branching panicle vs. dsRNAiRFL

city: Bangalore

first: Nagashree

middle: N

last: Rao

state: Karnataka

address: C.V. Raman Avenue

department: Microbiology and Cell Biology

country: India

institute: Indian Institute of Science

description:
Image quality was checked with the help of-
1. Four green spots and each corner of the image
2. SpikeIn A and B control spots across the image
3. Evenness of the background in log-scale mode

hyb_protocol: Probe fragmentation: Fragmentation reaction was as- cRNA Cy3 750 ng,cRNA Cy5 750 ng,Blocking agent 50 ul,Water variable, 25 X fragmentation buffer,10 ul to 250 ul total volume. Incubate at 60C for 30 mins. Add 250 ul of 2X hybridization buffer. Use 490 ul for each slide and hybridize at 65C for 17 hrs at 5 rpm speed.

scan_protocol: Washing was done according to Agilent’s instructions using wash buffer 1 followed by wash buffer 2. Slides were scanned using Agilent DNA Microarray Scanner (G2565BA).

data_processing: The TIFF image was used to extract raw and processed data using Agilent’s Feature Extraction software (FE v8.1). The normalization was done using GeneSpring GX version 7.2 using the recommended Per Spot and Per Chip: Intensity dependent (Lowess) normalization. Number of non-control spots with ratio 0.25 and below were considered as down regulated spots.

organism: Oryza sativa

source_name: WT rice TP309 branching panicles

label_protocol: cDNA was synthesized from tortal RNA by RT-PCR and was used as templete for Cy3 labeled cRNA synthesis using T7 dependent in vitro transcription system.

extract_protocol: Total RNA was isolated from WT rice panicles using Tri Reagent (Sigma) and purified by RNeasy cleanup kit (Qiagen). RNA profile and integrity of RNA was checked by Agilent’s Bioanalyzer.

tag: Rice TP309; wild type branching panicles

source_name: Transgenic rice panicles knock down for RFL

label_protocol: cDNA was synthesized from tortal RNA by RT-PCR and was used as templete for Cy5 labeled cRNA synthesis using T7 dependent in vitro transcription system.

extract_protocol: Total RNA was isolated from RFL knock down rice panicles using Tri Reagent (Sigma) and purified by RNeasy cleanup kit (Qiagen). RNA profile and integrity of RNA was checked by Agilent’s Bioanalyzer.

tag: Transgenic rice branching panicles of similar developmental stage to WT where a transcription regulator, RFL has been knocked down by double stranded RNA interference


title: Soybean_Seed

source_name: Soybean seed


title: fetalliver-Rad23a-untreated-A

label_protocol: Details on the protocol can be found on http://www.nimblegen.com/technology/index.html


title: Peripheral blood_female_Pitta_techrep1_Ex.set1&3

status: Public on Jan 16 2008

city: New Delhi

first: Mitali

last: Mukerji

state: New Delhi

address: Sukhdev Vihar, Mathura Road

department: Functional Genomics and Molecular Medicine

institute: CSIR-Institute Of Genomics and Integrative Biology

description: Log2 normalized values of the analyzable spots commonly obtained between 1 and 3 experimental sets, for the first technical replicate of the Pitta female samples

hyb_protocol: The two cRNA samples of each prakriti, one labeled with Cy3 and another with Cy5, were pooled together, precipitated, washed and air-dried. The dried pellet was dissolved in RNAase free water (Sigma). Hybridization solution was prepared by mixing hybridization buffer (DIG Easy Hyb; Roche), 10mg/ml salmon testis DNA (0.05 mg/ml final concentration, Sigma) and 10mg/ml yeast tRNA (0.05 mg/ml final concentration, Sigma) and added to the labeled product. This mixture was denatured at 65ºC and applied onto cDNA microarray slides. Inter prakriti cohybridization was carried out at 37ºC for 16 hrs.

scan_protocol: Microarray slides were scanned at 10µm resolution in GenePix 4000A Microarray Scanner (Molecular Devices), using both green and red lasers. The 16 bit TIFF images were preprocessed and quantified using Gene Pix Pro 6.0 software (Molecular Devices).

data_processing: Analysis was carried out taking two experiments at a time, separately for male and female data. Background subtracted mean values were used for the analysis. All the negative values were removed and only those genes having positive values for all the samples were considered for further analysis.  Values were log2 transformed and lowess normalization. Across array normalization was carried out using quantile normalization method. One-way analysis of variance was adopted to identify differentially expressed genes in all three categories. F-test was carried out in order to reject the hypothesis of equality of three group means. in order to investigate further the nature of differentially expressed genes; we have drawn strip charts and carried out pair wise comparisons using t-test. p-values obtained from ANOVA have been adjusted for multiplicity using Bonferroni method for controlling family wise error rate. Genes at p0.1 level of significance were considered to be significantly different in expression between all three groups.

organism: Homo sapiens

source_name: Peripheral blood cells from pitta prakriti females

label_protocol: Three samples of each prakriti were pooled. Experiments for male and female were carried out separately. Double stranded cDNA was synthesized from 15 µg (5 µg each sample) of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. Each pool of Vata, Pitta and Kapha purified cDNA was divided into two halves, one half labeled with Cy5 and other with Cy3  (Amersham Biosciences) using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products were purified by Microarray Target Purification Kit (Roche).

extract_protocol: Using EZ-RNA isolation kit (Biological Industries) as per manufacturers protocol.

tag: total RNA from peripheral blood cells of first set of pitta prakriti females of age group 18-40yrs labeled with Cy5, and compared with values obtained in set 3


title: Appressorium induced by cAMP Replicate 2

city: Raleigh

first: Yeon Yee

last: Oh

state: NC

address: NCSU Campus Box 7251

department: Plant Pathology

institute: NCSU

description: Biological replicate 1 of 4. Control germinating cells, untreated, harvested after several passages.

hyb_protocol: The 4 chips were hybridized with their labeled targets for 17 h at 60 °C in the dark. After hybridization, slides were washed sequential according to Agilent Technologies protocol

scan_protocol: Scanned on an Agilent G256BA microarray scanner Images were quantified using Agilent Feature Extraction Software (version 1.6.1.1)

data_processing: LOWESS normalization

organism: Pyricularia grisea

source_name: 50mM cAMP treated; Conidia with appressoria

label_protocol: 1ug of total RNA was labelled by reverse transcriptional incorporation of cyanine 3 (Cy3) or cyanine 5 (Cy5) labelled dCTP, using an oligo(dT) primer. The Agilent Fluorescent Linear Amplification Kit protocol for fluorescent cRNA synthesis (Agilent Technologies) was used.

growth_protocol: RNA from spore germinated on hydrophilic surface of Gelbond for 9 hours,  labeled with Cyanine-3 (green).

extract_protocol: Total RNA extracted using RNAeasy Plant Mini Kit (Qiagen Inc., Valencia, CA) following manufacturer's instructions

tag: 50mM cAMP treated

tag: Conidia with appressoria

source_name: Mock treated; Conidia without appressoria

growth_protocol: RNA from spore germinated on hydrophilic surface of Gelbond for 9 hours, labeled with Cyanine-5 (red).

tag: Mock treated

tag: Conidia without appressoria


title: Bone CTL-OA AMC 3118 20

status: Public on Jan 14 2008

city: Adelaide

first: Blair

last: Hopwood

state: South Australia

address: Frome Road

department: Tissue Pathology

country: Australia

institute: Institute of Medical and Veterinary Science

description: This sample is part of a series (CTL-OA-OP human IT PF Bone study series) that spanned two array print runs (slides AMC_2609 - AMC_2638 and AMC_3104 - AMC_3119).

hyb_protocol: see the Adelaide Microarray Facility website

scan_protocol: Slides were scanned with a GenePix 3000B Scanner (Axon Instruments) twice at slightly different PMT voltage.

data_processing: Images were visually inspected for artefacts and boxplots and image plots of Red and Green channels examined. Arrays with poor hybridisation efficiency, or gross artefacts were excluded and repeated. Image analysis and spot identification and intensity extraction was performed using the Spot software package (see the CSIRO Australia SPOT web page. Spot uses a seeded region growing algorithm to identify spots and is able to identify non-uniform shaped spots. Each estimated grid was visually inspected to ensure accurate spot identification. Morphological opening background correction was applied to mean spot signal intensities. Arrays were normalised using intensity-dependent print-tip loess normalization followed by within slide scale normalisation (as implemented in the LIMMA package of BioConductor). As the design of this experiment did not include any technical replication, data obtained from duplicate scans were used for this purpose. Duplicate correlation was calculated in LIMMA and incorporated into the calculations similarly to the treatment commonly used for duplicate spots on the same array.

source_name: CTL46 - Total RNA from human CTL trabecular bone labelled with Cyanine-5 (red)

label_protocol: RNA was purified using RNeasy columns (Qiagen) according to the manufacturers instructions. RNA (5 micro grams) was amplified using a Message Amp II kit (Ambion) with indirect amino allyl-mediated incorporation of Cy5 (Amersham Biosciences) according to the manufacturers instructions. 5 micro grams of the labelled sample was used for hybridisation.

extract_protocol: As described in Kuliwaba et al Journal Bone & Mineral Research 2000 15:332-341

tag: CTL bone Age

value: 50 years  Sex:male

source_name: OA56 - Total RNA from human OA trabecular bone, labelled with Cyanine-3 (green)

label_protocol: RNA was purified using RNeasy columns (Qiagen) according to the manufacturers instructions. RNA (5 micro grams) was amplified using a Message Amp II kit (Ambion) with indirect amino allyl-mediated incorporation of Cy3 (Amersham Biosciences) according to the manufacturers instructions. 5 micro grams of the labelled sample was used for hybridisation.

tag: OA bone Age

value: 50 years Sex:male


title: fetalliver-Beta-globin-DRB

source_name: 4C sample obtained from cultured 14.5 dpc fetal liver cells, digested with HindIII and NlaIII

treatment_protocol: The cultured fetal liver cells were treated for 3 hours with 100 micromolar DRB.

tag: 4C sample containing DNA amplified by inverse PCR using primers specific for a HindIII restriction fragment encompassing the promoter of the murine beta-globin gene.


title: WT Rice branching panicle vs. dsRNAiRFL Sample B_SWAP


title: Bone CTL-OA AMC 3112 14

source_name: CTL40 - Total RNA from human CTL trabecular bone labelled with Cyanine-5 (red)

value: 71 years  Sex:male

source_name: OA50 - Total RNA from human OA trabecular bone, labelled with Cyanine-3 (green)

value: 70 years Sex:male


title: Bone CTL-OA AMC 3115 17

source_name: CTL43 - Total RNA from human CTL trabecular bone labelled with Cyanine-3 (green)

tag: CTL bone 64 years  Sex

value: male

source_name: OA53 - Total RNA from human OA trabecular bone, labelled with Cyanine-5 (red)

value: 63 years Sex:male


title: Bone CTL-OA AMC 3110 12

source_name: CTL38 - Total RNA from human CTL trabecular bone labelled with Cyanine-5 (red)

value: 73 years  Sex:male

source_name: OA48 - Total RNA from human OA trabecular bone, labelled with Cyanine-3 (green)

value: 77 years Sex:male


title: Bone CTL-OA AMC 3109 11

source_name: CTL37 - Total RNA from human CTL trabecular bone labelled with Cyanine-3 (green)

value: 85 years  Sex:male

source_name: OA47 - Total RNA from human OA trabecular bone, labelled with Cyanine-5 (red)

value: 85 years Sex:male


title: Soybean_Flower

source_name: Soybean flower


title: Medicago_Root

source_name: Medicago root


title: WT Rice branching panicle vs. RFL antisense

source_name: WT rice TP309 panicles

source_name: Transgenic rice panicles expressing antisense RFL RNA

tag: Transgenic rice panicles of similar developmental stage to WT where a transcription regulator, RFL has been partially knocked down by antisensense based approach


title: Bone CTL-OA AMC 3114 16

source_name: CTL42 - Total RNA from human CTL trabecular bone labelled with Cyanine-5 (red)

value: 69 years  Sex:male

source_name: OA52 - Total RNA from human OA trabecular bone, labelled with Cyanine-3 (green)


title: Bone CTL-OA AMC 3113 15

source_name: CTL41 - Total RNA from human CTL trabecular bone labelled with Cyanine-3 (green)

value: 70 years  Sex:male

source_name: OA51 - Total RNA from human OA trabecular bone, labelled with Cyanine-5 (red)

value: 69 years Sex:male


title: Bone CTL-OA AMC 3107 6

description: This sample is part of a series (CTL-OA-OP human IT PF Bone study series) that spanned two array print runs (slides AMC_2609 - AMC_2638 and AMC_3104 - AMC_3119)

scan_protocol: Slides were scanned with a GenePix 3000B Scanner (Axon Instruments) twice at slightly different PMT voltage

data_processing: Images were visually inspected for artefacts and boxplots and image plots of Red and Green channels examined. Arrays with poor hybridisation efficiency, or gross artefacts were excluded and repeated. Image analysis and spot identification and intensity extraction was performed using the Spot software package (see the CSIRO Australia SPOT web page. Spot uses a seeded region growing algorithm to identify spots and is able to identify non-uniform shaped spots. Each estimated grid was visually inspected to ensure accurate spot identification. Morphological opening background correction was applied to mean spot signal intensities. Arrays were normalised using intensity-dependent print-tip loess normalization followed by within slide scale normalisation (as implemented in the LIMMA package of BioConductor). As the design of this experiment did not include any technical replication, data obtained from duplicate scans were used for this purpose. Duplicate correlation was calculated in LIMMA and incorporated into the calculations similarly to the treatment commonly used for duplicate spots on the same array

source_name: CTL5 - Total RNA from human CTL trabecular bone labelled with Cyanine-5 (red)

label_protocol: RNA was purified using RNeasy columns (Qiagen) according to the manufacturers instructions. RNA (5 micro grams) was amplified using a Message Amp II kit (Ambion) with indirect amino allyl-mediated incorporation of Cy5 (Amersham Biosciences) according to the manufacturers instructions. 5 micro grams of the labelled sample was used for hybridisation

value: 68 years  Sex:female

source_name: OA21 - Total RNA from human OA trabecular bone, labelled with Cyanine-3 (green)

label_protocol: RNA was purified using RNeasy columns (Qiagen) according to the manufacturers instructions. RNA (5 micro grams) was amplified using a Message Amp II kit (Ambion) with indirect amino allyl-mediated incorporation of Cy3 (Amersham Biosciences) according to the manufacturers instructions. 5 micro grams of the labelled sample was used for hybridisation

value: 68 years Sex:female


title: Bone CTL-OA AMC 3111 13

source_name: CTL39 - Total RNA from human CTL trabecular bone labelled with Cyanine-3 (green)

source_name: OA49 - Total RNA from human OA trabecular bone, labelled with Cyanine-5 (red)

value: 73 years Sex:male


title: WT Rice branching panicle vs. RFL antisense_SWAP

source_name: WT rice TP309 branching panicles

source_name: Transgenic rice branching panicles expressing RFL antisense RNA

tag: Transgenic rice branching panicles of similar developmental stage to WT where a transcription regulator, RFL has been partially knocked down by antisense based approach


title: Bone CTL-OA AMC 3117 19

source_name: CTL45 - Total RNA from human CTL trabecular bone labelled with Cyanine-3 (green)

value: 57 years  Sex:male

source_name: OA55 - Total RNA from human OA trabecular bone, labelled with Cyanine-5 (red)

value: 57 years Sex:male


title: fetalliver-Rad23a-untreated-B

source_name: 4C sample obtained from cultured 14.5 dpc fetal liver cells, digested with HindIII and Sau3A


title: Medicago_Nodule

source_name: Medicago nodule


title: Bone OP-OA AMC 2638 30

source_name: OP33 - Total RNA from human OP trabecular bone labelled with Cyanine-3 (green)

tag: OP bone Age

value: 74 years  Sex:female

source_name: OA17 - Total RNA from human OA trabecular bone, labelled with Cyanine-5 (red)

tag: OA bone 66 years Sex

value: female


title: Bone OP-OA AMC 3108 22

source_name: OP27 - Total RNA from human OP trabecular bone labelled with Cyanine-3 (green)

value: 87 years  Sex:female

source_name: OA12 - Total RNA from human OA trabecular bone, labelled with Cyanine-5 (red)

value: 83 years Sex:female


title: Soybean_Stem

source_name: Soybean stem

tag: Enriched for genomic DNA at all sequenced contexts


title: Bone OP-OA AMC 2633 25

source_name: OP29 - Total RNA from human OP trabecular bone labelled with Cyanine-5 (red)

value: 81 years  Sex:female

source_name: OA24 - Total RNA from human OA trabecular bone, labelled with Cyanine-3 (green)

value: 78 years Sex:female


title: Bone OP-OA AMC 2635 27

source_name: OP36 - Total RNA from human OP trabecular bone labelled with Cyanine-5 (red)

value: 78 years  Sex:female

source_name: OA16 - Total RNA from human OA trabecular bone, labelled with Cyanine-3 (green)

value: 77 years Sex:female


title: fetalliver-Beta-globin-alpha-amanitin-A

source_name: 4C sample obtained from cultured 14.5 dpc fetal liver cells, digested with HindIII and NlaIII


title: fetalliver-Beta-globin-alpha-amanitin-B


title: Bone CTL-OA AMC 3104 3

source_name: CTL2 - Total RNA from human CTL trabecular bone labelled with Cyanine-3 (green)

value: 83 years  Sex:female

source_name: OA14 - Total RNA from human OA trabecular bone, labelled with Cyanine-5 (red)

value: 82 years Sex:female


title: Bone OP-OA AMC 3119 29

source_name: OP32 - Total RNA from human OP trabecular bone labelled with Cyanine-5 (red)

source_name: OA21 - Total RNA from human OA trabecular bone, labelled with Cyanine-3 (green)


title: Bone OP-OA AMC 2629 21

source_name: OP26 - Total RNA from human OP trabecular bone labelled with Cyanine-5 (red)

value: 91 years  Sex:female

source_name: OA22 - Total RNA from human OA trabecular bone, labelled with Cyanine-3 (green)

value: 87 years Sex:female


title: Medicago_Seed

source_name: Medicago seed


title: Bone CTL-OA AMC 3105 4

source_name: CTL3 - Total RNA from human CTL trabecular bone labelled with Cyanine-3 (green)

value: 72 years  Sex:female

source_name: OA15 - Total RNA from human OA trabecular bone, labelled with Cyanine-5 (red)


title: fetalliver-Beta-globin-untreated-B

treatment_protocol: no treatment


title: Bone OP-OA AMC 2634 26

source_name: OP35 - Total RNA from human OP trabecular bone labelled with Cyanine-3 (green)


title: Bone CTL-OP AMC 2628 40

source_name: CTL6- Total RNA from human CTL trabecular bone labelled with Cyanine-5 (red)

value: 68 years  Sex:female

source_name: OP33 - Total RNA from human OP trabecular bone, labelled with Cyanine-3 (green)

value: 74 years Sex:female


title: Bone OP-OA AMC 2631 23

source_name: OP34 - Total RNA from human OP trabecular bone labelled with Cyanine-5 (red)

source_name: OA13 - Total RNA from human OA trabecular bone, labelled with Cyanine-3 (green)


title: Bone CTL-OP AMC 2627 39

source_name: CTL5 - Total RNA from human CTL trabecular bone labelled with Cyanine-5 (red)

source_name: OP32 - Total RNA from human OP trabecular bone, labelled with Cyanine-3 (green)


title: Bone OP-OA AMC 2632 24

source_name: OP28 - Total RNA from human OP trabecular bone labelled with Cyanine-3 (green)

value: 84 years  Sex:female

source_name: OA23 - Total RNA from human OA trabecular bone, labelled with Cyanine-5 (red)

value: 79 years Sex:female


title: Bone CTL-OP AMC 2624 32

source_name: CTL2 - Total RNA from human CTL trabecular bone labelled with Cyanine-5 (red)

source_name: OP27 - Total RNA from human OP trabecular bone, labelled with Cyanine-3 (green)


title: Bone CTL-OP AMC 2623 35

source_name: CTL11 - Total RNA from human CTL trabecular bone labelled with Cyanine-3 (green)

value: 74 years  Sex:female

source_name: OP29 - Total RNA from human OP trabecular bone, labelled with Cyanine-5 (red)

value: 81 years Sex:female


title: Fetalliver-Beta-globin-untreated-A

source_name: 4C sample obtained from cultured 14.5 dpc fetal liver cells, digested with HindIII and NlaIII


title: Bone CTL-OP AMC 2625 36

source_name: CTL4 - Total RNA from human CTL trabecular bone labelled with Cyanine-3 (green)

source_name: OP36 - Total RNA from human OP trabecular bone, labelled with Cyanine-5 (red)


title: Medicago_Leaf

source_name: Medicago leaf


title: Bone CTL-OP AMC 2622 34

source_name: CTL10 - Total RNA from human CTL trabecular bone labelled with Cyanine-5 (red)

source_name: OP28 - Total RNA from human OP trabecular bone, labelled with Cyanine-3 (green)

value: 84 years Sex:female


title: Bone CTL-OP AMC 2621 33

source_name: CTL2 - Total RNA from human CTL trabecular bone labelled with Cyanine-3 (green)

source_name: OP34 - Total RNA from human OP trabecular bone, labelled with Cyanine-5 (red)


title: Bone CTL-OA AMC 2612 5

source_name: CTL4 - Total RNA from human CTL trabecular bone labelled with Cyanine-5 (red)

value: 72 years Sex:female

source_name: OA16 - Total RNA from human OA trabecular bone, labelled with Cyanine-3 (green)


title: Bone CTL-OA AMC 2615 7

source_name: CTL6 - Total RNA from human CTL trabecular bone labelled with Cyanine-3 (green)

source_name: OA17 - Total RNA from human OA trabecular bone, labelled with Cyanine-5 (red)

value: 66 years Sex:female


title: Medicago_Flower

source_name: Medicago flower


title: Bone CTL-OP AMC 2626 37

source_name: CTL3 - Total RNA from human CTL trabecular bone labelled with Cyanine-5 (red)

source_name: OP30 - Total RNA from human OP trabecular bone, labelled with Cyanine-3 (green)


title: Liver_animal_2049_high_presure_ 1min

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: The differential expression of immediate-early and delayed genes in the liver remnant was studied under two predefined pressure situations; low portal venous pressure and thus low sinusoidal pressure (62 % resection) and high portal venous pressure and high sinusoidal pressure (75 % resection). Gene expression profiles were obtained from biopsies sampled in the liver remnant at time points 1, 30, 90, minutes and 3, 4 and 6 hours after resection.

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 LocalFeature as background measurement.

data_processing: Statistical analysis was carried out in the R computing environment (version 2.3.1 for Windows) using the package Linear Models for Microarray Analysis (Limma, version 2.7.10) which is part of the Bioconductor project. The median intensities were background corrected by using the ""normexp"" function on the median background intensities. Following background correction, the log2-transformed ratios of Alexa-594 to Alexa-488 were normalized within-slide using printtip-loess 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 time points within treatment as well as between treatments. Time point contrasts were formed referring to the sample taken at time point 1 min. followed by multiple testing across genes and contrasts with p-values below 0.001 considered as significant. The features of the arrays were mapped to a LocusLink identifier and an annotation package was built using the Bioconductor package AnnBuilder (version 1.9.14). Tests for significantly (P < 0.05) overrepresentation of gene ontology (GO) terms were conducted using the GOHyperG function of the Bioconductor package GOstats (ver 1.5.5). The sets of overrepresented GO terms were further analysed by utilising information from Online Mendelian Inheritance in Man (OMIM) to group the genes by function.

organism: Sus scrofa

source_name: Liver_animal_2049_high_presure_ 1min

label_protocol: 20 µg total RNA was labelled by using the Superscript Indirect cDNA Labeling System (Invitrogen) in combination with ARES cDNA labeling kits (Molecular Probes/Invitrogen) following the enclosed protocols. Spike-in RNA from the Lucidea Universal ScoreCard (Amersham Biosciences) was added to the cDNA reactions. ""Green"" spike-in RNA was added to the common reference samples and ""red"" spike-in RNA was added to the samples.

growth_protocol: Animals were acclimatized in the animal department for at least 48 hours prior to experiments. Conditions were set to room temperature of 20±1ºC, relative humidity of 55±10%, and a 12-hour light/dark cycle. The animals were fed Combi Fri™ chow (Felleskjøpet, Trondheim, Norway), but were fasted overnight prior to the experiment with free access to water.

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

treatment_protocol: Animals were premedicated with an intramuscular injection of ketamine (20 mg/kg) and atropin (1mg). Anaesthesia was induced with an intravenous bolus of pentobarbital (10 mg/kg) and fentanyl (10 µg/kg) and later maintained with continuous infusions of pentobarbital (4 mg/kg), fentanyl (0,02 mg/kg) and midazolam (0,3 mg/kg). All animals received a preoperative intravenous volume load consisting of 500mL 0,9 % NaCl containing 625 mg of glucose. Volume infusion was continued thereafter with 20mL/kg/hr 0,9% NaCl and 10% glucose plus 20% human albumin at 3mL/kg/hr. The animals were ventilated via a tracheotomy on a Servo Ventilator 900 (Elema-Schønander, Sweden). PCO2 was kept in the range 4,0 - 4,5 kPa by tidal volume adjustment. Core body temperature was maintained at 38,5 ± 1ºC with a heating blanket. A 16G central venous catheter (CVK, Secalon® T) was placed in the left external jugular vein for administration of anaesthesia and infusions. A 5 French Swan-Ganz catheter (Edwards Lifesciences) was floated via the right external jugular vein to the pulmonary artery for cardiac output (CO) measurements. A 16G CVK (Secalon® T) was placed in the left femoral artery for continuous arterial blood pressure monitoring. A 7 French 110 cm angiographic catheter (external diameter 2.3 mm, internal diameter 1.2 mm, 12 sideholes) (Cordis®, Johnson&Johnson) was placed in the hepatic vein draining segments V and VIII via the right internal jugular vein for blood pressure monitoring and blood sampling. Correct placement was ensured by direct palpation after laparotomy and later controlled by post-mortem dissection. A 5 French Swan-Ganz catheter (Edwards Lifesciences™) was placed in the hepatic vein draining segments II and III by direct transhepatic placement for pressure monitoring and blood sampling. A 4 French, 2 lumen 13 cm paediatric CVK (Arrow® International) was placed in the portal vein with the tip approximately 5 cm from the liver hilus. This was used for pressure monitoring and blood sampling. The bladder was drained via a cystostomy. Calibrated transducers (Transpac 3™, Abbott Critical Care Systems, Chicago, IL, USA) were used for continuous pressure registration. The transducers were connected to an amplifier (Gould, 2800S, Ohio, USA). Pulsatile signals were displayed on a monitor, digitalised and stored electronically (Advantech, Industrial Computer). All recordings were logged every fourth second. For graphic presentation the data was processed by Labview version 6.0™ (National instruments, Austin, TX, USA). Perivascular ultrasonic flow probes (CardioMed Systems, Medistim A/S, Oslo, Norway) were placed around the portal vein (12 mm probe), right hepatic artery (2 mm probe), left hepatic artery (3 mm probe) and around the aortoportal shunt (5 mm probe). Signals were displayed on a monitor and stored electronically (Advantech, Industrial Computer). Cardiac output was measured by the thermo dilution technique using 5 ml 0,9 % NaCl chilled to < 5 ºC, via a 5F Swan-Ganz catheter (Vigilance™ Volumetrics, Edwards Lifesciences™). Measurements were made in triplicate and documented as the average value. The same investigator made all measurements. A rectal probe recorded core body temperature. Three pigs (2048, 2055 and 2056) underwent a 62% liver resection (low-pressure resection, LPR) and three (2045, 2047 and 2049) underwent a 75% resection (high-pressure resection, HPR). Operative procedures: after a midline laparotomy and placement of all catheters as described above, the hepatic artery supplying segments II and III (left lateral lobe) together with these segments' portal branch were ligated using an absorbable polyfilament suture on a large needle. Thereafter the lobe was strangulated with a 0,5 cm wide cotton ribbon and then removed and weighed. Segments IV, V and VIII were removed in a similar manner in the LPR series leaving segments VI, VIII and I in place. In the HPR series, the resection was continued removing segments VI and VII as well. Biopsies were sampled from the remaining segments VI, VII in the LPR series and from segment I in the HPR series and placed immediately in RNALater (Ambion®). Sampling time points were 1, 5, 10, 30, 60, 90 minutes, 2, 3, 4, 5 and 6 hours after completion of resection. All biopsies were stored overnight in 4ºC and thereafter in - 70 ºC until further processing. The pigs were sacrificed with an intravenous overdose of 100 mg pentobarbital and 20mmol KCl intracardially on completion of the experiment.

tag: Breed

value: landrace, gender:male-castrates, age:3 months, weight:30 Kg, tissue:liver, animal:2049, treatment:partial hepatectomy - high presure, time point:1min

value: DLY X Hampshire, gender:female, tissue:liver, animal:2971-2, project:RN


title: Bone CTL-OA AMC 2617 9

source_name: CTL8 - Total RNA from human CTL trabecular bone labelled with Cyanine-3 (green)

value: 56 years  Sex:female

source_name: OA19 - Total RNA from human OA trabecular bone, labelled with Cyanine-5 (red)

tag: OA bone 56 years Sex

value: female


title: Bone CTL-OA AMC 2616 8

source_name: CTL7 - Total RNA from human CTL trabecular bone labelled with Cyanine-5 (red)

value: 60 years  Sex:female

source_name: OA18 - Total RNA from human OA trabecular bone, labelled with Cyanine-3 (green)

value: 60 years Sex:female


title: Bone CTL-OA AMC 2610 2

source_name: CTL2 - Total RNA from human CTL trabecular bone labelled with Cyanine-5 (red)

value: 83 years Sex:female

source_name: OA13 - Total RNA from human OA trabecular bone, labelled with Cyanine-3 (green)

value: 82 years Sex:female


title: Bone CTL-OA AMC 2618 10

source_name: CTL9 - Total RNA from human CTL trabecular bone labelled with Cyanine-5 (red)

value: 43 years Sex:female

source_name: OA20 - Total RNA from human OA trabecular bone, labelled with Cyanine-3 (green)

value: 49 years Sex:female


title: Bone OP-OA AMC 2620 28

source_name: OP35 - Total RNA from human OP trabecular bone labelled with Cyanine-3 (green)

value: 78 years Sex:female

source_name: OA25 - Total RNA from human OA trabecular bone, labelled with Cyanine-5 (red)

value: 73 years Sex:female


title: Bone CTL-OP AMC 2613 38

source_name: CTL3 - Total RNA from human CTL trabecular bone labelled with Cyanine-3 (green)

value: 72 years  Sex:female

source_name: OP31 - Total RNA from human OP trabecular bone, labelled with Cyanine-5 (red)

value: 75 years Sex:female


title: Liver_animal_2045_high_presure_ 30min

source_name: Liver_animal_2045_high_presure_ 30min

value: landrace, gender:male-castrates, age:3 months, weight:30 Kg, tissue:liver, animal:2045, treatment:partial hepatectomy - high presure, time point:30min


title: Liver_animal_2047_high_presure_ 6h

source_name: Liver_animal_2047_high_presure_ 6h

value: landrace, gender:male-castrates, age:3 months, weight:30 Kg, tissue:liver, animal:2047, treatment:partial hepatectomy - high presure, time point:6h


title: Liver_animal_2056_low_presure_1min

value: landrace, gender:male-castrates, age:3 months, weight:30 Kg, tissue:liver, animal:2056, treatment:partial hepatectomy - low presure, time point:1min


title: Liver_animal_2047_high_presure_ 1min

source_name: Liver_animal_2047_high_presure_ 1min

value: landrace, gender:male-castrates, age:3 months, weight:30 Kg, tissue:liver, animal:2047, treatment:partial hepatectomy - high presure, time point:1min


title: Liver_animal_2056_low_presure_90min

value: landrace, gender:male-castrates, age:3 months, weight:30 Kg, tissue:liver, animal:2056, treatment:partial hepatectomy - low presure, time point:90min

value: DLY X Hampshire, gender:female, tissue:liver, animal:2971-2, project:RN


title: Liver_animal_2049_high_presure_ 3h

source_name: Liver_animal_2049_high_presure_ 3h

value: landrace, gender:male-castrates, age:3 months, weight:30 Kg, tissue:liver, animal:2049, treatment:partial hepatectomy - high presure, time point:3h


title: Liver_animal_2045_high_presure_ 4h

source_name: Liver_animal_2045_high_presure_ 4h

value: landrace, gender:male-castrates, age:3 months, weight:30 Kg, tissue:liver, animal:2045, treatment:partial hepatectomy - high presure, time point:4h


title: Bone CTL-OA AMC 2609 1

source_name: CTL1 - Total RNA from human CTL trabecular bone labelled with Cyanine-3 (green)

value: 85 years Sex:female

source_name: OA12 - Total RNA from human OA trabecular bone, labelled with Cyanine-5 (red)


title: Liver_animal_2048_low_presure_6h

value: landrace, gender:male-castrates, age:3 months, weight:30 Kg, tissue:liver, animal:2048, treatment:partial hepatectomy - low presure, time point:6h


title: Liver_animal_2048_low_presure_90min

value: landrace, gender:male-castrates, age:3 months, weight:30 Kg, tissue:liver, animal:2048, treatment:partial hepatectomy - low presure, time point:90min


title: Liver_animal_2048_low_presure_4h

value: landrace, gender:male-castrates, age:3 months, weight:30 Kg, tissue:liver, animal:2048, treatment:partial hepatectomy - low presure, time point:4h


title: Liver_animal_2047_high_presure_ 90min

source_name: Liver_animal_2047_high_presure_ 90min

value: landrace, gender:male-castrates, age:3 months, weight:30 Kg, tissue:liver, animal:2047, treatment:partial hepatectomy - high presure, time point:90min


title: Liver_animal_2045_high_presure_ 90min

source_name: Liver_animal_2045_high_presure_ 90min

value: landrace, gender:male-castrates, age:3 months, weight:30 Kg, tissue:liver, animal:2045, treatment:partial hepatectomy - high presure, time point:90min


title: Liver_animal_2055_low_presure_90min

value: landrace, gender:male-castrates, age:3 months, weight:30 Kg, tissue:liver, animal:2055, treatment:partial hepatectomy - low presure, time point:90min


title: Liver_animal_2045_high_presure_ 1min

source_name: Liver_animal_2045_high_presure_ 1min

value: landrace, gender:male-castrates, age:3 months, weight:30 Kg, tissue:liver, animal:2045, treatment:partial hepatectomy - high presure, time point:1min


title: Liver_animal_2048_low_presure_3h

value: landrace, gender:male-castrates, age:3 months, weight:30 Kg, tissue:liver, animal:2048, treatment:partial hepatectomy - low presure, time point:3h


title: Liver_animal_2055_low_presure_6h

value: landrace, gender:male-castrates, age:3 months, weight:30 Kg, tissue:liver, animal:2055, treatment:partial hepatectomy - low presure, time point:6h


title: Liver_animal_2048_low_presure_1min

value: landrace, gender:male-castrates, age:3 months, weight:30 Kg, tissue:liver, animal:2048, treatment:partial hepatectomy - low presure, time point:1min


title: 3_min_36_wk_50_mg/kg/d_spironolactone

status: Public on Jan 12 2008

city: Ann Arbor

first: Seetha

middle: U

last: Monrad

state: MI

address: 1500 E Medical Center Dr, SPC 5358

department: Internal Medicine

institute: University of Michigan

description: final images saved in .tif format

hyb_protocol: per manufacturer's protocol

scan_protocol: chemiluminescent array image recorded using X-ray film exposure for 45 seconds and digitized using a flatbed desktop scanner

data_processing: Raw data was analyzed using Superarray's data analysis software; this corrected for background (minimum value) and normalized to the median. Average density was obtained and clover setting was off.

label: biotin

source_name: whole kidney tissue

label_protocol: per manufacturer's protocol

extract_protocol: Extracted using TriPure per manufacturer's protocol and further purified using an RNEasy Mini Kit.

tag: Strain

value: NZB/W F1

tag: Female

tag: 36 weeks of age

tag: 50 mg/kg/day spironolactone treated


title: 3_min_36_wk_Vehicle_treated

description: final images saved in .tif format

source_name: whole kidney

tag: Vehicle treated


title: 3_min_36_wk_25_mg/Kg_spironolactone

description: final images saved in .tif format

tag: 25 mg/kg/day spironolactone treated


title: Liver_animal_2047_high_presure_ 3h

source_name: Liver_animal_2047_high_presure_ 3h

value: landrace, gender:male-castrates, age:3 months, weight:30 Kg, tissue:liver, animal:2047, treatment:partial hepatectomy - high presure, time point:3h


title: Liver_animal_2047_high_presure_ 30min

source_name: Liver_animal_2047_high_presure_ 30min

value: landrace, gender:male-castrates, age:3 months, weight:30 Kg, tissue:liver, animal:2047, treatment:partial hepatectomy - high presure, time point:30min


title: Liver_animal_2055_low_presure_4h

value: landrace, gender:male-castrates, age:3 months, weight:30 Kg, tissue:liver, animal:2055, treatment:partial hepatectomy - low presure, time point:4h

value: DLY X Hampshire, gender:female, tissue:liver, animal:2971-2, project:RN


title: Liver_animal_2049_high_presure_ 6h

source_name: Liver_animal_2049_high_presure_ 6h

value: landrace, gender:male-castrates, age:3 months, weight:30 Kg, tissue:liver, animal:2049, treatment:partial hepatectomy - high presure, time point:6h


title: Liver_animal_2045_high_presure_ 3h

source_name: Liver_animal_2045_high_presure_ 3h

value: landrace, gender:male-castrates, age:3 months, weight:30 Kg, tissue:liver, animal:2045, treatment:partial hepatectomy - high presure, time point:3h


title: Liver_animal_2056_low_presure_4h

value: landrace, gender:male-castrates, age:3 months, weight:30 Kg, tissue:liver, animal:2056, treatment:partial hepatectomy - low presure, time point:4h


title: Liver_animal_2049_high_presure_ 90min

source_name: Liver_animal_2049_high_presure_ 90min

value: landrace, gender:male-castrates, age:3 months, weight:30 Kg, tissue:liver, animal:2049, treatment:partial hepatectomy - high presure, time point:90min


title: Liver_animal_2049_high_presure_ 4h

source_name: Liver_animal_2049_high_presure_ 4h

value: landrace, gender:male-castrates, age:3 months, weight:30 Kg, tissue:liver, animal:2049, treatment:partial hepatectomy - high presure, time point:4h


title: Liver_animal_2047_high_presure_ 4h

source_name: Liver_animal_2047_high_presure_ 4h

value: landrace, gender:male-castrates, age:3 months, weight:30 Kg, tissue:liver, animal:2047, treatment:partial hepatectomy - high presure, time point:4h


title: Liver_animal_2056_low_presure_6h

value: landrace, gender:male-castrates, age:3 months, weight:30 Kg, tissue:liver, animal:2056, treatment:partial hepatectomy - low presure, time point:6h


title: Liver_animal_2049_high_presure_ 30min

source_name: Liver_animal_2049_high_presure_ 30min

value: landrace, gender:male-castrates, age:3 months, weight:30 Kg, tissue:liver, animal:2049, treatment:partial hepatectomy - high presure, time point:30min


title: Liver_animal_2048_low_presure_30min

value: landrace, gender:male-castrates, age:3 months, weight:30 Kg, tissue:liver, animal:2048, treatment:partial hepatectomy - low presure, time point:30min


title: Patient_MU1

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description: frozen-tissue tumor samples were collected from patients with histological confirmed OSCC after approval by the institutional review

hyb_protocol: Hybridization was carried out at 37°C in UltraHyb buffer (Ambion) on a GeneTAC hybridization station (Genomic Solutions).

scan_protocol: hybridised arrays werde scaned using an Agilent Microarray Scanner G2505 B (Agilent Technologies, Santa Clara, CA) dual laser scanner.

data_processing: spot replicates were averaged. Spots not recognized by the image analysis software "GenePix Pro 6.0" (Axon Instruments) were excluded from the calculations. Raw fluorescence intensities were normalized applying the variance stabilization method (W. Huber et al., Bioinformatics 18 Suppl. 1, 2002). To eliminate low quality data, the data points were ranked according to spot homogeneity, as assayed by the ratio of median to mean fluorescence intensity, the ratio of spot to local background intensity and the standard deviation of the log2 ratios between spot replicates. Those data points ranked among the lower 20% were removed from the data set. Genes that could not be quantified in more than 33% of all experiments of the experimental series after filtering were excluded as well.

label: Cy3 Chip1, Cy5 Chip2

source_name: MU1 / universal human reference total RNA (Stratagene #740000)

label_protocol: aRNA produced by T7 amplification was reversely transcribed and subsequently labeled using Klenow fragment and Cy-dUTPs.

extract_protocol: Nucleic acid extraction of high-molecular-weight RNA from frozen tumor tissue was carried out by ultracentrifugation

tag: Mucosa from healthy NON-Tumor Patients

label: Cy5 Chip1, Cy3 Chip2

source_name: universal human reference total RNA (Stratagene #740000) / MU1

extract_protocol: see Product Manual of refernce RNA (Stratagene)

tag: TNM unknown


title: Patient_MU2

source_name: MU2 / universal human reference total RNA (Stratagene #740000)

source_name: universal human reference total RNA (Stratagene #740000) / MU2


title: Patient_MU6

source_name: MU6 / universal human reference total RNA (Stratagene #740000)

source_name: universal human reference total RNA (Stratagene #740000) / MU6


title: Patient_H85

source_name: H85 / universal human reference total RNA (Stratagene #740000)

tag: TNM

value: T4N2cM0 Age:66 Sex:f

source_name: universal human reference total RNA (Stratagene #740000) / H85


title: Patient_MU5

source_name: MU5 / universal human reference total RNA (Stratagene #740000)

source_name: universal human reference total RNA (Stratagene #740000) / MU5


title: Patient_MU4

source_name: MU4 / universal human reference total RNA (Stratagene #740000)

source_name: universal human reference total RNA (Stratagene #740000) / MU4


title: Patient_H102

source_name: H102 / universal human reference total RNA (Stratagene #740000)

value: T3N0M0 Age:71 Sex:m

source_name: universal human reference total RNA (Stratagene #740000) / H102


title: Patient_H89

source_name: H89 / universal human reference total RNA (Stratagene #740000)

value: T1N0M0 Age:55 Sex:m

source_name: universal human reference total RNA (Stratagene #740000) / H89


title: Patient_MU3

source_name: MU3 / universal human reference total RNA (Stratagene #740000)

source_name: universal human reference total RNA (Stratagene #740000) / MU3


title: Patient_H79

source_name: H79 / universal human reference total RNA (Stratagene #740000)

value: T4N0M0 Age:57 Sex:m

source_name: universal human reference total RNA (Stratagene #740000) / H79


title: Liver_animal_2045_high_presure_ 6h

source_name: Liver_animal_2045_high_presure_ 6h

value: landrace, gender:male-castrates, age:3 months, weight:30 Kg, tissue:liver, animal:2045, treatment:partial hepatectomy - high presure, time point:6h


title: Patient_H67

source_name: H67 / universal human reference total RNA (Stratagene #740000)

value: T4N2bM0 Age:60 Sex:f

source_name: universal human reference total RNA (Stratagene #740000) / H67


title: Patient_H91

source_name: H91 / universal human reference total RNA (Stratagene #740000)

value: T4N2cM0 Age:45 Sex:m

source_name: universal human reference total RNA (Stratagene #740000) / H91


title: Patient_H70

source_name: H70 / universal human reference total RNA (Stratagene #740000)

value: T2N0M1 Age:73 Sex:m

source_name: universal human reference total RNA (Stratagene #740000) / H70


title: Patient_H103

source_name: H103 / universal human reference total RNA (Stratagene #740000)

value: T2N0M0 Age:52 Sex:f

source_name: universal human reference total RNA (Stratagene #740000) / H103


title: Patient_H101

source_name: H101 / universal human reference total RNA (Stratagene #740000)

value: T3N0M0 Age:76 Sex:m

source_name: universal human reference total RNA (Stratagene #740000) / H101


title: Patient_H94

source_name: H94 / universal human reference total RNA (Stratagene #740000)

value: T2N0M0 Age:77 Sex:f

source_name: universal human reference total RNA (Stratagene #740000) / H94


title: Patient_H71

source_name: H71 / universal human reference total RNA (Stratagene #740000)

value: T2N0M0 Age:53 Sex:m

source_name: universal human reference total RNA (Stratagene #740000) / H71


title: Patient_H90

source_name: H90 / universal human reference total RNA (Stratagene #740000)

value: T2N0M0 Age:50 Sex:f

source_name: universal human reference total RNA (Stratagene #740000) / H90


title: Patient_H86

source_name: H86 / universal human reference total RNA (Stratagene #740000)

value: T2N2bM0 Age:59 Sex:m

source_name: universal human reference total RNA (Stratagene #740000) / H86


title: Patient_H78

source_name: H78 / universal human reference total RNA (Stratagene #740000)

value: T4N1M0 Age:37 Sex:m

source_name: universal human reference total RNA (Stratagene #740000) / H78


title: Patient_H63

source_name: H63 / universal human reference total RNA (Stratagene #740000)

value: T4N0M0 Age:61 Sex:m

source_name: universal human reference total RNA (Stratagene #740000) / H63


title: Patient_H73

source_name: H73 / universal human reference total RNA (Stratagene #740000)

value: T2N2cM0 Age:47 Sex:m

source_name: universal human reference total RNA (Stratagene #740000) / H73


title: Patient_H81

source_name: H81 / universal human reference total RNA (Stratagene #740000)

value: T3N2bM0 Age:63 Sex:m

source_name: universal human reference total RNA (Stratagene #740000) / H81


title: hepatocellular carcinoma-normal liver-54

status: Public on Jan 06 2009

city: Shanghai

first: xuping

last: fu

country: China

institute: Institute of Genetics, Fudan University

description: hepatocellular carcinoma versus normal liver tissue

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

source_name: normal liver tissue

tag: normal liver tissue

source_name: hepatocellular carcinoma

tag: AGE

value: 65 SEX:Male Size of tumor:6*6 Differentiation:Poorly-differentiated


title: Patient_H93

source_name: H93 / universal human reference total RNA (Stratagene #740000)

value: T4N2cM0 Age:49 Sex:m

source_name: universal human reference total RNA (Stratagene #740000) / H93


title: Patient_H104

source_name: H104 / universal human reference total RNA (Stratagene #740000)

value: T4N2cM0 Age:64 Sex:m

source_name: universal human reference total RNA (Stratagene #740000) / H104


title: Patient_H68

source_name: H68 / universal human reference total RNA (Stratagene #740000)

value: T4N2bM0 Age:65 Sex:m

source_name: universal human reference total RNA (Stratagene #740000) / H68


title: Patient_H64

source_name: H64 / universal human reference total RNA (Stratagene #740000)

value: T4N2cM1 Age:77 Sex:m

source_name: universal human reference total RNA (Stratagene #740000) / H64


title: Patient_H66

source_name: H66 / universal human reference total RNA (Stratagene #740000)

value: T4N2cM0 Age:58 Sex:m

source_name: universal human reference total RNA (Stratagene #740000) / H66


title: Patient_H95

source_name: H95 / universal human reference total RNA (Stratagene #740000)

value: T4N2bM1 Age:69 Sex:m

source_name: universal human reference total RNA (Stratagene #740000) / H95


title: Patient_H99

source_name: H99 / universal human reference total RNA (Stratagene #740000)

value: T4N2bM0 Age:86 Sex:m

source_name: universal human reference total RNA (Stratagene #740000) / H99


title: Patient_H105

source_name: H105 / universal human reference total RNA (Stratagene #740000)

source_name: universal human reference total RNA (Stratagene #740000) / H105


title: Patient_H83

source_name: H83 / universal human reference total RNA (Stratagene #740000)

value: T2N0M0 Age:83 Sex:f

source_name: universal human reference total RNA (Stratagene #740000) / H83


title: Patient_H77

source_name: H77 / universal human reference total RNA (Stratagene #740000)

value: T2N2cM0 Age:50 Sex:m

source_name: universal human reference total RNA (Stratagene #740000) / H77


title: Patient_H65

source_name: H65 / universal human reference total RNA (Stratagene #740000)

value: T4N2cM0 Age:60 Sex:m

source_name: universal human reference total RNA (Stratagene #740000) / H65


title: Patient_H76

source_name: H76 / universal human reference total RNA (Stratagene #740000)

value: T2N0M0 Age:68 Sex:m

source_name: universal human reference total RNA (Stratagene #740000) / H76


title: Patient_H92

source_name: H92 / universal human reference total RNA (Stratagene #740000)

value: T4N2cM0 Age:64 Sex:f

source_name: universal human reference total RNA (Stratagene #740000) / H92


title: MCF7_AZT_azaC_6hour_sample3

city: Heidelberg

first: George

last: Reid

address: Meyerhofstrasse 1

institute: European Molecular Biology Organisation

description: This sample is the 3rd sample treated with 5 micromolar azacytidine for six hours

hyb_protocol: Centrifuge samples for 5 sec at max speed. Heat hybridistion cocktail to 90C for 5 min. Cool tubes on ice for 5 min. Load arrays within 30 min of denatured cRNA. Hybridize at 37 C for 18-24 hours. Prepare 0.75x TNT buffer for 46C over night. Wash 3x in TNT covered from light. Put in Cy5-Strep solution, incubate 30 min at RT proteced from light. Repeat TNT washes 4x. Incubate in a large reservoir of 0.1xSSC/0.05%Tween20 for 30 seconds, centrifuge for 3 min at 200 rpm.

scan_protocol: Scanning was performed according to the CodeLink manual, paragraph 7, page 9. GenePix software and the following settings were used: expand setting file name: Expression_5um.gps: whole genome products Expression_10um.gps: 10K and 20K products wavelength: 635 nm PMT voltage: 600 V laser power: 100% pixel size: 5 um for Whole Genome products

data_processing: Raw intensity values were median background subtracted and normalized to the median of the chip intensity

source_name: MCF7 cells

label_protocol:
Synthesis of cRNA by IVT:
Component 1x reaction
10x T7 reaction buffer 4,0ul
T7 ATP solution 4ul
T7 GTP solution 4ul
T7 CTP solution 4ul
T7 UTP solution 3ul
10mM biotin-16-UTP 7,5ul
10x T7 enzyme mix 4ul
30,5 ul of mixture was added to each sample and incubated at 37C for 14 hours.
Cleanup and Quantification of Biotin Labeled cRNA
Add 60ul Rnase free water and 350 ul buffer RLT to the IVT reaction, mix thoroughly. Add 250 ul ethanol (96-100%), mix well. Apply sample to an RNeasy spin column in a collection tube (2mL tube). Centrifuge for 15 seconds at 8000g (10000rpm). Add 500 ul buffer RPE Wash. Centrifuge for 15 seconds at 8000g (10000rpm). Repeat the last two steps. Replace the 2mL collection tube. Centrifuge for 2 minutes at 8000g (10000rpm). New 1,5mL collection tube: Add 50 ul nuclease-free water onto the filtermembrane. Incubate for 10 minutes at RT. Centrifuge for 1 minute at 8000g (10000rpm). Repeat the last three steps.

extract_protocol: ells were lysed in 10 ml Trizol, incubated for 5 min at room temperature. After addition of 1 ml chloroform, the lysate was mixed and incubated for 5 min at room temperature. The pahses were seperated by 12000xg for 15 min, the aquous phase was removed and 2-propanol was added. After a 10 min incubation at RT, the tubes were spun at 10000 rpm at 4C for 10 minutes, washed with 75% ethanol and finally, total RNA was dissolved in water and quantified.

treatment_protocol: MCF7 cells at 80% confluency were treated with 5 micromolar azacytidine for six hours

tag: MCF7 ERAlpha positive Breast Adenocarcinoma cell line


title: Patient_H88

source_name: H88 / universal human reference total RNA (Stratagene #740000)

value: T2N1M0 Age:51 Sex:m

source_name: universal human reference total RNA (Stratagene #740000) / H88


title: Patient_H82

source_name: H82 / universal human reference total RNA (Stratagene #740000)

value: T4N2bM1 Age:89 Sex:f

source_name: universal human reference total RNA (Stratagene #740000) / H82


title: MCF7_AZT_azaC_6hour_sample1

description: This sample is the 1st sample treated with 5 micromolar azacytidine for six hours

treatment_protocol: MCF7 cells at 80% confluency were treated with 5 micromolar azacytidine for four hours


title: MCF7_AZT_azaC_12hour_sample1

description: This sample is the 1st sample treated with 5 micromolar azacytidine for twelve hours

treatment_protocol: MCF7 cells at 80% confluency were treated with 5 micromolar azacytidine for twelve hours


title: Patient_H84

source_name: H84 / universal human reference total RNA (Stratagene #740000)

value: T2N1M0 Age:53 Sex:m

source_name: universal human reference total RNA (Stratagene #740000) / H84


title: MCF7_AZT_azaC_12hour_sample2

description: This sample is the 2nd sample treated with 5 micromolar azacytidine for twelve hours

extract_protocol: Cells were lysed in 10 ml Trizol, incubated for 5 min at room temperature. After addition of 1 ml chloroform, the lysate was mixed and incubated for 5 min at room temperature. The pahses were seperated by 12000xg for 15 min, the aquous phase was removed and 2-propanol was added. After a 10 min incubation at RT, the tubes were spun at 10000 rpm at 4C for 10 minutes, washed with 75% ethanol and finally, total RNA was dissolved in water and quantified.


title: Patient_H72

source_name: H72 / universal human reference total RNA (Stratagene #740000)

value: T4N2M0 Age:58 Sex:m

source_name: universal human reference total RNA (Stratagene #740000) / H72


title: MCF7_AZT_azaC_6hour_sample2

description: This sample is the 2nd sample treated with 5 micromolar azacytidine for six hours


title: MCF7_AZT_azaC_12hour_sample3

description: This sample is the 3rd sample treated with 5 micromolar azacytidine for twelve hours


title: 45_sec_36_week_50_mg_spironolactone

description: final images saved in .tif format

hyb_protocol: Per Superarray protocol

data_processing: Raw data was analyzed using Superarray's data analysis software; this corrected for background and normalized to the median. Average density was obtained and clover setting was off.

source_name: whole mouse kidney

label_protocol: Per Superarray protocol

value: NZB/W F1


title: MCF7_AZT_azaC_4hour_sample3

description: This sample is the 3rd sample treated with 5 micromolar azacytidine for four hours


title: 45_sec_36_week_25_mg_spironolactone_treated

description: final images saved in .tif format

source_name: whole kidney tissue


title: 45_sec_36_wk_vehicle_treated

description: final images saved in .tif format

source_name: whole homogenized kidney


title: MCF7_AZT_azaC_3hour_sample3

description: This sample is the 3rd sample treated with 5 micromolar azacytidine for three hours

scan_protocol: Expression_5um.gps: whole genome products Expression_10um.gps: 10K and 20K products wavelength: 635 nm PMT voltage: 600 V laser power: 100% pixel size: 5 um for Whole Genome products

treatment_protocol: MCF7 cells at 80% confluency were treated with 5 micromolar azacytidine for two hours


title: MCF7_AZT_azaC_4hour_sample2

description: This sample is the 2nd sample treated with 5 micromolar azacytidine for four hours


title: MCF7_AZT_azaC_1hour_sample2

description: This sample is the 2nd sample treated with 5 micromolar azacytidine for one hour

extract_protocol: Cells were lysed in 10 ml Trizol, incubated for 5 min at room temperature. After addition of 1 ml chloroform, the lysate was mixed and incubated for 5 min at room temperature. The pahses were seperated by 12000xg for 15 min, the aquous phase was removed and 2-propanol was added. After a 10 min incubation at RT, the tubes were spun at 10000 rpm at 4C for 10 minutes, washed with 75% ethanol and finally, total RNA was dissolved in water and quantitated.

treatment_protocol: MCF7 cells at 80% confluency were treated with 5 micromolar azacytidine for one hour


title: MCF7_AZT_azaC_1hour_sample3

description: This sample is the 3rd sample treated with 5 micromolar azacytidine for one hour


title: MCF7_AZT_Control3

description: This sample is the 3rd untreated control sample

label_protocol:
Synthesis of cRNA by IVT:
Component 1x reaction
10x T7 reaction buffer 4,0ul
T7 ATP solution 4ul
T7 GTP solution 4ul
T7 CTP solution 4ul
T7 UTP solution 3ul
10mM biotin-16-UTP 7,5ul
10x T7 enzyme mix 4ul
30,5 ul of mixture was added to each sample and incubated at 37C for 14 hours.
Cleanup and Quantification of Biotin Labeled cRNA
Add 60ul Rnase free water and 350 ul buffer RLT to the IVT reaction, mix thoroughly. Add 250 ul ethanol (96-100%), mix well. Apply sample to an RNeasy spin column in a collection tube (2mL tube). Centrifuge for 15 seconds at 8000g (10000rpm). Add 500 ul buffer RPE Wash. Centrifuge for 15 seconds at 8000g (10000rpm). Repeat the last two steps. Replace the 2mL collection tube. Centrifuge for 2 minutes at 8000g (10000rpm). New 1,5mL collection tube: Add 50 ul nuclease-free water onto the filtermembrane. Incubate for 10 minutes at RT. Centrifuge for 1 minute at 8000g (10000rpm0. Repeat the last three steps.


title: MCF7_AZT_azaC_2hour_sample1

description: This sample is the 1st sample treated with 5 micromolar azacytidine for two hours


title: MCF7_AZT_azaC_3hour_sample2

description: This sample is the 2nd sample treated with 5 micromolar azacytidine for three hours


title: The genome of Streptomyces rimosus M4018 shows a novel structure compared to other Streptomyces

status: Public on Jan 11 2008

city: Taipei

first: Ralph

last: Kirby

address: Li-Nong Road

country: Taiwan

institute: National Yang-Ming University

description: A comparison of the Streptomyces rimosus and mutants with Streptomyces coelicolor A3(2) using DNA/DNA microarray comparison based on the University of Surrey Microarray derived from the Bentley et al. (2002) genome sequence

hyb_protocol: see Hsiao Nai-hua & Ralph Kirby. Comparative genomics of Streptomyces avermitilis, Streptomyces cattleya, Streptomyces rimosus and Kitasatospora aureofaciens using a Streptomyces coelicolor microarray system Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology (2008) 93, 1-25

data_processing: normalization procedure discussed in Hsiao Nai-hua & Ralph Kirby. Comparative genomics of Streptomyces avermitilis, Streptomyces cattleya, Streptomyces rimosus and Kitasatospora aureofaciens using a Streptomyces coelicolor microarray system Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology (2008) 93, 1-25

organism: Streptomyces rimosus

source_name: Streptomyces rimosus M4018

label_protocol: Random Primer Labeling

extract_protocol: Total Genomic DNA extraction

tag: Strain derived by mutation and selection from Streptomyces rimosus G7

organism: Streptomyces coelicolor A3(2)

source_name: Streptomyces coelicolor A3(2) 104

extract_protocol: Total Genomic DNA Extraction

tag: Strain derived after mutation and selection by Professor David Hopwood


title: The genome of Streptomyces rimosus G37 shows a novel structure compared to other Streptomyces

scan_protocol: see Hsiao Nai-hua & Ralph Kirby. Comparative genomics of Streptomyces avermitilis, Streptomyces cattleya, Streptomyces rimosus and Kitasatospora aureofaciens using a Streptomyces coelicolor microarray system Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology (2008) 93, 1-25

source_name: Streptomyces rimosus G37

tag: Strain derived by mutation and selection by Professor David Hopwood


title: MCF7_AZT_azaC_1hour_sample1

description: This sample is the 1st sample treated with 5 micromolar azacytidine for one hour


title: The genome of Streptomyces rimosus S15883 shows a novel structure compared to other Streptomyces

source_name: Streptomyces rimosus S15883

tag: Strain derived using mutation and selection by Professor David Hopwood


title: MCF7_AZT_Control2

description: This sample is the 2nd untreated control sample

data_processing: Raw intensity values were  median background subtracted and normalized to the median of the chip intensity

label_protocol:
Synthesis of cRNA by IVT:
Component 1x reaction
10x T7 reaction buffer 4,0ul
T7 ATP solution 4ul
T7 GTP solution 4ul
T7 CTP solution 4ul
T7 UTP solution 3ul
10mM biotin-16-UTP 7,5ul
10x T7 enzyme mix 4ul
30,5 ul of mixture was added to each sample and incubated at 37C for 14 hours.
Cleanup and Quantification of Biotin Labeled cRNA
Add 60ul Rnase free water and 350 ul buffer RLT to the IVT reaction, mix thoroughly. Add 250 ul ethanol (96-100%), mix well. Apply sample to an RNeasy spin column in a collection tube (2mL tube). Centrifuge for 15 seconds at 8000g (10000rpm). Add 500 ul buffer RPE Wash. Centrifuge for 15 seconds at 8000g (10000rpm). Repeat the last two steps. Replace the 2mL collection tube. Centrifuge for 2 minutes at 8000g (10000rpm). New 1,5mL collection tube: Add 50 ul nuclease-free water onto the filtermembrane. Incubate for 10 minutes at RT. Centrifuge for 1 minute at 8000g (10000rpm. Repeat the last three steps.


title: MCF7_AZT_azaC_4hour_sample1

description: This sample is the 1st sample treated with 5 micromolar azacytidine for four hours


title: The genome of Streptomyces rimosus G7 shows a novel structure compared to other Streptomyces

source_name: Streptomyces rimosus G7

tag: Type strain of Streptomyces rimosus rimosus used to create a series of high antibiotic production mutants

tag: Strain obtained by mutation and selection by Professor David Hopwood


title: MCF7_AZT_azaC_3hour_sample1

description: This sample is the 1st sample treated with 5 micromolar azacytidine for three hours

source_name: MCF7 cells


title: MCF7_AZT_Control1

description: This sample is the 1st untreated control sample

source_name: MCF7 Cells


title: MCF7_AZT_azaC_2hour_sample3

description: This sample is the 3rd sample treated with 5 micromolar azacytidine for two hours


title: LS174T tet-on NICD1 0h vs 24h (dye-swap)

city: Tokyo

first: Ryuichi

last: Okamoto

state: Please Select

address: Tokyo Medical and Dental University

country: Japan

institute: Tokyo Medical and Dental University

description: Dye flip experiment of sample2

hyb_protocol: Target soution containing  5 µg of Cy3 or Cy5 coupled aRNA were combined and added to the hybridization buffer (Acegene hybridization solution supplemented with 5xSSC, 0.5%SDS, 4x Denhardt Solution, 100μg/ml  salmon sperm DNA, 10% formamide) , which were applied to microarrays enclosed in hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Gene pix 4000B scanner. Images were quantified using GenePix Pro software (version 4.1.1.42).

data_processing: Median normalized, background subtracted data obtained from log2 of processed Cy3 signal/processed Cy5 signal. An expression profile of a single timepoint was confirmed by dye-flip analysis.

source_name: Total RNA from LS174Ttet-onNICD1 cell

label_protocol: 5 µg of total RNA were coupled with either Cy3 or Cy5 using the Amino Allyl Message Amp aRNA kit (Ambion).

growth_protocol: Cells were grown in MEM supplemented with 10% FCS and 4mM l-glutamine.

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

treatment_protocol: For induction of NICD1 expression, Doxycycline at a final concentration of 100ng/ml  was added to the medium.

tag: LS174T cell line before Doxycycline addition

source_name: LS174Ttet-onNICD1 24h

tag: LS174T cell line 24 hours after Doxycycline addition


title: The genome of Streptomyces rimosus 23383 shows a novel structure compared to other Streptomyces

description: A comparison of the Streptomyces rimosus rimosus and mutants with Streptomyces coelicolor A3(2) using DNA/DNA microarray comparison based on the University of Surrey Microarray derived from the Bentley et al. (2002) genome sequence

source_name: Streptomyces rimosus 23383

tag: Derivatived from Streptomyces coelicolor by mutation and selection in the laboratory of Professor David Hopwood


title: Unloaded3

city: Berkeley

first: Justyn

middle: Wayne

last: Jaworski

state: CA

address: 1 Cyclotron Rd

department: Bioengineering

institute: UC Berkeley/ LBNL

description: Human dermal fibroblasts embedded in collagen 1 hydrogel scaffold under no loading condition at 37 degrees Celsius

hyb_protocol: Hybridization performed according to Affymetrix protocol and performed by Boston University Microarray Core Facility.  See Affymetrix I. Gene Chip(R) Expression Analysis Technical Manual. In: Affymetrix I, editor. Technical Support Manuals; 2004.

scan_protocol: Scanning performed according to Affymetrix protocol and performed by Boston University Microarray Core Facility.  See Affymetrix I. Gene Chip(R) Expression Analysis Technical Manual. In: Affymetrix I, editor. Technical Support Manuals; 2004.

data_processing: Robust Multichip Analysis Data (background correction and normalized expression data)

label_protocol: Labeling performed according to Affymetrix protocol and performed by Boston University Microarray Core Facility.  See Affymetrix I. Gene Chip(R) Expression Analysis Technical Manual. In: Affymetrix I, editor. Technical Support Manuals; 2004.

extract_protocol: Total RNA was extracted from fibroblast seeded gels using the TRIspin method.

tag: Primary human dermal fibroblasts were isolated from neonatal foreskins via tissue explant procedure and cultured in Dulbecco's Modified Eagle Medium


title: Unloaded2

source_name: Human dermal fibroblasts embedded in collagen 1 hydrogel scaffold


title: Unloaded1


title: Loaded1

description: Human dermal fibroblasts embedded in collagen 1 hydrogel scaffold under cyclic loading of 0.1Hz for 180 minutes at 37 degrees Celsius


title: Loaded2


title: LS174T tet-on NICD1 0h vs 12h (dye-swap)

description: Dye flip experiment of sample1

source_name: LS174Ttet-onNICD1 12h

tag: LS174T cell line 12 hours after Doxycycline addition


title: LS174T tet-on NICD1 0h vs 24h

description: Expression compared between before and 24 hours after doxycycline addition


title: JJ5 Mut S.aureus treated with triclosan 3

city: Newark

first: Virginie

middle: Marie

last: Aris

state: NJ

address: W420M, 225 Warren St

department: Center For Applied Genomics

institute: PHRI-UMNDJ

description:
Isolated ciprofloxacin/triclosan resistant mutant of S. aureus.The mutants were created by serial passage of wild-type S. aureus in increasing concentrations of triclosan (ranging from 0.25-1.25 ug/ml). The triclosan/ciprofloxacin resistant mutant JJ5 does not have alterations in the genes encoding fabI, gyrA, grlA, and grlB.
Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.

hyb_protocol: The purified cDNA was fragmented by incubation with DNase I.  Following heat inactivation of DNase I, the cDNA fragments were labeled with biotin at the 3’ end using the GeneChip DNA Labeling Reagent (Affymetrix).  The labeled cDNA was hybridized to the GeneChip S. aureus Genome Array at 45oC overnight.  The S. aureus Genome Array contains probe sets to over 3,300 S. aureus open reading frames and over 4,800 intergenic regions. Following hybridization, the hybridization mixture was removed and the arrays were washed and stained with R-phycoerythrin streptavin (Molecular Probes) using the GeneChip Fluidics Station 450 ProkGE-WS2_450 fluidics protocol.

scan_protocol: The chips were scanned using the GeneChip Scanner 3000

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

organism: Staphylococcus aureus

source_name: Mutant JJ5 strain treated with Triclosan (1.0 ug/ml for 1 hour at 37C)

label_protocol: Biotin-labeled cDNA was synthesized from total RNA following the procedure described in Section 3, Prokaryotic Sample and Array Processing, of the Expression Analysis Technical Manual (Affymetrix).  Briefly, total RNA (10 ?g) was converted to cDNA using SuperScript II (Invitrogen) and random primers.  The RNA was degraded by incubation with NaOH and the cDNA purified with the MiniElute PCR Purification Kit (Qiagen) following the manufacturer’s protocol.

growth_protocol: 18-24 hour cultures of the wild-type and JJ5 mutant S. aureus strains were washed three times and diluted in TSB to obtain a final A600 of 0.1.  The strains were grown in triplicate at 37oC with constant shaking for an additional 2 hours until they reached an A600 of 0.7. Then they were either treated with 1.0 ug/ml triclosan or not treated and incubated at 37oC with constant shaking for another hour.

extract_protocol: RNeasy Maxi-prep kit (Qiagen)

treatment_protocol: 18-24 hour cultures of the wild-type and JJ5 mutant S. aureus strains were washed three times and diluted in TSB to obtain a final A600 of 0.1.  The strains were grown in triplicate at 37oC with constant shaking for an additional 2 hours until they reached an A600 of 0.7.  1.0 ug/ml triclosan was then added to each of the cultures and the cultures were incubated at 37oC with constant shaking for 1 hour.  Control cultures were also grown under the same conditions in the absence of triclosan.  Following the 1 hour incubation, the cells were pelleted by centrifugation at 10000 g for 20 minutes at 4oC and washed three times with TSB.  The cell pellets from the final wash were resuspended into 500 ug/ml lysis buffer (20 mM Tris HCl, pH 7.5, 145 mM NaCl) containing 0.5 mg/ml lysostaphin (Sigma) and incubated at room temperature for 30 minutes in order for lysis to occur.  Total cellular RNA was then isolated using an RNeasy Maxi-prep kit (Qiagen) according to the manufacturers instructions.  RNA concentrations were determined spectrophotometrically at A260.  RNA integrity was determined by running 5.0 ug of each sample on a 1.2% agarose/0.66 M formaldehyde gel.


title: WT S.aureus treated with triclosan 2

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.

source_name: Wild type S. aureus from ATCC

tag: Wild type strain  treated with Triclosan (1.0 ug/ml for 1 hour at 37C)


title: WT S.aureus treated with triclosan 3

tag: Wild type strain treated with Triclosan (1.0 ug/ml for 1 hour at 37C)


title: WT S.aureus treated with tricolsan 1


title: Loaded3


title: JJ5 Mut S.aureus untreated 2

source_name: Mutant JJ5 strain not treated

tag: Mutant JJ5 strain not treated

tag: JJ5 does not have alterations in the genes encoding fabI, gyrA, grlA, and grlB.


title: JJ5 Mut S.aureus treated with triclosan 2

tag: Mutant JJ5 strain treated with Triclosan (1.0 ug/ml for 1 hour at 37C)


title: JJ5 Mut S.aureus treated with triclosan 1


title: LS174T tet-on NICD1 0h vs 12h

description: Expression compared between before and 12 hours after doxycycline addition


title: JJ5 Mut S.aureus untreated 1


title: WT S.aureus untreated 2

tag: Wild type strain not treated


title: WT S.aureus untreated 3


title: JJ5 Mut S.aureus untreated 3


title: WT S.aureus untreated 1


title: Campylobacter jejuni strain F38011_12h_rep1

status: Public on Jan 10 2008

type: mixed

city: Albany

first: Craig

middle: T

last: Parker

address: 800 Buchanan St

department: PSM

institute: USDA ARS

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

hyb_protocol: Labeled reference genomic DNA and test cDNAs were combined in 45 µl Pronto! cDNA hybridization solution (Corning, Corning, NY) and heated to 95°C for 5 min. Then, 15 µl of the hybridization mixture was put onto a microarray slide and sealed with a cover slip. The microarray slide was placed in a hybridization chamber (Corning) and incubated at 42°C for 18 h. Following hybridization, the slides were washed twice in 2× SSC, 0.1% sodium dodecyl sulfate at 42°C for 10 min, followed by twice in 1× SSC at room temperature for 10 min, and finally twice in 0.2× SSC at room temperature for 5 min. The microarray slides were dried by centrifugation at 300 × g for 10 min before scanning.

scan_protocol: Axon GenePix4000B, 10nm resolution. GenePix software. Optimize intensities manually.

data_processing: Data normalization was performed as described by Malik-Kale, P., et al. 2007. Appl. Environ. Microbiol. 73:3123-3136

organism: Campylobacter jejuni

label_protocol: Genomic DNA labeled using protocol described in Parker et al. J Clin Microbiol 2006, 44(11):4125-4135.

extract_protocol: Genomic DNA isolated using protocol described in Parker et al. J Clin Microbiol 2006, 44(11):4125-4135.

tag: Campylobacter jejuni strain F38011 genomic DNA.

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

source_name: Campylobacter jejuni strain F38011 total RNA

label_protocol: Total RNA was labeled directly using protocol described by Malik-Kale, P., et al. 2007. Appl. Environ. Microbiol. 73:3123-3136

growth_protocol: The C. jejuni F38011 strain was cultured on Mueller-Hinton (MH) agar plates supplemented with 5% bovine citrated blood (MH-blood) under microaerobic conditions (5% O2, 10% CO2, 85% N2) at 37ºC.

extract_protocol: Total RNA was isolated using protocol described by Malik-Kale, P., et al. 2007. Appl. Environ. Microbiol. 73:3123-3136


title: Campylobacter jejuni strain F38011_12h_rep2

source_name: Campylobacter jejuni strain F38011 genomic DNA

source_name: Campylobacter jejuni strain F38011, 12h, total RNA


title: Campylobacter jejuni strain F38011_12h_rep3

tag: DNA labelled with Cy5-dUTP and laser scanned at 635nm with background subtracted from feature signal.

tag: Campylobacter jejuni strain F38011, 12h, total RNA


title: Campylobacter jejuni strain F38011_12h_Deoxycholate_rep3

source_name: Campylobacter jejuni strain F38011, 12h, 0.1% sodium deoxycholate, total RNA

growth_protocol: The C. jejuni F38011 strain was cultured on Mueller-Hinton (MH) agar plates supplemented with 5% bovine citrated blood (MH-blood) and with 0.1% sodium deoxycholate under microaerobic conditions (5% O2, 10% CO2, 85% N2) at 37ºC.

tag: Campylobacter jejuni strain F38011 total RNA

tag: 0.1% sodium deoxycholate


title: Campylobacter jejuni strain F38011_12h_Deoxycholate_rep1


title: MCF7_AZT_azaC_2hour_sample2

description: This sample is the 2nd sample treated with 5 micromolar azacytidine for two hours

tag: MCF7 ERAlpha positive Breast Adenocarcinoma cell line


title: Campylobacter jejuni strain F38011_12h_Deoxycholate_rep2

growth_protocol: The C. jejuni F38011 strain was cultured on Mueller-Hinton (MH) agar plates supplemented with 5% bovine citrated blood (MH-blood) andwith 0.1% sodium deoxycholate under microaerobic conditions (5% O2, 10% CO2, 85% N2) at 37ºC.


title: C. albicans SMP_Tr_Vs_Un_A

status: Public on Jan 09 2008

city: University

first: Ameeta

last: Agarwal

state: MS

address: NCNPR, Room 2049

department: National Center for Natural Products Research

institute: University of Mississippi

description: C. albicans SMP Treated vs. Untreated A

hyb_protocol: Hybridization and washing protocols from the Corning UltraGAPS Coated Slides Instruction Manual (www.corning.com/lifesciences)

scan_protocol: Default parameters on ScanArray 5000 scanner (Perkin Elmer)

data_processing: Image analysis was performed using QuantArray v3.0 software (Perkin Elmer).  Differentially expressed genes were identified using default parameters of BRB Array Tools v3.2.3 software developed by Dr. Richard Simon and Amy Peng Lam (http://linus.nci.nih.gov/BRB-ArrayTools.html).  Data normalization was done using Lowess algorithm available in BRB ArrayTools.

organism: Candida albicans

source_name: C.albicans SC5314 cells treated with solvent (0.25% DMSO)

label_protocol: Aminoallyl labeling protocol from The Institute for Genomic Research (www.tigr.com)

extract_protocol: Qiagen RNeasy Midi-kit

tag: C. albicans SC5314 cells at OD 0.2 were treated with solvent (0.25% DMSO), allowed to grow to OD 0.5, then harvested and frozen.  Three biological replicate samples were generated.

source_name: C.albicans SC5314 cells treated with sampangine (SMP)

tag: C. albicans SC5314 cells at OD 0.2 were treated with sampangine (SMP) at IC50 concentration (6.13 ug/ml), allowed to grow to OD 0.5, then harvested and frozen.  Three biological replicate samples were generated.


title: BABA3

first: Laurent

last: Zimmerli

address: Roosevelt road

institute: National Taiwan University

description:
Simple annotation: Chemical effects, Heat-shock
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33706.gif

hyb_protocol: not provided

scan_protocol: not provided

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)

organism: Arabidopsis thaliana

source_name: BABA-treated

label_protocol: not provided

extract_protocol: not provided

tag: Arabidopsis Col-0 plants

source_name: water


title: White adipose tissue, 24 h-fasted #10

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

description: No additional information

hyb_protocol: Following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Rattus norvegicus

source_name: white adipose tissue

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 2 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolatedusing ISOGEN (Nippon Gene Co., Ltd., Toyama, Japan), then purified with an RNeasy mini kit (Qiagen K.K., Tokyo, Japan).

tag: Strain

value: Wistar

tag: Gender

value: male

tag: Age

value: 8 weeks

tag: Tissue

value: perinephrial white adipose tissue


title: C. albicans SMP_Tr_Vs_Un_B

description: C. albicans SMP Treated vs. Untreated B


title: BABA4

description:
Simple annotation: Chemical effects, Heat-shock
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33707.gif


title: Liver, 24 h-fasted #10

description: No additional information

source_name: liver

value: liver


title: C. albicans SMP_Tr_Vs_Un_C

description: C. albicans SMP Treated vs. Untreated C


title: BABA1

description:
Arabidopsis Col-0 plants were grown in ProMix HP (Premier Horticulture, Red Hill, PA, USA) for 14 days and the soil was drenched with a 0.25 mM BABA solution 1 day prior to harvesting samples for RNA preparation. These plants were grown in a growth chamber at 21C with a 14-hr photoperiod. All plants were grown at a light intensity of about 100 ? 150 ?E m-2 s-1. BABA (mixed isomers, Sigma, Milwaukee, WI, USA) was diluted in water at indicated concentration. A biological sample represents a comparison between plants that were water-treated (green channel) to plants drenched with BABA (red channel).
Simple annotation: Chemical effects, Heat-shock
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33704.gif


title: Liver, 24 h-fasted #6

description: No additional information


title: Liver, 24 h-fasted #8

description: No additional information


title: Liver, fed #1

description: No additional information


title: White adipose tissue, 24 h-fasted #9

description: No additional information


title: White adipose tissue, 24 h-fasted #8

description: No additional information


title: Liver, 24 h-fasted #9

description: No additional information


title: BABA2

description:
Simple annotation: Chemical effects, Heat-shock
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33705.gif


title: Liver, fed #5

description: No additional information


title: White adipose tissue, 24 h-fasted #6

description: No additional information


title: Liver, fed #2

description: No additional information


title: Liver, fed #4

description: No additional information


title: White adipose tissue, fed #5

description: No additional information


title: NZ7618 gshF::cam vs. WCFS1 (004_2_4)

city: Wageningen

first: L.

middle: Mariela

last: Serrano

address: Nieuwe Kanaal 9A

institute: TI Food and Nutrition

hyb_protocol: Agilent hybridization  protocol for Two-color  microarray-based Gene  expression analysis.  Version 5.5

scan_protocol: Using the Scan Array  Express microarray  scanner. 1.Turn on the scanner and  the computer (in this order) 2.Login: scanner 3.Double click the  'ScanArray Express' icon 4.Switch on lasers 1 and 3  at least 15 minutes prior to  scanning  arrays 5.Click the 'File' button This is to prevent you from  accidentally turning off the  laser  after the 15 minutes  warming-up phase 6.Insert the slide with the  array-side up and the label  towards  the outside. On Agilent  slides the array side is the  side with the  label that has the word  "Agilent" on it 7.Press 'Scan | Prescan' 8.Put resolution at 50  m,  select both labels used,  and set PMT  values for both channels  9.Press 'Start' 10.Press 'Palette,' 'Green'  as soon as projection of  the image has  started (first dye), select  the red colour as soon as  scanning of  the second layer (second  dye) has started 11.Adjust PMT values to  balance signals obtained  for both  channels. If necessary do  a few low-resolution scans  to obtain a  optimal balance 12.Click the 'Scan' button  again 13.Select frame for high  resolution scan, adjust  resolution (to 10   m) and scan the array for  both dyes 14.Press 'File | Save' to  save the files, 'Save all'  saves both  dye layers "Create a new folder for  each array "'Save all' saves the  signals from both layers in  individual files 15.Switch off the lasers

data_processing: 1.-Used script to split  8-array imagene file of cy3  intensity into eight separate  cy3 files. 2.-Used script to split  8-array imagene file of cy3  intensity into eight separate  cy5 files. 3.-For each indidivual  array, a merge file was  produced consisting of  merging the cy3 and cy5  intensity files created in  step 1 and 2. The merged  file is provided as  supplementary file for each  array.  4.-Background correction  (Mean values)

organism: Lactiplantibacillus plantarum

label_protocol: Annealing Mix 	x µl	 RNA preparation (=5µg) 	y µl	 nuclease-free water 	1 µl	 Random Nonamers 	11 µl	 TOTAL  1.	mix Annealing  Mix in a 200 µl PCR  tube gently by pipetting  up and down 2.	incubate for  5’ 70°C 3.	cool at room  temperature for 10’  (annealing) 4.	spin down the  mixture to the bottom of  the tube 5.	place on ice  Reverse transcription  Reverse Transcription  Mix 	4 µl	5x  buffer 	2 µl	0.1  M DTT 	1 µl	 dNTP-mix 	1 µl	 AA-dUTP 	1 µl  	 TMIII (keep only briefly  outside  20°C) 	20 µl	 TOTAL  1.	Mix by very  gently by pipetting up  and down (vigorous  pipetting will denature  the enzyme!) 2.	Incubate for 3  hrs at 42°C (in  PCR-machine) 3.	Cool on ice  for immediate  purification or place at   20°C  for storage  Degradation of mRNA 1.	Add 2 µl 2,5  M NaOH 2.	Mix (vortex)  and spin down 3.	Incubate for  15 min. at 37°C 4.	Add 10 µl 2 M  HEPES free acid 5.	Mix (vortex)  and spin down 6.	Ready for  purification or store at   20°C    Labelling and  purification of cDNA  with cyanine dyes  Followed Ge Healthcare  kit "Amersham CyDye  (Cy3/Cy5)Reactive Dye  Protocols for Post  Labelling  Aminoallyl-cDNA and  Aminoallyl-aRNA"  code RPN5661  Labelling of amino  allyl-modified cDNA with  CyDye 1.	Add the  amino allyl modified  cDNA (in 0.1 M sodium  bicarbonate) directly into  one aliquot of CyDye  NHS Ester.  Resuspend the ester  completely by pipetting  several times and  transfer the solution to  an amber 1.5 ml tube 2.	Incubate at  room temperature, in the  dark for 60 to 90  minutes 3.	Add 15 µl 4 M  Hydroxylamine to each  coupling reaction 4.	Mix by stirring  and incubate at room  temperature, in the  dark, for 15 minutes 5.	Proceed  directly to purification of  CyDye-labelled cDNA  Purification of CyDye  labelled cDNA Followed Ge Healthcare  kit "Amersham CyDye  (Cy3/Cy5)Reactive Dye  Protocols for Post  Labelling  Aminoallyl-cDNA and  Aminoallyl-aRNA"  code RPN5661

extract_protocol: Collecting cells Quenching Buffer 66.7 mM	HEPES (pH  6.5) 60%Methanol Extraction Mixture  (Prepared in a  screw-cap tube) -500 µll  phenol/Chloroform -30 µl10% SDS -30 µl3 M NaAc (pH 5.2) -500 mg glass-beads  (75-150 µm) -400 µlTE buffer    1.For each sample  prepare a tube with  Extraction Mixture 2.Harvest cells and  quench them  immediately in  Quenching Buffer.  Add 4 volumes of  Quenching Buffer (  40°C) to 1 volume of cell  culture 3.Mix and store the  sample at -40°C 4.Centrifuge cells at  -20  C at 9000 rpm for 10  minutes  (Centrifuge RC5B) 5.Discard the  supernatant; keep the  cell pellet cooled and  work  quickly to prevent  condensation of water.  Transfer the pellet with  a pre-cooled spatula to  a screw-crap tube with  Extraction Mixture 6.Mix the cell pellet  thoroughly with  Extraction Mixture by  shaking by hand 7.Freeze the tube  immediately in liquid  nitrogen 8.Break cells in the  Savant FastPrep  FP120. Three times 40  seconds  at speed 4.0 (cool cells  between steps if  necessary) 9.Centrifuge for 5  minutes at 4°C in an  Eppendorf centrifuge at  10.000 rpm 10.Transfer 500 µl of  the supernatant to a  new tube. Add 400 µl  chloroform (chloroform  should be cooled at  4°C) 11.Centrifuge for 2  minutes in an Eppendorf  centrifuge at full  speed (4°C) 5.Continue with the  "High Pure RNA  Isolation Kit" from  Roche  (order # 1 828 665) 6.Incubate for 60  minutes with DnaseI,  elute with 50 µl elution  buffer 7.Store the RNA in at  least 2 aliquots, one of  20 µl (for  concentration and  quality analysis and  labelling) and one  back-up  of 30 µl at  80°C.

tag: L. plantarum strain NZ7618 gshF::cam

tag: L. plantarum strain WCFS1


title: WCFS1 after 30 min 10 mM H2O2 vs. WCFS1 after 10 min 10 mM H2O2 (004_2_2)

tag: L. plantarum strain WCFS1 after 30 minutes 10 mM H2O2 stress.

tag: L. plantarum strain WCFS1 after 10 minutes 10 mM H2O2 stress.


title: White adipose tissue, fed #1

description: No additional information


title: WCFS1 vs. WCFS1 after 30 min 10 mM H2O2 (004_2_3)


title: White adipose tissue, fed #2

description: No additional information


title: WCFS1 after 10 min 10 mM H2O2 vs. NZ7618 gshF::cam after 10 min 10 mM H2O2 (004_2_1)

tag: L. plantarum strain NZ7618 gshF::cam after 10 minutes 10 mM H2O2 stress.


title: NZ7618 gshF::cam after 30 min 10 mM H2O2 vs. WCFS1 after 10 min 10 mM H2O2 (004_1_2)

tag: L. plantarum strain NZ7618 gshF::cam after 30 minutes 10 mM H2O2 stress.


title: Brown adipose tissue, fed #5

description: No additional information

source_name: brown adipose tissue

value: interscapular brown adipose tissue


title: NZ7618 gshF::cam after 10 min 10 mM H2O2 vs. WCFS1 after 30 min 10 mM H2O2 (004_1_4)


title: Brown adipose tissue, fed #2

description: No additional information


title: White adipose tissue, fed #4

description: No additional information


title: Brown adipose tissue, 24 h-fasted #6

description: No additional information


title: WCFS1 after 30 min 10 mM H2O2 vs. NZ7618 gshF::cam after 30 min 10 mM H2O2 (003_2_2)


title: Brown adipose tissue, 24 h-fasted #8

description: No additional information


title: Brown adipose tissue, 24 h-fasted #9

description: No additional information


title: NZ7618 gshF::cam after 10 min 10 mM H2O2 vs. WCFS1 after 30 min 10 mM H2O2 (004_1_1)


title: WCFS1 vs. WCFS1 after 10 min 10 mM H2O2 (003_2_4)


title: NZ7618 gshF::cam after 30 min 10 mM H2O2 vs. WCFS1 after 10 min 10 mM H2O2 (004_1_3)


title: Brown adipose tissue, fed #4

description: No additional information


title: NZ7618 gshF::cam after 30 min 10 mM H2O2 vs. NZ7618 gshF::cam after 10 min 10 mM H2O2 (003_2_1)


title: Brown adipose tissue, 24 h-fasted #10

description: No additional information


title: WCFS1 after 10 min 10 mM H2O2 vs. WCFS1 after 30 min 10 mM H2O2 (003_2_3)


title: NZ7618 gshF::cam cultivated in CDM containing vs. NZ7618 gshF::cam cultivated in CDM containing (003_1_4)

tag: L. plantarum strain NZ7618 gshF::cam cultivated in CDM containing


title: NZ7618 gshF::cam vs. WCFS1 (003_1_3)


title: Brown adipose tissue, fed #1

description: No additional information


title: NZ7618 gshF::cam after 10 min 10 mM H2O2 vs. NZ7618 gshF::cam after 30 min 10 mM H2O2 (003_1_2)


title: S. cerevisiae SMP_Treated_A

description: S. cerevisiae SMP_Treated_A

hyb_protocol: Affymetrix GenChip Hybridization protocol, and GeneChip Fluidics Station 450 default protocol

scan_protocol: Affymetrix GeneChip Scanner 3000 default parameters

data_processing: Image analysis, scaling (TGT = 500), and probeset-level data analysis using default parameters in GCOS v1.1

label: Biotin

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae Strain S288C cells treated with sampangine (SMP)

label_protocol: Affymetrix One Cycle Target Labeling kit

tag: S. cerevisiae S288C cells at OD 0.2 were treated with sampangine (SMP) at IC50 concentration (1.17 ug/ml), allowed to grow to OD 0.5, then harvested and frozen.  Three biological replicate samples were generated.


title: S. cerevisiae SMP_Control_C

description: S. cerevisiae SMP_Control_C

source_name: S. cerevisiae Strain S288C cells treated with solvent (0.25% DMSO)

tag: S. cerevisiae S288C cells at OD 0.2 were treated with solvent (0.25% DMSO), allowed to grow to OD 0.5, then harvested and frozen.  Three biological replicate samples were generated.


title: S. cerevisiae SMP_Control_A

description: S. cerevisiae SMP_Control_A


title: NZ7618 gshF::cam after 30 min 10 mM H2O2 vs. NZ7618 gshF::cam (003_1_1)


title: S. cerevisiae SMP_Treated_C

description: S. cerevisiae SMP_Treated_C


title: S. cerevisiae SMP_Treated_B

description: S. cerevisiae SMP_Treated_B


title: S. cerevisiae SMP_Control_B

description: S. cerevisiae SMP_Control_B


title: Breast cancer cell antigen Grb10_immuno high vaccine_rep2

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

hyb_protocol: Complete CodeLink protocol with Cy5-streptavidin staining

scan_protocol: Axon 4000B scanner, 10um resolution, TIFF image data extracted with CodeLink v.4.1 software.

data_processing: CodeLink v. 4.1 software used to extract raw data from TIFF image.  All data normalized to the median raw value of the array

label: Biotin-UTP

source_name: Mouse fibroblasts, DNA transfected, immuno high vaccine

label_protocol: MessageAmp II (standard protocol)

extract_protocol: Ribopure (Ambion)

tag: Strain C3H/He, female, 8-12 weeks old, DNA transfected fibroblasts