title: CDC80

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC80 (human isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC80 (human isolate)


title: CDC78

status: Public on Feb 01 2008

type: genomic

city: Ithaca

first: Tavan

last: Janvilisri

state: NY

address: Veterinary Research Tower, College of Veterinary Medicine, Cornell University

country: USA

institute: Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC78 (food isolate)

hyb_protocol: Genomic DNA from C. difficile 630 was used as a reference DNA for all hybridizations. Dye swaps were performed to test dye-incorporation bias. The microarray slides were prehybridized using a solution containing 25% formamide, 5x SSC (1x SSC consists of 0.15M NaCl with 0.015M sodium citrate), 0.2% (w/v) sarcosyl, and 10 mg/ml bovine serum albumin at 42 °C for 1 h. The slides were then washed in MilliQ water and blow dried using compressed nitrogen gas. Equivalent amounts of labeled probes from reference and tested strains were pooled, lyophilized, and resuspended in 70 µl of hybridization buffer (25% formamide, 5x SSC, 0.2% sodium dodecyl sulfate (SDS), 1 mg/ml salmon sperm DNA, and 1 mg/ml yeast tRNA). The probes were then denatured at 99 °C for 5 min, centrifuged briefly at 13,800 x g and applied to the microarray under a 22 x 60mm LifterSlip (Erie Scientific Co.). Hybridizations were performed at 42 °C for 16 h in a sealed humidified hybridization chamber (Corning). Following the hybridization, excess hybridization solution and unbound probes were washed away during four washing steps including 5 min in 2x SSC, 1% SDS at 42 °C and 5 min in 0.1% SSC at room temperature for three times. The slides were then dried and scanned immediately.

scan_protocol: Arrays were scanned using a GenePix 4000B scanner (Axon Instruments).

data_processing: The Cy3 and Cy5 signals and the local background intensities were quantified using GenePix Pro 6.1 software. The local background value was subtracted from the intensity of each spot. Spots were examined manually, and poor spots were flagged for elimination from the analysis. All subsequent data analyses were performed by using Microsoft Excel and a genomotyping analysis software GACK to determine present/divergent genes.

molecule: genomic DNA

organism: Clostridioides difficile

source_name: Genomic DNA from Clostridium difficile strain CDC78 (food isolate)

label_protocol: Three micrograms of genomic DNA from each strain was fragmented by DraI digestion at 37°C for 3 h and cleaned up with QIAquick PCR purification kit (Qiagen). Fragmented DNA was then labeled with 10 µg of exo-resistant random primers (Fermentas), 25 U of Klenow fragment (New England Biolabs), dNTP mix (0.12 mM each dATP, dCTP, and dGTP and 0.03 mM dTTP), and 0.1 mM of either Cy3- or Cy5-dUTP (Amersham Biosciences). Probes were purified from unincorporated dyes using the QIAquick PCR purification kit (Qiagen). Labeled DNA sample yields and dye incorporation efficiencies were determined using spectrometry.

extract_protocol: Genomic DNA was isolated from C. difficile by using DNeasy Blood and Tissue Mini Kit (Qiagen) as described in the manufacturer’s protocol for gram-positive bacteria.

tag: Food isolate

source_name: Genomic DNA from Clostridium difficile reference strain 630

tag: Sequenced strain 630 (Human isolate)


title: Zeamays_hcf136_Mcells_052_B

type: RNA

first: Thomas

middle: P.

last: Brutnell

address: Cornell University

institute: Boyce Thompson Institute for Plant Research

description: The mutant hcf136 lacks functional PSII components and granal stacking in its mesophyll (M) plastids. This severe disruption in photosynthetic functionality may result in changes to transcriptional profiles of spatially regulated C4 photosynthetic genes. As such, the M cell transcriptome of this mutant was assayed in comparison to its wild-type siblings using microarray analysis. M protoplasts were isolated by enzymatic digestion from the second leaves of wild-type and hcf136 plants at the third-leaf emerging stage of growth. Total RNA was isolated from the M cells, and M transcript profiles were compared between wild-type and hcf136 mutants using six biological replicates in a two-label direct comparison. The microarray experiments were performed using the Array 900MPX Expression Array Detection Kit (Genisphere), according to the prescribed company protocol.

hyb_protocol: Followed Genisphere Array 900MPX instructions using buffer 6. cDNA hybridization overnight at 55°C. Washed slides in 2X SSC, 0.5%SDS; 0.5X SSC; 0.05X SSC for 5 min each. First wash buffer was used at 55°C.

data_processing: Lowess normalization. See: Sawers, R.J., Liu, P., Anufrikova, K., Hwang, J.T., and Brutnell, T.P. (2007). A multi-treatment experimental system to examine photosynthetic differentiation in the maize leaf. BMC Genomics 8, 12.

molecule: total RNA

organism: Zea mays

source_name: wild-type sibling of hcf136 mutant, mesophyll cells, replicate set 6

growth_protocol: Grown for 13 days in growth chamber (16h/8h light/darkness, 50% humidity, 28°C, approx 40 µmol/s-1/m-2) in soil. BS cells collected from second leaves of 3rd leaf emerging stage seedlings.

extract_protocol:
M protoplasts were isolated as previously described with slight modification; only second leaf blades were used. For full protocol see Markelz, N.H., Costich, D.E., and Brutnell, T.P. (2003). Photomorphogenic responses in maize seedling development. Plant Physiol 133, 1578-1591.
RNA was isolated as in Sheehan, M.J., Farmer, P.R., and Brutnell, T.P. (2004). Structure and expression of maize phytochrome family homeologs. Genetics 167, 1395-1405.

tag: W22 cultivar, hcf136 segregating line, harvested at 3rd leaf emerging stage


title: CDC74

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC74 (human isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC74 (human isolate)

tag: Human isolate


title: Zeamays_hcf136_Mcells_055_B

scan_protocol: See: Sawers, R.J., Liu, P., Anufrikova, K., Hwang, J.T., and Brutnell, T.P. (2007). A multi-treatment experimental system to examine photosynthetic differentiation in the maize leaf. BMC Genomics 8, 12.

source_name: wild-type sibling of hcf136 mutant, mesophyll cells, replicate set 5

label_protocol: Followed Genisphere Array 900MPX instructions using buffer 6. cDNA hybridization overnight at 55°C. Washed slides in 2X SSC, 0.5%SDS; 0.5X SSC; 0.05X SSC for 5 min each. First wash buffer was used at 55°C.


title: CDC75

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC75 (human isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC75 (human isolate)


title: Zeamays_hcf136_Mcells_051_B

source_name: wild-type sibling of hcf136 mutant, mesophyll cells, replicate set 4


title: CDC76

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC76 (food isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC76 (food isolate)


title: CDC53

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC53 (human isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC53 (human isolate)


title: CDC59

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC59 (human isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC59 (human isolate)


title: CDC77

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC77 (food isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC77 (food isolate)


title: CDC69

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC69 (human isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC69 (human isolate)


title: Control__09.14.04 75 HG Focus

city: Davis

first: Michael

last: Hornsby

state: CA

address: County Road 98 and Hutchison Drive

institute: University of California, Davis

description: Stomach Biopsy uninfected control

hyb_protocol: Hybridization to Affymetrix HumanFL (HuFL) chips were done according to the recommendations of the manufacturer (Affymetrix, Santa Clara, Calif.).

scan_protocol: Arrays were scanned with an Agilent GeneArray scanner according to manufacturer recommentations.

data_processing: Data were collated and scaled in Microarray Suite 5.0 (MAS 5.0, Affymetrix, Santa Clara, CA). Of 8,793 probe sets, approximately 5,000 passed filtering and were analyzed with BRB ArrayTools (version 3.3). Triple comparisons were performed (Control, WT, KO) for the data at weeks 1 and 13 using an F statistic, with p<0.01.

label: Biotin

organism: Macaca mulatta

source_name: Stomach Biopsy uninfected control

label_protocol: Labeling to Affymetrix HumanFL (HuFL) chips were done according to the recommendations of the manufacturer (Affymetrix, Santa Clara, Calif.). Briefly, biotin-labeled RNA was prepared by first reverse transcribing the RNA into double-stranded cDNA (Superscript II; Invitrogen Life Technologies, Carlsbad, Calif.) with an oligo(dT)24 primer containing a T7 RNA polymerase promoter. Then an in vitro transcription reaction was carried out (Enzo High Yield RNA Transcript Labeling kit; Enzo Biochem, Farmingdale, N.Y.) during which biotin-labeled ribonucleotides were incorporated into the cRNA followed by fragmentation of cRNA by heating to 94°C for 35 min.

extract_protocol: Ten gastric biopsy specimens were pooled, ground with a glass pestle in Trizol reagent (Sigma), and RNA was isolated according to protocols provided by the manufacturer. All RNA samples were treated with DNase I (Roche Applied Science, Mannheim, Germany), purified with an RNeasy kit (Qiagen, Valencia, Calif.) according to the RNA cleanup protocol, and resuspended in molecular-biology-grade water (BioWhittaker, Rockland, Maine).

tag: SPF Macaque stomach antrum and corpus pooled biopsy


title: CDC58

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC58 (human isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC58 (human isolate)


title: Zeamays_hcf136_Mcells_050_B

source_name: wild-type sibling of hcf136 mutant, mesophyll cells, replicate set 3


title: CDC51

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC51 (human isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC51 (human isolate)


title: Zeamays_hcf136_BScells_128_B

description: The mutant hcf136 lacks functional PSII components and granal stacking in its mesophyll (M) plastids. This severe disruption in photosynthetic functionality may result in changes to transcriptional profiles of spatially regulated C4 photosynthetic genes. As such, the bundle sheath (BS) cell transcriptome of this mutant was assayed in comparison to its wild-type siblings using microarray analysis. BS strands were isolated by mechanical extraction from the second leaves of wild-type and hcf136 plants at the third-leaf emerging stage of growth. Total RNA was isolated from the BS cells, and BS transcript profiles were compared between wild-type and hcf136 mutants using six biological replicates in a two-label direct comparison. The microarray experiments were performed using the Array 900MPX Expression Array Detection Kit (Genisphere), according to the prescribed company protocol.

source_name: wild-type sibling of hcf136 mutant, bundle sheath cells, replicate set 3

extract_protocol:
BS strands were isolated as previously described with slight modification; only second leaf blades were used. For full protocol see Markelz, N.H., Costich, D.E., and Brutnell, T.P. (2003). Photomorphogenic responses in maize seedling development. Plant Physiol 133, 1578-1591.
RNA was isolated as in Sheehan, M.J., Farmer, P.R., and Brutnell, T.P. (2004). Structure and expression of maize phytochrome family homeologs. Genetics 167, 1395-1405.


title: CDC38

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC38 (swine isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC38 (swine isolate)

tag: Swine isolate


title: CDC49

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC49 (human isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC49 (human isolate)

source_name: Genomic DNA from Clostridium difficile reference strain 630


title: CDC43

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC43 (human isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC43 (human isolate)


title: CDC71

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC71 (human isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC71 (human isolate)


title: CDC42

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC42 (human isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC42 (human isolate)


title: Zeamays_hcf136_BScells_133_B

source_name: wild-type sibling of hcf136 mutant, bundle sheath cells, replicate set 4


title: Zeamays_hcf136_Mcells_039_B

source_name: wild-type sibling of hcf136 mutant, mesophyll cells, replicate set 1


title: Zeamays_hcf136_BScells_118_B

source_name: wild-type sibling of hcf136 mutant, bundle sheath cells, replicate set 1


title: CDC37

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC37 (swine isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC37 (swine isolate)


title: CDC36

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC36 (swine isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC36 (swine isolate)


title: Zeamays_hcf136_BScells_120_B

source_name: wild-type sibling of hcf136 mutant, bundle sheath cells, replicate set 5


title: Zeamays_hcf136_BScells_117_B

source_name: wild-type sibling of hcf136 mutant, bundle sheath cells, replicate set 2


title: CDC35

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC35 (swine isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC35 (swine isolate)


title: Zeamays_hcf136_BScells_131_B

source_name: wild-type sibling of hcf136 mutant, bundle sheath cells, replicate set 6


title: Zeamays_hcf136_Mcells_049_B

description: The mutant hcf136 lacks functional PSII components and granal stacking in its mesophyll (M) plastids. This severe disruption in photosynthetic functionality may result in changes to transcriptional profiles of spatially regulated C4 photosynthetic genes. As such, the M cell transcriptome of this mutant was assayed in comparison to its wild-type siblings using microarray analysis. M protoplasts were isolated by enzymatic digestion from the second leaves of wild-type and hcf136 plants at the third-leaf emerging stage of growth. Total RNA was isolated from the M cells, and M transcript profiles were compared between wild-type and hcf136 mutants using six biological replicates in a two-label direct comparison. The microarray experiments were performed using the Array 900MPX Expression Array Detection Kit (Genisphere), according to the prescribed company protocol.

source_name: wild-type sibling of hcf136 mutant, mesophyll cells, replicate set 2


title: CDC34

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC34 (swine isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC34 (swine isolate)


title: CDC33

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC33 (swine isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC33 (swine isolate)


title: CDC27

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC27 (human isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC27 (human isolate)


title: CDC17

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC17(swine isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC17(swine isolate)

source_name: Genomic DNA from Clostridium difficile reference strain 630


title: CDC18

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC18 (swine isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC18 (swine isolate)


title: CDC31

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC31 (human isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC31 (human isolate)


title: Control__09.14.04 72 HG Focus

description: Stomach Biopsy uninfected control

source_name: Stomach Biopsy uninfected control


title: CDC19

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC19 (human isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC19 (human isolate)


title: CDC6

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC6 (human isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC6 (human isolate)


title: CDC13

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC13 (human isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC13 (human isolate)


title: B676

description: Comparative Genomic Hybridization of Clostridium difficile strain 676 (bovine isolate)

source_name: Genomic DNA from Clostridium difficile strain 676 (bovine isolate)

tag: Bovine isolate


title: B672

description: Comparative Genomic Hybridization of Clostridium difficile strain 672 (bovine isolate)

source_name: Genomic DNA from Clostridium difficile strain 672 (bovine isolate)


title: CDC3

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC3 (human isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC3 (human isolate)


title: CDC14

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC14 (human isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC14 (human isolate)


title: CDC21

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC21 (human isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC21 (human isolate)


title: B674

description: Comparative Genomic Hybridization of Clostridium difficile strain 674 (bovine isolate)

source_name: Genomic DNA from Clostridium difficile strain 674 (bovine isolate)


title: CDC25

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC25 (human isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC25 (human isolate)


title: B668

description: Comparative Genomic Hybridization of Clostridium difficile strain 668 (bovine isolate)

source_name: Genomic DNA from Clostridium difficile strain 668 (bovine isolate)


title: B670

description: Comparative Genomic Hybridization of Clostridium difficile strain 670 (bovine isolate)

source_name: Genomic DNA from Clostridium difficile strain 670 (bovine isolate)


title: B664

description: Comparative Genomic Hybridization of Clostridium difficile strain 664 (bovine isolate)

source_name: Genomic DNA from Clostridium difficile strain 664 (bovine isolate)


title: B662

description: Comparative Genomic Hybridization of Clostridium difficile strain 662 (bovine isolate)

source_name: Genomic DNA from Clostridium difficile strain 662 (bovine isolate)

source_name: Genomic DNA from Clostridium difficile reference strain 630


title: CDC24

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC24 (human isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC24 (human isolate)


title: H125

description: Comparative Genomic Hybridization of Clostridium difficile strain 125 (equine isolate)

source_name: Genomic DNA from Clostridium difficile strain 125 (equine isolate)

tag: Equine isolate


title: B660

description: Comparative Genomic Hybridization of Clostridium difficile strain 660 (bovine isolate)

source_name: Genomic DNA from Clostridium difficile strain 660 (bovine isolate)


title: H538

description: Comparative Genomic Hybridization of Clostridium difficile strain 538 (equine isolate)

source_name: Genomic DNA from Clostridium difficile strain 538 (equine isolate)


title: H539

description: Comparative Genomic Hybridization of Clostridium difficile strain 539 (equine isolate)

source_name: Genomic DNA from Clostridium difficile strain 539 (equine isolate)


title: H121

description: Comparative Genomic Hybridization of Clostridium difficile strain 121 (equine isolate)

source_name: Genomic DNA from Clostridium difficile strain 121 (equine isolate)


title: H124

description: Comparative Genomic Hybridization of Clostridium difficile strain 124 (equine isolate)

source_name: Genomic DNA from Clostridium difficile strain 124 (equine isolate)


title: B656

description: Comparative Genomic Hybridization of Clostridium difficile strain 656 (bovine isolate)

source_name: Genomic DNA from Clostridium difficile strain 656 (bovine isolate)


title: B658

description: Comparative Genomic Hybridization of Clostridium difficile strain 658 (bovine isolate)

source_name: Genomic DNA from Clostridium difficile strain 658 (bovine isolate)


title: H126

description: Comparative Genomic Hybridization of Clostridium difficile strain 126 (equine isolate)

source_name: Genomic DNA from Clostridium difficile strain 126 (equine isolate)


title: H114

description: Comparative Genomic Hybridization of Clostridium difficile strain 114 (equine isolate)

source_name: Genomic DNA from Clostridium difficile strain 114 (equine isolate)


title: H115

description: Comparative Genomic Hybridization of Clostridium difficile strain 115 (equine isolate)

source_name: Genomic DNA from Clostridium difficile strain 115 (equine isolate)


title: H112

description: Comparative Genomic Hybridization of Clostridium difficile strain 112 (equine isolate)

source_name: Genomic DNA from Clostridium difficile strain 112 (equine isolate)


title: H113

description: Comparative Genomic Hybridization of Clostridium difficile strain 113 (equine isolate)

source_name: Genomic DNA from Clostridium difficile strain 113 (equine isolate)


title: H109

description: Comparative Genomic Hybridization of Clostridium difficile strain 109 (equine isolate)

source_name: Genomic DNA from Clostridium difficile strain 109 (equine isolate)


title: H104

description: Comparative Genomic Hybridization of Clostridium difficile strain 104 (equine isolate)

source_name: Genomic DNA from Clostridium difficile strain 104 (equine isolate)


title: DK1622 (wt), 15h dev., Exp.3

city: Marburg

first: Lotte

last: Sogaard-Andersen

address: Karl-von-Frisch-Str.

department: Ecophysiology

country: Germany

institute: Max Planck Institute for Terrestrial Microbiology

description: fruiting body starvation response: developmental time course

hyb_protocol: Probes were mixed with final concentrations of 3x SSC, 0.5 µg/µl yeast tRNA (Sigma), and 0.3% SDS. The hybridization solution was boiled at 100°C for 2 min and cooled at room temperature for 5 min before application to a slide. Hybridizations were carried out under a 22- by 40-mm lifter slip in a total volume of 60 µl. The hybridization chamber was assembled, sealed, and submerged in a water bath at 60°C for 5 to 16 h. After hybridization, slides were washed for 5 min in 2x SSC-0.1% SDS, for 5 min in 0.2x SSC-0.1% SDS, and for 5 min in 0.2x SSC, followed by a short rinse in H2O. Slides were dried by centrifugation and scanned immediately (Overgaard et al. 2006, J. of Bact. Vol.188, No.12, p.4384-4394)

scan_protocol: GenePix 6.0

data_processing: spot finding algorithm GenePix 6.0; ratio-normalized (mean ratio of medians = 1); Signal to noise ratio in ch1 or ch2 at least >=2

organism: Myxococcus xanthus

source_name: dev. cells DK1622 (wt) 15h

label_protocol: Synthesis of Cy3- or Cy5-labeled cDNA probes was carried out using 25 µg of DNA-free total RNA and a CyScribe postlabeling kit (Amersham Biosciences) according to the protocol provided by the manufacturer (Overgaard et al. 2006, J. of Bact. Vol.188, No.12, p.4384-4394)

growth_protocol: M. xanthus strains were grown at 32°C in 1% CTT broth (21) or on CTT medium supplemented with 1.5% agar. Gentamicin (10 µg/ml), kanamycin (40 µg/ml), or oxytetracycline (10 µg/ml) was added when appropriate (Overgaard et al. 2006, J. of Bact. Vol.188, No.12, p.4384-4394)

extract_protocol: Total RNA was prepared from mid-exponential-phase liquid cultures of M. xanthus. Cells were transferred to a centrifuge tube on ice containing RNase stop solution (1/10 culture volume of 5% phenol in 96% ethanol). RNA was extracted by the hot-phenol method (Overgaard et al. 2006, J. of Bact. Vol.188, No.12, p.4384-4394)

tag: dev. cells DK1622 (wt) 15h

source_name: vegetative cells DK1622 (wt)

tag: vegetative cells DK1622 (wt)


title: DK1622 (wt), 18h dev., Exp.3

source_name: dev. cells DK1622 (wt) 18h

tag: dev. cells DK1622 (wt) 18h


title: DK1622 (wt), 24h dev., Exp.3

source_name: dev. cells DK1622 (wt) 24h

tag: dev. cells DK1622 (wt) 24h


title: DK1622 (wt), 12h dev., Exp.3

source_name: dev. cells DK1622 (wt) 12h

tag: dev. cells DK1622 (wt) 12h


title: CDC45

description: Comparative Genomic Hybridization of Clostridium difficile strain CDC45 (human isolate)

source_name: Genomic DNA from Clostridium difficile strain CDC45 (human isolate)

source_name: Genomic DNA from Clostridium difficile reference strain 630


title: H101

description: Comparative Genomic Hybridization of Clostridium difficile strain 101 (equine isolate)

source_name: Genomic DNA from Clostridium difficile strain 101 (equine isolate)


title: DK1622 (wt), 6h dev., Exp.3

source_name: dev. cells DK1622 (wt) 6h

tag: dev. cells DK1622 (wt) 6h


title: DK1622 (wt), 9h dev., Exp.3

source_name: dev. cells DK1622 (wt) 9h

tag: dev. cells DK1622 (wt) 9h


title: DK1622 (wt), 2h dev., Exp.3

source_name: dev. cells DK1622 (wt) 2h

tag: dev. cells DK1622 (wt) 2h


title: DK1622 (wt), 4h dev., Exp.3

source_name: dev. cells DK1622 (wt) 4h

tag: dev. cells DK1622 (wt) 4h


title: DK1622 (wt), 9h dev., Exp.2


title: DK1622 (wt), 12h dev., Exp.2


title: DK1622 (wt), 18h dev., Exp.2


title: DK1622 (wt), 15h dev., Exp.2


title: DK1622 (wt), 0h dev., Exp.3

source_name: veg. cells DK1622 (wt)


title: DK1622 (wt), 24h dev., Exp.2


title: Zeamays_hcf136_Mcells_052_A

description: The mutant hcf136 lacks functional PSII components and granal stacking in its mesophyll (M) plastids. This severe disruption in photosynthetic functionality may result in changes to transcriptional profiles of spatially regulated C4 photosynthetic genes. As such, the M cell transcriptome of this mutant was assayed in comparison to its wild-type siblings using microarray analysis. M protoplasts were isolated by enzymatic digestion from the second leaves of wild-type and hcf136 plants at the third-leaf emerging stage of growth. Total RNA was isolated from the M cells, and M transcript profiles were compared between wild-type and hcf136 mutants using six biological replicates in a two-label direct comparison. The microarray experiments were performed using the Array 900MPX Expression Array Detection Kit (Genisphere), according to the prescribed company protocol.

source_name: wild-type sibling of hcf136 mutant, mesophyll cells, replicate set 6


title: Zeamays_hcf136_Mcells_051_A

source_name: wild-type sibling of hcf136 mutant, mesophyll cells, replicate set 4


title: mex-3 pal-1 230 B

city: Haifa

first: Itai

last: Yanai

address: Technion City

department: Biology

country: Israel

institute: Technion - Israel Institute of Technology

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA

label: biotin

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: mex-3 pal-1 230 B

label_protocol: standard Affymetrix protocol

extract_protocol: standard Affymetrix protocol

tag: mex-3 pal-1 230 B


title: mex-3 pal-1 230 A

source_name: mex-3 pal-1 230 A

tag: mex-3 pal-1 230 A


title: mex-3 pal-1 186 C

source_name: mex-3 pal-1 186 C

tag: mex-3 pal-1 186 C


title: mex-3 pal-1 186 B

source_name: mex-3 pal-1 186 B

tag: mex-3 pal-1 186 B


title: mex-3 pal-1 186 A

source_name: mex-3 pal-1 186 A

tag: mex-3 pal-1 186 A


title: Zeamays_hcf136_Mcells_050_A

source_name: wild-type sibling of hcf136 mutant, mesophyll cells, replicate set 3

tag: W22 cultivar, hcf136 segregating line, harvested at 3rd leaf emerging stage


title: Zeamays_hcf136_Mcells_048_A

source_name: wild-type sibling of hcf136 mutant, mesophyll cells, replicate set 5


title: Zeamays_hcf136_Mcells_039_A

source_name: wild-type sibling of hcf136 mutant, mesophyll cells, replicate set 1


title: DK1622 (wt), 6h dev., Exp.2

source_name: vegetative cells DK1622 (wt)


title: Zeamays_hcf136_Mcells_049_A

source_name: wild-type sibling of hcf136 mutant, mesophyll cells, replicate set 2


title: mex-3 pal-1 143 C

source_name: mex-3 pal-1 143 C

tag: mex-3 pal-1 143 C


title: DK1622 (wt), 2h dev., Exp.2


title: DK1622 (wt), 4h dev., Exp.2


title: DK1622 (wt), 24h dev., Exp.1

source_name: dev. cells DK1622 (wt) 24h


title: Zeamays_hcf136_BScells_131_A

description: The mutant hcf136 lacks functional PSII components and granal stacking in its mesophyll (M) plastids. This severe disruption in photosynthetic functionality may result in changes to transcriptional profiles of spatially regulated C4 photosynthetic genes. As such, the bundle sheath (BS) cell transcriptome of this mutant was assayed in comparison to its wild-type siblings using microarray analysis. BS strands were isolated by mechanical extraction from the second leaves of wild-type and hcf136 plants at the third-leaf emerging stage of growth. Total RNA was isolated from the BS cells, and BS transcript profiles were compared between wild-type and hcf136 mutants using six biological replicates in a two-label direct comparison. The microarray experiments were performed using the Array 900MPX Expression Array Detection Kit (Genisphere), according to the prescribed company protocol.

source_name: wild-type sibling of hcf136 mutant, bundle sheath cells, replicate set 6


title: DK1622 (wt), 0h dev., Exp.2


title: Zeamays_hcf136_BScells_120_A

source_name: wild-type sibling of hcf136 mutant, bundle sheath cells, replicate set 5


title: H123

description: Comparative Genomic Hybridization of Clostridium difficile strain 123 (equine isolate)

source_name: Genomic DNA from Clostridium difficile strain 123 (equine isolate)

tag: Equine isolate

source_name: Genomic DNA from Clostridium difficile reference strain 630

tag: Sequenced strain 630 (Human isolate)


title: DK1622 (wt), 12h dev., Exp.1

source_name: dev. cells DK1622 (wt) 12h

tag: vegetative cells DK1622 (wt)


title: DK1622 (wt), 9h dev., Exp.1

source_name: dev. cells DK1622 (wt) 9h


title: mex-3 pal-1 101 A

source_name: mex-3 pal-1 101 A

tag: mex-3 pal-1 101 A


title: Zeamays_hcf136_BScells_124_A

source_name: wild-type sibling of hcf136 mutant, bundle sheath cells, replicate set 3


title: mex-3 pal-1 143 B

source_name: mex-3 pal-1 143 B

tag: mex-3 pal-1 143 B


title: DK1622 (wt), 18h dev., Exp.1

source_name: dev. cells DK1622 (wt) 18h

tag: dev. cells DK1622 (wt) 18h


title: DK1622 (wt), 15h dev., Exp.1

source_name: dev. cells DK1622 (wt) 15h

tag: dev. cells DK1622 (wt) 15h


title: mex-3 hnd-1 186 C

source_name: mex-3 hnd-1 186 C

tag: mex-3 hnd-1 186 C


title: mex-3 hlh-1 230 B

source_name: mex-3 hlh-1 230 B

tag: mex-3 hlh-1 230 B


title: DK1622 (wt), 0h dev., Exp.1

source_name: veg. cells DK1622 (wt)

source_name: vegetative cells DK1622 (wt)


title: DK1622 (wt), 4h dev., Exp.1

source_name: dev. cells DK1622 (wt) 4h

tag: dev. cells DK1622 (wt) 4h


title: DK1622 (wt), 6h dev., Exp.1

source_name: dev. cells DK1622 (wt) 6h

tag: dev. cells DK1622 (wt) 6h


title: DK1622 (wt), 2h dev., Exp.1

source_name: dev. cells DK1622 (wt) 2h

tag: dev. cells DK1622 (wt) 2h


title: mex-3 nhr-25 230 C


title: mex-3 elt-3 186 B

source_name: mex-3 elt-3 186 B

tag: mex-3 elt-3 186 B


title: mex-3 vab-7 186 C

source_name: mex-3 vab-7 186 C

tag: mex-3 vab-7 186 C


title: S. griseus IFO13350 vs adpA deficient mutant 1st

city: Bunkyo-ku

first: Yasuo

last: Ohnishi

state: Tokyo

address: 1-1-1 Yayoi

department: Biotechnology

country: Japan

institute: University of Tokyo

description: To correct for non-specific (background) signal for each channel (each dye), the mean signal of 10% of the probes in each sub grid with the lowest intensity was subtracted from that of all probes in the corresponding sub grid.

hyb_protocol: Microarray hybridization was carried out at 42°C for 18 h with mixing by using 120 μl per slide of SlideHyb#1 hybridization solution (Ambion) in a GeneTac HybStation (Genomic Solution). The posthybridization washing consisted of three cycles of 20-second incubations with each of the following solutions: 2× SSC plus 0.1% SDS (medium stringency) at 42°C, 0.1× SSC plus 0.05% SDS (high stringency) at 25°C, and 0.1× SSC (low stringency) at 25°C. After being washed, the slides were dried by centrifugation for 5 min at 350 × g at room temperature.

scan_protocol: The slides scanned with with a 428 array scanner (Affymetrix). The spot intensities were quantified using Imagene 6.1 (BioDiscovery, Inc.).

data_processing: Expression ratios were normalized using the Limma loess method by ArrayPipe 2.0. Average normalized expression ratios (S. griseus IFO13350/ΔadpA mutant) were calculated for each gene and tested for significance (p < 0.05). Ratio of S. griseus IFO13350 compared with ΔadpA were further screened for difference from ΔadpA mutant, which was defined as having an expression ratio of either >2.0 or <0.5.

organism: Streptomyces griseus subsp. griseus NBRC 13350

source_name: experiment

label_protocol: Cy3 labeled cDNA were prepared by indirect labeling.

extract_protocol: Total RNA was isolated by RNAqueous mini kit (Ambion) and carried out DNaseI treatment to remove contaminated genomic DNA.

tag: wild type

source_name: control

label_protocol: Cy5 labeled cDNA were prepared by indirect labeling.

tag: adpA deficient mutant


title: S. griseus IFO13350 vs adpA deficient mutant 3rd


title: mex-3 elt-3 186 C

source_name: mex-3 elt-3 186 C

tag: mex-3 elt-3 186 C


title: mex-3 scrt-1 186 C

source_name: mex-3 scrt-1 186 C

tag: mex-3 scrt-1 186 C


title: S. griseus IFO13350 vs adpA deficient mutant 4th


title: mex-3 vab-7 186 B

source_name: mex-3 vab-7 186 B

tag: mex-3 vab-7 186 B


title: S. griseus IFO13350 vs adpA deficient mutant 2nd


title: Zeamays_hcf136_BScells_118_A

source_name: wild-type sibling of hcf136 mutant, bundle sheath cells, replicate set 1

tag: W22 cultivar, hcf136 segregating line, harvested at 3rd leaf emerging stage


title: mex-3 pal-1 143 A

source_name: mex-3 pal-1 143 A

tag: mex-3 pal-1 143 A


title: Zeamays_hcf136_BScells_126_A

source_name: wild-type sibling of hcf136 mutant, bundle sheath cells, replicate set 4


title: mex-3 scrt-1 143 B

source_name: mex-3 scrt-1 143 B

tag: mex-3 scrt-1 143 B


title: mex-3 lin-26 186 B


title: mex-3 lin-26 230 A


title: mex-3 lin-26 230 B


title: Zeamays_hcf136_BScells_117_A

source_name: wild-type sibling of hcf136 mutant, bundle sheath cells, replicate set 2


title: mex-3 hnd-1 143 C

source_name: mex-3 hnd-1 143 C

tag: mex-3 hnd-1 143 C


title: mex-3 hnd-1 186 A

source_name: mex-3 hnd-1 186 A

tag: mex-3 hnd-1 186 A


title: mex-3 lin-26 186 A


title: mex-3 unc-120 230 C


title: mex-3 scrt-1 143 A

source_name: mex-3 scrt-1 143 A

tag: mex-3 scrt-1 143 A


title: mex-3 hnd-1 186 B

source_name: mex-3 hnd-1 186 B

tag: mex-3 hnd-1 186 B


title: Control LM2 Cell on HMVEC-L Replicate 3

city: Princeton

first: Yibin

last: Kang

state: NJ

address: LTL 254, Washington Road

department: Molecular Biology

institute: Princeton University

description: LM2 cancer cells were cultured alone or on top of a monolayer of human lung endothelial HMVEC-L cells

hyb_protocol: Sample RNA was hybridized on the two color Agilent human 4x4k arrays with reference RNA. Agilent Gene Expression Hybridization kit was used.

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version A.9.5).

data_processing: gMedian and rMedian signal were used. Array values were normalized to equal median.

organism: Homo sapiens

source_name: Total RNA from LM2 cells labeled with Cyanine-5 (red).

label_protocol: Labeled with Agilent Low RNA Input Amplification kit following manufacturer's instructions.

extract_protocol: Total RNA extracted using Qiagen RNAeasy mini kit following manufacturer's instructions. In the co-culture condition, LM2 cells were labeled with GFP, and HMVEC-L cells were labeled with SNARF before co-culture. LM2 cells were isolated by FACS 48 hours after co-culture.

tag: LM2 cells cultured with HMVEC-L and then purified by FACS

source_name: Human universal reference RNA labeled with Cyanine-3 (green).

tag: Purchased from Stratagene, Inc.


title: mex-3 unc-120 230 B


title: Control LM2 Cell on HMVEC-L Replicate 2


title: Knockdown Cell on HMVEC-L Replicate 1

tag: transfected with pSuper-shMTDH, cultured with HMVEC-L and then purified by FACS


title: mex-3 scrt-1 186 B

source_name: mex-3 scrt-1 186 B

tag: mex-3 scrt-1 186 B


title: mex-3 hnd-1 143 A

source_name: mex-3 hnd-1 143 A

tag: mex-3 hnd-1 143 A


title: mex-3 unc-120 230 A


title: Knockdown Cell Replicate 1

tag: transfected with pSuper-shMTDH


title: Knockdown Cell on HMVEC-L Replicate 3


title: Knockdown Cell on HMVEC-L Replicate 2


title: Knockdown Cell Replicate 2


title: mex-3 unc-120 186 C


title: mex-3 hnd-1 143 B

source_name: mex-3 hnd-1 143 B

tag: mex-3 hnd-1 143 B


title: Knockdown Cell Replicate 3


title: Control LM2 Cell Replicate 1

tag: LM2 cells


title: Control LM2 Cell on HMVEC-L Replicate 1


title: mex-3 unc-120 186 B


title: Control LM2 Cell Replicate 2


title: Control LM2 Cell Replicate 3


title: mex-3 unc-120 186 A


title: mex-3 nob-1 230 B

source_name: mex-3 nob-1 230 B

tag: mex-3 nob-1 230 B


title: mex-3 nob-1 230 A

source_name: mex-3 nob-1 230 A

tag: mex-3 nob-1 230 A


title: 12_drought&heat_Cy3_vs_drought_Cy5

city: Oak Ridge

first: David

middle: J

last: Weston

state: TN

department: Environmental Sciences Division

institute: David Weston

hyb_protocol: Three µg of labeled aRNA were subsequently used for hybridization onto Arabidopsis slides printed with Operon v 3.1, 70 mer oligos obtained from the laboratory of Dr. David Galbraith at the University of Arizona (www.cals.arizona.edu/microarray).  A formamide-based (50%) hybridization solution was applied at 42 ˚C for 14 h and then washed according to Galbraith protocols (http://ag.arizona.edu/microarray/methods.html).

scan_protocol: Arrays were imaged with a Scan Array 5000 system (Perkin Elmer, Wellesley, MA) and the resultant image files were imported into Imagene v.6.0 for data extraction and initial data diagnostics.

data_processing: All statistical calculations were performed using the limma (v.2.10.5) Bioconductor open access package run in the R statistical framework (R Development Core Team, 2005).  Quality of the hybridization was assessed with the Bioconductor packages arrayMagic v.1.14.0 and arrayQuality v.1.12.0.  Log-fold (M) over variance (A) plots (M-A plots) were used to determine the most appropriate background correction method.  We used basic subtraction in this study, but quantile, print-tip lowess, and global lowess were all investigated.  Using limma, a linear model was fitted to compare control to all treatment conditions as contrasts and empirical Bayes was used to compute a moderated t-statistic.  Multiple testing errors were accounted for by using a false discovery rate (FDR) correction.

organism: Arabidopsis thaliana

source_name: Arabidopsis shoots exposed to combined drought and heat conditions

label_protocol: RNA was transcribed into cDNA primed with T7 Oligo (dT).  Amino Allyl-modified RNA was then amplified and purified using manufacturer directions (Ambion) as modified by the Vicki Chandler lab (refer to www.maizearray.org/maize_protocols _factsheet.shtml for protocol). Six µg of each amplified RNA (aRNA) sample was coupled to either CY3 or CY5 monochromeric dye (Amersham) also according to the Chandler protocols

growth_protocol: Seedlings were transferred to holes cored into a Styrofoam lid floating atop a 10L plastic tub filled with 1 mM N nutrient solution (1.0 mM KNO3, 1.5 mM CaCl2, 1.0 mM MgSO4 ·7H20, 1.0 mM K3PO4·7H20, 0.5 mM NH4Cl; micronutrients and Fe-EDTA as described in Norén et al. 2004; and 0.5 gL-1 MES, pH 5.7). Tubs were transferred to a Conviron BWD80-controlled growth room programmed for 10 h, 22 ºC days/ 16 h, 18 º C nights, 80% RH with aeration provided by aquarium stones attached via tubing to an air pump. Metal halide and tungsten incandescent lamps provided an average of 110 μmol m-2 s-1 within the growth chamber. Seedlings were misted twice daily for approximately one week and lightly covered with a dome to reduce desiccation. A series of shadecloth coverage (70%-50%-30%-no shade) was used to acclimate the plants to MH lights over the course of 7-10 d. During the fourth week the plants were gradually introduced to lower humidity by loosening and finally removing domed lids (week 5).  Plants were harvested at the end of 11 weeks.

extract_protocol: Total RNA was isolated and labeled from control and treatment shoot tissue using methods from the Chandler Lab (www.maizearray.org/maize_protocols _factsheet.shtml).  Briefly, the TRIZOL reagent procedure was initially used to isolate total RNA that was further purified with RNA clean-up spin columns (Qiagen).  This two-step process ensured for high quality RNA determined spectrophotometircally (Nanodrop) and with denaturing agarose gels.

treatment_protocol: 24 plants were randomly chosen and six each were subjected to the following treatments: (1) Drought- systems drained and roots exposed to air until ~10 % fresh weight had been lost; (2) Heat - systems placed in 38 ºC chamber for 3 h; (3) plants subjected to combined treatments 1 & 2; and (4) no change (control).  At the end of the treatment, plant shoots were harvested and immediately flash frozen in liquid nitrogen for subsequent RNA isolation.

tag: Arabidopsis thaliana ‘Columbia’ was used. After treatment, plant shoots were harvested at the end of 11 weeks and immediately flash frozen in liquid nitrogen for subsequent RNA isolation.

source_name: Arabidopsis shoots exposed to drought conditions


title: 11_drought_Cy3_vs_heat_Cy5

label_protocol: For each treatment, RNA was transcribed into cDNA primed with T7 Oligo (dT).  Amino Allyl-modified RNA was then amplified and purified using manufacturer directions (Ambion) as modified by the Vicki Chandler lab (refer to www.maizearray.org/maize_protocols _factsheet.shtml for protocol). Six µg of each amplified RNA (aRNA) sample was coupled to either CY3 or CY5 monochromeric dye (Amersham) also according to the Chandler protocols.  Three µg of labeled aRNA were subsequently used for hybridization onto Arabidopsis slides printed with Operon v 3.1, 70 mer oligos obtained from the laboratory of Dr. David Galbraith at the University of Arizona (www.cals.arizona.edu/microarray).

source_name: Arabidopsis shoots exposed to heat conditions


title: mex-3 nob-1 186 C

source_name: mex-3 nob-1 186 C

tag: mex-3 nob-1 186 C


title: mex-3 nob-1 186 A

source_name: mex-3 nob-1 186 A

tag: mex-3 nob-1 186 A


title: mex-3 nob-1 186 B

source_name: mex-3 nob-1 186 B

tag: mex-3 nob-1 186 B


title: mex-3 elt-3 186 A

source_name: mex-3 elt-3 186 A

tag: mex-3 elt-3 186 A


title: mex-3 elt-3 230 C

source_name: mex-3 elt-3 230 C

tag: mex-3 elt-3 230 C


title: 10_heat_Cy3_vs_heat&drought_Cy5

source_name: Arabidopsis shoots exposed to combined heat and drought conditions


title: 8_heat_Cy3_vs_drought_Cy5


title: 7_drought_Cy3_vs_heat_Cy5


title: 1_heat_Cy3_vs_control_Cy5

source_name: Arabidopsis shoots exposed to control conditions


title: mex-3 nhr-25 186 B


title: mex-3 nob-1 230 C

source_name: mex-3 nob-1 230 C

tag: mex-3 nob-1 230 C


title: mex-3 hlh-1 230 A

source_name: mex-3 hlh-1 230 A

tag: mex-3 hlh-1 230 A


title: mex-3 elt-3 230 B

source_name: mex-3 elt-3 230 B

tag: mex-3 elt-3 230 B


title: 6_drought&heat_Cy3_vs_control_Cy5


title: mex-3 nhr-25 230 A


title: mex-3 nhr-25 186 C


title: 9_drought&heat_Cy3_vs_heat_Cy5


title: mex-3 nhr-25 230 B


title: mex-3 hlh-1 186 B

source_name: mex-3 hlh-1 186 B

tag: mex-3 hlh-1 186 B


title: mex-3 elt-3 230 A

source_name: mex-3 elt-3 230 A

tag: mex-3 elt-3 230 A


title: mex-3 nhr-25 186 A


title: 2_control_Cy3_vs_heat_Cy5


title: 3_drought_Cy3_vs_control_Cy5


title: 4_control_Cy3_vs_drought_Cy5

source_name: Arabidopsis shoots exposed to control conditions.

source_name: Arabidopsis shoots exposed to drought conditions.


title: 5_control_cy3_vs_drought&heat_Cy5

source_name: Arabidopsis shoots exposed to combined drought to heat conditions


title: mex-3 vab-7 230 A

source_name: mex-3 vab-7 230 A

tag: mex-3 vab-7 230 A


title: mex-3 elt-1 186 C

source_name: mex-3 elt-1 186 C

tag: mex-3 elt-1 186 C


title: mex-3 vab-7 230 B

source_name: mex-3 vab-7 230 B

tag: mex-3 vab-7 230 B


title: mex-3 vab-7 186 A

source_name: mex-3 vab-7 186 A

tag: mex-3 vab-7 186 A


title: mex-3 hlh-1 186 A

source_name: mex-3 hlh-1 186 A

tag: mex-3 hlh-1 186 A


title: mex-3 elt-1 143 C

source_name: mex-3 elt-1 143 C

tag: mex-3 elt-1 143 C


title: mex-3 elt-1 186 B

source_name: mex-3 elt-1 186 B

tag: mex-3 elt-1 186 B


title: mex-3 tbx-8,9 186 A


title: mex-3 tbx-8,9 143 B


title: mex-3 elt-1 143 B

source_name: mex-3 elt-1 143 B

tag: mex-3 elt-1 143 B


title: mex-3 vab-7 230 C

source_name: mex-3 vab-7 230 C

tag: mex-3 vab-7 230 C


title: mex-3 tbx-8,9 143 C


title: mex-3 scrt-1 186 A

source_name: mex-3 scrt-1 186 A

tag: mex-3 scrt-1 186 A


title: mex-3 elt-1 143 A

source_name: mex-3 elt-1 143 A

tag: mex-3 elt-1 143 A


title: mex-3 230 A


title: mex-3 elt-1 186 A

source_name: mex-3 elt-1 186 A

tag: mex-3 elt-1 186 A


title: mex-3 tbx-8,9 143 A


title: mex-3 186 A

source_name: C. elegans embryos

tag: see publication


title: Mouse lung Day 6 (infected with Plasmodium berghei ANKA) technical replicate

status: Public on Jan 31 2008

city: Toronto

first: Fiona

middle: E

last: Lovegrove

state: ON

address: 1 King's College Circle, MSB Rm 7318

department: Institute of Medical Science

country: Canada

institute: University of Toronto

description: Each array was hybridized with cDNA transcribed from an RNA pool of 5 C57BL/6 mice per timepoint (Day 0 and 6) and technical replicates (dye-swap) experiments were performed for both time points.

hyb_protocol: Cy3 and Cy5-labeled cDNA pairs and Agilent control spots were added to a final volume of 0.5ml hybridization buffer (1 M NaCl, 0.5% sodium sarcosine, 50 mM methyl ethane sulfonate (MES), pH 6.5, 33% formamide and 40µg salmon sperm DNA (Invitrogen)). Hybridizations were performed in Agilent hybridization (Agilent, Palo Alto CA) chambers at 42°C with rotation for 18-24 hours.

scan_protocol: Slides were washed in 6X SSPE, 0.005% sarcosine, followed by 0.06X SSPE, allowed to dry and scanned with a 4000A microarray scanner (Axon Instruments, Union City CA). TIFF images were quantified with GenePix (Axon Instruments).

data_processing: Variance stabilizing normalization and loess smoothing were applied in Bioconductor and the data were transformed to log2 scale.

organism: Mus musculus

source_name: Whole lung

label_protocol: cDNA with incorporated 5-(3-aminoallyl)-2’deoxyuridine-5’-triphosphate (AAdUTP; Sigma, Oakville ON) was reverse-transcribed from 1-2 µg mRNA. Purified cDNA was coupled with N-hydroxysuccinimide esters of Cy3 or Cy5 (GE Lifesciences, Baie d'Urfe QC).

extract_protocol: Trizol and RNEasy cleanup, oligo dT purification of mRNA

tag: Male C57BL/6 mice, 6-8 weeks old, infected with 1x10^6 P berghei ANKA parasitized erythrocytes


title: mex-3 230 B


title: Mouse lung Day 6 post Plasmodium berghei infection

source_name: Mouse whole lung (infected with P. berghei ANKA)

tag: Male C57bl/6 mice age 6-8 weeks, infected with 1x10^6 P berghei ANKA parasitized erythrocytes


title: shRNA_3D_1

city: Berkeley

first: Terumi

last: Kohwi-shigematsu

address: 1 Cyclotron road

department: Life Science

institute: LBNL

description: Gene expression data from MDA-MB-231-SATB1_shRNA1 cultured on matrigel coated dishes (3D)

hyb_protocol: Following fragmentation, 10 ?g of cRNA were hybridized for 16 hr at 45C.

scan_protocol: GeneChips were scanned according to manufacturer's instructions (2001 Affymetrix Genechip technical Manual)

data_processing: Probe set based gene expression measurements were generated from .CEL files using the RMA algorithm from the GeneSpring software (SiLicon Genetics).

source_name: SATB1-shRNA trasnfected MDA-MB-231 cells grown on 3D culture

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

growth_protocol: grown on matrigel coated culture dish (3D culture)

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

treatment_protocol: MDA-MB-231 cells stably trasnfected with pSUPER_ SATB1-shRNA1was cloned.

tag: SATB1-knocked down (by shRNA) human breast cancer cell line


title: Mouse lung Day 0

source_name: Whole lung tissue

tag: C57BL/6 male age 6-8 weeks, mRNA pool from 5 mice


title: mex-3 186 B


title: Mouse Lung Day 0 (Technical replicate)

tag: Male C57BL/6 mice age 6-8 weeks


title: Embryonic hatching muscle age 28 control replica 3

city: Raleigh

first: Jean

middle: Eduardo

last: de Oliveira

state: NC

address: 2711 Founders Dr

department: Poultry Science

institute: North Carolina State University

description: Slide 80-Embryonic hatching muscle: age 24 control replica 2 vs age 28 control replica 3

hyb_protocol: mix of 33 pmol of both samples was resuspended with 33 µl Pronto! Long Oligo Hybridization solution and applied to pre-hybrydized microarray slides with spotted area coved with a 25 X 40 mm glass coverslip; slides were hybridized in Corning Hybridization Chambers immersed in 42C water bath, protected from light, for 16h. After hybridization, slides were sequencenly washed according to manufacturer's instructions (Pronto! Universal Microarray Hybridization Kit, Corning Inc.)

scan_protocol: scanned on ScanArray Gx Plus (PerkinElmer) set to 65% lazer power Images were quantified using ScanAlyze Software (version 2.50).

data_processing: Log2 transformed data was submitted to ratio analysis and LOWESS normalization using JMP Genomics Software (SAS Institute)

organism: Meleagris gallopavo

source_name: Total RNA from hatching muscle enbryos day 28 labeled with cyanine-5 (red)

label_protocol: 5µg of total RNA were primed with 3µg of random primers and 2µg of oligo(dt) primer, heated at 70C for 10 min, then reverse transcribed at 42C for 2h with 3.2 µl ChipShot Reverse Transcriptase and 4 µl aminoallyl-sNTPs; cDNA was indirect labeled with CyDye NHS Esters (Cy3 or Cy5) by adding 60 µl of cDNA eluted to dried 40,000 pmol CyDye aliquot and hybrydized at room temperature for 1h, followed by purification steps as indicated by manufacturer's instructions (ChipShot Indirect Labeling System and Membrane Clean-Up System, Promega Corp)

growth_protocol: turkey eggs incubated under standard conditions

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions (Molecular Research Center, Inc.)

treatment_protocol: 16 eggs were sampled at each age (22, 24, 25, 26 and 28 days of incubation) to harvest the hatching muscle; tissue preserved in RNA Later solution (Ambion, Inc). In ovo injection was performed on day 24 of incuibation. Samples from days 25, 26 and 28 of incubation were collected for both: control and in ovo fed embryos.

tag: Tissue

value: hatching muscle

tag: 28E control


title: shRNA_3D_2


title: mex-3 143 A


title: MDA231_3D_1

description: Gene expression data from MDA-MB-231-control_shRNA cultured on 3D culture

source_name: Control MDA-MB231 cells grown on 3D culture

treatment_protocol: Parental MDA-MB-231 cells with pSUPER_control-shRNA transfection

tag: Aggressive human breast cancer cell line


title: mex-3 143 B


title: MDA231_3D_2


title: Embryonic hatching muscle age 28 IOF replica 3

description: Slide 79-Embryonic hatching muscle: age 22 control replica 2 vs age 28 IOF replica 3

tag: 28E IOF


title: Embryonic hatching muscle age 22 control replica 1

description: Slide 78-Embryonic hatching muscle: age 28 control replica 4 vs age 22 control replica 1

source_name: Total RNA from hatching muscle enbryos day 22 labeled with cyanine-5 (red)

tag: 22E control


title: BM55p3

description: Gene expression data from MDA-MB-231-SATB1_shRNA1 cultured on plastic dishes

source_name: SATB1-shRNA trasnfected MDA-MB-231 cells grown on 2D culture

growth_protocol: grown on plastic culture dish (2D culture)

treatment_protocol: MDA-MB-231 cells stably trasnfected with pSUPER_ SATB1-shRNA1 was cloned.


title: Embryonic hatching muscle age 26 IOF replica 3

description: Slide 75-Embryonic hatching muscle: age 28 IOF replica 2 vs age 26 IOF replica 3

source_name: Total RNA from hatching muscle enbryos day 26 labeled with cyanine-5 (red)

tag: 26E IOF


title: Embryonic hatching muscle age 28 control replica 1

description: Slide 76-Embryonic hatching muscle: age 28 IOF replica 4 vs age 28 control replica 1


title: Embryonic hatching muscle age 28 IOF replica 1

description: Slide 74-Embryonic hatching muscle: age 26 control replica 4 vs age 28 IOF replica 1


title: AM55p3


title: Embryonic hatching muscle age 26 control replica 1

description: Slide 72-Embryonic hatching muscle: age 26 IOF replica 4 vs age 26 control replica 1

tag: 26E control


title: Embryonic hatching muscle age 25 IOF replica 3

description: Slide 71-Embryonic hatching muscle: age 26 IOF replica 2 vs age 25 IOF replica 3

source_name: Total RNA from hatching muscle enbryos day 25 labeled with cyanine-5 (red)

tag: 25E IOF


title: Embryonic hatching muscle age 22 control replica 3

description: Slide 68-Embryonic hatching muscle: age 25 IOF replica 2 vs age 22 control replica 3


title: Embryonic hatching muscle age 25 control replica 1

description: Slide 69-Embryonic hatching muscle: age 25 IOF replica 4 vs age 25 control replica 1

tag: 25E control


title: Embryonic hatching muscle age 25 IOF replica 1

description: Slide 66-Embryonic hatching muscle: age 24 control replica 4 vs age 25 IOF replica 1


title: Embryonic hatching muscle age 26 IOF replica 1

description: Slide 70-Embryonic hatching muscle: age 25 control replica 4 vs age 26 IOF replica 1


title: Embryonic hatching muscle age 24 control replica 3

description: Slide 67-Embryonic hatching muscle: age 25 control replica 2 vs age 24 control replica 3

source_name: Total RNA from hatching muscle enbryos day 24 labeled with cyanine-5 (red)

tag: 24E control


title: BMDA231p3

description: Gene expression data from MDA-MB-231-control_shRNA cultured on plastic dishes

source_name: Parental MDA-MB231 cells grown on 2D culture


title: Embryonic hatching muscle age 26 control replica 3

description: Slide 77-Embryonic hatching muscle: age 28 control replica 2 vs age 26 control replica 3


title: Embryonic hatching muscle age 24 control replica 2

description: Slide 80-Embryonic hatching muscle: age 24 control replica 2 vs age 28 control replica 3

source_name: Total RNA from hatching muscle enbryos day 24 labeled with cyanine-3 (green)


title: Embryonic hatching muscle age 28 IOF replica 2

source_name: Total RNA from hatching muscle enbryos day 28 labeled with cyanine-3 (green)


title: AMDA231p3


title: Embryonic hatching muscle age 26 control replica 4

source_name: Total RNA from hatching muscle enbryos day 26 labeled with cyanine-3 (green)


title: Embryonic hatching muscle age 28 control replica 4


title: Embryonic hatching muscle age 26 control replica 2

description: Slide 73-Embryonic hatching muscle: age 26 control replica 2 vs age 25 control replica 3


title: Embryonic hatching muscle age 25 control replica 3


title: Embryonic hatching muscle age 26 IOF replica 4


title: Embryonic hatching muscle age 28 IOF replica 4


title: Embryonic hatching muscle age 28 control replica 2


title: Embryonic hatching muscle age 25 control replica 4

source_name: Total RNA from hatching muscle enbryos day 25 labeled with cyanine-3 (green)


title: Embryonic hatching muscle age 26 IOF replica 2


title: Embryonic hatching muscle age 24 control replica 1

description: Slide 65-Embryonic hatching muscle: age 22 control replica 4 vs age 24 control replica 1


title: Embryonic hatching muscle age 25 IOF replica 4


title: Embryonic hatching muscle age 24 control replica 4


title: Embryonic hatching muscle age 25 control replica 2


title: Embryonic hatching muscle age 22 control replica 2

description: Slide 79-Embryonic hatching muscle: age 22 control replica 2 vs age 28 IOF replica 3

source_name: Total RNA from hatching muscle enbryos day 22 labeled with cyanine-3 (green)


title: Embryonic ileum age 22 control replica 1

description: Slide 30-Embryonic ileum: age 28 control replica 4 vs age 22 control replica 1

source_name: Total RNA from ileum enbryos day 22 labeled with cyanine-5 (red)

treatment_protocol: 16 eggs were sampled at each age (22, 24, 25, 26 and 28 days of incubation) to harvest the ileum; tissue preserved in RNA Later solution (Ambion, Inc). In ovo injection was performed on day 24 of incuibation. Samples from days 25, 26 and 28 of incubation were collected for both: control and in ovo fed embryos.

value: ileum


title: Embryonic hatching muscle age 22 control replica 4


title: Embryonic ileum age 26 IOF replica 3

description: Slide 27-Embryonic ileum: age 28 IOF replica 2 vs age 26 IOF replica 3

source_name: Total RNA from ileum enbryos day 26 labeled with cyanine-5 (red)


title: Embryonic ileum age 28 control replica 1

description: Slide 28-Embryonic ileum: age 28 IOF replica 4 vs age 28 control replica 1

source_name: Total RNA from ileum enbryos day 28 labeled with cyanine-5 (red)


title: Embryonic ileum age 26 control replica 3

description: Slide 29-Embryonic ileum: age 28 control replica 2 vs age 26 control replica 3


title: Embryonic ileum age 28 control replica 3

description: Slide 32-Embryonic ileum: age 24 control replica 2 vs age 28 control replica 3


title: Embryonic ileum age 28 IOF replica 3

description: Slide 31-Embryonic ileum: age 22 control replica 2 vs age 28 IOF replica 3


title: Embryonic ileum age 28 IOF replica 1

description: Slide 26-Embryonic ileum: age 26 control replica 4 vs age 28 IOF replica 1


title: Embryonic ileum age 26 control replica 1

description: Slide 24-Embryonic ileum: age 26 IOF replica 4 vs age 26 control replica 1


title: Embryonic ileum age 25 IOF replica 3

description: Slide 23-Embryonic ileum: age 26 IOF replica 2 vs age 25 IOF replica 3

source_name: Total RNA from ileum enbryos day 25 labeled with cyanine-5 (red)


title: Embryonic ileum age 25 control replica 3

description: Slide 25-Embryonic ileum: age 26 control replica 2 vs age 25 control replica 3


title: Embryonic ileum age 25 control replica 1

description: Slide 21-Embryonic ileum: age 25 IOF replica 4 vs age 25 control replica 1


title: Embryonic ileum age 26 IOF replica 1

description: Slide 22-Embryonic ileum: age 25 control replica 4 vs age 26 IOF replica 1


title: Embryonic hatching muscle age 25 IOF replica 2

description: Slide 68-Embryonic hatching muscle: age 25 IOF replica 2 vs age 22 control replica 3


title: Embryonic ileum age 22 control replica 3

description: Slide 20-Embryonic ileum: age 25 IOF replica 2 vs age 22 control replica 3


title: Embryonic ileum age 24 control replica 1

description: Slide 17-Embryonic ileum: age 22 control replica 4 vs age 24 control replica 1

source_name: Total RNA from ileum enbryos day 24 labeled with cyanine-5 (red)


title: Embryonic ileum age 24 control replica 2

source_name: Total RNA from ileum enbryos day 24 labeled with cyanine-3 (green)


title: Embryonic ileum age 24 control replica 3

description: Slide 19-Embryonic ileum: age 25 control replica 2 vs age 24 control replica 3


title: Embryonic ileum age 22 control replica 2

source_name: Total RNA from ileum enbryos day 22 labeled with cyanine-3 (green)


title: Embryonic ileum age 28 control replica 4

source_name: Total RNA from ileum enbryos day 28 labeled with cyanine-3 (green)


title: Embryonic ileum age 25 IOF replica 1

description: Slide 18-Embryonic ileum: age 24 control replica 4 vs age 25 IOF replica 1


title: Embryonic ileum age 28 IOF replica 4


title: Embryonic ileum age 28 IOF replica 2


title: Embryonic ileum age 26 control replica 4

source_name: Total RNA from ileum enbryos day 26 labeled with cyanine-3 (green)


title: Embryonic ileum age 28 control replica 2


title: Embryonic ileum age 26 IOF replica 2


title: Embryonic ileum age 26 IOF replica 4


title: Embryonic ileum age 26 control replica 2


title: Embryonic ileum age 25 control replica 2

source_name: Total RNA from ileum enbryos day 25 labeled with cyanine-3 (green)


title: Embryonic ileum age 25 IOF replica 4


title: Embryonic ileum age 25 IOF replica 2


title: Embryonic ileum age 25 control replica 4


title: Embryonic duodenum age 28 IOF replica 3

description: Slide 63-Embryonic duodenum: age 22 control replica 2 vs age 28 IOF replica 3

source_name: Total RNA from duodenum enbryos day 28 labeled with cyanine-5 (red)

treatment_protocol: 16 eggs were sampled at each age (22, 24, 25, 26 and 28 days of incubation) to harvest the duodenum; tissue preserved in RNA Later solution (Ambion, Inc). In ovo injection was performed on day 24 of incuibation. Samples from days 25, 26 and 28 of incubation were collected for both: control and in ovo fed embryos.

value: duodenum


title: Embryonic duodenum age 28 control replica 3

description: Slide 64-Embryonic duodenum: age 24 control replica 2 vs age 28 control replica 3


title: Embryonic duodenum age 22 control replica 1

description: Slide 62-Embryonic duodenum: age 28 control replica 4 vs age 22 control replica 1

source_name: Total RNA from duodenum enbryos day 22 labeled with cyanine-5 (red)


title: Embryonic ileum age 22 control replica 4


title: Embryonic duodenum age 26 control replica 3

description: Slide 61-Embryonic duodenum: age 28 control replica 2 vs age 26 control replica 3

source_name: Total RNA from duodenum enbryos day 26 labeled with cyanine-5 (red)


title: Embryonic duodenum age 26 IOF replica 3

description: Slide 59-Embryonic duodenum: age 28 IOF replica 2 vs age 26 IOF replica 3


title: Embryonic duodenum age 28 control replica 1

description: Slide 60-Embryonic duodenum: age 28 IOF replica 4 vs age 28 control replica 1


title: Embryonic duodenum age 28 IOF replica 1

description: Slide 58-Embryonic duodenum: age 26 control replica 4 vs age 28 IOF replica 1


title: Embryonic duodenum age 26 control replica 1

description: Slide 56-Embryonic duodenum: age 26 IOF replica 4 vs age 26 control replica 1


title: Embryonic duodenum age 25 control replica 3

description: Slide 57-Embryonic duodenum: age 26 control replica 2 vs age 25 control replica 3

source_name: Total RNA from duodenum enbryos day 25 labeled with cyanine-5 (red)


title: Embryonic duodenum age 26 IOF replica 1

description: Slide 54-Embryonic duodenum: age 25 control replica 4 vs age 26 IOF replica 1


title: Embryonic duodenum age 25 control replica 1

description: Slide 53-Embryonic duodenum: age 25 IOF replica 4 vs age 25 control replica 1


title: Embryonic ileum age 24 control replica 4


title: Embryonic duodenum age 22 control replica 3

description: Slide 52-Embryonic duodenum: age 25 IOF replica 2 vs age 22 control replica 3


title: Embryonic duodenum age 25 IOF replica 3

description: Slide 55-Embryonic duodenum: age 26 IOF replica 2 vs age 25 IOF replica 3


title: Embryonic duodenum age 25 IOF replica 1

description: Slide 50-Embryonic duodenum: age 24 control replica 4 vs age 25 IOF replica 1


title: Embryonic duodenum age 28 control replica 4

source_name: Total RNA from duodenum enbryos day 28 labeled with cyanine-3 (green)


title: Embryonic duodenum age 24 control replica 3

description: Slide 51-Embryonic duodenum: age 25 control replica 2 vs age 24 control replica 3

source_name: Total RNA from duodenum enbryos day 24 labeled with cyanine-5 (red)


title: Embryonic duodenum age 24 control replica 1

description: Slide 49-Embryonic duodenum: age 22 control replica 4 vs age 24 control replica 1


title: Embryonic duodenum age 24 control replica 2

source_name: Total RNA from duodenum enbryos day 24 labeled with cyanine-3 (green)


title: Embryonic duodenum age 26 control replica 4

source_name: Total RNA from duodenum enbryos day 26 labeled with cyanine-3 (green)


title: Embryonic duodenum age 28 IOF replica 2


title: Embryonic duodenum age 28 control replica 2


title: Embryonic duodenum age 26 control replica 2


title: Embryonic duodenum age 25 control replica 4

source_name: Total RNA from duodenum enbryos day 25 labeled with cyanine-3 (green)


title: Embryonic duodenum age 26 IOF replica 4


title: Embryonic duodenum age 26 IOF replica 2


title: Embryonic duodenum age 22 control replica 2

source_name: Total RNA from duodenum enbryos day 22 labeled with cyanine-3 (green)


title: Embryonic breast muscle age 28 control replica 3

description: Slide 48-Embryonic breast muscle: age 24 control replica 2 vs age 28 control replica 3

source_name: Total RNA from breast muscle enbryos day 28 labeled with cyanine-5 (red)

treatment_protocol: 16 eggs were sampled at each age (22, 24, 25, 26 and 28 days of incubation) to harvest the breast muscle; tissue preserved in RNA Later solution (Ambion, Inc). In ovo injection was performed on day 24 of incuibation. Samples from days 25, 26 and 28 of incubation were collected for both: control and in ovo fed embryos.

value: breast muscle


title: Embryonic duodenum age 25 IOF replica 2


title: Embryonic duodenum age 22 control replica 4


title: Embryonic duodenum age 25 control replica 2


title: Embryonic duodenum age 24 control replica 4


title: Embryonic duodenum age 25 IOF replica 4


title: Embryonic duodenum age 28 IOF replica 4


title: Embryonic breast muscle age 28 IOF replica 3

description: Slide 47-Embryonic breast muscle: age 22 control replica 2 vs age 28 IOF replica 3


title: Embryonic breast muscle age 26 control replica 3

description: Slide 45-Embryonic breast muscle: age 28 control replica 2 vs age 26 control replica 3

source_name: Total RNA from breast muscle enbryos day 26 labeled with cyanine-5 (red)


title: Embryonic breast muscle age 22 control replica 1

description: Slide 46-Embryonic breast muscle: age 28 control replica 4 vs age 22 control replica 1

source_name: Total RNA from breast muscle enbryos day 22 labeled with cyanine-5 (red)


title: Embryonic breast muscle age 28 control replica 1

description: Slide 44-Embryonic breast muscle: age 28 IOF replica 4 vs age 28 control replica 1


title: Embryonic breast muscle age 25 IOF replica 3

description: Slide 39-Embryonic breast muscle: age 26 IOF replica 2 vs age 25 IOF replica 3

source_name: Total RNA from breast muscle enbryos day 25 labeled with cyanine-5 (red)


title: Embryonic breast muscle age 28 IOF replica 1

description: Slide 42-Embryonic breast muscle: age 26 control replica 4 vs age 28 IOF replica 1


title: Embryonic breast muscle age 26 IOF replica 3

description: Slide 43-Embryonic breast muscle: age 28 IOF replica 2 vs age 26 IOF replica 3


title: Embryonic breast muscle age 25 control replica 3

description: Slide 41-Embryonic breast muscle: age 26 control replica 2 vs age 25 control replica 3


title: Embryonic duodenum age 26 replica 4

description: Slide 528-Embryonic duodenum: age 26 biological replica 4 vs age 28 biological replica 1

source_name: Total RNA from duodenum embryos day 26 labeled with Cyanine-3 (green).

treatment_protocol: 24 eggs were sampled at each age (20, 22, 24, 26 and 28 days of incubation) to harvest the duodenum; tissue preserved in RNA Later solution (Ambion, Inc)

tag: Age

value: e26 d


title: Embryonic duodenum age 24 replica 4

description: Slide 684-Embryonic duodenum: age 26 biological replica 1 vs age 24 biological replica 4

source_name: Total RNA from duodenum embryos day 24 labeled with Cyanine-5 (red).

value: e24 d


title: Embryonic duodenum age 28 replica 1

source_name: Total RNA from duodenum embryos day 28 labeled with Cyanine-5 (red).

value: e28 d


title: Embryonic duodenum age 28 replica 2

description: Slide 641-Embryonic duodenum: age 24 biological replica 3 vs age 28 biological replica 2


title: Embryonic duodenum age 26 replica 3

description: Slide 635-Embryonic duodenum: age 20 biological replica 2 vs age 26 biological replica 3

source_name: Total RNA from duodenum embryos day 26 labeled with Cyanine-5 (red).


title: Embryonic duodenum age 20 replica 1

description: Slide 530-Embryonic duodenum: age 20 biological replica 1 vs age 28 biological replica 4

source_name: Total RNA from duodenum embryos day 20 labeled with Cyanine-5 (red).

value: e20 d


title: Embryonic duodenum age 26 replica 2

description: Slide 733-Embryonic duodenum: age 22 biological replica 3 vs age 26 biological replica 2


title: Embryonic duodenum age 24 replica 1

description: Slide 628-Embryonic duodenum: age 22 biological replica 4 vs age 24 biological replica 1


title: Embryonic duodenum age 22 replica 2

description: Slide 514-Embryonic duodenum: age 28 biological replica 3 vs age 22 biological replica 2

source_name: Total RNA from duodenum embryos day 22 labeled with Cyanine-5 (red).

value: e22 d


title: Embryonic duodenum age 20 replica 3

description: Slide 602-Embryonic duodenum: age 20 biological replica 3 vs age 24 biological replica 2


title: Embryonic duodenum age 22 replica 1

description: Slide 612-Embryonic duodenum: age 20 biological replica 4 vs age 22 biological replica 1


title: Embryonic duodenum age 26 replica 1


title: Embryonic duodenum age 24 replica 3

source_name: Total RNA from duodenum embryos day 24 labeled with Cyanine-3 (green).


title: Embryonic breast muscle age 26 control replica 1

description: Slide 40-Embryonic breast muscle: age 26 IOF replica 4 vs age 26 control replica 1


title: Embryonic duodenum age 22 replica 3

source_name: Total RNA from duodenum embryos day 22 labeled with Cyanine-3 (green).


title: Embryonic breast muscle age 22 control replica 3

description: Slide 36-Embryonic breast muscle: age 25 IOF replica 2 vs age 22 control replica 3


title: Embryonic breast muscle age 24 control replica 3

description: Slide 35-Embryonic breast muscle: age 25 control replica 2 vs age 24 control replica 3

source_name: Total RNA from breast muscle enbryos day 24 labeled with cyanine-5 (red)


title: Embryonic breast muscle age 24 control replica 1

description: Slide 33-Embryonic breast muscle: age 22 control replica 4 vs age 24 control replica 1


title: Embryonic breast muscle age 26 IOF replica 1

description: Slide 38-Embryonic breast muscle: age 25 control replica 4 vs age 26 IOF replica 1


title: Embryonic breast muscle age 25 control replica 1

description: Slide 37-Embryonic breast muscle: age 25 IOF replica 4 vs age 25 control replica 1


title: Embryonic breast muscle age 22 control replica 2

description: Slide 47-Embryonic breast muscle: age 22 control replica 2 vs age 28 IOF replica 3

source_name: Total RNA from breast muscle enbryos day 22 labeled with cyanine-3 (green)


title: Embryonic breast muscle age 24 control replica 2

description: Slide 48-Embryonic breast muscle: age 24 control replica 2 vs age 28 control replica 3

source_name: Total RNA from breast muscle enbryos day 24 labeled with cyanine-3 (green)


title: Embryonic breast muscle age 25 IOF replica 1

description: Slide 34-Embryonic breast muscle: age 24 control replica 4 vs age 25 IOF replica 1


title: Embryonic duodenum age 28 replica 3

source_name: Total RNA from duodenum embryos day 28 labeled with Cyanine-3 (green).


title: Embryonic breast muscle age 28 control replica 2

description: Slide 45-Embryonic breast muscle: age 28 control replica 2 vs age 26 control replica 3

source_name: Total RNA from breast muscle enbryos day 28 labeled with cyanine-3 (green)


title: Embryonic duodenum age 20 replica 4

source_name: Total RNA from duodenum embryos day 20 labeled with Cyanine-3 (green).


title: Embryonic breast muscle age 28 control replica 4

description: Slide 46-Embryonic breast muscle: age 28 control replica 4 vs age 22 control replica 1


title: Embryonic duodenum age 24 replica 2


title: Embryonic duodenum age 20 replica 2

description: Slide 635-Embryonic duodenum: age 20 biological replica 2 vs age 26 biological replica 3


title: Embryonic breast muscle age 28 IOF replica 2

description: Slide 43-Embryonic breast muscle: age 28 IOF replica 2 vs age 26 IOF replica 3


title: Embryonic duodenum age 28 replica 4

description: Slide 530-Embryonic duodenum: age 20 biological replica 1 vs age 28 biological replica 4


title: Embryonic hatching muscle age 28 replica 2

description: Slide 825-Embryonic hatching muscle: age 24 biological replica 3 vs age 28 biological replica 2

source_name: Total RNA from hatching muscle embryos day 28 labeled with Cyanine-5 (red).

treatment_protocol: 24 eggs were sampled at each age (20, 22, 24, 26 and 28 days of incubation) to harvest the hatching muscles; tissue preserved in RNA Later solution (Ambion, Inc)


title: Embryonic hatching muscle age 24 replica 1

description: Slide 989-Embryonic hatching muscle: age 22 biological replica 4 vs age 24 biological replica 1

source_name: Total RNA from hatching muscle embryos day 24 labeled with Cyanine-5 (red).


title: Embryonic breast muscle age 26 control replica 2

description: Slide 41-Embryonic breast muscle: age 26 control replica 2 vs age 25 control replica 3

source_name: Total RNA from breast muscle enbryos day 26 labeled with cyanine-3 (green)


title: Embryonic hatching muscle age 26 replica 2

description: Slide 991-Embryonic hatching muscle: age 22 biological replica 3 vs age 26 biological replica 2

source_name: Total RNA from hatching muscle embryos day 26 labeled with Cyanine-5 (red).


title: Embryonic breast muscle age 26 control replica 4

description: Slide 42-Embryonic breast muscle: age 26 control replica 4 vs age 28 IOF replica 1


title: Embryonic breast muscle age 28 IOF replica 4

description: Slide 44-Embryonic breast muscle: age 28 IOF replica 4 vs age 28 control replica 1


title: Embryonic hatching muscle age 22 replica 2

description: Slide 030-Embryonic hatching muscle: age 28 biological replica 3 vs age 22 biological replica 2

source_name: Total RNA from hatching muscle embryos day 22 labeled with Cyanine-5 (red).


title: Embryonic breast muscle age 26 IOF replica 2

description: Slide 39-Embryonic breast muscle: age 26 IOF replica 2 vs age 25 IOF replica 3


title: Embryonic breast muscle age 26 IOF replica 4

description: Slide 40-Embryonic breast muscle: age 26 IOF replica 4 vs age 26 control replica 1


title: Embryonic hatching muscle age 28 replica 1

description: Slide 988-Embryonic hatching muscle: age 26 biological replica 4 vs age 28 biological replica 1


title: Embryonic hatching muscle age 24 replica 4

description: Slide 114-Embryonic hatching muscle: age 26 biological replica 1 vs age 24 biological replica 4


title: Embryonic duodenum age 22 replica 4

description: Slide 628-Embryonic duodenum: age 22 biological replica 4 vs age 24 biological replica 1


title: Embryonic hatching muscle age 22 replica 1

description: Slide 592-Embryonic hatching muscle: age 20 biological replica 4 vs age 22 biological replica 1


title: Embryonic breast muscle age 25 control replica 4

description: Slide 38-Embryonic breast muscle: age 25 control replica 4 vs age 26 IOF replica 1

source_name: Total RNA from breast muscle enbryos day 25 labeled with cyanine-3 (green)


title: Embryonic hatching muscle age 26 replica 3

description: Slide 386-Embryonic hatching muscle: age 20 biological replica 2 vs age 26 biological replica 3


title: Embryonic hatching muscle age 20 replica 1

description: Slide 829-Embryonic hatching muscle: age 20 biological replica 1 vs age 28 biological replica 4

source_name: Total RNA from hatching muscle embryos day 20 labeled with Cyanine-5 (red).


title: Embryonic hatching muscle age 20 replica 3

description: Slide 281-Embryonic hatching muscle: age 20 biological replica 3 vs age 24 biological replica 2


title: Embryonic breast muscle age 25 IOF replica 2

description: Slide 36-Embryonic breast muscle: age 25 IOF replica 2 vs age 22 control replica 3


title: Embryonic breast muscle age 25 IOF replica 4

description: Slide 37-Embryonic breast muscle: age 25 IOF replica 4 vs age 25 control replica 1


title: Embryonic breast muscle age 25 control replica 2

description: Slide 35-Embryonic breast muscle: age 25 control replica 2 vs age 24 control replica 3


title: Embryonic breast muscle age 24 control replica 4

description: Slide 34-Embryonic breast muscle: age 24 control replica 4 vs age 25 IOF replica 1


title: Embryonic hatching muscle age 26 replica 4

source_name: Total RNA from hatching muscle embryos day 26 labeled with Cyanine-3 (green).


title: Embryonic hatching muscle age 22 replica 4

description: Slide 989-Embryonic hatching muscle: age 22 biological replica 4 vs age 24 biological replica 1

source_name: Total RNA from hatching muscle embryos day 22 labeled with Cyanine-3 (green).


title: Embryonic hatching muscle age 26 replica 1


title: Embryonic breast muscle age 22 control replica 4

description: Slide 33-Embryonic breast muscle: age 22 control replica 4 vs age 24 control replica 1


title: Embryonic liver age 28 control replica 3

description: Slide 16-Embryonic liver: age 24 control replica 2 vs age 28 control replica 3

source_name: Total RNA from liver enbryos day 28 labeled with cyanine-5 (red)

treatment_protocol: 16 eggs were sampled at each age (22, 24, 25, 26 and 28 days of incubation) to harvest the liver; tissue preserved in RNA Later solution (Ambion, Inc). In ovo injection was performed on day 24 of incuibation. Samples from days 25, 26 and 28 of incubation were collected for both: control and in ovo fed embryos.

value: liver


title: Embryonic liver age 22 control replica 1

description: Slide 14-Embryonic liver: age 28 control replica 4 vs age 22 control replica 1

source_name: Total RNA from liver enbryos day 22 labeled with cyanine-5 (red)


title: Embryonic liver age 28 IOF replica 3

description: Slide 15-Embryonic liver: age 22 control replica 2 vs age 28 IOF replica 3


title: Embryonic hatching muscle age 28 replica 3

description: Slide 030-Embryonic hatching muscle: age 28 biological replica 3 vs age 22 biological replica 2

source_name: Total RNA from hatching muscle embryos day 28 labeled with Cyanine-3 (green).


title: Embryonic hatching muscle age 22 replica 3

description: Slide 991-Embryonic hatching muscle: age 22 biological replica 3 vs age 26 biological replica 2


title: Embryonic liver age 28 control replica 1

description: Slide 12-Embryonic liver: age 28 IOF replica 4 vs age 28 control replica 1


title: Embryonic liver age 26 control replica 3

description: Slide 13-Embryonic liver: age 28 control replica 2 vs age 26 control replica 3

source_name: Total RNA from liver enbryos day 26 labeled with cyanine-5 (red)


title: Embryonic hatching muscle age 20 replica 4

description: Slide 592-Embryonic hatching muscle: age 20 biological replica 4 vs age 22 biological replica 1

source_name: Total RNA from hatching muscle embryos day 20 labeled with Cyanine-3 (green).


title: Embryonic liver age 26 IOF replica 3

description: Slide 11-Embryonic liver: age 28 IOF replica 2 vs age 26 IOF replica 3


title: Embryonic liver age 28 IOF replica 1

description: Slide 10-Embryonic liver: age 26 control replica 4 vs age 28 IOF replica 1


title: Embryonic hatching muscle age 24 replica 2

description: Slide 281-Embryonic hatching muscle: age 20 biological replica 3 vs age 24 biological replica 2

source_name: Total RNA from hatching muscle embryos day 24 labeled with Cyanine-3 (green).


title: Embryonic liver age 25 control replica 3

description: Slide 9-Embryonic liver: age 26 control replica 2 vs age 25 control replica 3

source_name: Total RNA from liver enbryos day 25 labeled with cyanine-5 (red)


title: Embryonic breast muscle age 28 replica 1

description: Slide 81-Embryonic breast muscle: age 26 biological replica 4 vs age 28 biological replica 1

source_name: Total RNA from breast muscle embryos day 28 labeled with Cyanine-5 (red).

treatment_protocol: 24 eggs were sampled at each age (20, 22, 24, 26 and 28 days of incubation) to harvest the pectoralis muscle; tissue preserved in RNA Later solution (Ambion, Inc)


title: Embryonic hatching muscle age 20 replica 2

description: Slide 386-Embryonic hatching muscle: age 20 biological replica 2 vs age 26 biological replica 3


title: Embryonic hatching muscle age 28 replica 4

description: Slide 829-Embryonic hatching muscle: age 20 biological replica 1 vs age 28 biological replica 4


title: Embryonic hatching muscle age 24 replica 3

description: Slide 825-Embryonic hatching muscle: age 24 biological replica 3 vs age 28 biological replica 2


title: Embryonic breast muscle age 28 replica 2

description: Slide 79-Embryonic breast muscle: age 24 biological replica 3 vs age 28 biological replica 2


title: Embryonic breast muscle age 24 replica 1

description: Slide 85-Embryonic breast muscle: age 22 biological replica 4 vs age 24 biological replica 1

source_name: Total RNA from breast muscle embryos day 24 labeled with Cyanine-5 (red).


title: Embryonic liver age 26 IOF replica 1

description: Slide 6-Embryonic liver: age 25 control replica 4 vs age 26 IOF replica 1


title: Embryonic breast muscle age 24 replica 4

description: Slide 78-Embryonic breast muscle: age 26 biological replica 1 vs age 24 biological replica 4


title: Embryonic breast muscle age 26 replica 2

description: Slide 77-Embryonic breast muscle: age 22 biological replica 3 vs age 26 biological replica 2

source_name: Total RNA from breast muscle embryos day 26 labeled with Cyanine-5 (red).


title: Embryonic liver age 25 control replica 1

description: Slide 5-Embryonic liver: age 25 IOF replica 4 vs age 25 control replica 1


title: Embryonic liver age 22 control replica 3

description: Slide 4-Embryonic liver: age 25 IOF replica 2 vs age 22 control replica 3


title: Embryonic liver age 24 control replica 3

description: Slide 3-Embryonic liver: age 25 control replica 2 vs age 24 control replica 3

source_name: Total RNA from liver enbryos day 24 labeled with cyanine-5 (red)


title: Embryonic breast muscle age 22 replica 2

description: Slide 74-Embryonic breast muscle: age 28 biological replica 3 vs age 22 biological replica 2

source_name: Total RNA from breast muscle embryos day 22 labeled with Cyanine-5 (red).


title: Embryonic liver age 26 control replica 1

description: Slide 8-Embryonic liver: age 26 IOF replica 4 vs age 26 control replica 1


title: Embryonic breast muscle age 20 replica 3

description: Slide 72-Embryonic breast muscle: age 20 biological replica 3 vs age 24 biological replica 2

source_name: Total RNA from breast muscle embryos day 20 labeled with Cyanine-5 (red).


title: Embryonic liver age 25 IOF replica 1

description: Slide 2-Embryonic liver: age 24 control replica 4 vs age 25 IOF replica 1


title: Embryonic breast muscle age 26 replica 3

description: Slide 82-Embryonic breast muscle: age 20 biological replica 2 vs age 26 biological replica 3


title: Embryonic breast muscle age 20 replica 1

description: Slide 73-Embryonic breast muscle: age 20 biological replica 1 vs age 28 biological replica 4


title: Embryonic breast muscle age 26 replica 1

source_name: Total RNA from breast muscle embryos day 26 labeled with Cyanine-3 (green).


title: Embryonic liver age 22 control replica 2

description: Slide 15-Embryonic liver: age 22 control replica 2 vs age 28 IOF replica 3

source_name: Total RNA from liver enbryos day 22 labeled with cyanine-3 (green)


title: Embryonic liver age 28 control replica 4

description: Slide 14-Embryonic liver: age 28 control replica 4 vs age 22 control replica 1

source_name: Total RNA from liver enbryos day 28 labeled with cyanine-3 (green)


title: Embryonic liver age 25 IOF replica 3

description: Slide 7-Embryonic liver: age 26 IOF replica 2 vs age 25 IOF replica 3


title: Embryonic breast muscle age 24 replica 3

description: Slide 79-Embryonic breast muscle: age 24 biological replica 3 vs age 28 biological replica 2

source_name: Total RNA from breast muscle embryos day 24 labeled with Cyanine-3 (green).


title: Embryonic breast muscle age 22 replica 1

description: Slide 75-Embryonic breast muscle: age 20 biological replica 4 vs age 22 biological replica 1


title: Embryonic liver age 24 control replica 1

description: Slide 1-Embryonic liver: age 22 control replica 4 vs age 24 control replica 1


title: Embryonic breast muscle age 22 replica 4

description: Slide 85-Embryonic breast muscle: age 22 biological replica 4 vs age 24 biological replica 1

source_name: Total RNA from breast muscle embryos day 22 labeled with Cyanine-3 (green).


title: Embryonic liver age 28 control replica 2

description: Slide 13-Embryonic liver: age 28 control replica 2 vs age 26 control replica 3


title: Embryonic breast muscle age 22 replica 3

description: Slide 77-Embryonic breast muscle: age 22 biological replica 3 vs age 26 biological replica 2


title: Embryonic liver age 26 control replica 2

description: Slide 9-Embryonic liver: age 26 control replica 2 vs age 25 control replica 3

source_name: Total RNA from liver enbryos day 26 labeled with cyanine-3 (green)


title: Embryonic liver age 28 IOF replica 2

description: Slide 11-Embryonic liver: age 28 IOF replica 2 vs age 26 IOF replica 3


title: Embryonic liver age 24 control replica 2

description: Slide 16-Embryonic liver: age 24 control replica 2 vs age 28 control replica 3

source_name: Total RNA from liver enbryos day 24 labeled with cyanine-3 (green)


title: Embryonic liver age 28 IOF replica 4

description: Slide 12-Embryonic liver: age 28 IOF replica 4 vs age 28 control replica 1


title: Embryonic liver age 26 control replica 4

description: Slide 10-Embryonic liver: age 26 control replica 4 vs age 28 IOF replica 1


title: Embryonic breast muscle age 20 replica 4

source_name: Total RNA from breast muscle embryos day 20 labeled with Cyanine-3 (green).


title: Embryonic breast muscle age 26 replica 4

description: Slide 81-Embryonic breast muscle: age 26 biological replica 4 vs age 28 biological replica 1


title: Embryonic breast muscle age 28 replica 3

description: Slide 74-Embryonic breast muscle: age 28 biological replica 3 vs age 22 biological replica 2

source_name: Total RNA from breast muscle embryos day 28 labeled with Cyanine-3 (green).


title: Embryonic liver age 26 IOF replica 2


title: resistant_48hours_rep3

city: Ft. Detrick

first: katherine

last: schneider

state: MD

address: 1301 Ditto Ave

department: FDWSRU

institute: USDA

hyb_protocol: 45C, 60 rpms, 16 hours

scan_protocol: Affymetrix Gene Scanner 3000

data_processing: Only the Gma probes were used for the analysis.  After removal of the non-Gma proces in the R programming environment, the resulting data set was normalized, scaled and background subtracted using RMA.  We used the default options in the fitPLM fucntion in affyPLM: RMA convolution for background subtraction and quantile normalization.  Data for multiple spots referring to one transcript were summarized using RMA tranformation of probe level data to gene expression level data.  log2 expression values were tested for differences between Resistant and Susceptible using the moderated t statistic, and the results were filtered such that genes with a p,0.05 and and absolute fold change > 1.5 were considered significantly different.

organism: Glycine max

source_name: pooled soybean leaves inoculated with HW94-1 harvested 48 hours

label_protocol: Affymetrix one cycle labeling kit following manufacturer's instructions

growth_protocol: Glycine max (Merr.) cultivar Komata (USDA germplasm accession PI200492) was seeded, grown, and maintained in a greenhouse with supplemental lighting to achieve 16 hour days

extract_protocol: trizol/guanidium isothiocyanate extraction (Chomczynski and Sacchi, 1987), followed by lithium chloride precipitation, DNAse treatment

treatment_protocol: Urediniospores were harvested from infected soybeans and kept under liquid nitrogen.  Prior to inoculation, urediniospores were heat shocked at 40C fro 5 min and kept in a humid environment overnight.  Spores were suspended in a 0.01% (v/v) Tween20/water solution and adjusted to a concentration of 250,000 spores ml-1 with a hemacytometer.  Twenty-two day old soybeans (second trifoliate leaf stage) were treated with an atomizer with either of two isolates of P. pachyrhizi, HW94-1 or TW72-1, or water/tween solution at 2 ml per plant.  Plants were placed in a dew chamber at 20ºC for up to 24 h, and then placed in the greenhouse set at 25ºC.  Leaves were harvested from inoculated plants at 6, 12, 24, and 48 hours post inoculation and snap frozen in liquid nitrogen.  4-6 leaves were pooled for each sample

tag: Glycine max PI200492 21 days old (4-5 trifolates) grown in greenhouse in sterile soil with supplemental light 16 h days


title: Embryonic liver age 25 IOF replica 2

description: Slide 4-Embryonic liver: age 25 IOF replica 2 vs age 22 control replica 3

source_name: Total RNA from liver enbryos day 25 labeled with cyanine-3 (green)


title: Embryonic liver age 25 IOF replica 4

description: Slide 5-Embryonic liver: age 25 IOF replica 4 vs age 25 control replica 1


title: Embryonic breast muscle age 20 replica 2

description: Slide 82-Embryonic breast muscle: age 20 biological replica 2 vs age 26 biological replica 3


title: Embryonic breast muscle age 28 replica 4

description: Slide 73-Embryonic breast muscle: age 20 biological replica 1 vs age 28 biological replica 4


title: Embryonic liver age 25 control replica 4

description: Slide 6-Embryonic liver: age 25 control replica 4 vs age 26 IOF replica 1


title: susceptible_12hours_rep3

source_name: pooled soybean leaves inoculated with TW72-1 harvested 12 hours


title: resistant_24hours_rep3

source_name: pooled soybean leaves inoculated with HW94-1 harvested 24 hours


title: resistant_12hours_rep3

source_name: pooled soybean leaves inoculated with HW94-1 harvested 12hours


title: susceptible_48hours_rep3

source_name: pooled soybean leaves inoculated with TW72-1 harvested 48 hours


title: Embryonic liver age 25 control replica 2

description: Slide 3-Embryonic liver: age 25 control replica 2 vs age 24 control replica 3


title: Embryonic liver age 28 replica 1

description: Slide 81-Embryonic liver: age 26 biological replica 4 vs age 28 biological replica 1

source_name: Total RNA from liver embryos day 28 labeled with Cyanine-5 (red).

treatment_protocol: 24 eggs were sampled at each age (20, 22, 24, 26 and 28 days of incubation) to harvest the liver; tissue preserved in RNA Later solution (Ambion, Inc)


title: Embryonic liver age 28 replica 2

description: Slide 79-Embryonic liver: age 24 biological replica 3 vs age 28 biological replica 2


title: susceptible_24hours_rep3

source_name: pooled soybean leaves inoculated with TW72-1 harvested 24 hours


title: Embryonic liver age 24 control replica 4

description: Slide 2-Embryonic liver: age 24 control replica 4 vs age 25 IOF replica 1


title: Embryonic breast muscle age 24 replica 2

description: Slide 72-Embryonic breast muscle: age 20 biological replica 3 vs age 24 biological replica 2


title: susceptible_48hours_rep2


title: Embryonic liver age 22 control replica 4

description: Slide 1-Embryonic liver: age 22 control replica 4 vs age 24 control replica 1


title: susceptible_6hours_rep3

source_name: pooled soybean leaves inoculated with TW72-1 harvested 6 hours


title: resistant_6hours_rep3

source_name: pooled soybean leaves inoculated with HW94-1 harvested 6 hours


title: Embryonic liver age 24 replica 1

description: Slide 85-Embryonic liver: age 22 biological replica 4 vs age 24 biological replica 1

source_name: Total RNA from liver embryos day 24 labeled with Cyanine-5 (red).


title: susceptible_24hours_rep2


title: resistant_48hours_rep2


title: resistant_24hours_rep2


title: mock_0hours_rep3

source_name: pooled soybean leaves mock- inoculated harvested time 0


title: susceptible_12hours_rep2


title: Embryonic liver age 26 replica 2

description: Slide 77-Embryonic liver: age 22 biological replica 3 vs age 26 biological replica 2

source_name: Total RNA from liver embryos day 26 labeled with Cyanine-5 (red).


title: Embryonic liver age 24 replica 4

description: Slide 78-Embryonic liver: age 26 biological replica 1 vs age 24 biological replica 4


title: Embryonic liver age 26 IOF replica 4

description: Slide 8-Embryonic liver: age 26 IOF replica 4 vs age 26 control replica 1

source_name: Total RNA from liver enbryos day 26 labeled with cyanine-3 (green)


title: Embryonic liver age 22 replica 2

description: Slide 74-Embryonic liver: age 28 biological replica 3 vs age 22 biological replica 2

source_name: Total RNA from liver embryos day 22 labeled with Cyanine-5 (red).


title: Embryonic liver age 22 replica 1

description: Slide 75-Embryonic liver: age 20 biological replica 4 vs age 22 biological replica 1


title: Embryonic liver age 20 replica 3

description: Slide 72-Embryonic liver: age 20 biological replica 3 vs age 24 biological replica 2

source_name: Total RNA from liver embryos day 20 labeled with Cyanine-5 (red).


title: Embryonic liver age 26 replica 4

source_name: Total RNA from liver embryos day 26 labeled with Cyanine-3 (green).


title: Embryonic liver age 22 replica 4

source_name: Total RNA from liver embryos day 22 labeled with Cyanine-3 (green).


title: Embryonic liver age 24 replica 3

source_name: Total RNA from liver embryos day 24 labeled with Cyanine-3 (green).


title: Embryonic liver age 22 replica 3


title: Embryonic liver age 20 replica 2

description: Slide 82-Embryonic liver: age 20 biological replica 2 vs age 26 biological replica 3

source_name: Total RNA from liver embryos day 20 labeled with Cyanine-3 (green).


title: Embryonic liver age 26 replica 3


title: Embryonic liver age 28 replica 3

source_name: Total RNA from liver embryos day 28 labeled with Cyanine-3 (green).


title: Embryonic liver age 20 replica 4


title: Embryonic liver age 28 replica 4

description: Slide 73-Embryonic liver: age 20 biological replica 1 vs age 28 biological replica 4


title: Embryonic liver age 20 replica 1


title: Embryonic liver age 24 replica 2


title: susceptible_24hours_rep1 *failed QC*

description: A6  *failed QC*


title: susceptible_6hours_rep2


title: resistant_24hours_rep1 *failed QC*

description: A5  *failed QC*

source_name: pooled soybean leaves inoculated with HW94-1 harvested 24 hours


title: susceptible_48hours_rep1

source_name: pooled soybean leaves inoculated with TW72-1 harvested 48 hours


title: resistant_12hours_rep2

source_name: pooled soybean leaves inoculated with HW94-1 harvested 12hours


title: mock_0hours_rep2


title: Embryonic liver age 26 replica 1


title: resistant_6hours_rep2


title: susceptible_6hours_rep1


title: susceptible_12hours_rep1

source_name: pooled soybean leaves inoculated with TW72-1 harvested 12 hours


title: resistant_48hours_rep1

source_name: pooled soybean leaves inoculated with HW94-1 harvested 48 hours


title: resistant_6hours_rep1

source_name: pooled soybean leaves inoculated with HW94-1 harvested 6 hours


title: mock_0hours_rep1


title: resistant_12hours_rep1