title: S14-1

description:
Simple annotation: Kidney, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69907.gif
Disease State: stable
Individual: 14

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1200, 5800; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Timothy,,Meyer Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.21; Parameter Scan Time = 08:59:32; Parameter PMT Volts = 530; Parameter Scan Date = 2006-08-10; Parameter Pixel Size = 10; Parameter Laser on time = 12563; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.88; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 27.21; Parameter Scan Time = 08:59:32; Parameter PMT Volts = 740; Parameter Scan Date = 2006-08-10; Parameter Pixel Size = 10; Parameter Laser on time = 12578; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.87; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer

source_name: 1 ug I19-T aRNA 2rounds

tag: 1 ug I19-T aRNA 2rounds


title: wild type 24h growth vs. delta calA 24h growth dye swap

status: Public on Dec 23 2008

type: RNA

city: Ribeirão Preto

first: Gustavo

middle: Henrique

last: Goldman

state: São Paulo

address: Av do Café, s/n

country: Brazil

institute: Faculty of Pharmaceutical Sciences of Ribeirão Preto

description: This hybridization used the wild type RNA from 24 hours growth as reference. The test RNA was obtained from a delta calA mutant culture also gown for 24 hours.

hyb_protocol: Labeled cDNAs were mixed with 8 µl Liquid block RPN3601 Batch 24 (GE Health Care), 5.5 µl SDS 2% and 19 µl SSC (20X) and the volume adjusted to 110 µl. Slides were hybridized overnight (42°C) in a Gene-Tac Hybridization Station (Genomic Solutions, Inc.) and washed in 2x SSC 0.5% SDS, 0.5x SSC and 0.05x SSC. All washing steps consisted of 1 min of flow, followed by 5 min of incubation.

scan_protocol: Slides were dried by centrifugation and subjected to fluorescent detection with a GMS 418 Array Scanner (Affymetrix Inc., Santa Clara, CA).

data_processing: TIFF images generated were analyzed using TIGR Spotfinder (http://www.jcvi.org/cms/research/software/) to obtain relative transcript levels. Spotfinder uses a dynamic thresholding algorithm to identify spots and calculate local background and integrated fluorescence intensity for each of the Cy3 and Cy5 channels. This software was also useful in eliminating questionable spots (those for which shape deviates significantly from that of a true circle, or those with a low signal-to-noise ratio). Spots with very low intensity in one channel (and thus aberrantly high or low expression ratios) were removed and eliminated from future analyses. Data was normalized using a local regression technique LOWESS (LOcally WEighted Scatterplot Smoothing) for hybridizations with RNA-based samples and SD regularization of the Cy5/Cy3 ratio across all sectors (blocks) of the array using a software tool MIDAS (http://www.jcvi.org/cms/research/software/). Following normalization, the values for each gene's in-slide replicates were averaged (median variance <0.01), and corresponding flip-dye replicates were averaged to compensate for dye-specific effects. Differentially expressed genes at the 95% confidence level were determined using intensity-dependent Z-scores (with Z=1.96) as implemented in MIDAS and the union of all genes identified at each time point were considered significant in this experiment. The resulting data were organized and visualized based on similar expression vectors in genes using Euclidean distance and hierarchical clustering with average linkage clustering method to view the whole data set and k-means to group the genes in clusters with TIGR MEV (Multi Experiment Viewer), also available at http://www.jcvi.org/cms/research/software/.

molecule: total RNA

organism: Aspergillus fumigatus

source_name: Aspergillus fumigatus wild type conidia grown for 24 hours

label_protocol: The RNA samples were extracted with Trizol and further purified with the RNeasy kit (Qiagen, Germany) and directly labeled by incorporation of Cy3-dUTP (GE Health Care). Briefly, 30 µg of total RNA were mixed with 20 µg of Randon Primer Hexamers (Invitrogen), 100 pmol of oligo dTV (Invitrogen) in a volume of 13 µl and heated to 70°C for 5 minutes. The tubes were briefly chilled to 4°C for 5 minutes and mixed with 5 µl of 5X first-strand buffer (Invitrogen), 2 µl DTT (Invitrogen), 2 µl dNTP (5 mM dATP, 5 mM dCTP, 5 mM dGTP, 2 mM dTTP), 2 µl of Suprescript III (Invitrogen) and 1 µl of Cy3-dUTP (25 nmol). The reaction was then incubated at 25°C for 5 minutes and at 42°C for 3 hours. The RNA was degraded by adding 2.5 µl EDTA (0.5 M, pH 8) and 5 µl NaOH (1M) following an incubation at 37°C for 40 minutes. The resulting first strand labeled cDNA was purified and concentrated using a Microcon YM-50 cartridge.

extract_protocol: At each time point the mycelia was harvested by centrifugation and quickly frozen in liquid nitrogen. For total RNA isolation, the mycelia were disrupted by grinding in liquid nitrogen and total RNA was extracted with Trizol reagent (Invitrogen). Ten micrograms of RNA from each treatment were then fractionated in 2.2 M formaldehyde, 1.2% agarose gel, stained with ethidium bromide, and then UV-visualized. The presence of intact 25S and 17S ribosomal RNA bands was used as a criterion to assess the integrity of the RNA.

tag: For the time course microarray experiments, 1.0 x 109 conidia of both A. fumigatus wild type [CEA17 delta akuB(KU80)] and mutant strain (delta calA) were used to inoculate 400 ml of pre-warmed liquid cultures in complete medium (YG) in  1 L erlenmeyer flasks. Cultures were allowed to grow for 6, 8, 12, 18 and 24 hours in a reciprocal shaker (250 rpm) at 37°C. At each time point, germilings were harvested by centrifugation or filtration and total RNA was extracted. Hybridization experiments were competitive using Cy3 or Cy5 probes derived from both wild type and delta calA strain grown for 6, 8, 12, 18 and 24 hours. Hybridizations were performed using the wild type RNA as reference in comparison to the mutant strain (test RNA) for the same time point. Normalized signal intensities were used to generate relative hybridization ratios (query/reference).

source_name: Aspergillus fumigatus delta calA conidia grown for 24 hours


title: Trenbolone_4

city: Vicksburg

first: Natalia

last: Vinas

state: MS

address: 3909 Halls Ferry Rd

country: USA

institute: Mississippi State University

description: Biological replicate 4 of 4 trenbolone treated fish

hyb_protocol: Standard Agilent two-color protocol (Agilent 60-mer oligo microarray processing protocol)

data_processing: Microarray image processing and data pre-processing were performed using Agilent's Feature Extraction software v 9.5. The intensity of each spot was summarized by the median pixel intensity. A log10 transformed signal ratio between the experimental (Cy5) channel and the reference (Cy3) channel was calculated for each spot, followed by within-array lowess transformation and between array scale normalization on median intensities (Zahurak et al., 2007). Probes that did not hybridize were removed from consideration.

organism: Pimephales promelas

source_name: Fathead minnow ovary exposed to trenbolone

label_protocol: cDNA synthesis, cRNA labelling, amplification and hybridization were performed following the manufacturer's kits and protocols (Agilent Low RNA Input Fluorescent Linear Amplification Kit)

growth_protocol: Adult (ca. 6 month old) female FHM from an on-site culture (EPA’s Mid-Continent Ecology Division Laboratory, Duluth) were acclimated to test conditions (25oC, 16:8 light:dark photoperiod, and fed adult brine shrimp twice daily) over a period of one week as described in USEPA (2001).  Exposures were initiated by transferring fish from the acclimation tanks to randomly assigned treatment tanks, n = 6 fish per treatment tank.  Water quality conditions, monitored daily, were maintained within the guidelines established for fathead minnow reproduction tests.

extract_protocol: Total RNA was isolated from gonadal tissue with the RNA Stat-60 reagent (Tel-test, Friendswood, TX).

treatment_protocol: Fathead minnow ovary exposed for 48h to trenbolone, flutamide, a mix of tronbolone/flutamide or control

tag: RNA from fathead minnow ovary exposed to 0.5 ug/L trenbolone

source_name: Reference Pool

extract_protocol: Total RNA was isolated from tissue with the RNA Stat-60 reagent (Tel-test, Friendswood, TX).

treatment_protocol: Control fish

tag: The reference pool consisted of equal amounts of RNA from control fathead minnow female and male tissues (liver, brain and gonad).


title: wild type 12h growth vs. delta calA 12h growth dye swap

description: This hybridization used the wild type RNA from 12 hours growth as reference. The test RNA was obtained from a delta calA mutant culture also gown for 12 hours.

source_name: Aspergillus fumigatus wild type conidia grown for 12 hours

source_name: Aspergillus fumigatus delta calA conidia grown for 12 hours


title: P5-2

status: Public on Dec 24 2008

city: Innsbruck

first: Michael

last: Rudnicki

state: Tirol

address: Anichstrasse 35

department: Dept of Nephrology

country: Austria

institute: University of Innsbruck

description:
Simple annotation: Kidney, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65947.gif
Disease State: progressive
Individual: 19

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 840, 6080; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Timothy,,Meyer Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 22.27; Parameter Scan Time = 10:28:14; Parameter PMT Volts = 520; Parameter Scan Date = 2005-11-18; Parameter Pixel Size = 10; Parameter Laser on time = 11834; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.84; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 22.27; Parameter Scan Time = 10:28:14; Parameter PMT Volts = 730; Parameter Scan Date = 2005-11-18; Parameter Pixel Size = 10; Parameter Laser on time = 11848; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 4.02; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer

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: Homo sapiens

source_name: Stratagene Universal Human Reference RNA

label_protocol: not provided

extract_protocol: not provided

tag: 1 ug STR  aRNA 2rounds vom 27.04.04

source_name: 1 ug PD 15 no DNase aRNA 2rounds

extract_protocol: RNA was isolated using Pico Pure; RNA Isolation Kit (all Arcturus, Mountain View, CA). We performed two rounds of linear RNA amplification using RiboAmp; RNA Amplification Kit (Arcturus, Mountain View, CA). Reference RNA was as well amplified twice.

tag: 1 ug PD 15 no DNase aRNA 2rounds


title: wild type 18h growth vs. delta calA 18h growth dye swap

description: This hybridization used the wild type RNA from 18 hours growth as reference. The test RNA was obtained from a delta calA mutant culture also gown for 18 hours.

source_name: Aspergillus fumigatus wild type conidia grown for 18 hours

source_name: Aspergillus fumigatus delta calA conidia grown for 18 hours


title: wild type 24h growth vs. delta calA 24h growth


title: Trenbolone_3

description: Biological replicate 3 of 4 trenbolone treated fish

scan_protocol: Standard Agilent two-color protocol (Agilent 60-mer oligo microarray processing protocol)


title: Trenbolone_1

description: Biological replicate 1 of 4 trenbolone treated fish


title: MIX_3

description: Biological replicate 3 of 4 mixture treated fish

source_name: Fathead minnow ovary exposed to a mix of trenbolone and flutamide

tag: RNA from fathead minnow ovary exposed to a mix of 0.5 ug/L trenbolone and 500 ug/L flutamide


title: Trenbolone_2

description: Biological replicate 2 of 4 trenbolone treated fish


title: MIX_4

description: Biological replicate 4 of 4 mixture treated fish


title: wild type 18h growth vs. delta calA 18h growth


title: wild type 12h growth vs. delta calA 12h growth


title: P1-1

description:
Simple annotation: Kidney, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58614.gif
Disease State: progressive
Individual: 15

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1200, 4560; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Timothy,,Meyer Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 22.88; Parameter Scan Time = 09:16:52; Parameter PMT Volts = 500; Parameter Scan Date = 2005-01-12; Parameter Pixel Size = 10; Parameter Laser on time = 10032; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.78; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 22.88; Parameter Scan Time = 09:16:52; Parameter PMT Volts = 700; Parameter Scan Date = 2005-01-12; Parameter Pixel Size = 10; Parameter Laser on time = 10046; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 4.10; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer

source_name: 1 ug PD2-T aRNA 2rounds

tag: 1 ug PD2-T aRNA 2rounds


title: P3-1

description:
Simple annotation: Kidney, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2005-09/64138.gif
Disease State: progressive
Individual: 17

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 5720; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Timothy,,Meyer Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.29; Parameter Scan Time = 09:57:59; Parameter PMT Volts = 520; Parameter Scan Date = 2005-09-22; Parameter Pixel Size = 10; Parameter Laser on time = 11622; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.85; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 25.29; Parameter Scan Time = 09:57:59; Parameter PMT Volts = 650; Parameter Scan Date = 2005-09-22; Parameter Pixel Size = 10; Parameter Laser on time = 11636; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 4.08; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer

source_name: 1 ug PD 17  no DNase aRNA 2rounds

tag: 1 ug PD 17  no DNase aRNA 2rounds


title: MIX_2

description: Biological replicate 2 of 4 mixture treated fish


title: wild type 8h growth vs. delta calA 8h growth

description: This hybridization used the wild type RNA from 8 hours growth as reference. The test RNA was obtained from a delta calA mutant culture also gown for 8 hours.

source_name: Aspergillus fumigatus wild type conidia grown for 8 hours

source_name: Aspergillus fumigatus delta calA conidia grown for 8 hours


title: MG_An_138

city: Bethesda

first: Jackie

last: Lavigne

state: MD

address: 6120 Executive Blvd. Rm. 6114

department: DCEG

institute: NCI/NIH

description: Effects of calorie restriction and exercise alone or in association in mammary gland gene expression

hyb_protocol: Affymetrix recommended protocol was followed for hybridation process. Hybridation cocktail  was prepared by mixing Control oligo B2, 20X Euk. Hyb controls, Herring Sperm DNA, Acetylated BSA, 2X Hybridization Buffer  and RNase-free Water at the requested concentration. Following fragmentation, 15 ug of cRNA, were hybridized on Affymetrix GeneChip Mouse Expression Array 430A . The microarrays were than incubated for 16 hours (o/n) at 45˚C and 60rpm. (Takahashi et al Using DNA microarray analyses to elucidate the effects of genistein in androgen-responsive prostate cancer cells: identification of novel targets. Mol Carcinog 2004;41:108-19)

scan_protocol: Affymetrix equipment and recommended protocol were used for the scan process.  (Takahashi et al Using DNA microarray analyses to elucidate the effects of genistein in androgen-responsive prostate cancer cells: identification of novel targets. Mol Carcinog 2004;41:108-19)

data_processing: The signal values and detection calls of the probe sets were determined using Affymetrix GCOS (ver. 1) software.  Relative intensity variation across arrays was normalized by scaling to an average signal level of 500 counts, excluding low 2% and high 2% signals. These signal values were transformed to a logarithmic scale (base 2) for statistical calculations.

label: biotin

organism: Mus musculus

source_name: Bilateral thoracical C57BL/6 mouse mammary gland

label_protocol: Affymetrix recommended protocol was followed for labeling (Expression Analysis Technical Manual, 2001, Affymetrix). RNA was biotin-labeled using the Enzo Bioarray-High Yield-RNA Transcript Labeling Kit (Cat #42655-20)

extract_protocol: Total mammary gland RNA was isolated from pooled left and right thoracic mammary glands (approximately 60 mg each) prior to microarray analysis, using TRIzol extraction reagent (Invitrogen, Rockville, MD) and the RNeasy Midi Cleanup Kit (Qiagen, Valencia, CA) in accordance with the manufacturers’ protocols.  Total RNA concentration was determined by spectrophotometric evaluation of absorbance at 260 nm, and RNA integrity was confirmed by 1% agarose gel electrophoresis.  RNA quality of random samples was also tested on an Agilent 2100 bio-analyzer (Agilent Technologies, Palo Alto CA).

treatment_protocol: Female C57BL/6 mice (9 weeks old) were randomized into 4 experimental groups: 1) food consumed ad libitum (AL); 2) AL with access to running wheels (AL+EX); 3) 30% CR; and 4) 30% CR with access to running wheels (CR+EX). CR mice received 70% of calories but 100% of all other nutrients compared to AL mice.  Food consumption, weight gain, and physical activity levels were recorded for 6 weeks.  RNA samples from animal mammary glands were analysed by Affymetrix oligo-microarray platform, in particular 10 samples from AL group (control), 9 samples from AL+EX group,  9 samples from CR group and 9 samples from CR+EX group were analysed.

tag: Diet regimen

value: 30% Calorie Restriction (CR)


title: P5-1

description:
Simple annotation: Kidney, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2005-09/64137.gif
Disease State: progressive
Individual: 19

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 5240; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Timothy,,Meyer Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 24.92; Parameter Scan Time = 09:51:00; Parameter PMT Volts = 520; Parameter Scan Date = 2005-09-22; Parameter Pixel Size = 10; Parameter Laser on time = 11615; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.84; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 24.92; Parameter Scan Time = 09:51:00; Parameter PMT Volts = 700; Parameter Scan Date = 2005-09-22; Parameter Pixel Size = 10; Parameter Laser on time = 11630; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 4.03; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer

source_name: 1 ug PD 15  no DNase aRNA 2rounds

tag: 1 ug PD 15  no DNase aRNA 2rounds


title: MIX_1

description: Biological replicate 1 of 4 mixture treated fish


title: wild type 6h growth vs. delta calA 6h growth dye swap

description: This hybridization used the wild type RNA from 6 hours growth as reference. The test RNA was obtained from a delta calA mutant culture also gown for 6 hours.

source_name: Aspergillus fumigatus wild type conidia grown for 6 hours

source_name: Aspergillus fumigatus delta calA conidia grown for 6 hours


title: Flutamide_3

description: Biological replicate 3 of 4 flutamide treated fish

source_name: Fathead minnow ovary exposed to Flutamide

tag: RNA from fathead minnow ovary exposed to 500 ug/L flutamide


title: wild type 8h growth vs. delta calA 8h growth dye swap


title: Control_4

description: Biological replicate 4 of 4 control fish

source_name: Fathead minnows control ovary

tag: RNA from fathead minnow control ovary

source_name: Reference Pool


title: SP_Replicate 1_Tanzania 16 week old root sample was compared to Tanzania 3 week old root sample

city: Seibersdorf

first: Silvia

last: Fluch

address: Campus Seibersdorf

department: Biogenetics/Natural Resources

institute: Austrian Research Centers GmbH

description: Biological replicate 1 out of 2

hyb_protocol: Hybridization mixture was prepared containing 2μg of each cy3-and cy5-labelled aaRNA with 30μl Microarray hybridization solution (# PRK0325) buffer and 60 μl formamide in total volume of 120μl for each reaction. The hybridization reaction was carried out in Tecan HS 400.hybridization chamber for 6 hours at 420C. After completing the hybridisation, the slides were washed once with 1xSSC for 30 sec. at 230C, then once with 1x SSC + 0.2% SDS for 20 min. and 30 sec. at 500C, then once with 0.1x SSC + 0.2% SDS for 10 min. at 230C, then twice with 0.2% SSC for 5 min. at 230C. After washing the slides were dried for 2min. and 30 sec. with Nitrogen gas.

scan_protocol: Slides were scanned with Tecan LS 200 scanner with different PMT (Photo-multiplier tube) settings for each slide so as to obtain images having not more than 2 saturated spots.

data_processing: GenePix 5.0 software was used for identifying the spots and creating gpr files for further analysis in GeneSpring GX7 software environment. The raw data were normalised by intensity dependent Lowess method and dye swap. The experiment was setup by selecting time point as a single condition to calculate log of ratio. The error model for two colour data based on replicates was constructed using dye swap and individual identifier (biological replicates) as parameters, with average Base/Proportional of 154.3. One way ANOVA test was carried out taking time as a single parameter and Benjamini and Hochberg false discovery rate (0.05) as a multiple testing correction, with parametric test (assuming variances are not equal), to identify significantly expressed genes. The data was filtered for fold change by comparison of three week sample with 6, 10 and 16 week samples, where genes having more than log2 fold up and down-regulation were selected.

organism: Ipomoea batatas

source_name: Root

label_protocol: 2μg of mRNA was amplified using Amino Allyl MessageAmp™ II aRNA Amplification Kit from Ambion® according to manufacturer’s protocol. Using same kit and Amersham CyDye™ post-labeling reactive dye pack (Cat #RPN 5661), labelling reaction was carried out with 20μg of amplified aaRNA.

growth_protocol: For cDNA library construction five Sweetpotato accessions (INA100, Zapallo, SPK004, Feng Shu Bai and Wagabolige) grown on the experimental fields of CIP (International Potato Center - Centro Internacional de la Papa) were used. The roots were harvested from soil (3 plants/clone were taken for isolation of each RNA sample) and used for RNA extraction. Accessions used for probe RNA extraction were SPK004, Beauregard, Tanzania and Feng Shou Bai. The root material used was from 3, 6, 10 and 16 weeks of development stages of the sweet potato plant.

extract_protocol: Total RNA extraction by the TIGR hot phenol procedure (http://www.tigr.org/tdb/potato/images/SGED_SOP_3.2.1.pdf).

tag: Cultivar

value: Tanzania

tag: 16 weeks old root

tag: 3 weeks old root


title: Flutamide_2

description: Biological replicate 2 of 4 flutamide treated fish


title: SP_Replicate 1_Swap_Feng Shou Bai 16 week old root sample was compared to Tanzania 16 week old root sample

description: Biological replicate 1 out of 2

value: Feng Shou Bai


title: Control_3

description: Biological replicate 3 of 4 control fish


title: wild type 6h growth vs. delta calA 6h growth

source_name: A fumigatus wild type conidia grown for 6 hours

source_name: A fumigatus delta calA strain conidia grown for 6 hours


title: SP_Replicate 1_beauregard 10 week old root sample was compared to SPK004 10 week old root sample

description: Biological replicate 1 out of 2

value: Beauregard

tag: 10 weeks old root


title: Flutamide_1

description: Biological replicate 1 of 4 flutamide treated fish


title: SP_Replicate 1_Tanzania 3 week old root sample was compared to SPK004 3 week old root sample

description: Biological replicate 1 out of 2


title: Control_2

description: Biological replicate 2 of 4 control fish


title: SP_Replicate 1_Swap_Tanzania 3 week old root sample was compared to Tanzania 16 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 1_Swap_Feng Shou Bai 3 week old root sample was compared to Feng Shou Bai 6 week old root sample

description: Biological replicate 1 out of 2

tag: 6 weeks old root


title: SP_Replicate 1_Tanzania 16 week old root sample was compared to Feng Shou Bai 16 week old root sample

description: Biological replicate 1 out of 2


title: Control_1

description: Biological replicate 1 of 4 control fish


title: SP_Replicate 1_Swap_SPK004 3 week old root sample was compared to SPK004 6 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 1_Swap_SPK004 10 week old root sample was compared to beauregard 10 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 1_Swap_beauregard 3 week old root sample was compared to beauregard 10 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 1_Swap_beauregard 3 week old root sample was compared to beauregard 6 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 1_Swap_Feng Shou Bai 3 week old root sample was compared to Feng Shou Bai 16 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 1_Swap_SPK004 16 week old root sample was compared to beauregard 16 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 1_Swap_beauregard 6 week old root sample was compared to Feng Shou Bai 6 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 1_Swap_SPK004 3 week old root sample was compared to beauregard 3 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 1_Swap_SPK004 3 week old root sample was compared to Tanzania 3 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 1_Swap_SPK004 6 week old root sample was compared to beauregard 6 week old root sample

description: Biological replicate 1 out of 2


title: S2-1

description:
Simple annotation: Kidney, Kidney
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53605.gif
Disease State: stable
Individual: 2

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1410, 5060; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Timothy,,Meyer Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.60; Parameter Scan Time = 08:58:58; Parameter PMT Volts = 500; Parameter Scan Date = 2004-07-06; Parameter Pixel Size = 10; Parameter Laser on time = 8583; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 3.77; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.4; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.60; Parameter Scan Time = 08:58:58; Parameter PMT Volts = 650; Parameter Scan Date = 2004-07-06; Parameter Pixel Size = 10; Parameter Laser on time = 8586; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [90704]; Parameter Laser Power = 4.39; Parameter Scanning software version = 2.0.2.4; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Timothy,,Meyer

source_name: Stratagene Universal Human Reference RNA

source_name: 1 ug F1-T aRNA 2rounds

tag: 1 ug F1-T aRNA 2rounds


title: SP_Replicate 1_Swap_Feng Shou Bai 3 week old root sample was compared to Tanzania 3 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 1_Swap_Feng Shou Bai 3 week old root sample was compared to Feng Shou Bai 10 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 1_Swap_SPK004 3 week old root sample was compared to Feng Shou Bai 3 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 1_Swap_SPK004 3 week old root sample was compared to SPK004 10 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 1_Swap_beauregard 10 week old root sample was compared to Feng Shou Bai 10 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 1_Swap_beauregard 3 week old root sample was compared to Feng Shou Bai 3 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 1_SPK004 16 week old root sample was compared to SPK004 3 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 1_beauregard 3 week old root sample was compared to SPK004 3 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 1_Swap_Feng Shou Bai 6 week old root sample was compared to Tanzania 6 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 1_Swap_Tanzania 3 week old root sample was compared to Tanzania 6 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 1_Swap_beauregard 3 week old root sample was compared to beauregard 16 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 1_Swap_beauregard 16 week old root sample was compared to Feng Shou Bai 16 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 2_Feng Shou Bai 10 week old root sample was compared to beauregard 10 week old root sample

description: Biological replicate 2 out of 2


title: SP_Replicate 2_beauregard 6 week old root sample was compared to beauregard 3 week old root sample

description: Biological replicate 2 out of 2


title: SP_Replicate 2_Tanzania 3 week old root sample was compared to Feng Shou Bai 3 week old root sample

description: Biological replicate 2 out of 2


title: SP_Replicate 1_Swap_Tanzania 3 week old root sample was compared to Tanzania 10 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 1_SPK004 10 week old root sample was compared to SPK004 3 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 2_Feng Shou Bai 16 week old root sample was compared to Feng Shou Bai 3 week old root sample

description: Biological replicate 2 out of 2


title: SP_Replicate 2_Feng Shou Bai 16 week old root sample was compared to beauregard 16 week old root sample

description: Biological replicate 2 out of 2


title: SP_Replicate 2_beauregard 16 week old root sample was compared to SPK004 16 week old root sample

description: Biological replicate 2 out of 2


title: SP_Replicate 1_Swap_SPK004 3 week old root sample was compared to SPK004 16 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 2_Feng Shou Bai 6 week old root sample was compared to Feng Shou Bai 3 week old root sample

description: Biological replicate 2 out of 2


title: SP_Replicate 2_Feng Shou Bai 6 week old root sample was compared to beauregard 6 week old root sample

description: Biological replicate 2 out of 2


title: SP_Replicate 2_Feng Shou Bai 3 week old root sample was compared to SPK004 3 week old root sample

description: Biological replicate 2 out of 2


title: SP_Replicate 2_Tanzania 3 week old root sample was compared to SPK004 3 week old root sample

description: Biological replicate 2 out of 2


title: SP_Replicate 2_beauregard 10 week old root sample was compared to SPK004 10 week old root sample

description: Biological replicate 2 out of 2


title: SP_Replicate 1_Swap_Feng Shou Bai 10 week old root sample was compared to Tanzania 10 week old root sample

description: Biological replicate 1 out of 2


title: L. pneumophila strain AA100, sta phase, sample replicate 03, array replicate 01

city: New York

first: Sergey

last: Kalachikov

state: NY

address: NWC Bld, 550 West 120th Street Rm 1002

department: Chemical Engineering

institute: Columbia University

hyb_protocol: The microarray slides were prepared as described in GPL7283. The probes were UV-crosslinked to the slides using energy of 0.8 J/cm2 at 254 nm and the hybridization was set according to the recommendations provided with the Corning Ultra GAPS microarray slides. Slides were prehybridized in 5x SSC containing 0.1% sodium dodecyl sulfate (SDS) and 0.1mg/ml bovine serum albumin for 45 min at 37°C, rinsed in 0.1 x SSC and dried. Labeled cDNA (1.8 ug) was concentrated in Microcon 50 to an approximate volume of 5 uL, washed off the filter with 450 uL of hybridization solution (consisting of 40% formamide, 5x SSC, 0.1%SDS, 10mM Tris HCl (pH 7.5) and 1mg/ml of sonicated denatured human placental DNA), warmed up to 92 °C for 2 min and hybridized to microarrays in hybridization chambers (GraceBio Inc, Bend, OR) at 37°C overnight with rotation. After hybridization, slides were washed twice for five minutes in each of 5.0x SSC 0.1%SDS and 0.1x SSC 0.1%SDS at ambient temperature, briefly rinsed in 0.1x SSC and dried using compressed air.

scan_protocol: Slides were scanned at 5 µm resolution using ScanArray Express microarray scanner (Perkin Elmer Inc, Wellesley, MA) and the resulting images were analyzed using ProScanArray software v.3.0.0.0016 provided with the instrument.

data_processing:
The expression VALUE provided in the table was generated in the following way:
(1) for each probe spot on the array, the average local background intensity value measured in vicinity of the spot was subtracted from the average spot intensity value;
(2) the background-corrected intensity values were log-transformed at base 2;
(3) the resulting log-transformed intensity values in this sample were normalized against another 17 expression profiles analyzed in this study using normalize.lowess() R-function implemented in Bioconductor affy microarray analysis package (Gautier et al. 2004, Bioinf. 20: 307-315).
(4) the missing values in the resulting log-transformed normalized dataset were imputed using K-nearest neighbor prediction devised in (Troyanskaya et al. 2001, Bioinf. 17: 520-525)

label: Alexa Fluor 647

organism: Legionella pneumophila

source_name: AYE axenic culture at OD600=3.0

label_protocol:
twenty micrograms of total RNA were converted into cDNA by reverse transcription in the presence of allylamino-dUTP and the resulting amino-modified cDNA was coupled with Alexa Fluor 647 using conventional protocols. The cDNA yield for this sample was 1.9 ug.
The extent of the Alexa Fluor 647 label incorporation was 1.5% with respect to cDNA bases.

growth_protocol: 50 mL of fresh AYE in 250 mL baffled conical flask was innoculated with a fresh overnight Legionella culture at OD600=0.05 and the bacteria were grown in orbital shacker at 250 rpm at 37 °C. The growth was monitored by measuring the OD600 of the culture aliquotes diluted 10 times.

extract_protocol:
Bacterial pellets were removed from the -80 °C, resuspended in 200 uL of TE/lysozyme for 5 min and the total RNA was isolated using RNeasy mini RNA extraction kit (Qiagen, Valencia, CA) with strict conformity with the recommended protocol. The quantity and the integrity of the resulting total RNA sample was measured using Qbit and Agilent Bioanalyzer instruments.
The RNA yield for this sample was 34 ug. RIN(as E.coli, exp)=7.4

tag: Legionella pneumophila strain AA100


title: L. pneumophila strain AA100, sta phase, sample replicate 03, array replicate 02


title: SP_Replicate 2_Tanzania 10 week old root sample was compared to Feng Shou Bai 10 week old root sample

description: Biological replicate 2 out of 2


title: L. pneumophila strain AA100, sta phase, sample replicate 02, array replicate 01

source_name: AYE axenic culture at OD600=2.9

label_protocol:
twenty micrograms of total RNA were converted into cDNA by reverse transcription in the presence of allylamino-dUTP and the resulting amino-modified cDNA was coupled with Alexa Fluor 647 using conventional protocols. The cDNA yield for this sample was 1.2 ug.
The extent of the Alexa Fluor 647 label incorporation was 1.2% with respect to cDNA bases.

extract_protocol:
Bacterial pellets were removed from the -80 °C, resuspended in 200 uL of TE/lysozyme for 5 min and the total RNA was isolated using RNeasy mini RNA extraction kit (Qiagen, Valencia, CA) with strict conformity with the recommended protocol. The quantity and the integrity of the resulting total RNA sample was measured using Qbit and Agilent Bioanalyzer instruments.
The RNA yield for this sample was 45 ug. RIN(as E.coli, exp)=7.4


title: SP_Replicate 1_Tanzania 10 week old root sample was compared to Feng Shou Bai 10 week old root sample

description: Biological replicate 1 out of 2


title: L. pneumophila strain AA100, sta phase, sample replicate 02, array replicate 02


title: L. pneumophila strain AA100, sta phase, sample replicate 01, array replicate 01

label_protocol:
twenty micrograms of total RNA were converted into cDNA by reverse transcription in the presence of allylamino-dUTP and the resulting amino-modified cDNA was coupled with Alexa Fluor 647 using conventional protocols. The cDNA yield for this sample was 1.3 ug.
The extent of the Alexa Fluor 647 label incorporation was 1.9% with respect to cDNA bases.

extract_protocol:
Bacterial pellets were removed from the -80 °C, resuspended in 200 uL of TE/lysozyme for 5 min and the total RNA was isolated using RNeasy mini RNA extraction kit (Qiagen, Valencia, CA) with strict conformity with the recommended protocol. The quantity and the integrity of the resulting total RNA sample was measured using Qbit and Agilent Bioanalyzer instruments.
The RNA yield for this sample was 34 ug. RIN(as E.coli, exp)=7.9


title: L. pneumophila strain AA100, sta phase, sample replicate 01, array replicate 02


title: SP_Replicate 2_Swap_Feng Shou Bai 10 week old root sample was compared to Tanzania 10 week old root sample

description: Biological replicate 2 out of 2


title: SP_Replicate 2_Feng Shou Bai 3 week old root sample was compared to beauregard 3 week old root sample

description: Biological replicate 2 out of 2


title: SP_Replicate 2_beauregard 6 week old root sample was compared to SPK004 6 week old root sample

description: Biological replicate 2 out of 2


title: SP_Replicate 2_beauregard 16 week old root sample was compared to beauregard 3 week old root sample

description: Biological replicate 2 out of 2


title: SP_Replicate 2_beauregard 10 week old root sample was compared to beauregard 3 week old root sample

description: Biological replicate 2 out of 2


title: SP_Replicate 2_Swap_beauregard 10 week old root sample was compared to Feng Shou Bai 10 week old root sample

description: Biological replicate 2 out of 2


title: L. pneumophila strain AA100, exp phase, sample replicate 03, array replicate 02

label: Alexa Fluor 546

source_name: AYE axenic culture at OD600=0.84

label_protocol:
twenty micrograms of total RNA were converted into cDNA by reverse transcription in the presence of allylamino-dUTP and the resulting amino-modified cDNA was coupled with Alexa Fluor 546 using conventional protocols. The cDNA yield for this sample was 2.0 ug.
The extent of the Alexa Fluor 546 label incorporation was 2.35% with respect to cDNA bases.

extract_protocol:
Bacterial pellets were removed from the -80 °C, resuspended in 200 uL of TE/lysozyme for 5 min and the total RNA was isolated using RNeasy mini RNA extraction kit (Qiagen, Valencia, CA) with strict conformity with the recommended protocol. The quantity and the integrity of the resulting total RNA sample was measured using Qbit and Agilent Bioanalyzer instruments.
The RNA yield for this sample was 59 ug. RIN=8.2


title: L. pneumophila strain AA100, exp phase, sample replicate 02, array replicate 02

source_name: AYE axenic culture at OD600=0.9

label_protocol:
twenty micrograms of total RNA were converted into cDNA by reverse transcription in the presence of allylamino-dUTP and the resulting amino-modified cDNA was coupled with Alexa Fluor 546 using conventional protocols. The cDNA yield for this sample was 1.1 ug.
The extent of the Alexa Fluor 546 label incorporation was 2.3% with respect to cDNA bases.

extract_protocol:
Bacterial pellets were removed from the -80 °C, resuspended in 200 uL of TE/lysozyme for 5 min and the total RNA was isolated using RNeasy mini RNA extraction kit (Qiagen, Valencia, CA) with strict conformity with the recommended protocol. The quantity and the integrity of the resulting total RNA sample was measured using Qbit and Agilent Bioanalyzer instruments.
The RNA yield for this sample was 57 ug. RIN(as E.coli, exp)=8.6


title: SP_Replicate 2_Swap_SPK004 16 week old root sample was compared to beauregard 16 week old root sample

description: Biological replicate 2 out of 2


title: SP_Replicate 2_Swap_Feng Shou Bai 3 week old root sample was compared to Feng Shou Bai 6 week old root sample

description: Biological replicate 2 out of 2


title: L. pneumophila strain AA100, exp phase, sample replicate 02, array replicate 01


title: SP_Replicate 2_Swap_beauregard 3 week old root sample was compared to beauregard 16 week old root sample

description: Biological replicate 2 out of 2


title: L. pneumophila strain AA100, exp phase, sample replicate 01, array replicate 01

source_name: AYE axenic culture at OD600=0.86

label_protocol:
twenty micrograms of total RNA were converted into cDNA by reverse transcription in the presence of allylamino-dUTP and the resulting amino-modified cDNA was coupled with Alexa Fluor 546 using conventional protocols. The cDNA yield for this sample was 1.3 ug.
The extent of the Alexa Fluor 546 label incorporation was 2.6% with respect to cDNA bases.

extract_protocol:
Bacterial pellets were removed from the -80 °C, resuspended in 200 uL of TE/lysozyme for 5 min and the total RNA was isolated using RNeasy mini RNA extraction kit (Qiagen, Valencia, CA) with strict conformity with the recommended protocol. The quantity and the integrity of the resulting total RNA sample was measured using Qbit and Agilent Bioanalyzer instruments.
The RNA yield for this sample was 71 ug. RIN=7.9


title: SP_Replicate 2_Feng Shou Bai 10 week old root sample was compared to Feng Shou Bai 3 week old root sample

description: Biological replicate 2 out of 2


title: L. pneumophila strain AA100, exp phase, sample replicate 03, array replicate 01

extract_protocol:
Bacterial pellets were removed from the -80 °C, resuspended in 200 uL of TE/lysozyme for 5 min and the total RNA was isolated using RNeasy mini RNA extraction kit (Qiagen, Valencia, CA) with strict conformity with the recommended protocol. The quantity and the integrity of the resulting total RNA sample was measured using Qbit and Agilent Bioanalyzer instruments.
The RNA yield for this sample was 59 ug. RIN(as E.coli, exp)=8.2


title: L. pneumophila strain AA100, exp phase, sample replicate 01, array replicate 02

extract_protocol:
Bacterial pellets were removed from the -80 °C, resuspended in 200 uL of TE/lysozyme for 5 min and the total RNA was isolated using RNeasy mini RNA extraction kit (Qiagen, Valencia, CA) with strict conformity with the recommended protocol. The quantity and the integrity of the resulting total RNA sample was measured using Qbit and Agilent Bioanalyzer instruments.
The RNA yield for this sample was 71 ug. RIN(as E.coli, exp)=7.9


title: L. pneumophila AA100 PmrB mutant, post-exponential phase, sample replicate 03, array replicate 02

source_name: AYE axenic culture at OD600=3.7

label_protocol:
twenty micrograms of total RNA were converted into cDNA by reverse transcription in the presence of allylamino-dUTP and the resulting amino-modified cDNA was coupled with Alexa Fluor 647 using conventional protocols. The cDNA yield for this sample was 0.8 ug.
The extent of the Alexa Fluor 647 label incorporation was 2.0% with respect to cDNA bases.

extract_protocol:
Bacterial pellets were removed from the -80 °C, resuspended in 200 uL of TE/lysozyme for 5 min and the total RNA was isolated using RNeasy mini RNA extraction kit (Qiagen, Valencia, CA) with strict conformity with the recommended protocol. The quantity and the integrity of the resulting total RNA sample was measured using Qbit and Agilent Bioanalyzer instruments.
The RNA yield for this sample was 57 ug. RIN(as E.coli, exp)=6.7

tag: Legionella pneumophila strain AA100; PmrB (lpg1291) mutant


title: SP_Replicate 2_Swap_beauregard 6 week old root sample was compared to Feng Shou Bai 6 week old root sample

description: Biological replicate 2 out of 2


title: SP_Replicate 2_Swap_beauregard 3 week old root sample was compared to beauregard 10 week old root sample

description: Biological replicate 2 out of 2


title: L. pneumophila AA100 PmrB mutant, post-exponential phase, sample replicate 03, array replicate 01


title: L. pneumophila AA100 PmrB mutant, exp phase, sample replicate 03, array replicate 02

label_protocol:
twenty micrograms of total RNA were converted into cDNA by reverse transcription in the presence of allylamino-dUTP and the resulting amino-modified cDNA was coupled with Alexa Fluor 546 using conventional protocols. The cDNA yield for this sample was 1.9 ug.
The extent of the Alexa Fluor 546 label incorporation was 2.46% with respect to cDNA bases.

extract_protocol:
Bacterial pellets were removed from the -80 °C, resuspended in 200 uL of TE/lysozyme for 5 min and the total RNA was isolated using RNeasy mini RNA extraction kit (Qiagen, Valencia, CA) with strict conformity with the recommended protocol. The quantity and the integrity of the resulting total RNA sample was measured using Qbit and Agilent Bioanalyzer instruments.
The RNA yield for this sample was 56 ug. RIN(as E.coli, exp)=9.4


title: L. pneumophila AA100 PmrB mutant, post-exponential phase, sample replicate 02, array replicate 01

source_name: AYE axenic culture at OD600=3.8

label_protocol:
twenty micrograms of total RNA were converted into cDNA by reverse transcription in the presence of allylamino-dUTP and the resulting amino-modified cDNA was coupled with Alexa Fluor 647 using conventional protocols. The cDNA yield for this sample was 1.3 ug.
The extent of the Alexa Fluor 647 label incorporation was 2.92% with respect to cDNA bases.

extract_protocol:
Bacterial pellets were removed from the -80 °C, resuspended in 200 uL of TE/lysozyme for 5 min and the total RNA was isolated using RNeasy mini RNA extraction kit (Qiagen, Valencia, CA) with strict conformity with the recommended protocol. The quantity and the integrity of the resulting total RNA sample was measured using Qbit and Agilent Bioanalyzer instruments.
The RNA yield for this sample was 82 ug. RIN(as E.coli, exp)=6.5


title: L. pneumophila AA100 PmrB mutant, post-exponential phase, sample replicate 02, array replicate 02

label_protocol:
twenty micrograms of total RNA were converted into cDNA by reverse transcription in the presence of allylamino-dUTP and the resulting amino-modified cDNA was coupled with Alexa Fluor 647 using conventional protocols. The cDNA yield for this sample was 1.3 ug.
The extent of the Alexa Fluor 647 label incorporation was 2.9% with respect to cDNA bases.


title: L. pneumophila AA100 PmrB mutant, exp phase, sample replicate 03, array replicate 01


title: SP_Replicate 2_Tanzania 16 week old root sample was compared to Feng Shou Bai 16 week old root sample

description: Biological replicate 2 out of 2


title: L. pneumophila AA100 PmrB mutant, post-exponential phase, sample replicate 01, array replicate 01

source_name: AYE axenic culture at OD600=3.9

label_protocol:
twenty micrograms of total RNA were converted into cDNA by reverse transcription in the presence of allylamino-dUTP and the resulting amino-modified cDNA was coupled with Alexa Fluor 647 using conventional protocols. The cDNA yield for this sample was 1.3 ug.
The extent of the Alexa Fluor 647 label incorporation was 2.95% with respect to cDNA bases.

extract_protocol:
Bacterial pellets were removed from the -80 °C, resuspended in 200 uL of TE/lysozyme for 5 min and the total RNA was isolated using RNeasy mini RNA extraction kit (Qiagen, Valencia, CA) with strict conformity with the recommended protocol. The quantity and the integrity of the resulting total RNA sample was measured using Qbit and Agilent Bioanalyzer instruments.
The RNA yield for this sample was 84 ug. RIN(as E.coli, exp)=5.8


title: L. pneumophila AA100 PmrB mutant, exp phase, sample replicate 02, array replicate 02

label_protocol:
twenty micrograms of total RNA were converted into cDNA by reverse transcription in the presence of allylamino-dUTP and the resulting amino-modified cDNA was coupled with Alexa Fluor 546 using conventional protocols. The cDNA yield for this sample was 1.4 ug.
The extent of the Alexa Fluor 546 label incorporation was 2.34% with respect to cDNA bases.

extract_protocol:
Bacterial pellets were removed from the -80 °C, resuspended in 200 uL of TE/lysozyme for 5 min and the total RNA was isolated using RNeasy mini RNA extraction kit (Qiagen, Valencia, CA) with strict conformity with the recommended protocol. The quantity and the integrity of the resulting total RNA sample was measured using Qbit and Agilent Bioanalyzer instruments.
The RNA yield for this sample was 62 ug. RIN(as E.coli, exp)=9.5


title: L. pneumophila AA100 PmrB mutant, exp phase, sample replicate 02, array replicate 01


title: L. pneumophila AA100 PmrB mutant, exp phase, sample replicate 01, array replicate 02

source_name: AYE axenic culture at OD600=0.76

label_protocol:
twenty micrograms of total RNA were converted into cDNA by reverse transcription in the presence of allylamino-dUTP and the resulting amino-modified cDNA was coupled with Alexa Fluor 546 using conventional protocols. The cDNA yield for this sample was 1.5 ug.
The extent of the Alexa Fluor 546 label incorporation was 2.0% with respect to cDNA bases.

extract_protocol:
Bacterial pellets were removed from the -80 °C, resuspended in 200 uL of TE/lysozyme for 5 min and the total RNA was isolated using RNeasy mini RNA extraction kit (Qiagen, Valencia, CA) with strict conformity with the recommended protocol. The quantity and the integrity of the resulting total RNA sample was measured using Qbit and Agilent Bioanalyzer instruments.
The RNA yield for this sample was 82 ug. RIN=9.5


title: SP_Replicate 2_Swap_Tanzania 3 week old root sample was compared to Tanzania 16 week old root sample

description: Biological replicate 2 out of 2


title: SP_Replicate 2_Swap_Feng Shou Bai 6 week old root sample was compared to Tanzania 6 week old root sample

description: Biological replicate 2 out of 2


title: SP_Replicate 2_Tanzania 16 week old root sample was compared to Tanzania 3 week old root sample

description: Biological replicate 2 out of 2


title: SP_Replicate 2_Swap_Feng Shou Bai 3 week old root sample was compared to Feng Shou Bai 10 week old root sample

description: Biological replicate 2 out of 2


title: SP_Replicate 2_SPK004 16 week old root sample was compared to SPK004 3 week old root sample

description: Biological replicate 2 out of 2


title: Flutamide_4

description: Biological replicate 4 of 4 flutamide treated fish

source_name: Fathead minnow ovary exposed to Flutamide

label_protocol: cDNA synthesis, cRNA labelling, amplification and hybridization were performed following the manufacturer's kits and protocols (Agilent Low RNA Input Fluorescent Linear Amplification Kit)

extract_protocol: Total RNA was isolated from gonadal tissue with the RNA Stat-60 reagent (Tel-test, Friendswood, TX).

extract_protocol: Total RNA was isolated from tissue with the RNA Stat-60 reagent (Tel-test, Friendswood, TX).

tag: The reference pool consisted of equal amounts of RNA from control fathead minnow female and male tissues (liver, brain and gonad).


title: L. pneumophila AA100 PmrB mutant, post-exponential phase, sample replicate 01, array replicate 02

label_protocol:
wenty micrograms of total RNA were converted into cDNA by reverse transcription in the presence of allylamino-dUTP and the resulting amino-modified cDNA was coupled with Alexa Fluor 647 using conventional protocols. The cDNA yield for this sample was 1.3 ug.
The extent of the Alexa Fluor 647 label incorporation was 2.95% with respect to cDNA bases.


title: L. pneumophila AA100 PmrB mutant, exp phase, sample replicate 01, array replicate 01

extract_protocol:
Bacterial pellets were removed from the -80 °C, resuspended in 200 uL of TE/lysozyme for 5 min and the total RNA was isolated using RNeasy mini RNA extraction kit (Qiagen, Valencia, CA) with strict conformity with the recommended protocol. The quantity and the integrity of the resulting total RNA sample was measured using Qbit and Agilent Bioanalyzer instruments.
The RNA yield for this sample was 82 ug. RIN(as E.coli, exp)=9.5


title: SP_Replicate 2_SPK004 10 week old root sample was compared to SPK004 3 week old root sample

description: Biological replicate 2 out of 2

extract_protocol: Total RNA extraction by the TIGR hot phenol procedure (http://www.tigr.org/tdb/potato/images/SGED_SOP_3.2.1.pdf).


title: SP_Replicate 2_beauregard 3 week old root sample was compared to SPK004 3 week old root sample

description: Biological replicate 2 out of 2


title: SP_Replicate 2_Swap_Tanzania 3 week old root sample was compared to Tanzania 10 week old root sample

description: Biological replicate 2 out of 2


title: L. pneumophila AA100 PmrA mutant, post-exponential phase, sample replicate 03, array replicate 02

source_name: AYE axenic culture at OD600=2.63

label_protocol:
twenty micrograms of total RNA were converted into cDNA by reverse transcription in the presence of allylamino-dUTP and the resulting amino-modified cDNA was coupled with Alexa Fluor 647 using conventional protocols. The cDNA yield for this sample was 1.3 ug.
The extent of the Alexa Fluor 647 label incorporation was 2.25% with respect to cDNA bases.

extract_protocol:
Bacterial pellets were removed from the -80 °C, resuspended in 200 uL of TE/lysozyme for 5 min and the total RNA was isolated using RNeasy mini RNA extraction kit (Qiagen, Valencia, CA) with strict conformity with the recommended protocol. The quantity and the integrity of the resulting total RNA sample was measured using Qbit and Agilent Bioanalyzer instruments.
The RNA yield for this sample was 74 ug. RIN(as E.coli, exp)=6.4

tag: Legionella pneumophila strain AA100; PmrA (lpg1292) mutant


title: SP_Replicate 2_Swap_Tanzania 3 week old root sample was compared to Tanzania 6 week old root sample

description: Biological replicate 2 out of 2

label_protocol: 2μg of mRNA was amplified using Amino Allyl MessageAmp™ II aRNA Amplification Kit from Ambion® according to manufacturer’s protocol. Using same kit and Amersham CyDye™ post-labeling reactive dye pack (Cat #RPN 5661), labelling reaction was carried out with 20μg of amplified aaRNA.


title: SP_Replicate 2_Tanzania 6 week old root sample was compared to Feng Shou Bai 6 week old root sample

description: Biological replicate 2 out of 2


title: L. pneumophila AA100 PmrA mutant, exp phase, sample replicate 03, array replicate 02

label_protocol:
twenty micrograms of total RNA were converted into cDNA by reverse transcription in the presence of allylamino-dUTP and the resulting amino-modified cDNA was coupled with Alexa Fluor 546 using conventional protocols. The cDNA yield for this sample was 1.4 ug.
The extent of the Alexa Fluor 546 label incorporation was 2.2% with respect to cDNA bases.

extract_protocol:
Bacterial pellets were removed from the -80 °C, resuspended in 200 uL of TE/lysozyme for 5 min and the total RNA was isolated using RNeasy mini RNA extraction kit (Qiagen, Valencia, CA) with strict conformity with the recommended protocol. The quantity and the integrity of the resulting total RNA sample was measured using Qbit and Agilent Bioanalyzer instruments.
The RNA yield for this sample was 61 ug. RIN(as E.coli, exp)=8.8


title: SP_Replicate 2_Tanzania 6 week old root sample was compared to Tanzania 3 week old root sample

description: Biological replicate 2 out of 2


title: L. pneumophila AA100 PmrA mutant, post-exponential phase, sample replicate 02, array replicate 02

source_name: AYE axenic culture at OD600=2.69

label_protocol:
twenty micrograms of total RNA were converted into cDNA by reverse transcription in the presence of allylamino-dUTP and the resulting amino-modified cDNA was coupled with Alexa Fluor 647 using conventional protocols. The cDNA yield for this sample was 1.1 ug.
The extent of the Alexa Fluor 647 label incorporation was 4.0% with respect to cDNA bases.

extract_protocol:
of TE/lysozyme for 5 min and the total RNA was isolated using RNeasy mini RNA extraction kit (Qiagen, Valencia, CA) with strict conformity with the recommended protocol. The quantity and the integrity of the resulting total RNA sample was measured using Qbit and Agilent Bioanalyzer instruments.
The RNA yield for this sample was 65 ug. RIN(as E.coli, exp)=6.4


title: L. pneumophila AA100 PmrA mutant, post-exponential phase, sample replicate 03, array replicate 01

label_protocol:
twenty micrograms of total RNA were converted into cDNA by reverse transcription in the presence of allylamino-dUTP and the resulting amino-modified cDNA was coupled with Alexa Fluor 647 using conventional protocols. The cDNA yield for this sample was 1.3 ug.
The extent of the Alexa Fluor 647 label incorporation was 2.5% with respect to cDNA bases.

extract_protocol:
Bacterial pellets were removed from the -80 °C, resuspended in 200 uL of TE/lysozyme for 5 min and the total RNA was isolated using RNeasy mini RNA extraction kit (Qiagen, Valencia, CA) with strict conformity with the recommended protocol. The quantity and the integrity of the resulting total RNA sample was measured using Qbit and Agilent Bioanalyzer instruments.
The RNA yield for this sample was 74 ug. RIN=6.4


title: L. pneumophila AA100 PmrA mutant, post-exponential phase, sample replicate 02, array replicate 01


title: SP_Replicate 2_Swap_beauregard 3 week old root sample was compared to Feng Shou Bai 3 week old root sample

description: Biological replicate 2 out of 2

source_name: Root


title: SP_Replicate 2_Swap_SPK004 3 week old root sample was compared to Tanzania 3 week old root sample

description: Biological replicate 2 out of 2


title: SP_Replicate 2_Swap_SPK004 3 week old root sample was compared to SPK004 16 week old root sample

description: Biological replicate 2 out of 2


title: SP_Replicate 2_Swap_Feng Shou Bai 16 week old root sample was compared to Tanzania 16 week old root sample

description: Biological replicate 2 out of 2


title: L. pneumophila AA100 PmrA mutant, post-exponential phase, sample replicate 01, array replicate 01

source_name: AYE axenic culture at OD600=2.62

label_protocol:
twenty micrograms of total RNA were converted into cDNA by reverse transcription in the presence of allylamino-dUTP and the resulting amino-modified cDNA was coupled with Alexa Fluor 647 using conventional protocols. The cDNA yield for this sample was 1.3 ug.
The extent of the Alexa Fluor 647 label incorporation was 1.4% with respect to cDNA bases.

extract_protocol:
of TE/lysozyme for 5 min and the total RNA was isolated using RNeasy mini RNA extraction kit (Qiagen, Valencia, CA) with strict conformity with the recommended protocol. The quantity and the integrity of the resulting total RNA sample was measured using Qbit and Agilent Bioanalyzer instruments.
The RNA yield for this sample was 63 ug. RIN(as E.coli, exp)=6.4


title: L. pneumophila AA100 PmrA mutant, post-exponential phase, sample replicate 01, array replicate 02


title: SP_Replicate 1_beauregard 16 week old root sample was compared to beauregard 3 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 2_Tanzania 10 week old root sample was compared to Tanzania 3 week old root sample

description: Biological replicate 2 out of 2


title: SP_Replicate 2_Swap_SPK004 3 week old root sample was compared to beauregard 3 week old root sample

description: Biological replicate 2 out of 2


title: L. pneumophila AA100 PmrA mutant, exp phase, sample replicate 01, array replicate 02

source_name: AYE axenic culture at OD600=0.82

label_protocol:
twenty micrograms of total RNA were converted into cDNA by reverse transcription in the presence of allylamino-dUTP and the resulting amino-modified cDNA was coupled with Alexa Fluor 546 using conventional protocols. The cDNA yield for this sample was 1.8 ug.
The extent of the Alexa Fluor 546 label incorporation was 2.4% with respect to cDNA bases.

extract_protocol:
Bacterial pellets were removed from the -80 °C, resuspended in 200 uL of TE/lysozyme for 5 min and the total RNA was isolated using RNeasy mini RNA extraction kit (Qiagen, Valencia, CA) with strict conformity with the recommended protocol. The quantity and the integrity of the resulting total RNA sample was measured using Qbit and Agilent Bioanalyzer instruments.
The RNA yield for this sample was 40 ug. RIN(as E.coli, exp)=8.8


title: L. pneumophila AA100 PmrA mutant, exp phase, sample replicate 03, array replicate 01


title: L. pneumophila AA100 PmrA mutant, exp phase, sample replicate 01, array replicate 01

data_processing:
The expression VALUE provided in the table was generated in the following way:
(1) for each probe spot on the array, the average local background intensity value measured in vicinity of the spot was subtracted from the average spot intensity value;
(2)  the background-corrected intensity values were log-transformed at base 2;
(3) the resulting log-transformed intensity values in this sample were normalized against another 17 expression profiles analyzed in this study using normalize.lowess() R-function implemented in Bioconductor affy microarray analysis package (Gautier et al. 2004, Bioinf. 20: 307-315).
(4) the missing values in the resulting log-transformed normalized dataset were imputed using K-nearest neighbor prediction devised in (Troyanskaya et al. 2001, Bioinf. 17: 520-525)

growth_protocol:
50 mL of fresh AYE in 250 mL baffled conical flask was innoculated with a fresh overnight Legionella culture at OD600=0.05 and the bacteria were grown in orbital shacker at 250 rpm at 37 °C. The growth was monitored by measuring the OD600 of the culture aliquotes diluted 10 times.
When the OD600 reached ~0.8,  two 2 mL aliquotes were removed from the culture into 2 mL eppendoff tubes, the bacteria were pelleted by centrifugation at 10,000 rpm for 2 min and frozen at -80 °C.


title: L. pneumophila AA100 PmrA mutant, exp phase, sample replicate 02, array replicate 01

label_protocol:
twenty micrograms of total RNA were converted into cDNA by reverse transcription in the presence of allylamino-dUTP and the resulting amino-modified cDNA was coupled with Alexa Fluor 546 using conventional protocols. The cDNA yield for this sample was 1.5 ug.
The extent of the Alexa Fluor 546 label incorporation was 2% with respect to cDNA bases.

extract_protocol:
Bacterial pellets were removed from the -80 °C, resuspended in 200 uL of TE/lysozyme for 5 min and the total RNA was isolated using RNeasy mini RNA extraction kit (Qiagen, Valencia, CA) with strict conformity with the recommended protocol. The quantity and the integrity of the resulting total RNA sample was measured using Qbit and Agilent Bioanalyzer instruments.
The RNA yield for this sample was 49 ug. RIN(as E.coli, exp)=9.0


title: L. pneumophila AA100 PmrA mutant, exp phase, sample replicate 02, array replicate 02


title: SP_Replicate 2_Swap_SPK004 3 week old root sample was compared to SPK004 10 week old root sample

description: Biological replicate 2 out of 2


title: SP_Replicate 1_Tanzania 3 week old root sample was compared to Feng Shou Bai 3 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 2_Swap_SPK004 10 week old root sample was compared to beauregard 10 week old root sample

description: Biological replicate 2 out of 2


title: SP_Replicate 1_beauregard 16 week old root sample was compared to SPK004 16 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 1_Feng Shou Bai 3 week old root sample was compared to beauregard 3 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 1_beauregard 6 week old root sample was compared to beauregard 3 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 1_beauregard 10 week old root sample was compared to beauregard 3 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 1_Tanzania 6 week old root sample was compared to Tanzania 3 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 1_Feng Shou Bai 16 week old root sample was compared to beauregard 16 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 1_Feng Shou Bai 10 week old root sample was compared to beauregard 10 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 1_Feng Shou Bai 6 week old root sample was compared to Feng Shou Bai 3 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 2_Swap_Feng Shou Bai 3 week old root sample was compared to Feng Shou Bai 16 week old root sample

description: Biological replicate 2 out of 2


title: SP_Replicate 2_Swap_beauregard 3 week old root sample was compared to beauregard 6 week old root sample

description: Biological replicate 2 out of 2


title: SP_Replicate 1_Tanzania 10 week old root sample was compared to Tanzania 3 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 1_Feng Shou Bai 10 week old root sample was compared to Feng Shou Bai 3 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 1_Feng Shou Bai 6 week old root sample was compared to beauregard 6 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 2_SPK004 6 week old root sample was compared to SPK004 3 week old root sample

description: Biological replicate 2 out of 2


title: SP_Replicate 1_Feng Shou Bai 16 week old root sample was compared to Feng Shou Bai 3 week old root sample

description: Biological replicate 1 out of 2


title: WCE of Rpo21 ChIP (Wild type, Low phosphate medium)

type: genomic

city: Bunkyo-ku

first: Katsuhiko

last: Shirahige

state: Tokyo

address: 1-1-1 Yayoi

department: Research Center for Epigenetic Disease

country: Japan

institute: The University of Tokyo

description: Rpo21 binding profile in low phosphate medium wild type (WCE).

hyb_protocol: Hybridization, blocking and washing steps were carried out as previously described by Winzeler et al. (Science. 281, 1194-1197, 1998). Each sample was hybridized to the array in 150ul containing 6XSSPE, 0.005% TritonX-100, 15ug fragmented denatured salmon sperm DNA (Gibco-BRL), and 1nmole of a 3’-biotin control oligonucleotide (oligo B2 probes) that hybridized to the border features on the array. Samples were heated to 100°C for 10 min., and then cooled on ice. Samples were hybridized for 16h at 42°C in a hybridization oven (GeneChip hybri oven 320, Affymetrix, CA). Washing and staining protocol (Mini_euk1 ver2) provided by Affymetrix was performed automatically on a fluidics station (GeneChip fluidics station 400, Affymetrix, CA).

scan_protocol: Each array was scanned by HP GeneArray Scanner (Affymetrix, CA) at an emission wavelength of 560nm at 7.5uM resolution. Grids were aligned to the scanned images using the know feature of the array. Primary data analyses were carried out using the Affymetrix Microarray Suite Ver.5.0 software to obtain hybridization intensity, fold change value, change p-value, and detection p-value for each locus.

data_processing: For the discrimination of positive and negative signals for the binding, we compared ChIP fraction with Sup (supernatant) fraction by using three criteria as follows. First, the reliability of strength of signal was judged by detection p-value of each locus (p-value lower than 0.025 was considered as significant). Secondly, reliability of binding ratio was judged by change p-value (p-value lower than 0.025 was considered as significant). Thirdly, clusters consisted of at least three contiguous loci which filled above two criteria were selected as significantly enriched locus, because it is apparent that a single site of protein-DNA interaction will result in immuno-precipitation of DNA fragments that hybridized not only to the locus of the actual binding site but also to its neighbors. This third criterion is very unique, make the data highly reliable and can be only applicable to the chip data obtained by our high-resolution tiling array.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: WCE fraction DNA

label_protocol: DNA was end-labelled with Biotin-N6ddATP by Terminal Transferase as previously described by Winzeler et al. (Science. 281, 1194-1197, 1998)

extract_protocol: 1.5X10^8 cells were disrupted by MULTI-BEADS SHOCKER (MB400U, YASUI KIKAI, Osaka), which was able to keep cells precisely at lower than 6°C during disruption by glass beads. This enabled us to retrieve more than 60% of tagged proteins to soluble fraction routinely. Chromosomal DNA was shared into the average size of 400-600bp by sonication. Anti-HA monoclonal antibody HA.11 (16B12) (CRP Inc., Denver, PA) and anti-FLAG monoclonal antibody M2 (Sigma-Aldrich Co., St Louis, MO) were used for chromatin immuno-precipitation. Immunoprecipitated chromosomal DNA was subsequently purified following the protocol of Young’s lab (Genome wide location analysis web page, MIT). Purified DNA was random primed and amplified by the protocol of Brown’s lab (Stanford). 2ug of amplified DNA was digested with DNaseI to a mean size of 100bp and used for labeling as previously described by Winzeler et al. (Science. 281, 1194-1197, 1998).

tag: Rpo 21 distribution in Wild type (Low phosphate medium).


title: SP_Replicate 1_SPK004 6 week old root sample was compared to SPK004 3 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 2_Swap_SPK004 3 week old root sample was compared to SPK004 6 week old root sample

description: Biological replicate 2 out of 2


title: SP_Replicate 1_Feng Shou Bai 3 week old root sample was compared to SPK004 3 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 1_beauregard 6 week old root sample was compared to SPK004 6 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 1_Tanzania 6 week old root sample was compared to Feng Shou Bai 6 week old root sample

description: Biological replicate 1 out of 2


title: SP_Replicate 2_Swap_SPK004 6 week old root sample was compared to beauregard 6 week old root sample

description: Biological replicate 2 out of 2


title: SP_Replicate 2_Swap_Feng Shou Bai 3 week old root sample was compared to Tanzania 3 week old root sample

description: Biological replicate 2 out of 2


title: SP_Replicate 2_Swap_beauregard 16 week old root sample was compared to Feng Shou Bai 16 week old root sample

description: Biological replicate 2 out of 2


title: WCE of Rpo21 ChIP (Wild type, High phosphate medium)

description: Rpo21 binding profile in high phosphate medium wild type (WCE fraction).

tag: Rpo 21 distribution in wild type (high phosphate medium). WCE fraction.


title: SP_Replicate 2_Swap_SPK004 3 week old root sample was compared to Feng Shou Bai 3 week old root sample

description: Biological replicate 2 out of 2


title: kernel_susceptible2_water stress_vs_well watered_rep4

status: Public on Dec 22 2008

city: Milano

first: Rosanna

last: Marino

state: Milano

address: Via celoria 26

department: Department of biomolecular sciences and biothecnology

country: Italy

institute: Universita' degli studi di Milano

description: ch1/ch2 (water stress/well watered)

hyb_protocol: The slides were hybridized using the procol described in the MWG Array manual (http://ecom2.mwgdna.com/services/array/download)

scan_protocol: Images were acquired at 5µm resolution by ScanArray v3.1 software on SA4000 Scanner (Packard Bioscience, Wellesley, MA) and quantified using Quantarray v3.0 software (Packard Bioscience, Wellesley, MA)

data_processing: Local background subtraction, per chip LOWESS and 50th percentile within array normalization function were performed by Genespring (Agilent Techonologies, Palo Alto,CA)

organism: Zea mays

source_name: poly(A+) RNA from 10 DAP kernel collected from the susceptible RIL68 grown in water stress field condition and labeled with cyanine 3

label_protocol: 1µg of purified poly(A+) RNA was labeled according to the protocol of the Amersham CyScribe Post-Labeling Kit (GE Healthcare, NJ, USA)

growth_protocol: All plants were grown in open field in Foggia (Southern Italy) where in late spring and summer the temperature is high and the rainfall is usually very limited or absent. Therefore the water supply was tightly controlled by differential irrigation.

extract_protocol: Total RNA was extracted, from a pool of 6-9 kernels (2-3 seeds from 3 different ears) at 10 DAP, using LiCl based method. RNA quality was evaluated on agarose gels and assorbance 260/280 ratios between 1.8 and 2.2 were typically obtained. Poly(A+) RNA was purfied using the Amersham mRNA Purification Kit (GE Healthcare, NJ, USA).

treatment_protocol: Two levels of drought treatment were applied, well watered and water stress, with two randomized blocks for each level. For each block, two rows of fifteen plants per genotype were grown at a plant density of four plants/square meter. All trials were well irrigated from sowing to the start of the treatment. Thereafter, the well-watered trials received additional full irrigations maintaining soil moisture at about 30% expressed on a dry weight basis, while stressed plants received just enough water for surviving (soil moisture about 16%). The stress was applied strarting three weeks before flowering time.

tag: RIL from B73xH99

tag: phenotypically recorded as susceptible (RIL68)

tag: organ

value: 10days after pollination kernels

tag: water stress

value: 16% (expressed on a dry weight basis) soil moisture was maintained for the treatment

source_name: poly(A+) RNA from 10 DAP kernel collected from the susceptible RIL68 grown in well watered field condition and labeled with cyanine 5

tag: well watered

value: 30% (expressed on a dry weight basis) soil moisture was maintained for the treatment


title: kernel_susceptible2_water stress_vs_well watered_rep3

description: ch1/ch2 (water stress/well watered)


title: 3 weeks old transgenic plants (empty vector; inducible system), biological rep2

city: Postdam

first: Salma

last: Balazadeh

address: Am Muehlenberg 1

department: Stitt

country: Germany

institute: MPIMP

description:
Gene expression data from empty inducible vector
RMA_ANAC059 and EV data:GSM353587, GSM353588, GSM353589 and GSM353590 have been normalized together.
RMA_ANAC092 and EV data: GSM353591, GSM353592, GSM353593, GSM353584, GSM353585 and GSM353586 have been normalized together.
RMA_T-DNA ANAC059,ANAC092, WT data: GSM353594, GSM353595 and GSM353596 have been normalized together.

hyb_protocol: Affymetrix protocol, performed by Atlas Biolabs

data_processing: The data were analyzed with Robust Multi-array Average (Irizarry et al., 2003). GSM353585 raw files (CEL and CHP) are identical to GSM353590 raw files

organism: Arabidopsis thaliana

source_name: 3 weeks old transgenic plants (empty vector; inducible system), WT_col0

label_protocol: Labling procedure performed using MessageAmpTM II-Biotin Enhanced Kit

growth_protocol: Seeds were surface sterilized and sown in half-strength MS medium supplemented with 1% sucrose and solidified with 0.7% phytoagar and appropriate antibiotic. After inbibition, the seeds were strafied at 4C° for 3 days. The seeds were germinated at 22 C° under a 16-h day (140µmol m2- s1-) / 8-h night regime. The three weeks old Arabidopsis seedlings were removed carefully and subjected to the treatment. T-DNA insertion lines were grown in soil and germinated under controlled condition in a growth chamber with a 16-h day lenght provided by fluorescent light at 80 or 120 µmol m2- s1- and a days/night temperature of 20/16 C° and relative humidity 60/75%.

extract_protocol: RNA extraction performed using Rneasy Plant MiniKit (Qiagene)

treatment_protocol: Three weeks old Arabidopsis seedlings were treated with 10µM estradiole for 5 hourse and then shoots were carefully harvested.. The leaf no.11 of wt and ANAC059 and ANAC092 T-DNA insertion lines were carefully harvested.

tag: 5hr estradiole treated shoot


title: 3 weeks old transgenic plants (empty vector; inducible system), biological rep1

description:
Gene expression data from empty inducible vector
RMA_ANAC059 and EV data: GSM353587, GSM353588, GSM353589 and GSM353590 have been normalized together.
RMA_ANAC092 and EV data: GSM353591, GSM353592, GSM353593, GSM353584, GSM353585 and GSM353586 have been normalized together.
RMA_T-DNA ANAC059,ANAC092, WT data: GSM353594, GSM353595 and GSM353596 have been normalized together.

scan_protocol: Affymetrix protocol, performed by Atlas Biolabs

data_processing: The data were analyzed with Robust Multi-array Average (Irizarry et al., 2003). GSM353584 raw files (CEL and CHP) are identical to GSM353589 raw files


title: WCE of Rpo21 ChIP (pho4 deletion, low phosphate medium)

description: Rpo21 binding profile in Low phosphate medium in pho4 deletion strain (WCE fraction).

source_name: ChIP DNA

tag: Rpo 21 distribution in pho4 deletion mutant (low phosphate medium). WCE fraction.


title: kernel_susceptible1_water stress_vs_well watered_rep4

description: ch1/ch2 (water stress/well watered)

source_name: poly(A+) RNA from 10 DAP kernel collected from the susceptible RIL 66 grown in well water stress field condition and labeled with cyanine 5

tag: phenotypically recorded as susceptible (RIL66)

source_name: poly(A+) RNA from 10 DAP kernel collected from the susceptible RIL 66 grown in well watered field condition and labeled with cyanine 3


title: kernel_susceptible2_water stress_vs_well watered_rep1

description: ch2/ch1 (water stress/well watered)

source_name: poly(A+) RNA from 10 DAP kernel collected from the susceptible RIL68 grown in well watered field condition and labeled with cyanine 3

source_name: poly(A+) RNA from 10 DAP kernel collected from the susceptible RIL68 grown in water stress field condition and labeled with cyanine 5


title: kernel_susceptible1_water stress_vs_well watered_rep3

description: ch1/ch2 (water stress/well watered)


title: kernel_tolerant2_water stress_vs_well watered_rep3

description: ch1/ch2 (water stress/well watered)

source_name: poly(A+) RNA from 10 DAP kernel collected from the tolerant RIL78 grown in water stress field condition and labeled with cyanine 3

tag: phenotypically recorded as tolerant (RIL78)

source_name: poly(A+) RNA from 10 DAP kernel collected from the tolerant RIL78 grown in well watered field condition and labeled with cyanine 5


title: kernel_susceptible1_water stress_vs_well watered_rep1

description: ch2/ch1 (water stress/well watered)

source_name: poly(A+) RNA from 10 DAP kernel collected from the susceptible RIL 66 grown in well watered field condition and labeled with cyanine 5

source_name: poly(A+) RNA from 10 DAP kernel collected from the susceptible RIL 66 grown in well water stress field condition and labeled with cyanine 3


title: kernel_tolerant2_water stress_vs_well watered_rep1

description: ch2/ch1 (water stress/well watered)

source_name: poly(A+) RNA from 10 DAP kernel collected from the tolerant RIL78 grown in well watered field condition and labeled with cyanine 3

source_name: poly(A+) RNA from 10 DAP kernel collected from the tolerant RIL78 grown in water stress field condition and labeled with cyanine 5


title: kernel_tolerant1_water stress_vs_well watered_rep3

description: ch1/ch2 (water stress/well watered)

source_name: poly(A+) RNA from 10 DAP kernel collected from the tolerant RIL60 grown in water stress field condition and labeled with cyanine 3

tag: phenotypically recorded as tolerant (RIL60)

source_name: poly(A+) RNA from 10 DAP kernel collected from the tolerant RIL60 grown in well watered field condition and labeled with cyanine 5


title: kernel_tolerant1_water stress_vs_well watered_rep4

description: ch1/ch2 (water stress/well watered)


title: kernel_tolerant1_water stress_vs_well watered_rep2

description: ch2/ch1 (water stress/well watered)

source_name: poly(A+) RNA from 10 DAP kernel collected from the tolerant RIL60 grown in well watered field condition and labeled with cyanine 3

source_name: poly(A+) RNA from 10 DAP kernel collected from the tolerant RIL60 grown in water stress field condition and labeled with cyanine 5


title: kernel_susceptible1_water stress_vs_well watered_rep2

description: ch2/ch1 (water stress/well watered)


title: WCE of Rpo21 ChIP (pho4 deletion, high phosphate medium)

description: WCE fraction used for normalization of Rpo21 binding profile in High phosphate medium in pho4 deletion strain.

source_name: WCE fraction DNA

tag: WCE fraction after Rpo21 chip. WCE fraction used for normalization of GSM336972.


title: Obese_surgery biopsy_subject 9

city: Paris

first: David

middle: M

last: Mutch

address: Centre de Recherche des Cordeliers (CRC), 15 rue de l'école de médecine

department: Nutrition and Metabolism

country: France

institute: INSERM UMRS U872 (Eq 7) Nutriomique

description: Obese_surgery biopsy_subject 9

hyb_protocol: Agilent Low RNA Input Linear Amplification kit

scan_protocol: microarrays scanned using an AXON scanner and data visualized using GenePix software

data_processing: Lowess normalized using Goulphar software, background signal not removed

source_name: subcutaneous adipose tissue, obese surgery biopsy

extract_protocol: Qiagen RNeasy total RNA Mini kit

treatment_protocol: tissue samples stored at -80°C until used

tag: Gender

value: Female, Biopsy Technique:surgical

source_name: In-house adipose tissue reference pool

tag: subjects all undergoing plastic surgery


title: Rpo21 distribution in Wild type (High phosphate condition)

description: Rpo21 binding profile in high phosphate medium wild type.

source_name: ChIP DNA

tag: Rpo 21 distribution in wild type (high phosphate medium).


title: Rpo21 in pho4 deletion mutant (Low phosphate condition)

description: Rpo21 binding profile in Low phosphate medium in pho4 deletion strain.

tag: Rpo 21 distribution in pho4 deletion mutant (low phosphate medium).


title: Obese_surgery biopsy_subject 8

description: Obese_surgery biopsy_subject 8

label_protocol: Agilent Low RNA Input Linear Amplification kit


title: Obese_surgery biopsy_subject 7

description: Obese_surgery biopsy_subject 7


title: Obese_needle biopsy_subject 9

description: Obese_needle biopsy_subject 9

source_name: subcutaneous adipose tissue, obese needle biopsy


title: Obese_needle biopsy_subject 8

description: Obese_needle biopsy_subject 8


title: Rpo21 in pho4 deletion mutant (High phosphate medium)

description: Rpo21 binding profile in High phosphate medium in pho4 deletion strain.

tag: Rpo 21 distribution in pho4 deletion mutant (high phosphate medium).


title: Rpo21 distribution in Wild type (Low phosphate condition)

description: Rpo21 binding profile in low phosphate medium wild type.

tag: Rpo 21 distribution in Wild type (Low phosphate medium).


title: CD56_25_aGVHD(+)

city: Minato-ku

first: Naoyuki

last: Takahashi

address: 4-6-1, Shirokanedai

department: Research Hospital

institute: The Institute of Medical Science, The University of Tokyo

description: The probes for 8 positive control genes (ACTB, ATP5F1, GAPD, GTF2B, PLA2G5, RPS5, TFRC, and K-ALPHA-1/TUBA1B) were spotted on a total of 24 spots and those for 4 negative control genes (lambda A, lambda B, Omp A1, and Omp A2) were spotted on a total of 12 spots, while nothing was spotted on 33 spots.  Therefore, a total of 69 spot data were already eliminated from the whole 684 spot data on the Genopal array IMS human 0.6K v.2.

hyb_protocol: Hybridization was performed according to Mitsubishi Rayon’s protocol ver. 2.  Briefly, 10 μg of biotin-modified aRNA, which was fragmented using Fragmentation Reagents (Ambion), was suspended in buffer A1 containing 0.12 M Tris-HCl (pH 7.5), 0.12 M NaCl, and 0.05% Tween 20.  The hybridization mixture was heated to 94°C for 2 min, then cooled to 37°C and injected into a hybridization chamber (Mitsubishi Rayon).  Hybridization was carried out at 65°C for 16 hr with the chamber rotating slowly.  Microarrays were washed by soaking twice in buffer A1 at 65°C for 20 min, then once in buffer A2 containing 0.12 M Tris-HCl (pH 7.5) and 0.12 M NaCl, at 65°C for 10 min, and finally left at rest for 60 min at room temperature.  Microarrays were stained with 2 μg/ml Streptavidin-Cy5 (GE Healthcare) in buffer A2 at room temperature for 30 min, then washed 4 times by soaking in buffer A1 at room temperature each for 5 min.

scan_protocol: The arrays were then scanned to obtain images using a cooled CCD-type DNA chip image analyzer (Mitsubishi Rayon).  Fluorescent intensity of images was quantified automatically with the software developed by Mitsubishi Rayon Co., Ltd.

data_processing:
To identify differentially-expressed genes during acute GVHD versus recovery phase, the raw signal intensity data were processed as follows.
To obtain gene-specific signal intensity data, the raw value for lambda A (negative control) in the same block was subtracted.
Secondly, paired gene-specific data (aGVHD(+) vs. aGVHD(−)) were discarded, if both values were lower than a threshold of 100 counts/sec.  If only one of the paired gene-specific values was lower than 100 counts/sec, it was replaced by 100 counts/sec.
Thirdly, these filtered gene-specific data were normalized within each block.  Since each block on a microarray did not contain enough number of spots to justify an assumption that median log-ratio of all the genes within a block should be zero, we examined other normalization methods.  To this purpose, we compared M-A scatter plots (i.e., scatter plots of log-ratios (M) versus averages of log-intensities (A) for paired data) for each block, for the following normalization methods.  The first is median-centering of log-ratio for a selected set of housekeeping genes (GAPDH, ACTB, RPS5, and K-ALPHA-1/TUBA1B) which were abundantly expressed in every subset of PBMCs.  The second is normalization by GAPDH gene.  The third is lowess normalization using lowess function (‘stats’ package) in R language (http://www.r-project.org/), with the lowess smoothing parameter f set to 0.4.  Most of the M-A plots, especially for low intensity data spots, were distributed unequally around 0 value of M-axis, if normalization was performed by the selected housekeeping genes (first method) or GAPDH (second method).  It seemed, therefore, to be most appropriate to perform normalization by lowess method to avoid false positive results, especially for low intensity data spots.  Consequently, we used lowess normalized data in the subsequent analysis.
Finally, significance analysis of microarray (SAM) (Tusher VG et al. Proc Natl Acad Sci USA 98: 5116-5121, 2001) was carried out to evaluate differential gene expression during acute GVHD compared to recovery phase, with false discovery rate (FDR) lower than 10%, using 'samr' package in R language.

source_name: CD56+ subsets, case IMS25, aGVHD

label_protocol: Total RNA of each subset of PBMCs derived from 10 ml of peripheral blood, was reverse-transcribed with oligo (dT) primer bearing a T7 promoter and transcribed in vitro to synthesize biotin-modified antisense RNA (aRNA) using MessageAmp II-Biotin Enhanced kit (Ambion), according to Mitsubishi Rayon’s protocol ver. 2.  For some specimens, which contained too few cells to obtain enough amount of aRNA for array hybridization by single round amplification, amplification was performed two rounds, using MessageAmp II aRNA Amplification Kit (Ambion) in addition to MessageAmp II-Biotin Enhanced kit, according to the manufacturer’s protocol.

extract_protocol:
Ten milliliter of peripheral blood was centrifuged over Histopaque 1077 (Sigma, St. Louis, USA) at 500 × g for 15 minutes to isolate mononuclear cells, which were then washed with RPMI 1640 media.  CD8+, CD56+, CD4+, and CD14+ cell subsets were isolated from the peripheral blood mononuclear cells (PBMCs) in this order by employing CD8 MicroBeads, CD56 MicroBeads, CD4 MicroBeads, and CD14 MicroBeads, respectively (Miltenyi Biotec GmbH, Germany), and then lyzed immediately in TRIZOL® reagent (Invitrogen, California, USA).  Total RNA was extracted and then purified using RNeasy® Micro kit (Qiagen, Valencia, CA) with on-column DNase digestion, according to the manufacturer’s protocol.
For each subset of PBMCs of a patient, paired samples (taken during acute GVHD (aGVHD(+)) versus taken upon discharge (aGVHD(−))) were handled in the same way and in parallel for every step of the following procedure, from total RNA extracting to scanning the arrays, according to Mitsubishi Rayon’s protocol ver. 2.

tag: Subsets

tag: Status

value: during acute GVHD

tag: Case

tag: AGE

tag: SEX

value: M

tag: Diagnosis

value: ALL (L2)

tag: Grading of acute GVHD

value: 2 (skin; 3, gut; 0, liver; 0)


title: CD56_18_aGVHD(+)

source_name: CD56+ subsets, case IMS18, aGVHD

value: MDS (→AML)


title: Obese_needle biopsy_subject 7

description: Obese_needle biopsy_subject 7


title: Obese_surgery biopsy_subject 5

description: Obese_surgery biopsy_subject 5


title: Obese_surgery biopsy_subject 4

description: Obese_surgery biopsy_subject 4


title: Obese_needle biopsy_subject 1

description: Obese_needle biopsy_subject 1


title: Obese_surgery biopsy_subject 6

description: Obese_surgery biopsy_subject 6


title: CD56_25_aGVHD(-)

source_name: CD56+ subsets, case IMS25, recovery

value: during recovery phase


title: Obese_needle biopsy_subject 6

description: Obese_needle biopsy_subject 6


title: kernel_tolerant2_water stress_vs_well watered_rep4

description: ch1/ch2 (water stress/well watered)

source_name: poly(A+) RNA from 10 DAP kernel collected from the tolerant RIL78 grown in water stress field condition and labeled with cyanine 3

tag: RIL from B73xH99

tag: organ

tag: water stress

source_name: poly(A+) RNA from 10 DAP kernel collected from the tolerant RIL78 grown in well watered field condition and labeled with cyanine 5

tag: well watered


title: Obese_needle biopsy_subject 3

description: Obese_needle biopsy_subject 3

tag: Gender


title: CD56_18_aGVHD(-)

source_name: CD56+ subsets, case IMS18, recovery


title: Obese_needle biopsy_subject 4

description: Obese_needle biopsy_subject 4

tag: subjects all undergoing plastic surgery


title: Obese_surgery biopsy_subject 1

description: Obese_surgery biopsy_subject 1


title: Lean_surgical biopsy_subject 8

description: Lean_surgical biopsy_subject 8

source_name: subcutaneous adipose tissue, lean surgical biopsy


title: kernel_tolerant1_water stress_vs_well watered_rep1

description: ch2/ch1 (water stress/well watered)

tag: phenotypically recorded as tolerant (RIL60)


title: Obese_surgery biopsy_subject 2

description: Obese_surgery biopsy_subject 2


title: CD56_17_aGVHD(+)

source_name: CD56+ subsets, case IMS17, aGVHD

value: F

value: NHL (LBL)

value: 1 (skin; 2, gut; 0, liver; 0)


title: Obese_surgery biopsy_subject 3

description: Obese_surgery biopsy_subject 3


title: Obese_needle biopsy_subject 5

description: Obese_needle biopsy_subject 5


title: Lean_surgical biopsy_subject 9

description: Lean_surgical biopsy_subject 9


title: Obese_needle biopsy_subject 2

description: Obese_needle biopsy_subject 2


title: CD56_17_aGVHD(-)

source_name: CD56+ subsets, case IMS17, recovery


title: CD56_13_aGVHD(+)

source_name: CD56+ subsets, case IMS13, aGVHD

value: AML (M3)


title: Lean_surgical biopsy_subject 7

description: Lean_surgical biopsy_subject 7


title: CD56_13_aGVHD(-)

source_name: CD56+ subsets, case IMS13, recovery


title: Lean_surgical biopsy_subject 5

description: Lean_surgical biopsy_subject 5


title: Lean_surgical biopsy_subject 6

description: Lean_surgical biopsy_subject 6


title: CD56_11_aGVHD(+)

source_name: CD56+ subsets, case IMS11, aGVHD

value: AML (M2)


title: CD14_25_aGVHD(+)

source_name: CD14+ subsets, case IMS25, aGVHD


title: CD56_11_aGVHD(-)

source_name: CD56+ subsets, case IMS11, recovery


title: CD14_18_aGVHD(+)

source_name: CD14+ subsets, case IMS18, aGVHD


title: Lean_surgical biopsy_subject 4

description: Lean_surgical biopsy_subject 4

source_name: In-house adipose tissue reference pool


title: Lean_needle biopsy_subject 9

description: Lean_needle biopsy_subject 9

source_name: subcutaneous adipose tissue, lean needle biopsy


title: Lean_surgical biopsy_subject 1

description: Lean_surgical biopsy_subject 1


title: CD14_18_aGVHD(-)

source_name: CD14+ subsets, case IMS18, recovery


title: CD14_17_aGVHD(+)

source_name: CD14+ subsets, case IMS17, aGVHD


title: CD14_25_aGVHD(-)

source_name: CD14+ subsets, case IMS25, recovery


title: kernel_tolerant2_water stress_vs_well watered_rep2

description: ch2/ch1 (water stress/well watered)

source_name: poly(A+) RNA from 10 DAP kernel collected from the tolerant RIL78 grown in well watered field condition and labeled with cyanine 3

tag: phenotypically recorded as tolerant (RIL78)

source_name: poly(A+) RNA from 10 DAP kernel collected from the tolerant RIL78 grown in water stress field condition and labeled with cyanine 5


title: CD14_17_aGVHD(-)

source_name: CD14+ subsets, case IMS17, recovery


title: CD14_13_aGVHD(+)

source_name: CD14+ subsets, case IMS13, aGVHD


title: CD14_13_aGVHD(-)

source_name: CD14+ subsets, case IMS13, recovery


title: CD14_11_aGVHD(-)

source_name: CD14+ subsets, case IMS11, recovery


title: CD14_11_aGVHD(+)

source_name: CD14+ subsets, case IMS11, aGVHD


title: Lean_needle biopsy_subject 8

description: Lean_needle biopsy_subject 8


title: Lean_surgical biopsy_subject 2

description: Lean_surgical biopsy_subject 2

source_name: subcutaneous adipose tissue, lean surgical biopsy


title: CD8_25_aGVHD(+)

source_name: CD8+ subsets, case IMS25, aGVHD


title: Lean_needle biopsy_subject 7

description: Lean_needle biopsy_subject 7


title: CD8_25_aGVHD(-)

source_name: CD8+ subsets, case IMS25, recovery


title: Lean_needle biopsy_subject 6

description: Lean_needle biopsy_subject 6


title: Lean_needle biopsy_subject 3

description: Lean_needle biopsy_subject 3


title: Lean_needle biopsy_subject 5

description: Lean_needle biopsy_subject 5


title: Lean_needle biopsy_subject 4

description: Lean_needle biopsy_subject 4


title: Lean_needle biopsy_subject 1

description: Lean_needle biopsy_subject 1