title: Infected cells series 3, t=8 h after infection (inf_8h_rep3)

description: no additional information

organism:
Prochlorococcus marinus subsp. pastoris str. CCMP1986
Tiamatvirus PSSP7

tag: Infected cells


title: isw2 Nucleosomes Frag Biological Rep 1

status: Public on Sep 10 2007

type: genomic

city: Seattle

first: Toshio

last: Tsukiyama

state: WA

address: 1100 Fairview Ave N

country: USA

institute: FHCRC

description: Fragmented nucleosomal DNA ~50bp

hyb_protocol: Samples were hybridized according to the manufacturer's instructions.

scan_protocol: Samples were scanned according to the manufacturer's instructions.

data_processing: Data was processed using Affymetrix Tiling Array Software. Data was quantile normalized, and log2 signals from each probe were reported.

label: 7ug of each sample was labeled with biotin

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: isw2 Nucleosomes Frag Biological Rep 1

label_protocol: Samples were labeled according to the manufacturer's instructions.

growth_protocol: Yeast were grown in a shaking flask log phase (OD = 0.7), in  YPD 2% Glucose at 30º C

extract_protocol:
500ml of yeast cells were grown to mid log phase (OD = 0.7), and cross-linked with the addition of formaldehyde to a final concentration of 2% for 20 minutes and then quenched with the addition of glycine to a final concentration of 125mM for 10 minutes. Cells were digested with 3mg of Zymolase-100T (Seikagaku) in 30ml of buffer Z (50mM Tris:Cl pH 7.5, 1M sorbitol 10mM 2ME) for 30 minutes at 30ºC with constant agitation. Nuclei were pelleted and resuspended with the addition of 5ml of buffer Q (10mM Tris:Cl pH7.5, 50mM NaCl, 10mM MgCl2, 1mM CaCl2, 0.075% NP40) and nuclei were digested with the addition of ~700units of Micorococcal Nuclease (Worthington) and 100units Exonuclease III for 20 minutes at 37ºC with constant agitation. Reaction was stopped with the addition of 1ml solution S (5% SDS, 100mM EDTA). RNA and proteins were removed with sequential additions of with RNaseA and Proteinase K. Crosslinks were reversed by incubation at 65ºC for 16 hours. SDS was precipitated from the solution with the addition of 2.5ml 3M potassium acetate pH5.5 followed by a centrifugation at 4000g for 5 minutes. DNA fragments were harvested from the supernatant with use of a G500 genomic column (Qiagen) according to instructions. DNA was then resolved on a 1.7% agarose gel and the band corresponding to mononucleosomal DNA (~150bp) was excised. The gel slice was placed in a dialysis bag and DNA extracted by electroelution.
Generation of fragmented nucleosome DNA:
3µg of full length nucleosomal DNA was placed in a 50µl reaction containing 50mM Tris:Cl pH 6.8, 5mM MgCl2, 0.3µg/µl random hexamers. Reaction was incubated at 95ºC for 5 minutes then rapidly chilled on ice. 5µl of dNTP mix (1.2mM dGTP, 1.2mM dCTP, 1.2mM dATP, 0.95mM dTTP, 0.25mM dUTP) along with 50 units of Klenow Exo- (NEB) was added and the reaction allowed to proceed at 22ºC for 10 minutes and then 37ºC for 30 minutes. The reaction was then heated to 95ºC for 5 minutes and rapidly chilled on ice. A further 50 units of Klenow exo- was added and the reaction was incubated at 22ºC for 10 minutes and then 37ºC for 30 minutes. The reaction was stopped by phenol:chloroform extraction and unincorporated random hexamers were removed with a gel filtration spin column. The DNA was then fragmented with the use of the WT Terminal Labeling Kit (Affymetrix) according to instructions.

treatment_protocol: Log phase yeast cultures harvested by centrifugation

tag: S cerevisiae S288C  congenic to BY4741

tag: Genotype

value: delta_isw2 (MATa his3-1 leu2-0 met15-0 ura3-0 isw2::HisG)


title: Infected cells series 3, t=7 h after infection (inf_7h_rep3)

status: Public on Sep 07 2007

type: RNA

city: Haifa

first: Debbie

last: Lindell

address: Technion City

department: Department of Biology

country: Israel

institute: Technion - Israel Institute of Technology

description: no additional information

hyb_protocol: The cDNA was hybridized to the MD4-9313 custom Affymetrix array in aqueous hybridization solution (100 mM MES, 1 M NaCl, 20 mM EDTA, 0.01% Tween-20, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, 7.8 % DMSO and 3 nM prelabeled Affymetrix hybridization B2 oligo control probe mix) during a 16 h incubation at 45 °C in a GeneChip Hybridization Oven 320 rotating at 60 rpm. Washes and stains were carried out on a GeneChip Fluidics Station 450 (Affymetrix) following the ProkGE_WS2v3 Affymetrix protocol. Briefly, following two stringency washes the array was sequentially incubated with 10 µg/mL streptavidin (Pierce Chemical), 5 µg/mL biotinylated anti-streptavidin goat antibody (Vector Laboratories) and 0.1 mg/mL goat IgG (Sigma) and 10 µg/mL streptavidin-phycoerythrin conjugate (Mol. Probes) each for 10 min at 25 °C and given a final wash.

scan_protocol: The arrays were scanned with the GeneChip Scanner (Affymetrix) at a 2.5 µm resolution with excitation set for 570 nm.

data_processing: The probe set summaries were calculated from perfect match probe intensities in Affymetrix CEL files using robust multi-array average (RMA) analysis with quantile normalization (as implemented in the Bioconductor package affy).

label: biotin

molecule: total RNA

label_protocol: Synthesis of complementary DNA (cDNA), labeling, hybridization, staining and scanning was carried out according to Affymetrix protocols for E.coli with minor changes. Total RNA (2 µg) was denatured at 70 °C and annealed to random hexamer primers (25 ng/µl) at 25 °C for 10 min. The RNA was reverse transcribed to produce cDNA with Superscript II (25 U/µl – Invitrogen Life Technologies) and 0.5 mM dNTPs in the presence of 1 U/µl RNase Out RNase Inhibitor (Invitrogen). The mix was incubated at 25 °C for 10 min followed by 60 min incubations at 37 °C and 42 °C respectively. Superscript II was inactivated with a 10 min incubation at 70 °C. Sodium hydroxide (0.25 N) was used to remove RNA during a 30 min incubation at 65 °C, followed by neutralization with HCl. The cDNA was purified with MinElute PCR purification columns (Qiagen). Fragments of cDNA, 50-200 nt long, were produced from a 10 min incubation at 37 °C with DNase I (0.6 U per µg cDNA), followed by heat inactivation of the DNase I enzyme (10 min at 98 °C). The cDNA fragments were end-labeled with biotin using the BioArray Terminal Labeling Kit (Enzo) during a 60 min incubation at 37 °C. The reaction was stopped by freezing at –20 °C. The quality of biotin end-labeling was verified by gel-shift assays with NeutrAvidin (Pierce Chemicals) on 1% TBE agarose gels.

growth_protocol: Prochlorococcus MED4 was grown in the Pro99 seawater based medium amended with 10 mM HEPES (pH7.5) and 12 mM sodium bicarbonate at 21 °C under continuous white light at 25 µmol photon·m-1·s-1

extract_protocol: Total RNA was extracted using Ambion’s mirVana RNA isolation kit according to manufacturer’s instructions, after resuspending the pellet in 600 µl lysis/binding buffer from the kit. DNA was removed by DNase I digestion using the Turbo DNA-free kit (Ambion) according to manufacturer’s instructions. Eight µg of the nucleic acid extract was digested with 6 U of Turbo DNase during a 60 min incubation at 37 °C followed by DNase I inactivation with inactivation slurry. The RNA was purified and concentrated by sodium acetate/ethanol precipitation. DNA removal was verified by gel electrophoresis.

treatment_protocol: Prior to phage or spent medium addition, cells were concentrated to 108 cells·ml-1 by centrifugation (10,000 Xg for 10 min at 20 °C). The cultures were split into two subcultures. Just prior to t=0 h, phage or spent medium were added to the appropriate subcultures. Samples at different time points after treatment addition were collected by centrifugation (12,400 Xg for 15 min at 20 °C), resuspended in storage buffer (200 mM sucrose, 10 mM sodium acetate pH5.2, 5 mM EDTA), snap frozen in liquid nitrogen and stored at -80 °C. Prior to RNA extraction the samples were thawed on ice and the storage buffer was removed after spinning the cells for 2 min at 20,000 Xg at 20 °C.


title: Control cells series 4, t=0 h after infection (ctrl_0h_rep1)

description: no additional information

organism: Prochlorococcus marinus subsp. pastoris str. CCMP1986

tag: Uninfected control cells


title: Infected cells series 3, t=5 h after infection (inf_5h_rep3)

description: no additional information


title: Infected cells series 3, t=6 h after infection (inf_6h_rep3)

description: no additional information


title: KR_Isw2_ChIP_biological_rep_2

description: KR Isw2 ChIP sample rep 2

hyb_protocol: according to manufacturers instructions

scan_protocol: according to manufacturers instructions

label_protocol: Samples were amplified and labeled according to manufacturers instructions

growth_protocol: Yeast cells grown in YPD 2% glucose to OD = 0.7

extract_protocol: Chip Assay: 500ml of yeast cells were grown to mid log phase (OD = 0.7), and cross-linked with the addition of formaldehyde to a final concentration of 1% for 20 minutes and then quenched with the addition of glycine to a final concentration of 125mM for 10 minutes.Cells were pelleted and washed in H20 then were digested with 3mg of Zymolase-100T (Seikagaku) in 30ml of buffer Z (50mM Tris:Cl pH 7.5, 1M sorbitol 10mM 2ME, 1mM PMSF, 2uM pepstatin, 0.6uM leupeptin, 2mM Benzamidine, 2ug/ml chymostatin-A) for 30 minutes at 30ºC with constant agitation. Nuclei were pelleted and resuspended with the addition of 5ml of buffer Q (10mM Tris:Cl pH7.5, 50mM NaCl, 10mM MgCl2, 1mM CaCl2, 0.075% NP40, 1mM PMSF, 2uM pepstatin, 0.6uM leupeptin, 2mM Benzamidine, 2ug/ml chymostatin-A) and nuclei were digested with the addition of ~200units of Micorococcal Nuclease (Worthington) for 20 minutes at 37ºC with constant agitation. Sample was flash frozen and thawed and 880ul of Buffer L was added (500mM Hepes KOH, 1.4M Nacl, 10mM EDTA, 10% Triton, 1% sodium Deoxycholate, 1mM PMSF, 2uM pepstatin, 0.6uM leupeptin, 2mM Benzamidine, 2ug/ml chymostatin-A). 1ml of the extract was saved and used as “input” whereas 4ml of this extract was then used in ChIP assay. As described in McConnell AD, Gelbart ME, Tsukiyama T. Mol Cell Biol. 2004 Apr;24(7):2605-13.

tag: Isw2-K215R 3x Flag (MATa his3-1 leu2-0 met15-0 ura3-0 isw2::ISW2-K215R-3xFlag-KanMX)


title: WT Nucleosomes Frag Biological Rep 1

description: Fragmented nucleosomal ~50bp

scan_protocol: Samples were scaned according to the manufacturer's instructions.

source_name: WT Nucleosomes Frag Biological Rep 1

tag: Genotypes

value: WT (MATa his3-1 leu2-0 met15-0 ura3-0)


title: Infected cells series 3, t=3 h after infection (inf_3h_rep3)

description: no additional information


title: Infected cells series 3, t=2 h after infection (inf_2h_rep3)

description: no additional information


title: Infected cells series 3, t=1 h after infection (inf_1h_rep3)

description: no additional information


title: WT Nucleosomes Frag Biological Rep 2

description: Fragmented nucleosomal DNA ~50bp

source_name: WT Nucleosomes Frag Biological Rep 2


title: Infected cells series 3, t=4 h after infection (inf_4h_rep3)

description: no additional information


title: Infected cells series 3, t=0 h after infection (inf_0h_rep3)

description: no additional information


title: Infected cells series 2, t=8 h after infection (inf_8h_rep2)

description: no additional information


title: Infected cells series 2, t=5 h after infection (inf_5h_rep2)

description: no additional information


title: Infected cells series 2, t=4 h after infection (inf_4h_rep2)

description: no additional information


title: Infected cells series 2, t=6 h after infection (inf_6h_rep2)

description: no additional information


title: Infected cells series 2, t=3 h after infection (inf_3h_rep2)

description: no additional information


title: Infected cells series 2, t=0 h after infection (inf_0h_rep2)

description: no additional information


title: Infected cells series 2, t=2 h after infection (inf_2h_rep2)

description: no additional information


title: Infected cells series 1, t=7 h after infection (inf_7h_rep1)

description: no additional information


title: Patient 6_TB3354DB1000

city: Philadelphia

first: Jayanti

last: Jagannathan

state: PA

address: 34th & Civic center blvd

department: Oncology

institute: Childrens Hospital of Philadelphia

description: Blood

hyb_protocol: 48-72 h at 37 deg C on a slowly rotating platform. Slide washing was done using published protocols (Hodgson et al. 2001)

scan_protocol: Affymetrix 428 microarray scanner and analyzed with Genepix software (Axon)

data_processing: Normalized by global print-tip adjustment of the median dye ratio(Cy3/Cy5), quality filtered, replicate spots and dye swaps merged

organism: Homo sapiens

source_name: Blood

label_protocol: Random primer labeling kit (Invitrogen)

extract_protocol: Qiagen DNA extraction standard protocol

tag: Age

value: 29mos, INSS Stage:4, MYCN:Not Amplified


title: Infected cells series 2, t=1 h after infection (inf_1h_rep2)

description: no additional information


title: Infected cells series 1, t=6 h after infection (inf_6h_rep1)

description: no additional information


title: Const Del1_TB1304DB3000

description: Blood

value: 3mos, INSS Stage:4, MYCN:Not Amplified


title: Patient 5_TB3957DB1000

description: Blood

value: 33mos, INSS Stage:4, MYCN:Not Amplified


title: Infected cells series 1, t=5 h after infection (inf_5h_rep1)

description: no additional information


title: Patient 10_TB3970DB1000

description: Blood

value: 3wks, INSS Stage:3, MYCN:Not Amplified


title: Control cells series 6, t=0 h after infection (ctrl_0h_rep3)

description: no additional information


title: WT_Isw2_ChIP_biological_rep_1

description: Isw2 ChIP sample rep 1

tag: Strains

value: S cerevisiae, BY 4741

tag: Isw2 3x Flag (MATa his3-1 leu2-0 met15-0 ura3-0 isw2::ISW2-3xFlag-KanMX)


title: mixed stage non-polyadenylated RNA (fishout of polyadenylated RNA), three replicates

type: other

city: Buffalo

first: Tao

last: Liu

state: NY

address: Elm and Carlton St

department: Biostatistics and Bioinformatics

institute: Roswell Park Comprehensive Cancer Institute

description: non-polyadenylated RNA (fishout of polyadenylated RNA), three biological replicates

hyb_protocol: Following the protocol of GeneChip® Whole Transcript (WT) Double-Stranded Target Assay Manual, 2006, Affymetrix.

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

data_processing: The data were analyzed with Affymetrix Tiling analysis software (version 1.0.15) .

molecule: other

organism: Caenorhabditis elegans

source_name: non-polyadenylated RNA (fishout of polyadenylated RNA) extracted from mix-stage N2 worms total RNA

label_protocol: Biotinylated dsDNA were prepared according to the standard Affymetrix protocol (GeneChip® Whole Transcript (WT) Double-Stranded Target Assay Manual, 2006, Affymetrix).

growth_protocol: mixed stage wild type N2 strain worms cultivated at 20C

extract_protocol: RNA was extracted according to the Trizol (Invitrogen) protocol.

treatment_protocol: no special treament

tag: N2 worms, polyA- RNA, Stage

value: mix


title: Const Del 3_TB3608DB1000

description: Blood

value: 8mos, INSS Stage:4, MYCN:Not Amplified


title: mixed stage small non-polyadenylated RNA, two replicates

description: small non-polyadenylated RNA, two biological replicates

source_name: small non-polyadenylated RNA extracted from mix-stage N2 worms total RNA

tag: N2 worms, small polyA- RNA, Stage


title: Patient 7_TB3648DB1000

description: Blood

value: 51mos, INSS Stage:4, MYCN:Not known


title: Infected cells series 1, t=4 h after infection (inf_4h_rep1)

description: no additional information


title: Patient 9_TB3651DB1000

description: Blood

value: 18mos, INSS Stage:3, MYCN:Not Amplified


title: Infected cells series 1, t=3 h after infection (inf_3h_rep1)

description: no additional information


title: Infected cells series 1, t=2 h after infection (inf_2h_rep1)

description: no additional information


title: Infected cells series 1, t=8 h after infection (inf_8h_rep1)

description: no additional information


title: mixed stage polyadenylated RNA, two replicates

description: polyadenylated RNA, two biological replicates

molecule: polyA RNA

source_name: polyadenylated RNA extracted from mix-stage N2 worms total RNA

tag: N2 worms, polyA+ RNA, Stage


title: Infected cells series 2, t=7 h after infection (inf_7h_rep2)

description: no additional information


title: Infected cells series 1, t=1 h after infection (inf_1h_rep1)

description: no additional information


title: Infected cells series 1, t=0 h after infection (inf_0h_rep1)

description: no additional information


title: Patient 8_TB3956DB1000

description: Blood

value: 69mos, INSS Stage:4, MYCN:Not Amplified


title: Const Del 2_TB3530DB1000

description: Blood


title: LHP1-Dam_2

city: Los Angeles

first: Steve

middle: E

last: Jacobsen

state: CA

address: 621 Charles E. Young Dr. South

department: Molecular Cell and Developmental Biology

institute: University of California, Los Angeles

description: Enriched for DNA bound by LHP1

hyb_protocol: Whole Genome Tiling Array  was hybridized for 16 hrs, washed and stained with a streptavidin-phycoerythrin conjugate on the Affymetrix Fluidics Station 450 according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned on Affymetrix scanner 7G

data_processing: hybridization signals were quantile-normalized

organism: Arabidopsis thaliana

source_name: Rosette leaves

label_protocol: The samples was 3'-end-labelled with dd-UTP (Roche) by the terminal transferase (TdT, Roche) reaction for 1.5 h at 37 degrees C.

growth_protocol: Plants were grown on soil under 16 h light

extract_protocol: sample was prepared by adenine methylation-specific PCR

treatment_protocol: Untreated

tag: Enriched for DNA bound by LHP1


title: Patient 4_TB3107DB1000

description: Blood


title: MCF7

status: Public on Sep 06 2007

city: San Francisco

first: Antoine

last: Snijders

address: 2340 Sutter Street

department: Cancer Research Institute

institute: University of California San Francisco

description: MMR proficient cell line

hyb_protocol: We combined and precipitated 50 ml Cy3 labeled test DNA, 50 ml Cy5 labeled reference DNA and 100 mg human Cot-1 DNA by adding 0.1 volumes of 3 M sodium acetate (pH 5.2) and 2 volumes of ice-cold ethanol. We collected the precipitate by centrifugation and dissolved the pellet in a final hybridization mixture containing 50% formamide, 2xSSC and 4% SDS. We denatured the hybridization mixture at 75°C for 10-15 min and then incubated the samples at 37°C for 1 hour to block repetitive DNA sequences. We applied a ring of rubber cement closely around the array to form a well, into which we added 50 ml of a pre-incubation solution containing 250 mg salmon sperm DNA, 50% formamide, 2xSSC and 4% SDS.  After a 30 min incubation at room temperature, we removed ~30 ml of the pre-incubation solution and added the denatured and re-annealed hybridization mixture.  We placed a silicone gasket around each hybridization area, placed a microscope slide on top of the gasket, which was thick enough to prevent the microscope slide from contacting the hybridization solution and clamped the whole unit together using binder clips to create an air tight environment.  We carried out the hybridization to the arrays for ~48 hrs on a slowly rocking table at 37°C.  After disassembling the hybridization chamber, we rinsed off the excess hybridization fluid with PN buffer (PN: 0.1 M sodium phosphate, 0.1% nonidet P40, pH 8), then washed the arrays once in a solution containing 50% formamide in 2xSSC for 15 min. at 45°C and finally in PN buffer at room temperature for 15 min.  Subsequently, we removed the ring of rubber cement, drained excess liquid from the arrays, mounted them in a solution containing 90% glycerol, 10% PBS and 1 mM DAPI, and sealed them with a cover slip.

scan_protocol: We acquired 16 bit 1024x1024 pixel DAPI, Cy3 and Cy5 images using a custom built CCD camera system We used “UCSF SPOT” software to automatically segment the spots based on the DAPI images, perform local background correction and to calculate various measurement parameters, including log2ratios of the total integrated Cy3 and Cy5 intensities for each spot.  We used a second custom program SPROC to associate clone identities and a mapping information file with each spot so that the data could be plotted relative to the position of the BACs on the August, 2001 freeze of the draft human genome sequence (http://genome.ucsc.edu).

data_processing: SPROC also implements a filtering procedure to reject data based on a number of criteria, including low reference/DAPI signal intensity and low correlation of the Cy3 and Cy5 intensities with a spot.  The SPROC output consists of averaged ratios of the triplicate spots for each clone, standard deviations of the triplicates and plotting position for each clone on the array, as well as other clone information stored in the database, such as STS content.  We edited the data files to remove ratios on clones for which only one of the triplicates remained after SPROC analysis and/or the standard deviation of the log2ratios of the triplicates was > 0.2.

source_name: Genomic DNA from MMR proficient MCF7 cell line labeled with Cyanine-3

label_protocol: We labeled genomic DNA by random priming in a 50 ml reaction by combining 300 ng genomic DNA, 1x random primers solution (BioPrime DNA Labeling System, Gibco BRL), 1x dNTP solution (0.2 mM each of dATP, dTTP, dGTP, 0.05 mM dCTP, 1 mM Tris base (pH 7.6), 0.1 mM EDTA), 40 mM Cy3 or Cy5-dCTP (Amersham) and 40 U Klenow fragment (BioPrime DNA Labeling System, Gibco BRL).  We incubated the DNA and the random primers in a volume of 42 ml at 100°C for 10-15 min, placed the reaction on ice and added the dNTP solution, labeled nucleotides and Klenow fragment. We incubated the random priming reaction overnight at 37°C. We removed unincorporated nucleotides using a Sephadex spin-column.

extract_protocol: We incubated cells from a T75 flask overnight at 55°C in a 3 ml solution containing 0.01 M Tris, pH 7.5, 0.001 M EDTA, pH 8, 0.5% SDS and 0.1 mg/ml proteinase K. We precipitated the DNA with ethanol, recovered it by spooling and then dissolved it in ~300 ml H2O.

tag: cell line DNA

source_name: Genomic DNA isolated from blood

tag: genomic DNA from blood


title: LHP1-Dam_1

description: Enriched for DNA bound by LHP1


title: Dam_3

description: Enriched for DNA bound non-specifically by Dam


title: Day 10 T-dependent GC B cells in non-carrier-primed mice (pooled from 6 mice) 1

status: Public on Sep 05 2007

city: Canberra

first: Diego

middle: G

last: Silva

state: ACT

address: Mills Road

department: Division of Immunology and Genetics

country: Australia

institute: John Curtin School of Medical Research

description: Purification: FACS sort: GL7+ B220+

hyb_protocol: as per Affymetrix standard protocol

scan_protocol: as per Affymetrix standard protocol

data_processing: MAS 4

organism: Mus musculus

source_name: T dependent GC B cells

label_protocol: as per Affymetrix standard protocol

growth_protocol: Isolated from immunised and non-immunised mice

extract_protocol: RNAzol RNA extraction

treatment_protocol:
Immunization: Immunised with 50ug alum-precipitated NP-chicken gamma-globulin plus 1x10^9 heat-killed B.pertussis i.p.
Immunisation with T dependent and T independent antigens as described next to each sample

tag: QMxB6 F1 mice


title: LHP1-Dam_3

description: Enriched for DNA bound by LHP1


title: WT_brain_pMCAO_3h

city: Athens

first: Era

last: Taoufik

state: Attiki

address: 127 Vas. Sofias Avenue

department: Molecular Genetics

country: Greece

institute: Hellenic Pasteur Institute

description:
Sample RNA was extracted from the ipsilateral brain hemisphere of a wild-type mouse 3 hours following permanent occlusion of the left middle cerebral artery.
The data table represents the averaged results from duplicate hybridizations.

hyb_protocol: Labeled cDNA probe was hybridized to the Atlas mouse array membrane (PT3558-3) that contains 588 mouse cDNA fragments from known genes in duplicate, according to the BD Clontech protocol (PT3140-1).

scan_protocol: Membranes were exposed overnight on a Storm PhosphorImager  low radiation P33 Screen (Molecular Dynamics), scanned using the Molecular Dynamics Storm Scanner 600, and hybridization patterns were quantified using Image Quant 5.2.

data_processing: The signal for any given gene (shown in the VALUE column) was calculated as the average of the signals from the two duplicate DNA spots and was normalized to the average expression of the entire array (global normalization) to allow comparisons of multiple cDNA array images.

source_name: Brain, 3 hours after permanent ischemia

label_protocol: 5 micrograms of DNase-treated (Promega, UK) RNA sample was reverse transcribed to [α-33P]dATP-labeled cDNA according to the BD Clontech Atlas mouse cDNA array instructions (PT3140-1).

extract_protocol: Total RNA was extracted from the ipsilateral hemisphere of WT and TNFRIKO mice with TRIzol (InVitrogen, Paisley, UK) according to the manufacturer’s instructions. RNA samples chosen for hybridisation were DNase-treated (Promega, UK).

treatment_protocol: Permanent ischemia. All experiments were performed on mice under chloral hydrate anesthesia (500 mg/Kg). Surgical protocols were approved by the local ethic committee and conformed to national legislation. Focal ischemia was induced by permanent occlusion of the left middle cerebral artery (pMCAO) by electrocoagulation. During ischemia, physiological parameters remained in the normal range (body temperature (°C): 37 ± 0.3; PaCO2 (mm Hg): 40.9 ± 4.2; PaO2 (mm Hg); 131.73 ± 3.97; pH: 7.08 ± 0.08).

tag: C57BL/6, male


title: TNFRIKO_brain_pMCAO_6h

description:
Sample RNA was extracted from the ipsilateral brain hemisphere of TNFRI knock-out mouse 6 hours following permanent occlusion of the left middle cerebral artery.
The data table represents the averaged results from duplicate hybridizations.

source_name: brain, 6h after permanent ischemia


title: Dam_2

tag: Enriched for DNA bound non-specifically by Dam


title: Resting B cells (pooled from 9 mice) 2

description: Purification: FACS sort: GL7- B220+

source_name: resting B cells

treatment_protocol:
Immunization: Unimmunised
Immunisation with T dependent and T independent antigens as described next to each sample


title: Day 10 T-dependent GC B cells in non-carrier-primed mice (pooled from 6 mice) 2

description: Purification: FACS sort: GL7+ B220+


title: WT_brain_pMCAO_6h

description:
Sample RNA was extracted from the ipsilateral brain hemisphere of a wild-type mouse 6 hours following permanent occlusion of the left middle cerebral artery.
The data table represents the averaged results from duplicate hybridizations.

source_name: Brain, 6 hours after permanent ischemia


title: Day 4 T-independent GC B cells (pooled from 4 mice) 1

description: Purification: FACS sort: GL7+ B220+

source_name: T independent GC B cells

treatment_protocol:
Immunization: Immunised with 30ug NP-Ficoll i.p.
Immunisation with T dependent and T independent antigens as described next to each sample


title: Day 4 T-dependent GC B cells in carrier primed mice (pooled from 6 mice) 1

description: Purification: FACS sort: GL7+ B220+

treatment_protocol:
Immunization: Carrier primed with 50ug alum-precipitated chicken gamma-globulin plus 1x10^9 heat-killed B.pertussis i.p. Challengend 5 weeks later with 50ug soluble NP-CGG i.p.
Immunisation with T dependent and T independent antigens as described next to each sample


title: Day 4 T-dependent GC B cells in carrier primed mice (pooled from 9 mice) 2

description: Purification: FACS sort: GL7+ B220+


title: TNFRIKO_brain_pMCAO_3h

description:
Sample RNA was extracted from the ipsilateral brain hemisphere of TNFRI knock-out mouse 3 hours following permanent occlusion of the left middle cerebral artery.
The data table represents the averaged results from duplicate hybridizations.

source_name: TNFRIKO brain, 3h after permanent ischemia


title: HRD_overexpression_rep2

city: Blacksburg

first: Andy

last: Pereira

state: VA

address: Washington Street MC0477

department: Virginia Bioinformatics Institute

institute: Virginia Tech

description: Mutant was created using an activation tag insertion adjacent to the At2g36450 gene, an AP2/ERF-like transcription factor, which is overexpressed in the hrd-D mutant. This gain-of-function mutant hardy (hrd-D; 'D' denotes the dominant effect) was identified with the remarkable feature of having roots that were difficult to pull out from the soil, and dark green leaves that were smaller and thicker than normal WT plants.

hyb_protocol: After labeling and purification, the targets were mixed to 80 microl hybridization solution containing 2xSSC, 6%Liquid Blocking Reagent (Amersham Biosciences), and 0.08% SDS. After heating to 95 °C for 2 microin and then cooled on ice, the mixture was applied to the gap between the slides and coverslip (LifterSlip, Erie Scientific). Slides were incubated in a hybridization chamber for 9 h at 56 °C in an oven. Slides were washed at RT for 5 microin in solutions of 2×SSC with 0.5% SDS, 0.5×SSC, and 0.05×SSC sequentially and then spin dried for 10 min at 1000 rpm.

scan_protocol: Hybridized slides were scanned with the ScanArray Express HT scanner (Perkin Elmer), which generates Tiff images of both the Cy3 and Cy5 channels. ScanArray PMT voltage was set from 42 to 50 V depending upon the first sign of a saturated signal. The images were scanned and quantitated using ScanArray Express (PerkinElmer Life and Analytical Sciences, Inc., Boston, MA USA).

data_processing: Global lowess normalization of median intensities per microarray, background correction, filtering of low intensity and saturated spots marked by quantitation program, followed by total intensity normalization, per-block-lowess, standard-deviation regularization, and low-intensity filtering.

source_name: wild-type Arabidopsis thaliana ecotype Wassiliewskija (Ws), rosette leaf

label_protocol: RNA amplification was performed using Amino Allyl MessageAmp Kit (Ambion, Austin, TX, USA). Briefly, first strand cDNA synthesis was carried out by reverse transcription using 3 microg Total RNA and 1 ml T7 Oligo(dT) primer. Full length dsDNA was synthesized with the reaction containing 1× second strand buffer, 4 microl dNTP mix, 2 microl DNA polymerase, 1 microl RNase H, followed by incubation for 2 h at 16 °C. The cDNA was purified by applying to an equilibrated filter cartridge. The purified cDNA was concentrated and the volume adjusted to 14 microl. The anti-sense RNA amplification by T7 in vitro transcription was achieved in a solution containing 12 microl of ATP, CTP, GTP Mix (25 microM), 3 ml of aaUTP Solution (50mM), 3 ml of UTP Solution (50mM), 4 microl of 10 × reaction buffer, 4 microl of T7 enzyme mix at 37 °C for 8 h. Then the amplified aRNA was purified by applying to an equilibrated filter cartridge. The aRNA samples were coupled to mono-reactive NHS esters of Cy3 (Amersham Biosciences) for 2 hrs, used for dye quenching and purification and then mixed with hybridization solution.

extract_protocol: Total RNA was isolated using TRIZOL reagent (Life Technologies, Inc.) using two-four rosette leaves of Arabidopsis according to the manufacturer's instruction and purified using RNeasy Minelute Kit (Qiagen, Carlsbad, CA, USA).

tag: Strain

value: wild-type

tag: Tissue

value: rosette leaves 21 days

source_name: hardy-D mutant Arabidopsis thaliana ecotype Wassiliewskija (Ws), rosette leaf

label_protocol: RNA amplification was performed using Amino Allyl MessageAmp Kit (Ambion, Austin, TX, USA). Briefly, first strand cDNA synthesis was carried out by reverse transcription using 3 microg Total RNA and 1 ml T7 Oligo(dT) primer. Full length dsDNA was synthesized with the reaction containing 1× second strand buffer, 4 microl dNTP mix, 2 microl DNA polymerase, 1 microl RNase H, followed by incubation for 2 h at 16 °C. The cDNA was purified by applying to an equilibrated filter cartridge. The purified cDNA was concentrated and the volume adjusted to 14 microl. The anti-sense RNA amplification by T7 in vitro transcription was achieved in a solution containing 12 microl of ATP, CTP, GTP Mix (25 microM), 3 ml of aaUTP Solution (50mM), 3 ml of UTP Solution (50mM), 4 microl of 10 × reaction buffer, 4 microl of T7 enzyme mix at 37 °C for 8 h. Then the amplified aRNA was purified by applying to an equilibrated filter cartridge. The aRNA samples were coupled to mono-reactive NHS esters of Cy5 (Amersham Biosciences) for 2 hrs, used for dye quenching and purification and then mixed with hybridization solution.

value: mutant hrd-D (dominant activation tagged)


title: LHP1-Dam_4

description: Enriched for DNA bound by LHP1


title: DvH_60min._pH10__pH_repId354

status: Public on Sep 01 2007

type: mixed

city: Berkeley

first: Adam

middle: P.

last: Arkin

address: 1 Cyclotron Road

department: Physical Biosciences Division

institute: Virtual Institute for Microbial Stress and Survival

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with pH. This sample was treated with pH10  pH.  Treatment time point = 60 min.

hyb_protocol: He, Z., Wu, L., Li, X., Fields, M., and Zhou, J. 2005.  Empirical Establishment of Oligonucleotide Probe Design Criteria. Appl. Environ. Microbiol. 71:3753-3760.

scan_protocol: ImaGene software

data_processing: See Methods in: S. R. Chhabra, Q. He, K. H. Huang, S. P. Gaucher, E. J. Alm, Z. He, M. Z. Hadi, T. C. Hazen, J. D. Wall, J. Zhou, A.  . Arkin, and A. K. Singh, Global Analysis of Heat Shock Response in Desulfovibrio vulgaris Hildenborough, J Bacteriol. 2006 March; 188(5): 1817-1828. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16484192

organism: Nitratidesulfovibrio vulgaris str. Hildenborough

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 60min. pH10  pH

growth_protocol: 2L bottles containing 1.8L of  defined PIPES buffered medium LS4D (13, 27), amended with 60mM lactate and 50mM sulfate were inoculated with exponentially grown cultures (1:10) to generate three biological duplicate pairs of culture for experimentation.  Each pair consisted of a control and a test culture. The head space of the vessels was 5% H2, 5% CO2, and 90% N2. At the late exponential phase (ca. 0.4 OD600)   pH stress was applied to the test culture of each pair by the addition of 35 ml 2M KOH with vigorous stirring resulting in pH 10.0.  The control of each pair was treated by the addition of 35ml sterile anoxic distilled water.  Samples, 300ml of each, were taken for the gene expression analysis from each bottle at 30, 60, 120, and 240 min after the addition of stressor.  The 0 minute samples were taken prior to stressor addition.  Sample biomass was immediately chilled to 4°C during collection by pumping sample out of the vessel with a peristaltic pump through a 7 m long stainless steel tube immersed in an ice bath. Harvested biomass was centrifuged at 11,000  g for 10 min at 4°C.  Cell pellets were washed in 50ml anoxic 10mM phosphate buffered saline and centrifuged as above.  Cell pellets were immediately frozen in liquid N2 and stored at -80°C until RNA isolation.

treatment_protocol: 60min. pH10  pH.

tag: str. Hildenborough

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, genomic DNA.


title: HRD_overexpression_rep1

value: Arabidopsis thaliana ecotype Wassiliewskija (Ws)


title: DvH_30min._pH10__pH_repId353

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with pH. This sample was treated with pH10  pH.  Treatment time point = 30 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 30min. pH10  pH

label_protocol: He, Z., Wu, L., Li, X., Fields, M., and Zhou, J.  2005. Empirical Establishment of Oligonucleotide Probe Design Criteria. Appl. Environ. Microbiol. 71:3753-3760.

treatment_protocol: 30min. pH10  pH.


title: DvH_240min._pH10__pH_repId356

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with pH. This sample was treated with pH10  pH.  Treatment time point = 240 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 240min. pH10  pH

extract_protocol: He, Z., Wu, L., Li, X., Fields, M., and Zhou, J.  2005. Empirical Establishment of Oligonucleotide Probe Design Criteria. Appl. Environ. Microbiol. 71:3753-3760.

treatment_protocol: 240min. pH10  pH.


title: Leaf_salt_day17_rep2

city: Nashville

first: Suping

last: Zhou

state: TN

address: 3500 John A Merritt Blvd

department: IAGER

institute: Tennessee State University

description: no other description

hyb_protocol: A 70 μl of the probe preparation was loaded onto each slide. Hybridization was conducted at 43 oC dark for 16 h. After washes following the protocols at the microarray supplier’s website (http://bti.cornell.edu/CGEP).

scan_protocol: the microarrays were scanned using Genepix 4000B scanner and acquisition software according to the manufacturer's instructions (Molecular Probes).

data_processing: A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.

organism: Solanum lycopersicum

source_name: Leaf treated with salt, day 17, rep2

label_protocol: To prepare the fluorescent probes, total RNA was amplified using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion, Texas) following the manufacture’s instructions. In brief, the first strand cDNA was synthesized from 1000 ng of total RNA with ArrayScript and then subsequently converted into ddcDNA. The amino allyl aRNA was obtained by in vitro transcription and amino allyl UTP nucleotide. 5 ug of this aRNA   was used to couple with the fluorescent cyanine Dye Cy3-dCTP and Cy5-dCTP (Amersham Biosciences). Generated aRNA targets were purified using the QIAquick PCR purification kit (Qiagen, Valencia, CA). The purified aRNA targets were dried to completion and then differentially coupled to ester-linked Cy3 (controls) or Cy5 (LiCl-treated) dye (Amersham, Piscataway, NJ). After quenching of unbound dye with 4M Hydroxylamine, Cy3- and Cy5-labeled cDNA target pairs were combined and cleaned up over QIAquick columns (Qiagen, Valencia, CA). 100 pmol of fluorescent aRNA (based on Cy3-reading on the Nanodrop spectrometer) probes were  fragmented with the fragmentation buffer (Ambion )  at 70 oC for 15min, and denatured in a final concentration of 0.075% SDS, 2 X SSC, 5.6% Liquid Block (GE Healthcare ) at 65 oC for 5 min.

extract_protocol: Total RNA extraction was using the RNA pure kit (Genhunter, USA). To remove genomic DNA, the total RNA was treated with RNase-free DNase (RQ1; Promega, USA) for 15 min at 37°C, extracted with phenol: chloroform (1:1) and chloroform, precipitated with ethanol, and finally re-suspended in diethyl pyrocarbonate-treated water. Quality and quantity of the RNA extraction was monitored on 2.0% denatured agarose gels and a ND-1000 nanodrop spectrometer (Nanodrop Technologies, USA). The DNA free RNA samples were used for further analysis.

treatment_protocol: The seeds were surface sterilized in 50% bleach for 10 min. After three washes in sterile water, 10 seeds were inoculated into 250 ml of a medium containing Gamborg basic minerals, MS vitamins and 10g/L sucrose, pH 5.0. The salt treatment was supplemented with NaCl at 0.4% (75mM). The culture was incubated at 25oC, 125rpm shaking for 17 d when the two cotyledons were open, but, no true leaves emerged.  The root and leaf (cotyledons with the shoot tips) were collected separately. Each sample represents a pool of same tissue 20 seedlings grown in two flasks.

tag: Component

value: Leaf

tag: Treatment

value: 75mM Salt

tag: Time

source_name: Leaf with no salt treatment day 17, rep2

value: 0 Salt


title: Resting B cells (pooled from 6 mice) 1

description: Purification: FACS sort: GL7- B220+


title: Leaf_salt_day17_rep1

description: no other description

source_name: Leaf treated with salt, day 17

source_name: Leaf with no salt treatment day 17


title: TTHB211 deletion mutant strain_8h_1

status: Public on Sep 04 2007

city: Hyogo

first: Akeo

last: Shinkai

address: 1-1-1, Kouto, Sayo

department: SPring-8 Center

country: Japan

institute: RIKEN Harima Institute

description: no additional information

hyb_protocol: 3’-terminal-labeled cDNA (2 micro g) was hybridized to a TTHB8401 GeneChip (Affymetrix, Santa Clara, CA).  The array was incubated for 16 h at 50oC in a solution comprising 180 mM MES, pH 6.6, 40 mM EDTA, 0.02% Tween 20, 7% dimethyl sulfoxide, 1 mg of herring sperm DNA (Promega), 0.5 mg of bovine serum albumin (BSA), the recommended amount of Eukaryotic Hybridization Control (Affymetrix), and Control Oligo B2 for the alignment signal (Affymetrix), and then the array was automatically washed and stained with streptavidin-phycoerythrin (Invitrogen) by using a GeneChip Fluidics Station, 450XP (Affymetrix).

scan_protocol: The Probe Array was scanned with a GeneArray Scanner (Affymetrix).

data_processing: The image data was scaled to the target intensity by one-step Tukey’s biweight algorithm using GeneChip Operating software, version 1.0 (Affymetrix, Santa Clara, CA).

organism: Thermus thermophilus HB8

source_name: TTHB211 deletion mutant grown on a rich (TT) medium for 8 h

label_protocol: cDNA was synthesized with SuperScript II (Invitrogen) reverse transcriptase in the presence of RNase inhibitor SUPERase (Ambion) and 6 base random primers (Invitrogen).  The cDNA was fragmented with 35 units of DNase I (GE Healthcare Bio-Science Corp.) at 37oC for 10 min, and after inactivation at 98oC for 10 min, the cDNA fragments were labeled with biotin-dideoxy UTP, using terminal transferase according to the manufacturer’s instructions (ENZO Biochem. Inc., Farmingdale, NY).

growth_protocol: TTHB211 deletion mutant strain was pre-cultured at 70oC for 16 h in 3 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH.  The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70oC for 8 h (OD600nm = ~ 4.5).

extract_protocol: Cells were collected from 15 ml of the culture medium, and then crude RNA was extracted by the addition of 1.4 ml of a solution comprising 5 mM Tris-HCl, pH 7.5, 5 mM EDTA, 0.25% SDS, and 50% of water-saturated phenol.  This mixture was incubated at 65oC for 5 min, chilled on ice for 5 min, and then centrifuged at 4oC.  Then, 750 micro l of TRIZOL LS (Invitrogen, Carlsbad, CA) was added to 0.2 ml of the aqueous phase.  After incubation for 5 min at room temperature, the RNA was extracted with 0.2 ml of chloroform.  The extraction was repeated with 0.5 ml of chloroform, and the aqueous phase was precipitated with isopropanol.  The pellet was dissolved in 0.2 ml of nuclease-free water, precipitated with ethanol, and then resuspended in 40 micro l of water.  The RNA was treated with DNase I (Ambion, Austin, TX) at 37oC for 20 min in a 25-micro l reaction mixture.  The reaction was terminated by the addition of 1 micro l of 0.5 M EDTA, followed by incubation at 70oC for 5 min.  Thereafter, the RNA was precipitated with ethanol in the presence of 1% glycogen and 1 M NH4OAc.

tag: TTHB211 deletion mutant strain grown on TT medium for 8 h


title: TTHB211 deletion mutant strain_8h_2

description: no additional information

source_name: TTHB211 deletion mutant strain grown on a rich (TT) medium for 8 h


title: TTHB211 deletion mutant strain_8h_3

description: no additional information


title: DvH_120min._pH10__pH_repId355

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with pH. This sample was treated with pH10  pH.  Treatment time point = 120 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 120min. pH10  pH

treatment_protocol: 120min. pH10  pH.


title: Dam_1

source_name: Rosette leaves


title: isw2 Nucleosomes Frag Biological Rep 2

description: Fragmented nucleosomal DNA ~50bp

source_name: isw2 Nucleosomes Frag Biological Rep 2

tag: S cerevisiae S288C  congenic to BY4741

tag: Genotype

value: delta isw2 (MATa his3-1 leu2-0 met15-0 ura3-0 isw2::HisG)


title: Dam_4


title: Leaf_salt_day17_rep3

description: no other description

source_name: Leaf treated with salt, day 17, rep3

source_name: Leaf with no salt treatment day 17, no salt, rep3


title: DvH_0min._pH10__pH_repId352

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with pH. This sample was treated with pH10  pH.  Treatment time point = 0 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 0min. pH10  pH

treatment_protocol: 0min. pH10  pH.


title: P1_vs_ST1

city: Rockville

first: Jia

state: MD

address: 9712 Medical Center Drive

institute: Plant Genomics

description: The goal of the current research is to identify factors that involved with heat induced russeting of the potato tuber skin. Potato plants of the variety Desirèe were grown in pots filled with perlite, in a greenhouse under natural winter conditions (Nov 2005- Jan 2006, average temperatures range of 10-18°C). For the exposure of tubers to heat stress (H) hot water (33-35°C) was circulated in tubes lined at the internal side of the pots. The heat was applied one week before tubers harvest. Tubers were harvested at two time points: 8 weeks post sprouting and a week post mechanical vine killing. The skin (S) of young tubers was peeled by hand, as the remaining phelloderm (PH) layers, the periderm of young tubers (P) and the periderm of mature tubers (ST) were peeled using a scalpel blade. Leaves (L) and tuber flesh (TF) samples were collected as well. For each RNA sample 4 biological replicates were prepared; each one represents pooled tissues from 4-6 plants grown at different location in the greenhouse. RNA was extracted using CTAB protocol, and was further purified by RNeasy Mini Kit (Qiagen) using the On-Column DNase Digestion protocol.

hyb_protocol: Hybridization with indirectly labeled mRNA (SGED_SOP_6.1.1, SGED_SOP_6.2.1-4)

scan_protocol: Axon 4000B scanner. Both the 635nm (red, Cy5) and 532nm (green, Cy3) channels are scanned simultaneously at 100% laser power, the PMT set between 600 and 950. Slides are scanned at a resolution of 10micron

data_processing: The TIFF images were quantified using Genepix 5.0. Local background was subtracted from the signal value and the data was normalized using the quantile method in the limma package of bioconductor.

organism: Solanum tuberosum

label_protocol: Amino allyl labeling and direct labeling (SGED_SOP_5.1.1 + SGED_SOP_6.1.1)

growth_protocol: Potato plants were grown in pots filled with perlite, in a greenhouse under natural winter conditions (Nov 2005- Jan 2006, average temperatures range of 10-18°C)

extract_protocol: Phenol method with carbohydrate-enriched tissue such as tubers and trizol for other tissues such as leaves (SGED_SOP_3.1.1 + SGED_SOP_3.3.1)

treatment_protocol: Control

tag: Solanum tuberosum, Periderm, Abiotic stress

treatment_protocol: Mechanical vine killing was applied 10 weeks post sprouting and tubers were collected a week later.

tag: Solanum tuberosum, Mature periderm, Abiotic stress


title: Day 4 T-independent GC B cells (pooled from 10 mice) 2

description: Purification: FACS sort: GL7+ B220+

source_name: T independent GC B cells


title: ST1_vs_P1


title: P2_vs_ST2


title: ST2_vs_P2


title: L1_vs_S1

tag: Solanum tuberosum, Leaves, Abiotic stress

tag: Solanum tuberosum, Skin, Abiotic stress


title: S2_vs_PH1

tag: Solanum tuberosum, Phelloderm, Abiotic stress


title: PH3_vs_TF2

tag: Solanum tuberosum, Tuber flesh, Abiotic stress


title: S4_vs_TF3


title: PH4_vs_L3


title: TF4_vs_PH[H]3

treatment_protocol: Heat stress was applied by circulating hot water (33-35°C) in tubes lined at the internal side of the pots one week before tubers harvest.


title: S[H]3_vs_L4


title: PH[H]2_vs_S[H]2


title: TF2_vs_PH3


title: PH2_vs_PH[H]1


title: isw2 Nucleosomes FL Biological Rep 2

description: Full length nucleosomal DNA ~150bp

source_name: isw2 Nucleosomes FL Biological Rep 2

extract_protocol: 500ml of yeast cells were grown to mid log phase (OD = 0.7), and cross-linked with the addition of formaldehyde to a final concentration of 2% for 20 minutes and then quenched with the addition of glycine to a final concentration of 125mM for 10 minutes. Cells were digested with 3mg of Zymolase-100T (Seikagaku) in 30ml of buffer Z (50mM Tris:Cl pH 7.5, 1M sorbitol 10mM 2ME) for 30 minutes at 30ºC with constant agitation. Nuclei were pelleted and resuspended with the addition of 5ml of buffer Q (10mM Tris:Cl pH7.5, 50mM NaCl, 10mM MgCl2, 1mM CaCl2, 0.075% NP40) and nuclei were digested with the addition of ~700units of Micorococcal Nuclease (Worthington) and 100units Exonuclease III for 20 minutes at 37ºC with constant agitation. Reaction was stopped with the addition of 1ml solution S (5% SDS, 100mM EDTA). RNA and proteins were removed with sequential additions of with RNaseA and Proteinase K. Crosslinks were reversed by incubation at 65ºC for 16 hours. SDS was precipitated from the solution with the addition of 2.5ml 3M potassium acetate pH5.5 followed by a centrifugation at 4000g for 5 minutes. DNA fragments were harvested from the supernatant with use of a G500 genomic column (Qiagen) according to instructions. DNA was then resolved on a 1.7% agarose gel and the band corresponding to mononucleosomal DNA (~150bp) was excised. The gel slice was placed in a dialysis bag and DNA extracted by electroelution and treated with CIP to remove terminal phosphates.

treatment_protocol: Log phase yeast cultures harvested by centrifugation


title: L2_vs_TF1


title: S3_vs_S[H]1


title: S[H]1_vs_S3


title: TF3_vs_S4


title: S1_vs_L1


title: L3_vs_PH4


title: L4_vs_S[H]3


title: PH1_vs_S2


title: PH[H]1_vs_PH2


title: PH[H]3_vs_TF4


title: ST3_vs_P3


title: S[H]2_vs_PH[H]2


title: Flesh_vs_Peel_stage3_3

description: The quality of the pepper fruit is significantly influenced by the properties of its surface such as color, glossiness and texture. The fruit surface is composed of a peel containing several layers including the cuticle, epidermis and the hypodermis. The peel acts as a protective barrier against biotic and abiotic stresses and is the most critical tissue affecting water loss during post harvest storage. The peel is composed of an outer epidermis with thick waxy (lipid) cuticle and few cell layers of thick-walled hypodermal cells. Despite its agronomic importance and due to the fact that the majority of studies in fruits have been conducted using flesh and peel tissues as a whole, the biochemical and genetic bases of variation in peel properties are largely unknown. In this proposal we aim to determine peel-specific gene expression in pepper by micro array hybridizations of peel and flesh RNA extracted at different developmental stages of the fruit.  The cultivar Celica (Capsicum annuum) that has a large blocky fruit will be used for studying gene expression in the peel and flesh. Plants were grown in the greenhouse during the spring of 2006. Fruits were harvested at three developmental stages: young- 10 days after anthesis, mature green- 30 days after anthesis and ripe red- 45 days after anthesis. These stages were chosen because each represents a distinct phase in fruit development. At each stage, a biological replicate consists of bulked tissue from 3 fruits from each of 3 plants (a total of 9 fruits). We have a total of 4 biological replicates. For each fruit, the peel was separated from the flesh by manual dissection using thin forceps and scalpel blade. Peel and flesh samples were immediately frozen in liquid nitrogen and stored at -800C until RNA extraction. Total RNA was extracted using the GenElute Mammalian Total RNA Miniprep kit (Sigma).

organism: Capsicum annuum

growth_protocol: Green house spring time of Israel

treatment_protocol: Peel from ripe fruit

tag: Capsicum annuum, Fruit peel, Development

treatment_protocol: Flesh from ripe fruit

tag: Capsicum annuum, Fruit flesh, Development


title: Flesh_vs_Peel_stage3_1


title: TF1_vs_L2


title: wt_vs_jai1_root12hr_3

description: Jasmonic acid (JA) is a fatty-acid derived signaling molecule that regulates a wide variety of plant developmental and stress-related responses. We identified a jasmonate-insensitive1 (jai1) mutant of tomato that is defective in the LeCOI1 gene, which plays an essential role in induced resistance of tomato to a broad spectrum of pests, and is also required for maternal control of seed and fruit development.  The present study is aimed at identifying genes involved in two JA-signaled processes that have not been studied in other plants. The first specific aim is to identify the set of JA/COI1-regulated genes in tomato reproductive tissues, with emphasis on genes expressed in maternal tissues. We hypothesize that JA/COI1 signaling regulates maternal processes that nurture the developing embryo and seed. The second aim of the study is to identify JA/COI1-regulated genes that are specifically expressed in tomato roots. Although it has been shown that JA promotes root defenses against various pests, virtually nothing is known about the JA-regulated transcriptome in roots.  Tomato (Solanum lycopersicum) cv Micro-Tom wild-type and jai1 seed were grown in peat pots and maintained in growth chambers. To identify COI1-regulated genes in reproductive tissues, flower buds, open flowers and immature fruit at 7 and 17 days post-pollination were collected from 8 to 10 week old plants. To identify COI1-regulated genes in roots, 3 week old plants were exposed to exogenous JA by a single soil drench with 0.1mM JA, and roots were collected after 1, 6, 12 and 24 hours. Plants treated with water were used for the 0hr time point. All tissue was snap-frozen in liquid nitrogen, and RNA was extracted and analyzed as described in the TIGR Potato Microarray protocol (phenol method). Three biological replicates were collected for this study.

growth_protocol: Grown for 21 days in growth chamber (17h/7h light/dark, 28C/18C) in peat pots

treatment_protocol: 0.1mM exogenous JA for 12 hr

tag: Solanum lycopersicum, Roots, Development


title: Flesh_vs_Peel_stage3_4


title: wt_vs_jai1_root24hr_3

treatment_protocol: 0.1mM exogenous JA for 24 hr


title: wt_vs_jai1_root24hr_1


title: wt_vs_jai1_root24hr_2


title: wt_vs_jai1_root12hr_2


title: Flesh_vs_Peel_stage2_2

treatment_protocol: Peel from mature green fruit

treatment_protocol: Flesh from mature green fruit


title: Flesh_vs_Peel_stage1_4

treatment_protocol: Peel from young fruit

treatment_protocol: Flesh from young fruit


title: wt_vs_jai1_root12hr_1


title: Flesh_vs_Peel_stage2_4


title: Flesh_vs_Peel_stage2_3


title: Flesh_vs_Peel_stage1_2


title: Flesh_vs_Peel_stage1_3


title: wt_vs_jai1_root6hr_3

treatment_protocol: 0.1mM exogenous JA for 6 hr


title: wt_vs_jai1_root24hr_3_FD


title: Flesh_vs_Peel_stage1_1


title: Flesh_vs_Peel_stage2_1


title: Flesh_vs_Peel_stage3_2


title: CtrlK_vs_ColdC_Stub_14d_Rep2

description: Healthy five-weeks old S. tuberosum (Red Pontiac) and S. commersonii (Oka 5040) were subjected to cold-acclimating temperature (2oC) in the growth chamber. Control plants at identical developmental stage were also grown in growth chamber at optimum conditions for growth (28oC, 14/10, light/dark, 65% RH). Leaf tissues were collected from the control (reference) and cold-acclimating (experimental treatment, 2oC) plants for each species at 2, 4, 7, 10 and 14 days after the initiation of the control and low temperature treatments. A total of two plants for each species were used for both the control and treatment experiments and tissue samples from each plant (within replicate) were pooled for RNA isolation. These experiments were performed twice in order to produce two sets of biological replicates for each species for all sampling time-points.

growth_protocol: Grown for 35 days in growth chamber (28C, 14h/10h light/dark, 65% RH); After 35 days, plants were transfered at 2C

treatment_protocol: Low temperature (2C) for 14 days

tag: Solanum tuberosum, Leaf, Abiotic stress

treatment_protocol: Control temperature (28C) for 14 days


title: wt_vs_jai1_root1hr_1

treatment_protocol: 0.1mM exogenous JA for 1 hr


title: wt_vs_jai1_root1hr_2


title: CtrlK_vs_ColdC_Stub_14d_Rep1


title: CtrlK_vs_ColdC_Scom_10d_Rep1_FD

treatment_protocol: Low temperature (2C) for 10 days

treatment_protocol: Control temperature (28C) for 10 days


title: CtrlK_vs_ColdC_Stub_10d_Rep2


title: P3_vs_ST3

treatment_protocol: Control

treatment_protocol: Mechanical vine killing was applied 10 weeks post sprouting and tubers were collected a week later.


title: CtrlK_vs_ColdC_Stub_7d_Rep1

treatment_protocol: Low temperature (2C) for 7 days

treatment_protocol: Control temperature (28C) for 7 days


title: CtrlK_vs_ColdC_Stub_10d_Rep1


title: wt_vs_jai1_root1hr_3


title: wt_vs_jai1_root6hr_1


title: wt_vs_jai1_root0hr_1

treatment_protocol: Untreated control


title: wt_vs_jai1_17dayfruit_2

growth_protocol: Grown in peat pots for 3 weeks in growth chamber (17h/7h light/dark, 28C/18C), then for 5-7 weeks in greenhouse in 2:1/2 Baccto:sand soil mix.

tag: Solanum lycopersicum, Fruit, Development


title: CtrlK_vs_ColdC_Stub_4d_Rep2

treatment_protocol: Low temperature (2C) for 4 days

treatment_protocol: Control temperature (28C) for 4days


title: wt_vs_jai1_17dayfruit_3


title: CtrlK_vs_ColdC_Stub_2d_Rep2

treatment_protocol: Low temperature (2C) for 2 days

treatment_protocol: Control temperature (28C) for 2 days


title: wt_vs_jai1_root0hr_3


title: wt_vs_jai1_openflowers_2

tag: Solanum lycopersicum, Flower, Development


title: wt_vs_jai1_17dayfruit_1


title: CtrlK_vs_ColdC_Stub_4d_Rep1

treatment_protocol: Control temperature (28C) for 4 days


title: CtrlK_vs_ColdC_Scom_14d_Rep1


title: wt_vs_jai1_openflowers_3


title: wt_vs_jai1_7dayfruit_3


title: wt_vs_jai1_openflowers_1


title: wt_vs_jai1_root0hr_2


title: wt_vs_jai1_buds_3


title: CtrlK_vs_ColdC_Scom_7d_Rep1

treatment_protocol: Low temperature (2C) for 7days


title: CtrlK_vs_ColdC_Stub_2d_Rep1


title: CtrlK_vs_ColdC_Scom_10d_Rep2


title: CtrlK_vs_ColdC_Scom_10d_Rep1


title: wt_vs_jai1_buds_2


title: wt_vs_jai1_buds_1


title: CtrlK_vs_ColdC_Scom_4d_Rep1


title: CtrlK_vs_ColdC_Scom_4d_Rep2

treatment_protocol: Low temperature (2C) for 4days


title: CtrlK_vs_ColdC_Scom_2d_Rep1


title: SNHc_vs_SITc_3

description: The primary objective of this project is to determine the physiological and developmental differences between photoperiod and root induced tuberization responses in potato using genomic techniques. These experiments will establish baseline genomic and proteomic response associated with a partially characterized root-produced compound (TIF) that either substitutes for, or over-rides, the primary leaf perceived photoperiod induction signal in potato. The proposed work will answer the following questions. Are photoperiod and root induced tuberization responses the same? Do photoperiod and root induced tuberization trigger the same developmental processes in the stolon? How are photoperiod and root induced signals expressed in the genome of the leaf, stolon and roots? The data from the proposed experiments will prove invaluable in identifying key pathways in specific tissues to target in subsequent experiments in order to determine identify of, and establish the mode of action of the TIF compound.

growth_protocol: 12 light, 12 hr dark cycle in controlled environment chamber( 300 umol m-1 s-1 PAR with  at  1500 ppm CO2, 23oC, 65% RH) using an asceptic shaking flask culture system.

treatment_protocol: 12/12 photoperiod w/ TIF solution

tag: Solanum tuberosum, Stolon, Development

growth_protocol: Grown for 4 weeks in greenhouse

treatment_protocol: Wounded systemic 4 hr

tag: Solanum tuberosum, Leaf, Development


title: ctrl_vs_LapA-SI_W_1h_Sys_3

description: LapA encodes an acidic leucine aminopeptidase that is wound-inducible and found only in tomato (Solanum lycopersicum) and a small subset of the Solanaceae.  LapA is expressed in developing flowers, fruit and in foliage after wounding, insect feeding (Manduca sexta), Pseudomonas syringae pv. tomato infection, salinity, and water-deficit stress. Using Agrobacterium tumefaciens, UC82b plants were transformed  with a chimeric gene containing the CaMV 35S promoter and LapA cDNA in the sense orientation. Kanamycin-resistant plants were screened by RNA and protein blots to  identify plants that did not accumulate and LAP-A protein upon wounding; these plants were designated LapA-silenced (LapA-SI) lines. The LapA-SI plants have an impaired wound response and do not accumulate wound response transcripts (proteinase inhibitors and polyphenol oxidase) to wild-type levels. LAP-A is the first aminopeptidase to be shown to have a regulatory role in plants.   LapA-SI and UC82b plants were germinated on filter paper for 7 days before being planted in soil. Plants were grown in a growth chamber, (16 hour days at 28°C, 8 hour nights at 24°C, 50% humidity) for three weeks. Plants were wounded by crushing each leaflet on each of two lower leaves with pliers. Wounded leaves were collected at 0, 1 and 8 hr (local wounded tissue). Two upper, unwounded leaves were collected from the same plants at the same times (systemically wounded tissue). Five to seven plants were pooled for each time point. The experiment was repeated three times. RNA was extracted using a hot phenol/LiCl protocol and purified and DNase treated using the SV Total RNA Isolation Kit from Promega.

growth_protocol: Germinated for 7 days on wet filter paper, planted in soil, grown in growth chamber (16h/8h light/darkness, 28°C day/24°C night temp, 50% humidity)

treatment_protocol: LapA-silenced (LapA-SI), Upper unwounded leaves (systemically wounded tissue), 1hr

tag: Solanum lycopersicum, Leaf, Biotic stress

treatment_protocol: Mixed reference pool


title: ctrl_vs_LapA-SI_W_8h_Lo_3

treatment_protocol: LapA-silenced (LapA-SI), Wounded/Crushed lower leaves (local wounded tissue), 8hr


title: SINc_vs_SNHc_3

growth_protocol: 12 light, 12 hr dark with 15 min light break 6hr into dark cycle in controlled environment chamber( 300 umol m-1 s-1 PAR with  at  1500 ppm CO2, 23oC, 65% RH) using an asceptic shaking flask culture system.

treatment_protocol: 12/6+6 photoperiod w/ Hoagland solution


title: SNHb_vs_SNTb_2

treatment_protocol: 12/6+6 photoperiod w/ TIF solution


title: ctrl_vs_UC82b_W_0h_3

treatment_protocol: WT, Unwounded, 0hr


title: SNHa_vs_SNTa_1


title: SNHc_vs_SNTc_3


title: SNHa_vs_SITa_1


title: RNHc_vs_RITc_3

tag: Solanum tuberosum, Roots, Development


title: ctrl_vs_UC82b_W_8h_Lo_3

treatment_protocol: WT, Wounded/Crushed lower leaves (local wounded tissue), 8hr


title: ctrl_vs_LapA-SI_W_8h_Sys_3

treatment_protocol: LapA-silenced (LapA-SI), Upper unwounded leaves (systemically wounded tissue), 8hr


title: ctrl_vs_LapA-SI_W_1h_Lo_3

treatment_protocol: LapA-silenced (LapA-SI), Wounded/Crushed lower leaves (local wounded tissue), 1hr


title: ctrl_vs_LapA-SI_W_8h_Lo_2


title: ctrl_vs_LapA-SI_W_0h_3

treatment_protocol: LapA-silenced (LapA-SI), Unwounded, 0hr


title: SIHc_vs_SITc_3


title: ctrl_vs_LapA-SI_W_8h_Sys_2


title: RNHa_vs_RITa_1


title: RNHb_vs_RITb_2


title: ctrl_vs_UC82b_W_1h_Sys_3

treatment_protocol: WT, Upper unwounded leaves (systemically wounded tissue), 1hr


title: SINb_vs_SNHb_2


title: SIHa_vs_SITa_1


title: ctrl_vs_LapA-SI_W_1h_Sys_2


title: ctrl_vs_UC82b_W_8h_Sys_3

treatment_protocol: WT, Upper unwounded leaves (systemically wounded tissue), 8hr


title: ctrl_vs_UC82b_W_1h_Lo_3

treatment_protocol: WT, Wounded/Crushed lower leaves (local wounded tissue), 1hr


title: SIHb_vs_SITb_2


title: SINa_vs_SNHa_1


title: wt_vs_jai1_root6hr_2

treatment_protocol: 0.1mM exogenous JA for 6 hr


title: ctrl_vs_LapA-SI_W_0h_2


title: RNHc_vs_RNTc_3


title: ctrl_vs_LapA-SI_W_1h_Lo_2


title: RNHb_vs_RNTb_2


title: ctrl_vs_UC82b_W_8h_Sys_2


title: RIHc_vs_RITc_3

treatment_protocol: Wounded 4 hr


title: RNHa_vs_RNTa_1


title: ctrl_vs_UC82b_W_8h_Lo_2


title: RIHb_vs_RITb_2

treatment_protocol: 12/12 photoperiod w/ TIF solution

treatment_protocol: Control 4 hr


title: RIHc_vs_RNHc_3


title: ctrl_vs_Lap-SI_W_8h_Sys_1


title: ctrl_vs_UC82b_W_0h_2


title: ctrl_vs_Lap-SI_W_8h_Lo_1


title: ctrl_vs_UC82b_W_1h_Lo_2


title: RIHa_vs_RITa_1


title: LNHc_vs_LITc_3

treatment_protocol: Wounded systemic 4 hr


title: LNHa_vs_LITa_1


title: LNHb_vs_LITb_2


title: ctrl_vs_LapA-SI_W_0h_1

treatment_protocol: Mixed reference pool


title: RIHb_vs_RNHb_2


title: ctrl_vs_LapA-SI_W_1h_Sys_1

treatment_protocol: LapA-silenced (LapA-SI), Upper unwounded leaves (systemically wounded tissue), 1hr


title: ctrl_vs_UC82b_W_8h_Sys_1


title: LNHc_vs_LNTc_3


title: RIHa_vs_RNHa_1

treatment_protocol: 12/6+6 photoperiod w/ Hoagland solution


title: ctrl_vs_UC82b_W_1h_Sys_1


title: LNHb_vs_LNTb_2

treatment_protocol: 12/6+6 photoperiod w/ TIF solution


title: ctrl_vs_UC82b_W_8h_Lo_1


title: ctrl_vs_UC82b_W_1h_Sys_2


title: ctrl_vs_LapA-SI_W_1h_Lo_1


title: LIHc_vs_LITc_3


title: LNHa_vs_LNTa_1


title: LIHb_vs_LITb_2


title: ctrl_vs_UC82b_W_0h_1

treatment_protocol: WT, Unwounded, 0hr


title: ctrl_vs_UC82b_W_1h_Lo_1


title: LIHc_vs_LNHc_3


title: Mg_vs_dex_9h_2_1

description: Tumor induction by Agrobacterium is due to transfer of T-DNA genes. We study the 6b T-DNA oncogene that induces tumors on species like Nicotiana glauca, but for which no precise growth induction mechanism has been found sofar. The 6b gene belongs to a larger group of T-DNA genes including rolB, rolC and orf13, no homologies are known with other genes. In N. tabacum, 6b modifies responses to auxins and cytokinins and induces strong morphological changes including cell enlargement, abnormal division, double flowers, enations and root shortening (Helfer et al., 2003, Grémillon et al., 2004). Others have localized 6b and rolB proteins in the nucleus, where they could modify transcription (Kitakura et al., 2002, Moriuchi et al., 2004).  Recently, we developed a system to study early  6b-induced growth changes, using a dexamethasone-inducible 6b gene (dex-T-6b). Leaves of homozygous dex-T-6b plants are infiltrated with a 10 mM MgSO4 solution, with or without 20 micromolar dex. In the presence of dex, a reproducible increase in glucose and fructose concentrations is observed. Such changes are also found in cultured leaf discs and in that case accompanied by an increase in expansion. 6b-induced changes are detected as early as 7 hours after dex infiltration. Western analysis shows that dex-T-6b plants have undetectable 6b protein levels without induction, and rapidly accumulate 6b protein upon induction. We propose to study gene expression in induced and non-induced leaves at different times of induction: 0-3-6-9 and 12 hours. The data will be used to establish whether the 6b gene induces specific genes, and whether these genes are involved in hexose changes and cell expansion. We will also test the effect of infiltrating tobacco leaves with 10 mM MgSO4 by comparison with non-infiltrated leaf tissues in order to correct for changes due to the infiltration procedure.

organism: Nicotiana tabacum

growth_protocol: Grown for 45 days in greenhouse, 16h/8h light/darkness, 50% humidity, 18°C-22°C, peat(65%)-clay(35%) substrate

treatment_protocol: Infiltrated with dex, 9h

tag: Nicotiana tabacum, Leaf, Development

treatment_protocol: Infiltrated with MgSO4, 10 mM, 9h


title: LIHb_vs_LNHb_2


title: Mg_vs_dex_6h_3_1

treatment_protocol: Infiltrated with dex, 6h

treatment_protocol: Infiltrated with MgSO4, 10 mM, 6h


title: Mg_vs_dex_9h_1


title: Mg_vs_dex_9h_3


title: LIHa_vs_LITa_1


title: Mg_vs_dex_3h_3

treatment_protocol: Infiltrated with dex, 3h

treatment_protocol: Infiltrated with MgSO4, 10 mM, 3h


title: Mg_vs_dex_6h_2


title: Mg_vs_dex_6h_1_1


title: Mg_vs_dex_3h_2


title: Mg_vs_dex_3h_1


title: Mg_vs_dex_12h_3

treatment_protocol: Infiltrated with dex, 12h

treatment_protocol: Infiltrated with MgSO4, 10 mM, 12h


title: LIHa_vs_LNHa_1


title: wildtype_vs_ced4_3.2.8

description: Transgenic tobacco (Nicotiana tabacum) expressing Caenorhabditis elegans cell death genes, Ced4 and Ced3, show evidence suggesting such expressions protect the plants from infestation by the plant parasitic nematode Meloidogyne incognita.  Although positive results have been correlated with the gene expressions (data in preparation for publication; a draft of the publication can be provided upon request), the mechanism by which the nematode protection is manifested is not clearly understood.  One possibility is that the C. elegans cell death proteins produced by the transgenic plants are being ingested and incorporated into the nematode’s own cell death pathway, leading to their demise.  Alternatively, it is also possible that expression of the C. elegans cell death genes promotes the endogenous resistance genes of the plant, leading to nematode resistance.  We want to test the later hypothesis by conducting a reference design microarray experiment to establish the expression profile of Ced3, and Ced4 homozygous plants and Ced3xCed4 double heterozygous plants in comparison with wild-type tobacco plants.  If the hypothesis is correct, we expect to detect increased expression of pathogenicity-related genes in the transgenic plants.  Furthermore, characterization of the expression profiles in these transgenic plants will provide us directionality for our future research on the elucidation of this resistance mechanism.

growth_protocol: Grown for 55+/-6days in incubator (14h/10h light/darkness, 26°C) on MS Plates

treatment_protocol: Transgenic

tag: Nicotiana tabacum, Whole plant, Other

treatment_protocol: Wildtype


title: Mg_vs_dex_12h_1


title: wildtype_vs_ced4_3.1.8


title: wildtype_vs_ced3X4_3.2.9


title: Mg_vs_dex_12h_2


title: wildtype_vs_ced3X4_3.1.9


title: wildtype_vs_ced3_3.2.7


title: wildtype_vs_ced3X4_3_FD


title: ctrl_vs_Mg_9h_3

treatment_protocol: Untreated, 9h


title: wildtype_vs_ced4_3_FD


title: ctrl_vs_Mg_9h_2_2


title: ctrl_vs_Mg_6h_3

treatment_protocol: Untreated, 6h


title: ctrl_vs_Mg_9h_2


title: ctrl_vs_Mg_6h_2


title: wildtype_vs_ced3X4_2_FD


title: wildtype_vs_ced3_3.1.7


title: ctrl_vs_Mg_9h_1


title: wildtype_vs_ced4_2_FD


title: wildtype_vs_ced3_3_FD


title: ctrl_vs_Mg_6h_1


title: ctrl_vs_Mg_6h_3_2


title: ctrl_vs_Mg_6h_1_2


title: wildtype_vs_ced4_2.2.5


title: ctrl_vs_Mg_3h_2

treatment_protocol: Untreated, 3h


title: wildtype_vs_ced3X4_2.2.6


title: wildtype_vs_ced3_2_FD


title: wildtype_vs_ced3X4_2.1.6


title: wildtype_vs_ced3_2.2.4


title: wildtype_vs_ced3_2.1.4


title: ctrl_vs_Mg_12h_3

treatment_protocol: Untreated, 12h


title: wildtype_vs_ced3X4_1.2.3


title: ctrl_vs_Mg_3h_1


title: ctrl_vs_Mg_3h_3


title: wildtype_vs_ced3X4_1_FD


title: ctrl_vs_Mg_12h_1


title: ctrl_vs_Mg_12h_2


title: ctrl_vs_ctrl_0h_3

treatment_protocol: Untreated, 0h


title: wildtype_vs_ced4_2.1.5


title: wildtype_vs_ced4_1.2.2


title: ctrl_vs_ctrl_0h_1


title: 9LOX_sys_control_vs_Psm_8hr_3

description: Oxylipins play a role in the response of plants to pathogens both as antimicrobial compounds and as signaling molecules. In potato, pathogen infection leads to the stimulation of the 9-lipoxygenase pathway (Göbel et al. 2001; 2002; Stumpe et al. 2001). In order to analyze whether 9-LOX-derived oxylipins such as colnele(n)ic acid (products of the 9-divinyl ether synthase reaction) act as signaling molecules for the activation of defense responses, transgenic potato plants (Solanum tuberosum cv. Désirée) were generated which express an RNAi construct directed against the pathogen-induced 9-lipoxygenase (Göbel et al. 2003) or against the pathogen-induced 9-divinyl ether synthase (Stumpe et al. 2001). Highly reduced transcript levels correlate with low levels of 9-lipoxygenase-derived oxylipins (Göbel et al. 2003).  Transgenic and wild type plants were grown as sterile plants on MS medium supplemented with agar in a phytochamber with 16 h of light [200 µE] at 22 °C. After transfer to soil, plants were kept in a phytochamber with 16 h of light [200 µE], 18 °C and 60 % humidity for four weeks. Lower leaves were infiltrated with a suspension of Pseudomonas syringae pv. maculicola at a concentration of 108 cfu/ml MgCl2 or, as a control, 10 mM MgCl2-solution. RNA was isolated both from the infiltrated leaves and the upper, non-treated leaves using the trizol method. Subsequently, RNA was digested with DNase and purified via Qiagen RNeasy Kit (Qiagen, Hilden, Germany) according to the manufacturer´s instructions.

growth_protocol: 16 hour light/8 hour dark at 22° C in soil/sand

treatment_protocol: Infiltration of Pseudomonas syringae pv. maculicola, 8h

tag: Solanum tuberosum, Leaves, Biotic stress

treatment_protocol: MgCl2, 8h


title: wild_sys_control_vs_Psm_24hr_3

treatment_protocol: Infiltration of Pseudomonas syringae pv. maculicola, 24h

treatment_protocol: MgCl2 24h


title: wild_sys_control_vs_Psm_8hr_3


title: wildtype_vs_ced4_1.1.2


title: ctrl_vs_ctrl_0h_2


title: 8004_vs_8523_2

description: Xanthomonas campestris pv. campestris (Xcc) is a major bacterial pathogen of cruciferous plants worldwide. The pathogen produces polysaccharides including extracellular cyclic glucan, xanthan, and extracellular enzymes that are key virulence factors. Different Xcc mutants (8397-defective in xanthan and 8523- defective in extracellular glucans) have been obtained and characterized in previously, wich shown to be less infective than the wild type strain when inoculated in N.benthamiana, wich has shown to be an excellent model for the study of Xcc-plant interaction. The objective of this work is evaluate this compounds functions in the plant-pathogen interaction, in particular in the plant transcriptoma modulation to confer susceptibility or resistance to the infection.     Plant gene expression profiles would be obtained from independently inoculated leaves of N.benthamiana with the following strains of xanthomonas: Xcc. 8004 (wild type), Xcc. 8397 (xanthan minus), Xcc. 8523 (glucan minus), ant water (control). Leaves discs will be collected at 24 hs post infection and immediately submerged in liquid N2. Total RNA will be extracted with plant RNA specific kits (RNA easy QIAGen), treated with DNase, purified and quantified.

organism: Nicotiana benthamiana

growth_protocol: Grown for 7 weeks at 25 C (day, 16 hr) and 22 C (night, 8 hr) and watered with nutrient solution

treatment_protocol: Inoculated with xanthomonas strain 8523 for 24 h

tag: Nicotiana benthamiana, Leaf, Biotic stress

treatment_protocol: Inoculated with xanthomonas strain 8004 for 24 h


title: wildtype_vs_ced3_1_FD


title: water_vs_8523_2

treatment_protocol: Inoculated with water for 24 h


title: 9LOX_sys_control_vs_Psm_24hr_3

treatment_protocol: MgCl2, 24h


title: 9LOX_sys_control_vs_Psm_8hr_FD


title: wildtype_vs_ced3_1.1.1


title: wild_sys_control_vs_Psm_8hr_2


title: 9DES_sys_control_vs_Psm_24hr_2


title: 8004_vs_8523_1


title: 8004_vs_8397_2

treatment_protocol: Inoculated with xanthomonas strain 8397 for 24 h


title: 9LOX_sys_control_vs_Psm_24hr_2


title: water_vs_8004_2FD


title: 9-DES_sys_control_vs_Psm_8hr_2


title: wild_sys_control_vs_Psm_24hr_2


title: water_vs_8523_1


title: wildtype_vs_ced4_1_FD


title: wild_sys_control_vs_Psm_24hr_1


title: water_vs_8397_2


title: 8004_vs_8397_1


title: water_vs_8397_1


title: 9LOX_sys_control_vs_Psm_8hr_2


title: water_vs_8004_1


title: R3_vs_R

description: Blackspot bruising is the tuber discoloration resulting from mechanical damage in susceptible crops and is a major quality and environmental problem for the potato industry. The present study is aimed at identifying differences in gene expression which are correlated with the development of bruise susceptibility or resistance in tubers.  This may produce markers or diagnostic tests for use in predicting enhanced bruise susceptibility in field grown potato crops.  Different potato cultivars were grown in field plots at ADAS Gleadthorpe, Nottinghamshire, UK during three growing seasons – 2003, 2004 and 2005.  Random samples of tubers (8) were harvested by hand and cores excised from the subdermal tissues of the stolon end of the tubers and immediately frozen and stored in liquid nitrogen for RNA isolations.  The remainder of the crops were stored at 4oC for bruise susceptibility testing - samples of tubers (30) from each crop were impacted and incubated for 48h at 30oC.  Bruise susceptibility was scored, according to the intensity of pigmentation and the volume of tuber tissue affected, on a scale of 0 (very resistant) – 10 (very susceptible). Crops representing 'very susceptible', 'susceptible', 'moderate' and 'resistant' to bruising, were selected for RNA isolation.  Total RNA’s were isolated from frozen cores by the TIGR hot phenol extraction method, precipitated by LiCl and treated with DNase.  RNA concentrations were adjusted to ~2ug/ul and analysed on 1% TBE gels after formamide treatment. Any RNA’s which were not pure enough or showed degradation were discarded. Total RNA’s were pooled and 25ul samples aliquotted according to the required hybridisations indicated in the Excel spreadsheet and the on-line information form.

growth_protocol: Prevailing field conditions

treatment_protocol: Standard fertilizer and irrigation practice

tag: Solanum tuberosum, Tubers, Development

growth_protocol: Cultivated for 4 weeks in greenhouse (16h daylength, 70% humidity, 25C in peat-clay mix)

treatment_protocol: Challenged with water for 24h

tag: Solanum tuberosum, Leaf and petiole, Development


title: 9LOX_sys_control_vs_Psm_24hr_1


title: 9DES_sys_control_vs_Psm_24hr_1


title: R2_vs_R

treatment_protocol: Challenged with P.infestans for 24h


title: R_vs_R2


title: R4_vs_VS_1


title: R4_vs_VS_2


title: wild_sys_control_vs_Psm_8hr_1


title: roots_uc_v_c_grosto_5d_FD_3

description: Sets of seven 2-week old potato plants carrying the nematode resistance gene H1, grown from tuber ‘chits’ in sandy loam at a constant temperature of 20 ºC and a light cycle of 16 hour light/8 hour dark, were each inoculated in the roots evenly with 2000 juveniles of the virulent potato cyst nematode Globodera pallida, or with the avirulent G. rostochiensis pathotype Ro1, or with water. Plants were manually watered throughout the duration of the experiment.   5, 17 and 33 days after inoculation, the roots were carefully washed and root tissue samples were individually flash-frozen in liquid nitrogen and stored at –80 ºC. Total RNA isolations were performed using the Qiagen RNeasy kit. All samples were treated with DNase. The experiment was replicated twice.

growth_protocol: 16 hour light/8 hour dark; 20 C; sandy loam

treatment_protocol: Challenged with G. rostochiensis Ro1, 5d

tag: Solanum tuberosum, Roots, Biotic stress

treatment_protocol: None, 5d


title: water_vs_8004_2


title: 9-DES_sys_control_vs_Psm_8hr_1


title: R_vs_R3


title: roots_grosto_v_gpallida_33d_3

treatment_protocol: Challenged with G. rostochiensis Ro1, 33d

treatment_protocol: Challenged with G. pallida, 33d


title: VS_vs_R4_1


title: roots_grosto_v_gpallida_5d_3

treatment_protocol: Challenged with G. pallida, 5d


title: 9LOX_sys_control_vs_Psm_8hr_1

treatment_protocol: Infiltration of Pseudomonas syringae pv. maculicola, 8h


title: roots_grosto_v_gpallida_17d_3

treatment_protocol: Challenged with G. rostochiensis Ro1, 17d

treatment_protocol: Challenged with G. pallida, 17d


title: VS_vs_R4_2


title: roots_uc_v_c_grosto_5d_3


title: VS_vs_S_2


title: roots_uc_v_c_grosto_33d_3

treatment_protocol: None, 33d


title: VS_vs_S_1


title: wildtype_vs_ced3_1.2.1

treatment_protocol: Transgenic

treatment_protocol: Wildtype


title: wildtype_vs_ced3X4_1.1.3


title: VS_vs_M1


title: roots_uc_v_c_gpallida_33d_3


title: roots_uc_v_c_gpallida_5d_3


title: VS_vs_M2


title: S_vs_R_2


title: roots_grosto_v_gpallida_33d_2


title: roots_grosto_v_gpallida_5d_2


title: VS_vs_R_2


title: roots_uc_v_c_gpallida_17d_3

treatment_protocol: None, 17d


title: roots_uc_v_c_grosto_33d_2


title: S_vs_R_1


title: S_vs_M1


title: roots_grosto_v_gpallida_17d_2


title: S_vs_M2


title: VS_vs_R_1


title: S_vs_VS_2


title: roots_uc_v_c_grosto_17d_2


title: M2_vs_S


title: roots_uc_v_c_gpallida_17d_2


title: roots_uc_v_c_grosto_5d_2


title: M1_vs_VS


title: M2_vs_VS


title: M2_vs_R


title: S_vs_VS_1


title: roots_uc_v_c_gpallida_17d_1


title: M1_vs_S


title: roots_uc_v_c_grosto_17d_1


title: roots_uc_v_c_grosto_33d_1


title: roots_uc_v_c_gpallida_33d_2


title: roots_grosto_v_gpallida_5d_1


title: roots_uc_v_c_gpallida_5d_2


title: R_vs_M2


title: R_vs_S_2


title: roots_uc_v_c_gpallida_5d_1


title: roots_grosto_v_gpallida_33d_1


title: M1_vs_R


title: R_vs_S_1


title: roots_uc_v_c_grosto_5d_1


title: R_vs_VS_1


title: R_vs_M1


title: R_vs_VS_2


title: roots_uc_v_c_grosto_17d_3


title: tgf_wt_vs_CP12_antisense_3

description: CP12 is a small nuclear encoded chloroplast protein that has been shown to form a complex with the Calvin cycle enzymes, PRK and GADPH. We have taken an antisense approach in order to address the importance of this regulatory protein on carbon assimilation. Transgenic Nicotiana tabacum cv. Samsun with reduced levels of the CP12 protein, produced by leaf disc transformation with a full length tobacco CP12 cDNA, regulated by the cauliflower mosaic virus 35S promoter. Agrobacterium tumefaciens-mediated transformation and selection on kanamycin produced primary transformants whose progeny segregate for severity of the antisense CP12 phenotype. Because of the impact of the antisense reductions in CP12 on carbon assimilation, these plants have abnormal morphology of leaves, floral organs, greatly reduced fertility and markedly slower growth rates. Our hypothesis is that the phenotype is exposing the regulatory nature of the CP12 protein. Intermediates leaving the Calvin cycle are essential for the synthesis of hormones and perturbation of hormone balances is a potential source of the morphological and development effects observed in the CP12 antisense plants. Our objective is to understand the CP12 phenotype by identifying changes in gene expression occurring at key stages in the life cycle of the CP12 antisense plants.  CP12 antisense and wild type control plants for microarray analysis were germinated in a growth chamber in agar medium with 1% sucrose and 1/2 strength MS; with a 16 h light/8 h dark cycle at 25°C. At 20 days plants were transferred to a controlled environment greenhouse and grown in Fisons Levington F2 compost at 25°C, with light levels above 500 umol m-2 s-1 ;using supplementary lighting in a 16 h light/8 h dark cycle. 3 independent sets of plants (both wild type and CP12 antisense) were grown for preparation of three independent biological replicate RNA samples. RNA was extracted according to the TIGR protocol from plants in the early in all samples.

growth_protocol: 25C 20d on MS medium followed by 30C in Fisons Levington F2; 16h day, 8hr night

tag: Nicotiana tabacum, Green flowers, Development


title: tgf_wt_vs_CP12_antisense_2


title: nfetl_wt_vs_CP12_antisense_3FD

tag: Nicotiana tabacum, Newly fully expanded leaf, Development


title: tgf_wt_vs_CP12_antisense_1


title: nfetl_wt_vs_CP12_antisense_3


title: tr_wt_vs_CP12_antisense_2

tag: Nicotiana tabacum, Roots, Development


title: tr_wt_vs_CP12_antisense_3


title: rpn8_vs_ev_10dpi_2

description: N. benthamiana plants were grown under 16 hour light/8 hour dark cycle in a plant growth room at 24°C for approximately six weeks before subjected to virus-induced gene silencing. Agrobacterium stain GV2260 (OD600=1.0) carrying silencing constructs were infiltrated into 2 fully expended leaves for inducing gene silencing.  Samples were collected at 8, 10, 12, 14, and 16 days post Agro-inoculation (DPI) for RPN9-silenced plants and N-silenced control. For RPN8-silencing, samples were collected at 8, 10, and 12 DPI, and the empty vector treated plants were used as a control. Each sample was a pool of 6 silenced leaves collected from 3 individual plants. All the samples were in biological triplicates from 3 sets of independently silenced plants. Total RNA was extracted using Trizol and DNA was removed with DNase I treatment before cDNA synthesis.

growth_protocol: Grown at 24C under 16h light/8h dark cycle in a growth room.

tag: Nicotiana benthamiana, Leaf, Development


title: tr_wt_vs_CP12_antisense_1


title: rpn8_vs_ev_8dpi_3


title: rpn8_vs_ev_10dpi_3


title: rpn8_vs_ev_8dpi_1


title: nfetl_wt_vs_CP12_antisense_2


title: rpn8_vs_ev_12dpi_2


title: rpn8_vs_ev_12dpi_3


title: rpn8_vs_ev_12dpi_1


title: ytl_wt_vs_CP12_antisense_1

tag: Nicotiana tabacum, Young leaves, Development


title: rpn9_vs_n_16dpi_3


title: rpn8_vs_ev_12dpi_1_FD


title: nfetl_wt_vs_CP12_antisense_1


title: rpn8_vs_ev_10dpi_1


title: stage2_28d_vs_stage2_35d_3

description: This investigation was aimed at studying global gene expression during the process of somatic embryogenesis in potato using internodal segments (INS) as explants. The INS explants from 4 to 6 week old potato cv. Desiree in vitro cultures were cultured on somatic embryogenesis induction for 2 weeks (stage-I) and expression/regeneration modified MS media for 3 weeks, respectively with (stage-II) and without (stage-III) 2, 4-dichlorophenoxy acetic acid (5 µM). The culturing frequency was 10 INS/petridish with 25 ml medium.  The in vitro cultures were incubated at 19±1°C, 16/8 hrs light/dark cycles and 90 µmol/m2/s light intensity. To study the molecular events of SE as affected by the absence or presence of auxin, the INS explants were divided into 2 groups after the induction phase. One-half of the induced INS explants were transferred to auxin free medium to evoke SE, the other half were subjected to a prolonged induction phase. The total RNA from INS explants at these critical stages of SE progression was isolated using TRIzol (Invitrogen) as per the manufacturer’s instructions. The on-column DNase treatment and clean-up steps were performed using Qiagen RNase free DNase and RNeasy midi kits. The selected time points used for the RNA isolation were day 0 (freshly cut INS), day 14 (INS on induction medium) and day 21, 28 & 35 (INS on expression medium as well as from prolonged induced phase). Except day 0, where the whole INS were used for RNA isolation, all other time point RNA was isolated from the callused part of the INS distal end. Each time point was replicated 3 times. The number of explants for each biological replicate varied from 30 to 300 owing to variability in tissue availability and corresponding RNA yield from explants of each time-point. The entire process from tissue excision to RNA isolation was completed on the same day to avoid any unintended change in tissue condition by storage.

growth_protocol: 16 hr light; 8 hr dark at 20C on modified MS media

treatment_protocol: 35 days on stage-II

tag: Solanum tuberosum, Callused part of internodal segment distal end, Development

treatment_protocol: 28 days on stage-II


title: ytl_wt_vs_CP12_antisense_3


title: rpn8_vs_ev_8dpi_2


title: stage2_35d_vs_stage2_14d_3_FD

treatment_protocol: Stage-II


title: rpn9_vs_n_14dpi_3


title: rpn9_vs_n_16dpi_2


title: rpn9_vs_n_16dpi_1


title: stage2_21d_vs_stage2_28d_3

treatment_protocol: 21 days on stage-II


title: rpn9_vs_n_14dpi_2


title: stage2_35d_vs_stage2_14d_3


title: ytl_wt_vs_CP12_antisense_2


title: rpn9_vs_n_12dpi_3


title: stage3_35d_vs_stage2_14d_3

treatment_protocol: 14 days on stage-II followed by 21 days on stage-III


title: rpn9_vs_n_14dpi_1


title: stage2_21d_vs_stage2_28d_2


title: stage2_14d_vs_stage2_21d_3


title: stage3_28d_vs_stage3_35d_3

treatment_protocol: 14 days on stage-II followed by 14 days on stage-III


title: rpn9_vs_n_10dpi_2


title: stage2_14d_vs_stage3_21d_3

treatment_protocol: 14 days on stage-II followed by 7 days on stage-III


title: rpn9_vs_n_12dpi_2


title: stage3_21d_vs_stage3_28d_3


title: stage2_28d_vs_stage2_35d_2


title: rpn9_vs_n_12dpi_1


title: rpn9_vs_n_10dpi_3


title: rpn9_vs_n_10dpi_1


title: rpn9_vs_n_8dpi_3


title: rpn9_vs_n_8dpi_2


title: stage2_14d_vs_stage2_21d_2


title: stage2_35d_vs_stage2_14d_2


title: stage3_28d_vs_stage3_35d_2


title: stage2_14d_vs_stage1_0d_3

growth_protocol: 16 hr light; 8 hr dark at 20C on plain MS media

treatment_protocol: Freshly cut explants from stage-I cultures

tag: Solanum tuberosum, Internodal segment, Development


title: stage2_14d_vs_stage1_0d_2


title: non_GM_E_vs_GM_B_water_3

description: The goal of this study was to calculate the degree of substantial equivalence between a GM potato line modified for late blight resistance and corresponding non-GM controls in the presence/absence of P. infestans inoculation. The GM phenotype was conferred through the introduction of the Rb gene which has been previously cloned from Solanum bulbocastanum (Song et al. 2003). The resulting GM phenotype was characterised by the expression of strong, partial resistance to P. infestans. By obtaining an expression profile from a GM and non-GM population before and after exposure to P. infestans, this effectively provides for the completion of two risk assessments: impact on the potato transcriptome of plus/minus genetic modification; before and after exposure to the pathogen.  For each biological replicate, individuals from three separate GM lines (A, B, C) and three separate non-GM lines (D, E, F) were randomly sorted and cultivated for analysis. Each GM line contained an independent, single transgene insertion, which was verified through Southern Blot analysis. One day prior to pathogen exposure, the 4-week-old potato plants were transferred into a growth chamber with a 16-h light period, 90% relative humidity at a temperature of 15C. Plants were randomly selected and 14 individuals/line were inoculated with a field isolate of P. infestans. An additional 14 plants/line were sprayed with water. Inoculations were made with a sporangial suspension of 20,000/mL and plants were sprayed until run-off. Twenty-four hours post-inoculation, leaf tissue was collected from 9 plants per treatment, flash frozen in liquid nitrogen and pooled. Total leaf RNA was extracted using Trizol and the whole experiment was repeated three times (three biological replicates).

treatment_protocol: Challenged with water for 24h

tag: Solanum tuberosum, Leaf and petiole, Biotic stress


title: stage2_14d_vs_stage3_21d_2


title: non_GM_D_vs_GM_A_water_3FD


title: rpn9_vs_n_8dpi_1


title: stage3_21d_vs_stage3_28d_2


title: stage3_35d_vs_stage2_14d_2


title: non_GM_F_vs_GM_C_Pinf_3

treatment_protocol: Challenged with P.infestans for 24h


title: non_GM_E_vs_GM_B_Pinf_3


title: stage2_28d_vs_stage2_35d_1


title: non_GM_F_vs_GM_C_water_2


title: non_GM_D_vs_GM_A_Pinf_3


title: non_GM_F_vs_GM_C_water_1


title: non_GM_F_vs_GM_C_Pinf_2


title: non_GM_D_vs_GM_A_water_3


title: stage3_28d_vs_stage3_35d_1


title: non_GM_E_vs_GM_B_water_2


title: stage2_14d_vs_stage1_0d_1


title: stage3_21d_vs_stage3_28d_1


title: aphid_vs_PLRV_28d_3

description: Potato plants (cv. Russet Burbank) were grown as in vitro plantlets, and transplanted into 12-cm pots in Sunshine Mix #2 (peat/perlite mix) supplemented with slow release fertilizer (Osmocoat) in the greenhouse.  The experiment was conducted in the summer of 2004 at Moscow, ID.  Plantings were staggered to facilitate collection of volatiles and leaf samples during a short harvest window for all times of all treatments.  Infectious Green Peach Aphids were raised on PLRV-infected potato plants; test plants were infected by placing 10 infectious aphids on a leaf in a clip cage for 48 h.  The control plants for PLRV were similarly treated with aphids that had been raised on uninfected potato plants.  A local isolate of PVYO was inoculated mechanically using purified virus (5 ìg ml-1) in buffer (50 mM Na2HPO4, 20 mM Na2SO3 pH 7.0) lightly rubbed onto a leaf previously dusted with carborundum.  Control plants for PVY were treated in the same manner using buffer without PVY.  The RNA samples were made from systemically affected leaves, excluding the actual leaves inoculated by aphids or that received the mechanical infection.  Leaf volatiles were concurrently collected from equivalent plants; aliquots of frozen leaf samples were sent for metabolite analysis prior to RNA extraction.  Leaf harvests were made 1, 3, 7, 14, and 28 d post-inoculation.

growth_protocol: Greenhouse, ambient + supplemental light (metal halide)

treatment_protocol: PLRV aphid-infected, 28d

tag: Solanum tuberosum, Leaf, Biotic stress

treatment_protocol: Sham Inoc - aphid control, 28d


title: non_GM_F_vs_GM_C_Pinf_1


title: stage2_21d_vs_stage2_28d_1


title: non_GM_E_vs_GM_B_water_1


title: stage2_14d_vs_stage3_21d_1


title: stage3_35d_vs_stage2_14d_1


title: aphid_vs_PLRV_28d_2

treatment_protocol: PLRV, aphid-infected 28d

treatment_protocol: PVY-Buffer control, 28d


title: stage2_35d_vs_stage2_14d_1


title: non_GM_E_vs_GM_B_Pinf_1


title: non_GM_D_vs_GM_A_Pinf_1


title: PLRV_vs_aphid_28d_2_FD

label_protocol: mino allyl labeling and direct labeling (SGED_SOP_5.1.1 + SGED_SOP_6.1.1)


title: non_GM_D_vs_GM_A_water_2


title: non_GM_E_vs_GM_B_Pinf_2


title: control_vs_PVY_28d_3

treatment_protocol: PVY innoculated, 28d


title: non_GM_D_vs_GM_A_water_1


title: control_vs_PVY_28d_2


title: stage2_14d_vs_stage2_21d_1


title: control_vs_PVY_28d_1


title: Mock3_vs_PNRSV3_systemic_leaf

description: Objectives: Our work focuses on the responses of Solanaceous plants to viruses that cause economically important diseases in tree fruits.  Using mock inoculated leaf tissue as a reference, we plan to compare the gene expression profiles of Nicotiana Benthamiana plants infected with one of three viruses; Plum Pox Potyvirus (PPV), Tomato Ringspot Nepovirus (ToRSV), and Prunus Nectrotic Ringspot Nepovirus (PNRSV).  Our goals are as follows: (1) Identify genes that are induced/repressed in response to individual viruses. (2) Identify genes that are induced/repressed in response to all 3 viruses. (3) Compare results to existing potato array data to look for similarities in responses to other pathogens.  Experimental Design: Nicotiana benthamiana plants were inoculated with one of three viruses: PPV, ToRSV, or PNRSV.  3 week old plants were inoculated by rubbing virus infected plant sap onto leaves dusted with carborundum.  Control plants were mock inoculated using sap from healthy plants.  All plants were maintained in a growth chamber at 22C for 18 days.  8 plants were inoculated with each virus or mock inoculated.  This experiment was repeated twice.  4 biological replicates derived from 2 virus infected plants from each replica experiment (4 plants) are to be used for hybridizations.  RNA from all mock inoculated plants was similarly pooled to create 4 biological replicates.  Each replicate control will serve as a universal reference sample that is to be hybridized pair wise with each of the three virus infected samples.  RNA extraction: After 18 days, un-inoculated leaves displaying clear symptoms were harvested and immediately frozen in liquid N2.  Total RNA was purified using Trizol according to TIGRs listed protocol.  RNA was subsequently treated with Turbo DNA-free RNase (Ambion cat#1907).  Finally, total RNA was further purified on RNeasy columns (Qiagen) according to manufacturer’s instructions and quantified using a Nanodrop spectrophotometer.

growth_protocol: Grown for 18 days in growth chamber (16h/8h light/darkness, 50% humidity, 22°C) in Jiffy mix 50/50.

treatment_protocol: Systemically infected with sap containing prunus necrotic ringspot virus

tag: Nicotiana benthamiana, Whole leaf, Biotic stress

treatment_protocol: Mock infected with sap from healthy plant


title: aphid_vs_PLRV_28d_1


title: aphid_vs_PLRV_14d_3

treatment_protocol: PLRV aphid-infected, 14d

treatment_protocol: Sham Inoc - aphid control, 14d


title: Mock2_vs_PNRSV2_systemic_leaf


title: control_vs_PVY_14d_3

treatment_protocol: PVY innoculated, 14d

treatment_protocol: PVY-Buffer control, 14d


title: control_vs_PVY_14d_2


title: aphid_vs_PLRV_14d_2


title: Mock1_vs_PNRSV1_systemic_leaf


title: control_vs_PVY_14d_1


title: aphid_vs_PLRV_14d_1


title: Mock3_vs_ToRSV3_systemic_leaf

treatment_protocol: Systemically infected with sap containing tomato ringspot virus


title: Mock4_vs_ToRSV4_systemic_leaf


title: PNRSV1_vs_Mock1_systemic_leaf


title: Mock2_vs_ToRSV2_systemic_leaf


title: control_vs_PVY_7d_3

treatment_protocol: PVY innoculated, 7d

treatment_protocol: PVY-Buffer control, 7d


title: control_vs_PVY_7d_2


title: Mock1_vs_ToRSV1_systemic_leaf


title: PNRSV4_vs_Mock4_systemic_leaf


title: aphid_vs_PLRV_7d_2

treatment_protocol: PLRV aphid-infected, 7d

treatment_protocol: Sham Inoc - aphid control, 7d


title: aphid_vs_PLRV_7d_1


title: PNRSV3_vs_Mock3_systemic_leaf


title: ToRSV3_vs_Mock3_systemic_leaf


title: non_GM_F_vs_GM_C_water_3

treatment_protocol: Challenged with water for 24h


title: control_vs_PVY_7d_1


title: ToRSV1_vs_Mock1_systemic_leaf


title: ToRSV2_vs_Mock2_systemic_leaf


title: Mock4_vs_PPV4_systemic_leaf

treatment_protocol: Systemically infected with plant sap containing plum pox virus


title: control_vs_PVY_3d_3

treatment_protocol: PVY innoculated, 3d

treatment_protocol: PVY-Buffer control, 3d


title: control_vs_PVY_3d_1


title: aphid_vs_PLRV_3d_1

treatment_protocol: PLRV aphid-infected, 3d

treatment_protocol: Sham Inoc - aphid control, 3d


title: Mock1_vs_PPV1_systemic_leaf


title: non_GM_D_vs_GM_A_Pinf_2

treatment_protocol: Challenged with P.infestans for 24h


title: control_vs_PVY_1d_3

treatment_protocol: PVY innoculated, 1d

treatment_protocol: PVY-Buffer control, 1d


title: PPV3_vs_Mock3_systemic_leaf

treatment_protocol: Mock infected with sap from healthy plant


title: aphid_vs_PLRV_3d_2


title: PPV4_vs_Mock4_systemic_leaf


title: Mock3_vs_PPV3_systemic_leaf