title: Yeast replication MMS 90min a

growth_protocol: Growth protocol 	Density transfer experiments were performed essentially as described to isotopically label newly replicated DNA (see the Fangman-Brewer lab website at UW). Cells were grown a minimum of 7 generations in minimal medium containing 13C and 15N as the sole carbon and nitrogen sources (dense media). Cells were synchronized with α-factor for 105 minutes. Cells were then filtered and transferred to complete media (YC) containing 12C and 14N (light media) in the continued presence of α-factor for 75 minutes prior to release (termed conditioning phase). MMS was added to 0.015% 15 minutes into the conditioning phase resulting in a 60-minute exposure during G1 arrest. After the conditioning phase, cells were filtered, washed, and released in light media in the presence or absence of 0.015% MMS. This sample was collected at 90 min after release.


title: BiMP ColBS+ normalized

status: Public on Nov 30 2007

type: genomic

city: Genève

first: Jon

last: Reinders

state: Genève

address: 30 quai Ernest-Ansermet

department: Department of Plant Biology

country: Switzerland

institute: Universite de Geneve

description: two sample analysis ((Col_bs+1, Col_bs+2, Col_bs+3) and (non-treated gDNA1, non-treated gDNA2, non-treated gDNA3)), as experimental and control, respectively.

hyb_protocol: Following a 2 hour fragmentation, 9 ug of DNA were hybridized for 16 hr at 45C on Arabidopsis Tiling 1.0R arrays . GeneChips were washed and stained as directed by Affymetrix

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

data_processing: Arabidopsis data (CEL) files were analyzed using the Tiling Analysis Software (TAS, Affymetrix) using the following parameters. The normalization parameters were scaled to an intensity of 100 on a log2 scale and the p-value was -10log10. The probe analysis was set to a bandwidth of 80 and perfect match/mismatch intensities were analyzed using a one-sided upper test. The interval analysis on intensity values was set to a threshold of 1-e5 with a maximum gap of 80 and a minimum run to 40, resulting in a “sliding window” analysis at a 161 bp length. For analyzing methylation polymorphisms, hypo- and hypermethylated intervals were calculated using TAS. Per entry, the three biological replicate bisulfite-treated DNA files and the three biological replicate non treated DNA files were selected as the treatment and control group files, respectively, in a two sample comparison analysis using quantile normalization of both groups together. The resulting ColBS+ and met1-3BS+ BAR files, for the above two-sample comparisons, were loaded into IGB (Affymetrix). Since IGB performs only a one-sided statistical test, hypomethylated and hypermethylated comparisons were made separately. The hypomethylation graph was the difference in the log2 scaled (Col_BS+) from (met1-3_BS+) results and the hypermethylation was the difference in the log2 scaled (met1-3_BS+) from (Col_BS+). The graphs of these comparisons were adjusted to zero and the positive cutoff of 4.0 was applied. Additionally, the three CEL files per entry were analyzed in TAS using the one sample detection analysis to create a single BAR files for each entry alone. The one sample parameter were as above and allowed further visual inspection and comparison.

label: biotin

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: see description for corresponding files

label_protocol: DNA was amplified using our BiMP amplification method. DNA labeling reaction with terminal deoxynucleotidyl transferase and DNA labeling reagent (Affymetrix) were added to each DNA sample

growth_protocol: Plants were grown in soil under under 8 hr light/16 hr dark. Leaf tissue from 9-12 individuals was pooled per DNA sample.  Thre replicate samples per entry were collected.

extract_protocol: For the bisulfite treatment, the EpiTect Bisulfite modification kit (Qiagen) was used as directed by the manufacturer.

treatment_protocol: CTAB extracted DNA samples were Rnase A and Proteinase K treated (Warnecke et al. 2002), phenol extracted (Sigma) and then ethanol precipitated. DNA samples (4.0μg) were digested with a 2-fold excess of DraI restriction enzyme (Promega), as recommended by the manufacturer, and phenol extracted (Sigma) and ethanol precipitated.

tag: Genotype

value: M/M; treatment:bisulfite +


title: Yeast replication MMS 45min a

city: Seattle

first: Jack

middle: A.

last: Vincent

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences

country: USA

institute: Fred Hutchinson CRC

description:
Unreplicated vs Replicated DNA during MMS treatment
45 min time-point

hyb_protocol: Hybridization protocol 	• hybridization buffer: 3X SSC + 10%SDS + 1 mg/mL poly(dA) • blocking agent: no prehybridization • slide blocking: no prehybridization • probe blocking: 1mg/mL polydA during hybridization • wash procedure: wash1: 1X SSC, 0.03% SDS wash2: 1X SSC dip slides 15 times wash3: 0.2X SSC: shake slides 75rpm for 20minutes wash4: 0.05X SSC: shake slides 75rpm for 10 minutes spin-dry slides in centrifuge 50g for 5 minutes. • quantity of labelled target used: all material generated from 0.5 ug of EcoRI digested genomic DNA • time, concentration, volume, temperature: 16h, 26 microliters at 63°C • Hybridization instrument: Manual, TelChem hybridization chambers in waterbath

scan_protocol: Scanning hardware GenePix 4000B scanner (Molecular Devices) Image analysis GenePix Pro v6.0 (Molecular Devices)

data_processing:
Percent replication for each spot was determined as described (Alvino, GM et al, Mol Cell Bio, 2007). The calculation of percent replication at each time point is dependent on two measurements; the percentage of total genomic replication in the population at each time point and the number of cycling cells over the entire time course.
• Total genomic % replication:
The total percent replication for the genome was determined after fractionation of each CsCl gradient. Fractions were blotted to a nylon membrane and then hybridized to a radiolabeled genomic probe (as described above). Percent replication was determined by quantifying the signal from each fraction (by phosphorimager), plotting the value for each fraction, and then comparing the area under the curve corresponding to replicated and unreplicated fractions (see http://fangman-brewer.genetics.washington.edu/density_transfer.html). The total % replication for this sample was as follows:
45min 31%
• Ratio of cycling cells:
The ratio of cycling cells to non-cycling cells was estimated from the maximum percentage of budded cells obtained during the time course. The maximum percent budded was 94% for WT experiments.

organism: Saccharomyces cerevisiae

source_name: S.cerevisiae, 45min post alpha factor, 0.015% MMS, unreplicated DNA

label_protocol: 0.5ug of each sample was labeled with either Cy3 or Cy5-dUTP (GE Biosciences). 21ul DNA solution was heat denatured at 100°C for 5 min then quick chilled in an ice slurry. The following was added while samples were still on ice: 5ul 10x dNTP Mix (1.2mM each dATP, dCTP, dGTP; 0.6mM dTTP; 10mM Tris 8.0), 3ul Cy-dUTP, 1ul exo- Klenow (50000 U/ml, New England Biolabs). Samples were incubated at 37°C for 1hr. Reaction was stopped by adding 5ul 0.5M EDTA. 60ul of 1mg/ml tRNA was added to each reaction and unincorporated nucleotides were removed using a Biospin 30 column (BioRad). Oppositely labeled samples (i.e. Cy3-replicated and Cy5-unreplicated) from the same timepoint were combined for cohybridization. 20ul polydA::dT (1mg/ml; Sigma) was added to each probe mix, then DNA was precipitated after addition of 1/10 volume 3M NaOAc and 2 volumes 100% ethanol.

growth_protocol: Growth protocol 	Density transfer experiments were performed essentially as described to isotopically label newly replicated DNA (see the Fangman-Brewer lab website at UW). Cells were grown a minimum of 7 generations in minimal medium containing 13C and 15N as the sole carbon and nitrogen sources (dense media). Cells were synchronized with α-factor for 105 minutes. Cells were then filtered and transferred to complete media (YC) containing 12C and 14N (light media) in the continued presence of α-factor for 75 minutes prior to release (termed conditioning phase). MMS was added to 0.015% 15 minutes into the conditioning phase resulting in a 60-minute exposure during G1 arrest. After the conditioning phase, cells were filtered, washed, and released in light media in the presence or absence of 0.015% MMS. This sample was collected at 45 min after release.

extract_protocol:
Standard Yeast genomic prep: Bead beating + phenol:chloroform extraction.
Unreplicated DNA was separated from replicated DNA in a CsCl gradient (see the Fangman-Brewer lab website at UW.)
The CsCl gradient was drip-fractionated. Fractions were then applied to slot blots and probed for DNA content. Fractions from the bottom of the gradient (the most dense fractions) contain unreplicated DNA, while fractions from the top of the gradient (least dense fractions) contain newly replicated DNA. Fractions containing unreplicated DNA (or replicated DNA) were pooled and EtOH precipitated.

tag: Strain

tag: Collected 45 minutes post alpha factor release.

tag: Treated with MMS at 0.015%

tag: Unreplicated DNA

source_name: S.cerevisiae, 45min post alpha factor, 0.015% MMS, replicated DNA

label_protocol: same as channel 1

growth_protocol: same as channel 1

extract_protocol: same as channel 1

tag: replicated DNA


title: Yeast replication MMS 45min b


title: S. pombe Rad21 binding pattern, ssl3-wt in HU (2)

city: Bethesda

first: Christine

middle: Katrin

last: Schmidt

state: MD

address: 41 Library Drive, Bldg. 41, C619

department: LRBGE

institute: NCI (NIH)

description: no additional information

hyb_protocol: Labeled DNA was hybridised to microarrays in an Affymterix Gene Chip Hybridisation Oven 640 for 16h at 42°C & 60rpm. For washing and staining the EukGe_WS1_v4_450 fluidics protocol was run on an Affymetrix Gene Chip Fluidics Station (version 450). Staining included only one step with SAPE.

scan_protocol: Microarray scanning was performed with an Affymetrix Gene Chip Scanner 3000.

data_processing: The Affymetrix Gene Chip Operating Software GCOS, version 1.4,  was used for data processing.

label: biotin-11-ddATP (NEL548)

organism: Schizosaccharomyces pombe

source_name: Chromatin-immunoprecipitated DNA

label_protocol: DNA was labeled with biotin-11-ddATP using terminal transferase TdT (Roche, 400U/µl).

extract_protocol: ChIP and microarray analysis were carried out essentially as previously described (Katou et al., 2003, see below). In short, 2x10^9 cells were fixed with 1% formaldehyde for half an hour at room temperature. Cell extracts were prepared using a multibeads shocker (Yasui Kikai). After sonication (Sanyo Soniprep150) genomic DNA fragments of 400-800bp were retrieved and taken for ChIP. We used anti-HA mouse monoclonal 12CA5 antibody (CRUK production) against the HA-tagged cohesin subunit Rad21 in conjunction with protein A magnetic dynabeads (Dynal). The eluted immunoprecipitates were incubated overnight at 65°C to reverse the cross-linking. The genomic DNA was purified and amplified by random primer PCR.

tag: strain 1785

value: h- leu1-32 ura4-D18 ade6-210 ssl3::ura4+ ars1-ssl3+-LEU2 rad21-3HA-kanR

tag: Cells were arrested for 9h at 20°C in rich medium (YE4S) in early S-phase using 20mM hydroxyurea, then shifted to 37°C for 3h using a fresh batch of 20mM hydroxyurea. Experiment was performed as a control in parallel to a strain with an ssl3-29ts background (20°C permissive, 37°C restrictive temperature for the ssl3 mutant)


title: S. pombe Rad21 binding pattern, ssl3-ts in HU (2)

description: no additional information

extract_protocol:
ChIP and microarray analysis were carried out essentially as previously described (Katou et al., 2003, see below). In short, 2x10^9 cells were fixed with 1% formaldehyde for half an hour at room temperature. Cell extracts were prepared using a multibeads shocker (Yasui Kikai). After sonication (Sanyo Soniprep150) genomic DNA fragments of 400-800bp were retrieved and taken for ChIP. We used anti-HA mouse monoclonal 12CA5 antibody (CRUK production) against the HA-tagged cohesin subunit Rad21 in conjunction with protein A magnetic dynabeads (Dynal). The eluted immunoprecipitates were incubated overnight at 65°C to reverse the cross-linking. The genomic DNA was purified and amplified by random primer PCR.
Reference:
Katou, Y., Kanoh, Y., Bando, M., Noguchi, H., Tanaka, H., Ashikari, T., Sugimoto, K. and Shirahige, K. (2003) S-phase checkpoint proteins Tof1 and Mrc1 form a stable replication-pausing complex. Nature, 424, 1078-1083.

tag: strain 1783

value: h- leu1-32 ura4-D18 ade6-210 ssl3::ura4+ ars1-ssl3-29ts-LEU2 rad21-3HA-kanR

tag: Cells were arrested for 9h at the permissive temperature of 20°C in rich medium (YE4S) in early S-phase using 20mM hydroxyurea. To inactivate Ssl3, cells were subsequently shifted to the restrictive temperature of 37°C for 3h using a fresh batch of 20mM hydroxyurea.


title: Yeast replication MMS 30min b

description:
Unreplicated vs Replicated DNA during MMS treatment
30 min time-point

data_processing:
Percent replication for each spot was determined as described (Alvino, GM et al, Mol Cell Bio, 2007). The calculation of percent replication at each time point is dependent on two measurements; the percentage of total genomic replication in the population at each time point and the number of cycling cells over the entire time course.
• Total genomic % replication:
The total percent replication for the genome was determined after fractionation of each CsCl gradient. Fractions were blotted to a nylon membrane and then hybridized to a radiolabeled genomic probe (as described above). Percent replication was determined by quantifying the signal from each fraction (by phosphorimager), plotting the value for each fraction, and then comparing the area under the curve corresponding to replicated and unreplicated fractions (see http://fangman-brewer.genetics.washington.edu/density_transfer.html). The total % replication for this sample was as follows:
30min 12%
• Ratio of cycling cells:
The ratio of cycling cells to non-cycling cells was estimated from the maximum percentage of budded cells obtained during the time course. The maximum percent budded was 94% for WT experiments.

source_name: S.cerevisiae, 30min post alpha factor, 0.015% MMS, replicated DNA

growth_protocol: Growth protocol 	Density transfer experiments were performed essentially as described to isotopically label newly replicated DNA (see the Fangman-Brewer lab website at UW). Cells were grown a minimum of 7 generations in minimal medium containing 13C and 15N as the sole carbon and nitrogen sources (dense media). Cells were synchronized with α-factor for 105 minutes. Cells were then filtered and transferred to complete media (YC) containing 12C and 14N (light media) in the continued presence of α-factor for 75 minutes prior to release (termed conditioning phase). MMS was added to 0.015% 15 minutes into the conditioning phase resulting in a 60-minute exposure during G1 arrest. After the conditioning phase, cells were filtered, washed, and released in light media in the presence or absence of 0.015% MMS. This sample was collected at 30 min after release.

extract_protocol:
Standard Yeast genomic prep: Bead beating + phenol:chloroform extraction.
Unreplicated DNA was separated from replicated in a CsCl gradient (see the Fangman-Brewer lab website at UW.)
The CsCl gradient was drip-fractionated. Fractions were then applied to slot blots and probed for DNA content. Fractions from the bottom of the gradient (the most dense fractions) contain unreplicated DNA, while fractions from the top of the gradient (least dense fractions) contain newly replicated DNA. Fractions containing unreplicated DNA (or replicated DNA) were pooled and EtOH precipitated.

tag: Collected 30 minutes post alpha factor release.

source_name: S.cerevisiae, 30min post alpha factor, 0.015% MMS, unreplicated DNA


title: Yeast replication MMS 30min a

hyb_protocol: •	hybridization buffer: 3X SSC + 10%SDS + 1 mg/mL poly(dA) •	blocking agent: no prehybridization •	slide blocking: no prehybridization •	probe blocking: 1mg/mL polydA during hybridization •	wash procedure: wash1: 1X SSC, 0.03% SDS wash2: 1X SSC dip slides 15 times wash3: 0.2X SSC: shake slides 75rpm for 20minutes wash4: 0.05X SSC: shake slides 75rpm for 10 minutes spin-dry slides in centrifuge 50g for 5 minutes. •	quantity of labelled target used: all material generated from 0.5 ug of EcoRI digested genomic DNA •	time, concentration, volume, temperature: 16h, 26 microliters at 63°C •	Hybridization instrument: Manual, TelChem hybridization chambers in waterbath

data_processing:
Percent replication for each spot was determined as described (Alvino, GM et al, Mol Cell Bio, 2007). The calculation of percent replication at each time point is dependent on two measurements; the percentage of total genomic replication in the population at each time point and the number of cycling cells over the entire time course.
•	Total genomic % replication:
The total percent replication for the genome was determined after fractionation of each CsCl gradient. Fractions were blotted to a nylon membrane and then hybridized to a radiolabeled genomic probe (as described above). Percent replication was determined by quantifying the signal from each fraction (by phosphorimager), plotting the value for each fraction, and then comparing the area under the curve corresponding to replicated and unreplicated fractions (see http://fangman-brewer.genetics.washington.edu/density_transfer.html). The total % replication for this sample was as follows:
30min	12%
•	Ratio of cycling cells:
The ratio of cycling cells to non-cycling cells was estimated from the maximum percentage of budded cells obtained during the time course. The maximum percent budded was 94% for WT experiments.

growth_protocol: Density transfer experiments were performed essentially as described to isotopically label newly replicated DNA (see the Fangman-Brewer lab website at UW). Cells were grown a minimum of 7 generations in minimal medium containing 13C and 15N as the sole carbon and nitrogen sources (dense media). Cells were synchronized with α−factor for 105 minutes. Cells were then filtered and transferred to complete media (YC) containing 12C and 14N (light media) in the continued presence of α−factor for 75 minutes prior to release (termed conditioning phase). MMS was added to 0.015% 15 minutes into the conditioning phase resulting in a 60-minute exposure during G1 arrest. After the conditioning phase, cells were filtered, washed, and released in light media in the presence or absence of 0.015% MMS. This sample was collected at 30 min after release.

label_protocol: Same as channel 1

tag: Replicated DNA


title: 13420186 - t-but+SA_1 vs SA_1

status: Public on Nov 29 2007

type: RNA

city: Evry Cedex

first: Agnes

last: Yu

address: 2 rue Gaston Cremieux CP 5708

department: URGV

country: France

institute: INRA

description: Our goal is to identify SA responsive genes dependent on PLD activation.

hyb_protocol: SA_1 Cy5 / t-but+SA_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 520V,laser power 100%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

molecule: total RNA

label_protocol: labelling Cy3 and Cy5 indirect, amplification=yes, 1 ug total RNA used for amplification (Ambion kit) to produce aRNA. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37°C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: cell culture - cells in Gamborg

extract_protocol: Qiagen RNeasy Plant Mini Kit

treatment_protocol: Name:PLD-SA_sterile-water1 - compound based treatment - compound addition,water:. 87.5 uL waterName: - compound based treatment - compound addition,salicylic acid:quantity .25mM . 15 min after first treatment : add 35 uL of SA 50 mM

tag: Arabidopsis thaliana (columbia)  - age:4.25hour

treatment_protocol: Name:PLD-SA_t-but - compound based treatment - compound addition,t-butanol:quantity .1percent . 87.5 uL of 8% t-butanolName: - compound based treatment - compound addition,salicylic acid:quantity .25mM . 15 min after first treatment : add 35 uL of SA 50 mM


title: Non-tumorous liver tissues of parkin-/- mice compared with normal livers of wild-type mice

city: Kyoto

first: mikio

last: fujiwra

address: 54 Kawahara-cho, Shogoin Sakyo-ku

country: Japan

institute: Kyoto University

description: There are no additional information.

hyb_protocol: First-strand cDNA was synthesized from 500 ng of total RNA in the presence of Cy5 or Cy3 dCTP. The Cy3- and Cy5-labeled samples derived from wild-type and parkin–/– mice at 72 weeks of age were injected simultaneously into the same spot of the whole mouse 60-mer oligo microarray (Agilent Technologies, Palo Alto, CA). After hybridization at 65 ℃ for 17 h, the slides were washed with 6 × SSC containing 0.005% TritonX-102, and dried using a nitrogen-filled air gun.

scan_protocol: feature extraction was performed using an Agilent G2565AA Microarray Scanner with feature extraction software (version 8.5.1.1; Agilent Technologies).

data_processing:
Data were analysed  using Agilent Feature Extraction Software version
8.5.1.1. A rank consistency filter and LOWESS were used for dye normalization.

organism: Mus musculus

source_name: non-tumorous liver tissues of parkin–/– mice

label_protocol:
The RNA was amplified and labeled by the Low RNA Input Fluorescent Linear Amplification Kit (Agilent). To synthesize cDNA, 500 ng total RNA
was used. Sample were labeled by cyanine5 (PerkinElmer Life Science, Inc., Boston, MA).

extract_protocol: total RNA was extracted from tissues using RNA assay Mini Kit (Qiagen)

tag: strain

value: 129/C57BL6SJL (75/25) genetic background (parkin-/- mice), age:72weeks, tissue:non-tumorous liver tissue

source_name: normal liver tissues of wild-type mice

tag: age

value: 72weeks, tissue:normal liver tissue


title: 13420194 - t-but_1 vs CO_1

hyb_protocol: CO_1 Cy5 / t-but_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:PLD-SA_sterile-water1 - compound based treatment - compound addition,water:. 87.5 uL waterName: - compound based treatment - compound addition,water:. 15 min after first treatment : add 35 uL water

treatment_protocol: Name:PLD-SA_t-but - compound based treatment - compound addition,t-butanol:quantity .1percent . 87.5 uL of 8% t-butanolName: - compound based treatment - compound addition,water:. 15 min after first treatment : add 35 uL water


title: Pombe Sup/WCE fraction (1)

description: no additional information

source_name: genomic DNA

extract_protocol:
Genomic DNA was prepared essentially as previously described (Katou et al., 2003, see below). 2x10^9 cells were fixed with 1% formaldehyde for half an hour at room temperature. Cell extracts were prepared using a multibeads shocker (Yasui Kikai). After sonication (Sanyo Soniprep150) genomic DNA fragments of 400-800bp were retrieved and a small fraction was directly taken for DNA purification, amplification and labeling (SUP sample).
Reference:
Katou, Y., Kanoh, Y., Bando, M., Noguchi, H., Tanaka, H., Ashikari, T., Sugimoto, K. and Shirahige, K. (2003) S-phase checkpoint proteins Tof1 and Mrc1 form a stable replication-pausing complex. Nature, 424, 1078-1083.


title: 13420181 - SA_2 vs t-but+SA_2

hyb_protocol: t-but+SA_2 Cy5 / SA_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13420189 - t-but_2 vs CO_2

hyb_protocol: CO_2 Cy5 / t-but_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13420193 - CO_1 vs t-but_1

hyb_protocol: t-but_1 Cy5 / CO_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Pombe Sup/WCE fraction (2)

description: no additional information

tag: Normalisation for pombe Rad21 binding patterns GSM209792 & GSM209796, HU arrested in YE4S, whole genomic DNA was used for hybridisation


title: Tumorous liver tissues of parkin-/- mice compared with normal livers of wild-type mice

description: There are no additional information.

source_name: tumorous liver tissues in parkin–/– mice

value: 129/C57BL6SJL (75/25) genetic background (parkin-/- mice), age:72weeks, tissue:tumorous liver tissue

source_name: normal liver tissues in wild-type mice

value: 72weeks, tissue:normal liver tissues


title: 13420185 - t-but+SA_2 vs SA_2

hyb_protocol: SA_2 Cy5 / t-but+SA_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13420188 - SA_1 vs t-but+SA_1

hyb_protocol: t-but+SA_1 Cy5 / SA_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: S. pombe Rad21 binding pattern, ssl3-29ts in HU

description: no additional information

extract_protocol:
ChIP and microarray analysis were carried out essentially as previously described (Katou et al., 2003, see below). In short, 2x10^9 cells were fixed with 1% formaldehyde for half an hour at room temperature. Cell extracts were prepared using a multibeads shocker (Yasui Kikai). After sonication (Sanyo Soniprep150) genomic DNA fragments of 400-800bp were retrieved and taken for ChIP. We used anti-HA mouse monoclonal 16B12 antibody (Babco) against the HA-tagged cohesin subunit Rad21 in conjunction with protein A magnetic dynabeads (Dynal). The eluted immunoprecipitates were incubated overnight at 65°C to reverse the cross-linking. The genomic DNA was purified and amplified by random primer PCR.
Reference:
Katou, Y., Kanoh, Y., Bando, M., Noguchi, H., Tanaka, H., Ashikari, T., Sugimoto, K. and Shirahige, K. (2003) S-phase checkpoint proteins Tof1 and Mrc1 form a stable replication-pausing complex. Nature, 424, 1078-1083.

tag: Cells were arrested for 8.5h at the permissive temperature of 20°C in rich medium (YE4S) in early S-phase using 20mM hydroxyurea. To inactivate Ssl3, cells were subsequently shifted to the restrictive temperature of 36°C for 3h using a fresh batch of 20mM hydroxyurea.


title: 13420195 - CO_2 vs t-but_2

hyb_protocol: t-but_2 Cy5 / CO_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13561541 - SA_2 vs n-but+SA_2

hyb_protocol: n-but+SA_2 Cy5 / SA_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 620V,laser power 100%

treatment_protocol: Name:PLD-SA_n-but - compound based treatment - compound addition,n-butanol:quantity .1percent . 87.5 uL of 8% n-butanolName: - compound based treatment - compound addition,salicylic acid:quantity .25mM . 15 min after first treatment : add 35 uL of SA 50 mM


title: 13561528 - n-but+SA_2 vs t-but+SA_2

hyb_protocol: t-but+SA_2 Cy5 / n-but+SA_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13561531 - n-but_2 vs CO_2

hyb_protocol: CO_2 Cy5 / n-but_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:PLD-SA_n-but - compound based treatment - compound addition,n-butanol:quantity .1percent . 87.5 uL of 8% n-butanolName: - compound based treatment - compound addition,water:. 15 min after first treatment : add 35 uL water


title: 13561416 - SA_2 vs CO_2

hyb_protocol: CO_2 Cy5 / SA_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13561539 - n-but+SA_1 vs SA_1

hyb_protocol: SA_1 Cy5 / n-but+SA_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13561542 - n-but+SA_2 vs SA_2

hyb_protocol: SA_2 Cy5 / n-but+SA_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13561529 - t-but+SA_2 vs n-but+SA_2

hyb_protocol: n-but+SA_2 Cy5 / t-but+SA_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13561530 - CO_2 vs n-but_2

hyb_protocol: n-but_2 Cy5 / CO_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13561527 - t-but+SA_1 vs n-but+SA_1

hyb_protocol: n-but+SA_1 Cy5 / t-but+SA_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: S. pombe Rad21 binding pattern, ssl3-wt in HU

description: no additional information

hyb_protocol: Labeled DNA was hybridised to microarrays in an Affymterix Gene Chip Hybridisation Oven 640 for 16h at 42°C & 60rpm. For washing and staining the EukGe_WS1_v4_450 fluidics protocol was run on an Affymetrix Gene Chip Fluidics Station (version 450). Staining included only one step with SAPE.

tag: Cells were arrested for 8.5h at 20°C in rich medium (YE4S) in early S-phase using 20mM hydroxyurea, then shifted to 36°C for 3h using a fresh batch of 20mM hydroxyurea. Experiment was performed as a control in parallel to a strain with an ssl3-29ts background (20°C permissive, 36°C restrictive temperature for the ssl3 mutant)


title: 13561415 - CO_2 vs SA_2

hyb_protocol: SA_2 Cy5 / CO_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13561544 - n-but_2 vs t-but_2

hyb_protocol: t-but_2 Cy5 / n-but_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13557364 - n-but_1 vs t-but_1

hyb_protocol: t-but_1 Cy5 / n-but_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13561519 - SA_1 vs n-but+SA_1

hyb_protocol: n-but+SA_1 Cy5 / SA_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13561412 - n-but+SA_1 vs t-but+SA_1

hyb_protocol: t-but+SA_1 Cy5 / n-but+SA_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13561408 - t-but_2 vs n-but_2

hyb_protocol: n-but_2 Cy5 / t-but_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13557362 - t-but_1 vs n-but_1

hyb_protocol: n-but_1 Cy5 / t-but_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13557353 - CO_1 vs SA_1

hyb_protocol: SA_1 Cy5 / CO_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13557361 - n-but_1 vs CO_1

hyb_protocol: CO_1 Cy5 / n-but_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13557358 - CO_1 vs n-but_1

hyb_protocol: n-but_1 Cy5 / CO_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13561410 - SA_1 vs CO_1

hyb_protocol: CO_1 Cy5 / SA_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Radioresistant tumor-24 hours post-IR-rep1

status: Public on Nov 28 2007

city: Chicago

first: Nikolai

middle: N.

last: Khodarev

state: IL

address: 5841 South Maryland Avenue

department: Radiation and Cellular Oncology

institute: The University of Chicago

description: Gene expression data from radioresistant tumor, 24 hours after irradiation at 3Gy

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on U133A Human GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Agilent GeneArray Scanner

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 700-800.

organism: Homo sapiens

source_name: tumor xenografts in nude mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: SCC-61 and nu61 xenografts were generated and allowed to grow to a volume of 150-200 mm3. At that time,tumors were either irradiated at 3Gy or left un-treated and 5 or 24 hours later they were collected for RNA purification

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

treatment_protocol: Tumors were excised, frozen in liquid nitrogen and stored at -80C

tag: Squamous cell carcinoma


title: Radiosensitive tumor-24 hours post-IR-rep2

description: Gene expression data from radiosensitive tumor, 24 hours after irradiation at 3Gy


title: Radiosensitive tumor-5 hours post-IR-rep3

description: Gene expression data from radiosensitive tumor, 5 hours after irradiation at 3Gy


title: Radioresistant tumor-24 hours post-IR-rep3


title: Radioresistant tumor-5 hours post-IR-rep1

description: Gene expression data from radioresistant tumor, 5 hours after irradiation at 3Gy


title: Radioresistant tumor-24 hours post-IR-rep2


title: Radiosensitive tumor-untreated-rep1 (c1)

description: Gene expression data from radiosensitive tumor


title: Radiosensitive tumor-irradiated-rep1

growth_protocol: SCC-61 and nu61 xenografts were generated and allowed to grow to a volume of 150-200 mm3. At that time,tumors were either irradiated at 3Gy or left un-treated and 5 hours later they were collected for RNA purification


title: Radiosensitive tumor-5 hours post-IR-rep1


title: Radioresistant tumor-untreated-rep3 (c3)

description: Gene expression data from radioresistant tumor


title: Radioresistant tumor-5 hours post-IR-rep2


title: Radiosensitive tumor-24 hours post-IR-rep3


title: Radiosensitive tumor-untreated-rep2 (c2)


title: Radioresistant tumor-5 hours post-IR-rep3


title: Radioresistant tumor-untreated-rep2 (c2)


title: Radiosensitive tumor-untreated-rep3


title: Radiosensitive tumor-irradiated-rep2


title: Radiosensitive tumor-irradiated-rep3


title: Radioresistant tumor-irradiated-rep2


title: Radiosensitive tumor-untreated-rep1


title: Radiosensitive tumor-untreated-rep3 (c3)


title: Radiosensitive tumor-5 hours post-IR-rep2


title: Radioresistant tumor-irradiated-rep3


title: Radiosensitive tumor-untreated-rep2


title: Radiosensitive tumor-24 hours post-IR-rep1


title: Radioresistant tumor-untreated-rep1 (c1)


title: Radioresistant tumor-untreated-rep3


title: Radioresistant tumor-irradiated-rep1


title: Radioresistant tumor-untreated-rep2


title: deltaZFS_BioRep1

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression analysis was conducted using C. Elegans Genome Genechip® arrays (Affymetrix, Santa Clara, CA).  Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3’ Amplification One-Cycle Target labeling kit according to manufacturer’s protocol.  For each array, 5ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.  Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450 with the Mini_euk2v3 protocol.  Arrays were then scanned with an Affymetrix Scanner 3000.  Data was obtained using the Genechip® Operating Software.

data_processing: The resulting files (.dat, .cel and .chp) were imported into the Rosetta Resolver system and the S. cerevisae probe sets were masked out prior to data pre-processing and error modeling (Weng et al., Bioinformatics, 2006).

source_name: S.pombe strain with zfs1 deficiency

growth_protocol: Strains were grown at 30°C in Edinburgh Minimal Medium (EMM) supplemented with 50 mg/l of adenine, histidine, leucine, lysine and uracil each (EMM+5S) or with SP minus leu (EMM+4S-Leu) when transformed (media and supplements were purchased from Q-biogene, Morgan, CA.

extract_protocol: Cells from 1.5 ml of culture were centrifuged at 16,100 × g for 1 min at room temperature and total RNA was harvested from the cell pellet after storage at -80°C using the MasterPure yeast RNA purification kit (Epicenter, Madison, WI).

tag: A Schizosaccharomyces pombe zfs1 gene-targeted strain (zfs1-deficient) was used in a direct comparison with a representative wild-type strain that was originally used as the background cell type for zfs1 gene targeting


title: deltaZFS_BioRep3

hyb_protocol: 5ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.

scan_protocol: Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450 with the Mini_euk2v3 protocol.  Arrays were then scanned with an Affymetrix Scanner 3000.  Data was obtained using the Genechip® Operating Software.

label_protocol: Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3’ Amplification One-Cycle Target labeling kit according to manufacturer’s protocol.


title: deltaZFS_BioRep4


title: deltaZFS_BioRep2


title: Day 22-35 Chronic infection GP33 specific-2_MG-U74B

status: Public on Nov 27 2007

city: Atlanta

first: Shruti

last: Subramaniam

state: GA

address: Clifton Road

institute: Emory University

description:
The array used was Murine Genome U74 Version 2 Set MG-U74A. There are 4 groups Naïve Effector Memory and Exhausted . Each group has 3 biological replicates. The biological replicates are numbered 1 to 4; except Effectors 1 to 3 .The
This sample is called Exhausted-2

hyb_protocol: Standard Affymetrix hybridization protocols for eukaryotic total RNA were used for the samples.All samples were hybed at 45C16 hours60 RPM in 640 Affymetrix Hyb oven. Affymetrix fludics program EUKGEWS2v4_450 was used for washing

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G Plus

data_processing: Genespring

source_name: Mouse Spleen CD8 T cells

label_protocol: Standard Affymetrix protocol

growth_protocol: T cells were isolated from naïve 4-6 week old mice on day 22-35 of chronic LCMV infection

treatment_protocol: Virus specific CD8 T cells were sorted by flow cytometry and purified cells were placed in Trizol Solution (GibcoBRL)

tag: Day 22-35 Chronic LCMV infection


title: Day 8 Acute infection GP33 specific-1_MG-U74B

description:
The array used was Murine Genome U74 Version 2 Set MG-U74B. There are 4 groups Naïve Effector Memory and Exhausted . Each group has 3 biological replicates. The biological replicates are numbered 1 to 4; except Effectors 1 to 3 . Th
This sample is called Effector-1

growth_protocol: T cells were isolated from naïve 4-6 week old mice on day 8 post acute LCMV infection

tag: Day 8 Acute LCMV infection


title: WT_BioRep2

source_name: Wildtype S.pombe strain


title: WT_BioRep3


title: Day 0 GP33-specific-1_MG-U74B

description:
The array used was Murine Genome U74 Version 2 Set MG-U74B. There are 4 groups Naïve Effector Memory and Exhausted . Each group has 3 biological replicates. The biological replicates are numbered 1 to 4; except Effectors 1 to 3 . Th
This sample is called Naïve-1

growth_protocol: T cells were isolated from naïve 4-6 week old mice prior to infection

tag: Day 0 Acute infection


title: WT_BioRep4


title: Day 22-35 Chronic infection GP276 specific-1_MG-U74B

description:
The array used was Murine Genome U74 Version 2 Set MG-U74A. There are 4 groups Naïve Effector Memory and Exhausted . Each group has 3 biological replicates. The biological replicates are numbered 1 to 4; except Effectors 1 to 3 .The
This sample is called Exhausted-1


title: WT_BioRep1


title: Day 22-35 Chronic infection GP276 specific-1_MG-U74C

description:
The array used was Murine Genome U74 Version 2 Set MG-U74C. There are 4 groups Naïve Effector Memory and Exhausted . Each group has 3 biological replicates. The biological replicates are numbered 1 to 4; except Effectors 1 to 3 .The
This sample is called Exhausted-1


title: Day 30+ Acute infection GP33 specific-1_MG-U74C

description:
The array used was Murine Genome U74 Version 2 Set MG-U74C. There are 4 groups Naïve Effector Memory and Exhausted . Each group has 3 biological replicates. The biological replicates are numbered 1 to 4; except Effectors 1 to 3 .The
This sample is called Memory-1

growth_protocol: T cells were isolated from naïve 4-6 week old mice on day 30+ post acute LCMV infection

tag: Day 30+ Acute LCMV infection


title: Day 22-35 Chronic infection GP33 specific-3_MG-U74A

description:
The array used was Murine Genome U74 Version 2 Set MG-U74A. There are 4 groups Naïve Effector Memory and Exhausted . Each group has 3 biological replicates. The biological replicates are numbered 1 to 4; except Effectors 1 to 3 . Th
This sample is called Exhausted-3

label_protocol: Standard Affymetrix protocol.


title: Day 8 Acute infection GP33 specific-1_MG-U74C

description:
The array used was Murine Genome U74 Version 2 Set MG-U74C. There are 4 groups Naïve Effector Memory and Exhausted . Each group has 3 biological replicates. The biological replicates are numbered 1 to 4; except Effectors 1 to 3 . Th
This sample is called Effector-1


title: Day 30+ Acute infection GP33 specific-4_MG-U74A

description:
The array used was Murine Genome U74 Version 2 Set MG-U74A. There are 4 groups Naïve Effector Memory and Exhausted . Each group has 3 biological replicates. The biological replicates are numbered 1 to 4; except Effectors 1 to 3 .  T
This sample is called Memory-4


title: Day 30+ Acute infection GP33 specific-1_MG-U74B

description:
The array used was Murine Genome U74 Version 2 Set MG-U74A. There are 4 groups Naïve Effector Memory and Exhausted . Each group has 3 biological replicates. The biological replicates are numbered 1 to 4; except Effectors 1 to 3 . Th
This sample is called Memory-1


title: Day 22-35 Chronic infection GP33 specific-2_MG-U74C

description:
The array used was Murine Genome U74 Version 2 Set MG-U74C. There are 4 groups Naïve Effector Memory and Exhausted . Each group has 3 biological replicates. The biological replicates are numbered 1 to 4; except Effectors 1 to 3 .The
This sample is called Exhausted-2


title: Day 22-35 Chronic infection GP33 specific-4_MG-U74A

description:
The array used was Murine Genome U74 Version 2 Set MG-U74A. There are 4 groups Naïve Effector Memory and Exhausted . Each group has 3 biological replicates. The biological replicates are numbered 1 to 4; except Effectors 1 to 3 . Th
This sample is called Exhausted-4


title: Day 22-35 Chronic infection GP33 specific-2_MG-U74A

description:
The array used was Murine Genome U74 Version 2 Set MG-U74A. There are 4 groups Naïve Effector Memory and Exhausted . Each group has 3 biological replicates. The biological replicates are numbered 1 to 4; except Effectors 1 to 3 . Th
This sample is calledExhausted-2


title: Day 0 GP33-specific-1_MG-U74C

description:
The array used was Murine Genome U74 Version 2 Set MG-U74C. There are 4 groups Naïve Effector Memory and Exhausted . Each group has 3 biological replicates. The biological replicates are numbered 1 to 4; except Effectors 1 to 3 . Th
This sample is called Naïve-1


title: Day 30+ Acute infection GP33 specific-1_MG-U74A

description:
The array used was Murine Genome U74 Version 2 Set MG-U74A. There are 4 groups Naïve Effector Memory and Exhausted . Each group has 3 biological replicates. The biological replicates are numbered 1 to 4; except Effectors 1 to 3 .  T
This sample is called Memory-1


title: Radioresistant tumor-untreated-rep1

description: Gene expression data from radioresistant tumor


title: Day 8 Acute infection GP33 specific-3_MG-U74A

description:
The array used was Murine Genome U74 Version 2 Set MG-U74A. There are 4 groups Naïve Effector Memory and Exhausted .Each group has 3 biological replicates. The biological replicates are numbered 1 to 4; except Effectors 1 to 3 . The
This sample is called  Effector-3


title: Day 30+ Acute infection GP33 specific-3_MG-U74A

description:
The array used was Murine Genome U74 Version 2 Set MG-U74A. There are 4 groups Naïve Effector Memory and Exhausted . Each group has 3 biological replicates. The biological replicates are numbered 1 to 4; except Effectors 1 to 3 .  T
This sample is called Memory-3


title: Day 30+ Acute infection GP33 specific-2_MG-U74A

description:
The array used was Murine Genome U74 Version 2 Set MG-U74A. There are 4 groups Naïve Effector Memory and Exhausted . Each group has 3 biological replicates. The biological replicates are numbered 1 to 4; except Effectors 1 to 3 .  T
This sample is called Memory-2


title: Rat Supporting cells from crista ampullaris_rep1

city: Milwaukee

first: Ashley

last: Wackym

state: WI

address: 9200 W. Wisconsin Ave

department: Otolaryngology

institute: Medical College of Wisconsin

description: Rat crista ampullaris, laser captured based on morphology

hyb_protocol: Arrays were hybridized at 37oC for 20h in a shaking incubator.

scan_protocol: Dried arrays were scanned with a  GenePixTM 4000B scanner (Molecular Devices, Axon Instruments, Union City, CA).

data_processing: Raw values represent the final number of the spot after the background is subtracted out.  Normalized values represent median global normalization method, i.e. raw intensity/median intensity of all spots on the array

organism: Rattus norvegicus

source_name: Rat crista ampullaris supporting cells

label_protocol: Biotin-labeled cRNA was prepared by linear amplification of the Poly(A)+ RNA population within the total RNA sample

extract_protocol: RNA was extracted using the Arcturus Picopur RNA Isolation Kit (Arcturus Bioscience, Mountain View, CA)

tag: Brown norwary rats, 6-8 weeks old, supporting cells


title: Day 22-35 Chronic infection GP276 specific-1_MG-U74A

description:
The array used was Murine Genome U74 Version 2 Set MG-U74A. There are 4 groups Naïve Effector Memory and Exhausted . Each group has 3 biological replicates. The biological replicates are numbered 1 to 4; except Effectors 1 to 3 .The
This sample is called Exhausted-1


title: Rat Supporting cells from crista ampullaris_rep2


title: Day 0 GP33-specific-2_MG-U74A

description:
The array used was Murine Genome U74 Version 2 Set MG-U74A. There are 4 groups Naïve Effector Memory and Exhausted . Each group has 3 biological replicates. The biological replicates are numbered 1 to 4; except Effectors 1 to 3 .The
This sample is called Naïve-2


title: Day 0 GP33-specific-1_MG-U74A

description:
The array used was Murine Genome U74 Version 2 Set MG-U74A. There are 4 groups Naïve Effector Memory and Exhausted . Each group has 3 biological replicates. The biological replicates are numbered 1 to 4; except Effectors 1 to 3 . Th
This sample is called Naïve-1


title: Day 0 GP33-specific-3_MG-U74A

description:
The array used was Murine Genome U74 Version 2 Set MG-U74A. There are 4 groups Naïve Effector Memory and Exhausted . Each group has 3 biological replicates. The biological replicates are numbered 1 to 4; except Effectors 1 to 3 . Th
This sample is called Naïve-3


title: Day 0 GP33-specific-4_MG-U74A

description:
The array used was Murine Genome U74 Version 2 Set MG-U74A. There are 4 groups Naïve Effector Memory and Exhausted . Each group has 3 biological replicates. The biological replicates are numbered 1 to 4; except Effectors 1 to 3 . Th
This sample is called Naïve-4


title: Day 8 Acute infection GP33 specific-1_MG-U74A

description:
The array used was Murine Genome U74 Version 2 Set MG-U74A. There are 4 groups Naïve Effector Memory and Exhausted . Each group has 3 biological replicates. The biological replicates are numbered 1 to 4; except Effectors 1 to 3 . Th
This sample is called Effector-1


title: Rat Hair cells from crista ampullaris_rep2

source_name: Rat crista ampullaris

tag: Brown norwary rats, 6-8 weeks old, crista ampullaris


title: 9_V71.I5U2.CEL, Experimental replicate 2

status: Public on Nov 26 2007

city: Blacksburg

first: sucheta

last: Tripathy

state: VA

address: 1, Washington street

department: Virginia  Bioinformatics Institute

institute: Virginia Tech

description:
V71-370 - P.sojae inoculated; 120 hrs (upper); ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points

hyb_protocol: hybridization cocktail is prepared, including the fragmented target, probe array controls, BSA, and herring sperm DNA. It is then hybridized to the probe array during a 16-hour incubation(Affymetrix technical manual - 2004)

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneChip Scanner 3000

data_processing: The data were analyzed with RMA suite from R package version 2.4.0. Background correction was using RMA followed by quantile normalization and data was summarized using median polish method

organism: Glycine max

source_name: Soybean cultivar V71-370 - pathogen(P.sojae) Inoculated: 120 hours post inoculation  : Sample taken from the upper side of the inoculation

label_protocol: The RNA samples isolated from each of the two inoculation replications were pooled in equal amounts before subjecting to microarray assay. RNA samples from mock inoculated tissue contain 0.03125-4% spike-in RNA from Phytophthora sojae mycellium grown in liquid sucrose-salts medium , depending upon resistance level and sampling time. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA. RNA is is first reverse transcribed using a T7-Oligo(dT) Promoter Primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA is purified and serves as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction is carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling. The biotinylated cRNA targets are then cleaned up, fragmented, and hybridized to GeneChip expression arrays(Affymetrix Technical manual - 2004)

growth_protocol: Soybean plants were grown in growth chambers and later transferred to trays with clothes soaked in water

extract_protocol: QIAGEN RNeasy Kit : As recommended by manufacturer

treatment_protocol: Inoculation assays were performed using the slant board technique (Olah and Schmitthenner, 1985).[ Briefly, 7-day-old soybean seedlings were thoroughly rinsed under tap water and placed in an inoculation tray (10 plants per tray, 3 trays per inoculation replication). The plants were wounded at 2 cm below the beginning of the root zone by scraping the epidermis with a scalpel and then inoculated with a mycelial slurry from a 7-day-old culture or agar alone. Samples of root tissues were collected at 3 and 5 days post inoculation (dpi) from 7.5 mm below and above the lesion margin from each seedling with characteristic lesions. For the mock-inoculated plants, tissue sections were taken 7.5 mm below and above the position corresponding to the average lesion length measured from the inoculated samples. The lesion length (mm) from the inoculation point up to the edge of the lesion margin was also measured 3 and 5 dpi. For each experimental replication, 2 replicates of 30 seedlings per condition were inoculated and harvested separately. All the plants for an experiment were grown in the same environmental growth chamber (Chagrin Falls, Ohio; Model M-48 with TC2 microcontroller unit) with day and night temperatures settings of 27C and 21C and relative humidity averaging 75 to 90%.

tag: cultivar - V71-370

tag: Tissue/Cell Type

value: Soybean root/hypocotyls - P.sojae mycelium from minimal medium

tag: total Soybean RNA


title: 9_VP9.M2W1.CEL, Experimental replicate 1

description:
VP-RIL9 - Mock inoculated; 48 hrs; ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar VP-RIL9 - Mock Inoculated (Inoculated with water + agar): 48 hours post inoculation

tag: cultivar - VP-RIL9

tag: total Soybean RNA Plus 1 % P.sojae RNA added


title: Day 8 Acute infection GP33 specific-2_MG-U74A

description:
The array used was Murine Genome U74 Version 2 Set MG-U74A. There are 4 groups Naïve Effector Memory and Exhausted .Each group has 3 biological replicates. The biological replicates are numbered 1 to 4; except Effectors 1 to 3 . The
This sample is called Effector-2


title: 8_SLO.I5L4.CEL, Experimental replicate 4

description:
SLOAN - P.sojae inoculated; 120 hrs (lower); ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar SLOAN - pathogen(P.sojae) Inoculated: 120 hours post inoculation  : Sample taken from the lower side of the inoculation

tag: cultivar - SLOAN


title: Rat Hair cells from crista ampullaris_rep1


title: 7_SLO.I1W4.CEL, Experimental replicate 4

description:
SLOAN - P.sojae inoculated; 24 hrs; ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar SLOAN - pathogen(P.sojae) Inoculated: 24 hours post inoculation


title: 7_V71.I2W2.CEL, Experimental replicate 2

description:
V71-370 - P.sojae inoculated; 48 hrs; ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar V71-370 - pathogen(P.sojae) Inoculated: 48 hours post inoculation


title: 6_V71.M3W1.CEL, Experimental replicate 1

description:
V71-370 - Mock inoculated; 72 hrs; ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar V71-370 - Mock Inoculated (Inoculated with water + agar): 72 hours post inoculation

tag: total Soybean RNA Plus 0.125 % P.sojae RNA added


title: 9_SLO.M1W3.CEL, Experimental replicate 3

description:
SLOAN - Mock inoculated; 24 hrs; ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar SLOAN - Mock Inoculated (Inoculated with water + agar): 24 hours post inoculation

tag: total Soybean RNA Plus 0.5 % P.sojae RNA added


title: 8_VP9.I5U1.CEL, Experimental replicate 1

description:
VP-RIL9 - P.sojae inoculated; 120 hrs (upper); ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar VP-RIL9 - pathogen(P.sojae) Inoculated: 120 hours post inoculation  : Sample taken from the upper side of the inoculation


title: 8_CON.I3U2.CEL, Experimental replicate 2

description:
CONRAD - P.sojae inoculated; 72 hrs (upper); ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar CONRAD - pathogen(P.sojae) Inoculated: 72 hours post inoculation  : Sample taken from the upper side of the inoculation

tag: cultivar - CONRAD


title: 9_SLO.I2W4.CEL, Experimental replicate 4

description:
SLOAN - P.sojae inoculated; 48 hrs; ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar SLOAN - pathogen(P.sojae) Inoculated: 48 hours post inoculation


title: 7_SLO.M3W3.CEL, Experimental replicate 3

description:
SLOAN - Mock inoculated; 72 hrs; ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar SLOAN - Mock Inoculated (Inoculated with water + agar): 72 hours post inoculation

tag: total Soybean RNA Plus 2 % P.sojae RNA added


title: 8_V71.M2W3.CEL, Experimental replicate 3

description:
V71-370 - Mock inoculated; 48 hrs; ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar V71-370 - Mock Inoculated (Inoculated with water + agar): 48 hours post inoculation

tag: total Soybean RNA Plus 0.0625 % P.sojae RNA added


title: 7_VP9.I5L1.CEL, Experimental replicate 1

description:
VP-RIL9 - P.sojae inoculated; 120 hrs (lower); ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar VP-RIL9 - pathogen(P.sojae) Inoculated: 120 hours post inoculation  : Sample taken from the lower side of the inoculation


title: 5_CON.M1W1.CEL, Experimental replicate 1

description:
CONRAD - Mock inoculated; 24 hrs; ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar CONRAD - Mock Inoculated (Inoculated with water + agar): 24 hours post inoculation

tag: total Soybean RNA Plus 0.03125 % P.sojae RNA added


title: 6_CON.M3W4.CEL, Experimental replicate 4

description:
CONRAD - Mock inoculated; 72 hrs; ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar CONRAD - Mock Inoculated (Inoculated with water + agar): 72 hours post inoculation


title: 6_V71.M1W2.CEL, Experimental replicate 2

description:
V71-370 - Mock inoculated; 24 hrs; ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar V71-370 - Mock Inoculated (Inoculated with water + agar): 24 hours post inoculation


title: 5_VP9.M5W4.CEL, Experimental replicate 4

description:
VP-RIL9 - Mock inoculated; 120 hrs; ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar VP-RIL9 - Mock Inoculated (Inoculated with water + agar): 120 hours post inoculation

tag: total Soybean RNA Plus 4 % P.sojae RNA added


title: 4_VP9.I3U4.CEL, Experimental replicate 4

description:
VP-RIL9 - P.sojae inoculated; 72 hrs (upper); ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar VP-RIL9 - pathogen(P.sojae) Inoculated: 72 hours post inoculation  : Sample taken from the upper side of the inoculation


title: 4_SLO.I3U1.CEL, Experimental replicate 1

description:
SLOAN - P.sojae inoculated; 72 hrs (upper); ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar SLOAN - pathogen(P.sojae) Inoculated: 72 hours post inoculation  : Sample taken from the upper side of the inoculation


title: 5_CON.I5U3.CEL, Experimental replicate 3

description:
CONRAD - P.sojae inoculated; 120 hrs (upper); ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar CONRAD - pathogen(P.sojae) Inoculated: 120 hours post inoculation  : Sample taken from the upper side of the inoculation


title: 5_VP9.I5L2.CEL, Experimental replicate 2

description:
VP-RIL9 - P.sojae inoculated; 120 hrs (lower); ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 6_VP9.I5L3.CEL, Experimental replicate 3

description:
VP-RIL9 - P.sojae inoculated; 120 hrs (lower); ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 4_SLO.I3L3.CEL, Experimental replicate 3

description:
SLOAN - P.sojae inoculated; 72 hrs (lower); ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar SLOAN - pathogen(P.sojae) Inoculated: 72 hours post inoculation  : Sample taken from the lower side of the inoculation


title: 4_SLO.I1W2.CEL, Experimental replicate 2

description:
SLOAN - P.sojae inoculated; 24 hrs; ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar SLOAN - pathogen(P.sojae) Inoculated: 24 hours post inoculation


title: 40_SLO.I3L4.CEL, Experimental replicate 4

description:
SLOAN - P.sojae inoculated; 72 hrs (lower); ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 40_V71.I3U2.CEL, Experimental replicate 2

description:
V71-370 - P.sojae inoculated; 72 hrs (upper); ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar V71-370 - pathogen(P.sojae) Inoculated: 72 hours post inoculation  : Sample taken from the upper side of the inoculation


title: 40_SLO.M2W3.CEL, Experimental replicate 3

description:
SLOAN - Mock inoculated; 48 hrs; ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar SLOAN - Mock Inoculated (Inoculated with water + agar): 48 hours post inoculation


title: 3_VP9.I3L2.CEL, Experimental replicate 2

description:
VP-RIL9 - P.sojae inoculated; 72 hrs (lower); ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar VP-RIL9 - pathogen(P.sojae) Inoculated: 72 hours post inoculation  : Sample taken from the lower side of the inoculation


title: 40_VP9.M5W1.CEL, Experimental replicate 1

description:
VP-RIL9 - Mock inoculated; 120 hrs; ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 3_SLO.M1W1.CEL, Experimental replicate 1

description:
SLOAN - Mock inoculated; 24 hrs; ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar SLOAN - Mock Inoculated (Inoculated with water + agar): 24 hours post inoculation


title: 39_CON.I5U2.CEL, Experimental replicate 2

description:
CONRAD - P.sojae inoculated; 120 hrs (upper); ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 38_V71.M2W2.CEL, Experimental replicate 2

description:
V71-370 - Mock inoculated; 48 hrs; ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 37_VP9.M1W2.CEL, Experimental replicate 2

description:
VP-RIL9 - Mock inoculated; 24 hrs; ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar VP-RIL9 - Mock Inoculated (Inoculated with water + agar): 24 hours post inoculation


title: 38_V71.I5L1.CEL, Experimental replicate 1

description:
V71-370 - P.sojae inoculated; 120 hrs (lower); ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar V71-370 - pathogen(P.sojae) Inoculated: 120 hours post inoculation  : Sample taken from the lower side of the inoculation


title: 38_VP9.M3W3.CEL, Experimental replicate 3

description:
VP-RIL9 - Mock inoculated; 72 hrs; ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar VP-RIL9 - Mock Inoculated (Inoculated with water + agar): 72 hours post inoculation


title: 3_CON.I5U4.CEL, Experimental replicate 4

description:
CONRAD - P.sojae inoculated; 120 hrs (upper); ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 39_V71.M1W3.CEL, Experimental replicate 3

description:
V71-370 - Mock inoculated; 24 hrs; ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 3_CON.M5W3.CEL, Experimental replicate 3

description:
CONRAD - Mock inoculated; 120 hrs; ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar CONRAD - Mock Inoculated (Inoculated with water + agar): 120 hours post inoculation

tag: total Soybean RNA Plus 0.25 % P.sojae RNA added


title: 39_VP9.I2W1.CEL, Experimental replicate 1

description:
VP-RIL9 - P.sojae inoculated; 48 hrs; ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar VP-RIL9 - pathogen(P.sojae) Inoculated: 48 hours post inoculation


title: 37_CON.M3W1.CEL, Experimental replicate 1

description:
CONRAD - Mock inoculated; 72 hrs; ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar CONRAD - Mock Inoculated (Inoculated with water + agar): 72 hours post inoculation


title: 38_CON.M1W4.CEL, Experimental replicate 4

description:
CONRAD - Mock inoculated; 24 hrs; ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar CONRAD - Mock Inoculated (Inoculated with water + agar): 24 hours post inoculation


title: 36_SLO.I3L1.CEL, Experimental replicate 1

description:
SLOAN - P.sojae inoculated; 72 hrs (lower); ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 37_CON.I3L3.CEL, Experimental replicate 3

description:
CONRAD - P.sojae inoculated; 72 hrs (lower); ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar CONRAD - pathogen(P.sojae) Inoculated: 72 hours post inoculation  : Sample taken from the lower side of the inoculation


title: 36_VP9.I1W4.CEL, Experimental replicate 4

description:
VP-RIL9 - P.sojae inoculated; 24 hrs; ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar VP-RIL9 - pathogen(P.sojae) Inoculated: 24 hours post inoculation


title: 35_VP9.I2W3.CEL, Experimental replicate 3

description:
VP-RIL9 - P.sojae inoculated; 48 hrs; ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 36_SLO.I3U3.CEL, Experimental replicate 3

description:
SLOAN - P.sojae inoculated; 72 hrs (upper); ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar SLOAN - pathogen(P.sojae) Inoculated: 72 hours post inoculation  : Sample taken from the upper side of the inoculation


title: 35_V71.I5L4.CEL, Experimental replicate 4

description:
V71-370 - P.sojae inoculated; 120 hrs (lower); ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 33_SLO.M3W1.CEL, Experimental replicate 1

description:
SLOAN - Mock inoculated; 72 hrs; ExpRep1
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar SLOAN - Mock Inoculated (Inoculated with water + agar): 72 hours post inoculation


title: 34_V71.I2W4.CEL, Experimental replicate 4

description:
V71-370 - P.sojae inoculated; 48 hrs; ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar V71-370 - pathogen(P.sojae) Inoculated: 48 hours post inoculation


title: 36_SLO.I2W2.CEL, Experimental replicate 2

description:
SLOAN - P.sojae inoculated; 48 hrs; ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar SLOAN - pathogen(P.sojae) Inoculated: 48 hours post inoculation


title: 33_CON.I3U4.CEL, Experimental replicate 4

description:
CONRAD - P.sojae inoculated; 72 hrs (upper); ExpRep4
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar CONRAD - pathogen(P.sojae) Inoculated: 72 hours post inoculation  : Sample taken from the upper side of the inoculation


title: 34_CON.M5W2.CEL, Experimental replicate 2

description:
CONRAD - Mock inoculated; 120 hrs; ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points


title: 34_V71.I1W3.CEL, Experimental replicate 3

description:
V71-370 - P.sojae inoculated; 24 hrs; ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar V71-370 - pathogen(P.sojae) Inoculated: 24 hours post inoculation


title: 33_CON.I5L3.CEL, Experimental replicate 3

description:
CONRAD - P.sojae inoculated; 120 hrs (lower); ExpRep3
Data was collected from the hypocotyl regions of Soybean plants at different time points

source_name: Soybean cultivar CONRAD - pathogen(P.sojae) Inoculated: 120 hours post inoculation  : Sample taken from the lower side of the inoculation


title: 35_SLO.M3W2.CEL, Experimental replicate 2

description:
SLOAN - Mock inoculated; 72 hrs; ExpRep2
Data was collected from the hypocotyl regions of Soybean plants at different time points