title: gene expression in monkey aorta with aging and gender YF4

status: Public on Dec 27 2007

type: RNA

city: newark

first: hongyu

last: qiu

state: NJ

address: 185 south orange ave

department: Cell biology and molecular medicine

country: USA

institute: UMDNJ

hyb_protocol: Labeled RNA was cleaned-up (Qiagen), fragmented by alkaline treatment and hybridized to the array overnight

scan_protocol: After hybridization, each array was washed, stained with streptavidin-phycoerythrin and scanned twice (Affymetrix gene Array scanner), and average intensity for each probe pair was generated.

data_processing: Data were first analyzed using Affymetrix Microarray Analysis Suite to assess quality of RNA and hybridization.  Probe sets for which fluorescent signals were not detected in at least four samples from each group were discarded.   All values from each array were normalized to the 75th percentile value of the array, which was arbitrarily set at 100.

label: biotin-labeled

molecule: total RNA

organism: Macaca fascicularis

source_name: monkey aorta

label_protocol: The DNA was subsequently transcribed into biotin-labeled synthetic antisense RNA, using the Bioarray RNA Labeling Kit (ENZO).

extract_protocol: Total RNA was extracted from each monkey thoracic aorta sample using phenol-chloroform  and reverse-transcribed into double-stranded DNA.   .

tag: aorta tissue in young female monkey; age

value: 7.2 years (average)


title: gene expression in monkey aorta with aging and gender OM1

tag: aorta tissue in old male monkey; age

value: 20.0 years (average)


title: gene expression in monkey aorta with aging and gender YF5


title: gene expression in monkey aorta with aging and gender OM6


title: gene expression in monkey aorta with aging and gender OF3

tag: aorta tissue in old female monkey; age

value: 21.2 years (average)


title: gene expression in monkey aorta with aging and gender YF3


title: gene expression in monkey aorta with aging and gender YF2


title: gene expression in monkey aorta with aging and gender YM5

tag: aorta tissue in young male monkey; age

value: 6.6 years (average)


title: gene expression in monkey aorta with aging and gender OM2


title: gene expression in monkey aorta with aging and gender OM3


title: gene expression in monkey aorta with aging and gender YM6


title: gene expression in monkey aorta with aging and gender YM2


title: gene expression in monkey aorta with aging and gender OF6


title: gene expression in monkey aorta with aging and gender YM4


title: gene expression in monkey aorta with aging and gender YF1


title: gene expression in monkey aorta with aging and gender YM1


title: CF416_lasR_stationary_rep2

status: Public on Dec 22 2007

city: Seattle

first: David

last: Dargenio

state: WA

department: Microbiology

institute: University of Washington

description: Bacteria from an overnight culture were used to inoculate 50 ml of LB broth to a starting A600 of 0.01 in 250 ml flasks.  These cultures, shaken at 300 rpm, were grown to early stationary phase (A600 of 1.2).  Twenty-five ml of the culture was centrifuged at 22°C, and total RNA was isolated using Trizol by standard procedures (Invitrogen).  RNA was purified using RNasy columns (Qiagen) followed by Ambion rDNase1 treatment and RNasy purification.  The absence of DNA was confirmed by PCR, and RNA integrity was validated by glyoxylate agarose gel electrophoresis (Ambion).  Fluorescently labeled cDNA was prepared using 10?g of RNA, and processed by Qiagen PCR purification.  cDNA hybridization was done according to the manufacturer's protocol (Agilent).  Microarray slides were scanned using an Agilent DNA microarray scanner and Agilent Feature Extractor software by the Center for Expression Arrays at the University of Washington.

data_processing: Standard Agilent processing

organism: Pseudomonas aeruginosa

growth_protocol: Grown to early stationary phase in LB broth (optical density at 600nm of 1.2).

tag: Pseudomonas aeruginosa earliest isolate from cystic fibrosis Patient 1 engineered with a lasR mutation.

tag: Pseudomonas aeruginosa earliest isolate from cystic fibrosis Patient 1.


title: gene expression in monkey aorta with aging and gender OM4

source_name: Monkey aorta


title: gene expression in monkey aorta with aging and gender Om5


title: gene expression in monkey aorta with aging and gender OF2


title: gene expression in monkey aorta with aging and gender YF6


title: gene expression in monkey aorta with aging and gender OF1


title: gene expression in monkey aorta with aging and gender OF4


title: gene expression in monkey aorta with aging and gender YM3


title: gene expression in monkey aorta with aging and gender OF5


title: KSAL15R01

status: Public on Dec 21 2007

city: Lubbock

first: Kameswara Rao

last: Kottapalli

state: TX

address: 3810 4th Street

department: Plant & Soil Science

institute: USDA-ARS Lubbock & Texas Tech University

description:
Keyword = rice
Keyword = Salt stress response

hyb_protocol: Standard protocol of Gene Expression Hybridization Kit from Agilent Technologies.

scan_protocol: Standard protocol of Agilent DNA Microarray Scanner

data_processing: Feature Extraction software Version 8.1 from Agilent Technologies

organism: Oryza sativa Indica Group

source_name: 15 min_IR24_Replication1

label_protocol: Standard Protocol of Agilent Low RNA Input Fluorescent Linear Amplification Kit

growth_protocol: Plants were grown under Growth chambers and samples were harvested on 14 DAS.

extract_protocol: Qiagen Rneasy Plant Maxi Kit and according to manufacturers protocol.

treatment_protocol: 14 days old plants were treated with 150 mM salt concentration.

tag: Plant samples from salt treated plants of IR24 collected after 15 minutes of treatment.

source_name: 15 min_FR13A_Replication1

tag: Plant samples from salt treated plants of FR13A collected after 15 minutes of treatment.


title: SP HU+ Syn chk1 120 min R2

status: Public on Dec 20 2007

city: Singapore

first: Zhaoqing

last: Chu

address: 60, Biopolis Streat

country: Singapore

institute: Genome Institute of Singapore

description: Schizosaccharomyces pombe elutriation centrifugation synchroinzed cells of wildtype and mutants indicated released to early G2 phase at indicated timepoints untreated (HU-) or treated (HU+) with 8 mM Hydroxyurea  vs Schizosaccharomyces pombe asynchronized mid log phase WT cells (OD600 was around 0.3) without supplement with HU.

data_processing: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software.  After background correction and removal of flagged values, features with low intensity (F/B<2 at either 635 or 532 channel) were removed.  Meidans of log base 2 expression ratios were given in the data table.

organism: Schizosaccharomyces pombe

source_name: Fission yeast cells

label_protocol: For fluorescence labeling of cDNAs, ~30 micro gramme total RNA was used to synthesize cDNA coupled with amino allyl-dUTP (aa-dUTP) by reverse transcriptase (Superscript-II, Invitrogen, Carlsbad, CA) according to manufacturer¡¯s instruction. cDNA was subsequently washed with Milli-Q water using microcon-YM30 (Millipore, Billerica,MA). ~1.5 micro gramme cDNA was used to couple with Cy5-fluorescence dye for 1 h in dark and purified through a spin column (Qiagen, Hilden, Germany) followed by washing on a micorcon YM-30.  Hybridization was performed using EasyHyb solution (Roche) in a MUAI mixer (BioMicro systems).  Hybridized slides were washed in a series of buffers containing various concentration of SSC (2x - 0.2x) with or without 1% SDS.

growth_protocol: Yeast cells were cultured at 30 degree centigrade.

extract_protocol: Total RNA of tissue samples were extracted using hot phenol methold describled in materials and metholds.

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of chk1 mutant released to early G2 phase at 120 min treated with 8 mM Hydroxurea (HU+) .

source_name: Fission yeast wildtype cells.

label_protocol: For fluorescence labeling of cDNAs, ~30 micro gramme total RNA was used to synthesize cDNA coupled with amino allyl-dUTP (aa-dUTP) by reverse transcriptase (Superscript-II, Invitrogen, Carlsbad, CA) according to manufacturer¡¯s instruction. cDNA was subsequently washed with Milli-Q water using microcon-YM30 (Millipore, Billerica,MA). ~1.5 micro gramme cDNA was used to couple with Cy3-fluorescence dye for 1 h in dark and purified through a spin column (Qiagen, Hilden, Germany) followed by washing on a micorcon YM-30.  Hybridization was performed using EasyHyb solution (Roche) in a MUAI mixer (BioMicro systems).  Hybridized slides were washed in a series of buffers containing various concentration of SSC (2x - 0.2x) with or without 1% SDS.

tag: Reference RNA was obtained by pooling equal amount of total RNA extracted from Schizosaccharomyces pombe mid-log phase cells (OD600 was around 0.3) growing at 30 degree centigrade without supplement with HU.


title: SP HU+ Syn chk1 080 min R2

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software.

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of chk1 mutant released to early G2 phase at 80 min treated with 8 mM Hydroxurea (HU+) .


title: KSAL15R02

source_name: 15 min_IR24_Replication2

source_name: 15 min_FR13A_Replication2


title: SP HU+ Syn chk1 200 min R1

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of chk1 mutant released to early G2 phase at 200 min treated with 8 mM Hydroxurea (HU+) .


title: KSAL24R01

source_name: 24 h_IR24_Replication1

growth_protocol: Plants were grown under Growth chambers and samples were harvested on 15 DAS.

tag: Plant samples from salt treated plants of IR24 collected after 24 h of treatment.

source_name: 24 h_FR13A_Replication1

tag: Plant samples from salt treated plants of FR13A collected after 24 h of treatment.


title: SP HU+ Syn chk1 120 min R1


title: KSALCR001

treatment_protocol: No treatment

tag: Plant samples from control plants of IR24

tag: Plant samples from control plants of FR13A


title: SP HU- Syn chk1 200 min R1

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of chk1 mutant released to early G2 phase at 200 min untreated with 8mM hydroxurea (HU-).


title: SP HU+ Syn chk1 160 min R1

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of chk1 mutant released to early G2 phase at 160 min treated with 8 mM Hydroxurea (HU+) .


title: KSALCR002


title: KSAL24R02

source_name: 24 h_IR24_Replication2

source_name: 24 h_FR13A_Replication2


title: SP HU+ Syn chk1 200 min R2


title: SP HU- Syn chk1 200 min R2


title: SP HU- Syn chk1 080 min R2

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of chk1 mutant released to early G2 phase at 80 min untreated with 8mM hydroxurea (HU-).


title: SP HU+ Syn chk1 040 min R1

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of chk1 mutant released to early G2 phase at 40 min treated with 8 mM Hydroxurea (HU+) .


title: SP HU+ Syn chk1 080 min R1


title: SP HU+ Syn chk1 160 min R2


title: SP HU- Syn chk1 160 min R1

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of chk1 mutant released to early G2 phase at 160 min untreated with 8mM hydroxurea (HU-).


title: SP HU- Syn chk1 120 min R2

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of chk1 mutant released to early G2 phase at 120 min untreated with 8mM hydroxurea (HU-).


title: SP HU+ Syn chk1 040 min R2


title: SP HU- Syn chk1 040 min R2

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of chk1 mutant released to early G2 phase at 40 min untreated with 8mM hydroxurea (HU-).


title: SP HU- Syn chk1 160 min R2


title: SP HU- Syn chk1 120 min R1


title: SP HU-/+ Syn chk1 000 min R2

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of chk1 mutant released to early G2 phase at 0 min (the time point to add HU) as control for both HU untreated and treated (HU-/+) cells of chk1 mutant.


title: SP HU- Syn chk1 080 min R1


title: SP HU- Syn chk1 040 min R1


title: SP HU-/+ Syn chk1 000 min R1


title: SP HU+ Syn cds1 200 min R2

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of cds1 mutant released to early G2 phase at 200 min treated with 8 mM Hydroxurea (HU+) .


title: SP HU+ Syn cds1 200 min R1


title: SP HU+ Syn cds1 040 min R2

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of cds1 mutant released to early G2 phase at 40 min treated with 8 mM Hydroxurea (HU+) .


title: SP HU- Syn cds1 200 min R2

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of cds1 mutant released to early G2 phase at 200 min untreated with 8mM hydroxurea (HU-).

tag: Reference RNA was obtained by pooling equal amount of total RNA extracted from Schizosaccharomyces pombe mid-log phase cells (OD600 was around 0.3) growing at 30 degree centigrade without supplement with HU.


title: SP HU+ Syn cds1 160 min R2

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of cds1 mutant released to early G2 phase at 160 min treated with 8 mM Hydroxurea (HU+) .


title: SP HU+ Syn cds1 080 min R1

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of cds1 mutant released to early G2 phase at 80 min treated with 8 mM Hydroxurea (HU+) .


title: SP HU+ Syn cds1 160 min R1


title: SP HU+ Syn cds1 120 min R1

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of cds1 mutant released to early G2 phase at 120 min treated with 8 mM Hydroxurea (HU+) .


title: SP HU+ Syn cds1 120 min R2


title: SP HU+ Syn cds1 040 min R1


title: SP HU+ Syn cds1 080 min R2


title: SP HU- Syn cds1 200 min R1


title: SP HU- Syn cds1 160 min R2

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of cds1 mutant released to early G2 phase at 160 min untreated with 8mM hydroxurea (HU-).


title: SP HU- Syn cds1 120 min R2

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of cds1 mutant released to early G2 phase at 120 min untreated with 8mM hydroxurea (HU-).


title: SP HU- Syn cds1 080 min R2

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of cds1 mutant released to early G2 phase at 80 min untreated with 8mM hydroxurea (HU-).


title: SP HU-/+ Syn cds1 000 min R1

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of cds1 mutant released to early G2 phase at 0 min (the time point to add HU) as control for both HU untreated and treated (HU-/+) cells of cds1 mutant.


title: SP HU- Syn cds1 120 min R1


title: SP HU- Syn cds1 160 min R1


title: SP HU-/+ Syn cds1 000 min R2


title: SP HU- Syn cds1 080 min R1


title: SP HU+ Syn rad3 120 min R2

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of rad3 mutant released to early G2 phase at 120 min treated with 8 mM Hydroxurea (HU+) .


title: SP HU+ Syn rad3 160 min R1

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of rad3 mutant released to early G2 phase at 160 min treated with 8 mM Hydroxurea (HU+) .


title: SP HU- Syn cds1 040 min R2

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of cds1 mutant released to early G2 phase at 40 min untreated with 8mM hydroxurea (HU-).


title: SP HU+ Syn rad3 200 min R1

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of rad3 mutant released to early G2 phase at 200 min treated with 8 mM Hydroxurea (HU+) .


title: SP HU- Syn cds1 040 min R1


title: SP HU+ Syn rad3 160 min R2


title: SP HU+ Syn rad3 080 min R2

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of rad3 mutant released to early G2 phase at 80 min treated with 8 mM Hydroxurea (HU+) .


title: SP HU+ Syn rad3 080 min R1


title: SP HU+ Syn rad3 040 min R2

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of rad3 mutant released to early G2 phase at 40 min treated with 8 mM Hydroxurea (HU+) .


title: SP HU- Syn rad3 160 min R2

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of rad3 mutant released to early G2 phase at 160 min untreated with 8mM hydroxurea (HU-).


title: SP HU+ Syn rad3 200 min R2


title: SP HU+ Syn rad3 120 min R1


title: SP HU- Syn rad3 040 min R2

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of rad3 mutant released to early G2 phase at 40 min untreated with 8mM hydroxurea (HU-).


title: SP HU+ Syn rad3 040 min R1


title: SP HU- Syn rad3 120 min R1

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of rad3 mutant released to early G2 phase at 120 min untreated with 8mM hydroxurea (HU-).


title: SP HU- Syn rad3 120 min R2

tag: Reference RNA was obtained by pooling equal amount of total RNA extracted from Schizosaccharomyces pombe mid-log phase cells (OD600 was around 0.3) growing at 30 degree centigrade without supplement with HU.


title: SP HU- Syn rad3 080 min R1

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of rad3 mutant released to early G2 phase at 80 min untreated with 8mM hydroxurea (HU-).


title: SP HU- Syn rad3 200 min R2

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of rad3 mutant released to early G2 phase at 200 min untreated with 8mM hydroxurea (HU-).


title: SP HU- Syn rad3 160 min R1


title: SP HU- Syn rad3 200 min R1


title: SP HU-/+ Syn rad3 000 min R2

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of rad3 mutant released to early G2 phase at 0 min (the time point to add HU) as control for both HU untreated and treated (HU-/+) cells of rad3 mutant.


title: SP HU- Syn rad3 040 min R1


title: SP HU+ Syn WT 200 min R2

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of wildtype (WT) released to early G2 phase at 200 min treated with 8 mM Hydroxurea (HU+) .


title: SP HU- Syn rad3 080 min R2


title: SP HU-/+ Syn rad3 000 min R1


title: SP HU+ Syn WT 160 min R2

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of wildtype (WT) released to early G2 phase at 160 min treated with 8 mM Hydroxurea (HU+) .


title: SP HU+ Syn WT 120 min R1

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of wildtype (WT) released to early G2 phase at 120 min treated with 8 mM Hydroxurea (HU+) .


title: SP HU+ Syn WT 120 min R2


title: SP HU+ Syn WT 200 min R1


title: SP HU- Syn WT 200 min R2

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of wildtype (WT) released to early G2 phase at 200 min untreated with 8mM hydroxurea (HU-).


title: SP HU+ Syn WT 160 min R1


title: SP HU+ Syn WT 040 min R1

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of wildtype (WT) released to early G2 phase at 40 min treated with 8 mM Hydroxurea (HU+) .


title: SP HU+ Syn WT 080 min R2

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of wildtype (WT) released to early G2 phase at 80 min treated with 8 mM Hydroxurea (HU+) .


title: SP HU- Syn WT 200 min R1


title: SP HU- Syn WT 160 min R2

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of wildtype (WT) released to early G2 phase at 160 min untreated with 8mM hydroxurea (HU-).


title: SP HU+ Syn WT 080 min R1


title: SP HU+ Syn WT 040 min R2


title: SP HU-/+ Syn WT 000 min R2

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of wildtype (WT) released to early G2 phase at 0 min (the time point to add HU) as control for both HU untreated and treated (HU-/+) cells of wildtype (WT).


title: SP HU- Syn WT 080 min R2

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of wildtype (WT) released to early G2 phase at 80 min untreated with 8mM hydroxurea (HU-).


title: SP HU- Syn WT 120 min R1

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of wildtype (WT) released to early G2 phase at 120 min untreated with 8mM hydroxurea (HU-).


title: SP HU- Syn WT 120 min R2


title: SP HU- Syn WT 080 min R1


title: SP HU- Syn WT 040 min R1

tag: Schizosaccharomyces pombe elutriation centrifugation synchronized (Syn) cells of wildtype (WT) released to early G2 phase at 40 min untreated with 8mM hydroxurea (HU-).


title: SP HU- Syn WT 040 min R2


title: SP HU- Syn WT 160 min R1


title: SP HU+ Asyn rad3sep1 060 min R1

description: Schizosaccharomyces pombe asynchronized mid log phase cells indicated treated with 8 mM for indicated timepoints vs Schizosaccharomyces pombe asynchronized mid log phase WT cells (OD600 was around 0.3) without supplement with HU.

label_protocol: For fluorescence labeling of cDNAs, ~30 micro gramme total RNA was used to synthesize cDNA coupled with amino allyl-dUTP (aa-dUTP) by reverse transcriptase (Superscript-II, Invitrogen, Carlsbad, CA) according to manufacturer¡¯s instruction. cDNA was subsequently washed with Milli-Q water using microcon-YM30 (Millipore, Billerica,MA). ~1.5 micro gramme cDNA was used to couple with Cy5-fluorescence dye for 1 h in dark and purified through a spin column (Qiagen, Hilden, Germany) followed by washing on a micorcon YM-30. Hybridization was performed using EasyHyb solution (Roche) in a MUAI mixer (BioMicro systems).Hybridized slides were washed in a series of buffers containing various concentration of SSC (2x - 0.2x) with or without 1% SDS.

tag: Schizosaccharomyces pombe asynchronized (Asyn) cells of rad3sep1 mutant treated with 8 mM Hydroxyurea (HU+) for 60 min.

label_protocol: For fluorescence labeling of cDNAs, ~30 micro gramme total RNA was used to synthesize cDNA coupled with amino allyl-dUTP (aa-dUTP) by reverse transcriptase (Superscript-II, Invitrogen, Carlsbad, CA) according to manufacturer¡¯s instruction. cDNA was subsequently washed with Milli-Q water using microcon-YM30 (Millipore, Billerica,MA). ~1.5 micro gramme cDNA was used to couple with Cy3-fluorescence dye for 1 h in dark and purified through a spin column (Qiagen, Hilden, Germany) followed by washing on a micorcon YM-30. Hybridization was performed using EasyHyb solution (Roche) in a MUAI mixer (BioMicro systems).  Hybridized slides were washed in a series of buffers containing various concentration of SSC (2x - 0.2x) with or without 1% SDS.


title: SP HU+ Asyn rad3sep1 120 min R2

tag: Schizosaccharomyces pombe asynchronized (Asyn) cells of rad3sep1 mutant treated with 8 mM Hydroxyurea (HU+) for 120 min.


title: SP HU+ Asyn rad3sep1 030 min R2

tag: Schizosaccharomyces pombe asynchronized (Asyn) cells of rad3sep1 mutant treated with 8 mM Hydroxyurea (HU+) for 30 min.

tag: Reference RNA was obtained by pooling equal amount of total RNA extracted from Schizosaccharomyces pombe mid-log phase cells (OD600 was around 0.3) growing at 30 degree centigrade without supplement with HU.


title: SP HU+ Asyn rad3sep1 010 min R2

tag: Schizosaccharomyces pombe asynchronized (Asyn) cells of rad3sep1 mutant treated with 8 mM Hydroxyurea (HU+) for 10 min.


title: SP HU+ Asyn rad3sep1 060 min R2


title: SP HU+ Asyn rad3sep1 030 min R1


title: SP HU-/+ Syn WT 000 min R1


title: SP HU+ Asyn chk1 120 min R3

tag: Schizosaccharomyces pombe asynchronized (Asyn) cells of chk1 mutant treated with 8 mM Hydroxyurea (HU+) for 120 min.


title: SP HU+ Asyn rad3sep1 000 min R1

tag: Schizosaccharomyces pombe asynchronized (Asyn) cells of rad3sep1 mutant (OD600 was around 0.25) treated with 8 mM Hydroxyurea (HU+) for 0 min.


title: SP HU+ Asyn rad3sep1 010 min R1


title: SP HU+ Asyn chk1 120 min R1


title: SP HU+ Asyn chk1 120 min R2


title: SP HU+ Asyn rad3sep1 000 min R2


title: SP HU+ Asyn chk1 060 min R2

tag: Schizosaccharomyces pombe asynchronized (Asyn) cells of chk1 mutant treated with 8 mM Hydroxyurea (HU+) for 60 min.


title: SP HU+ Asyn rad3sep1 120 min R1


title: SP HU+ Asyn chk1 060 min R1


title: SP HU+ Asyn chk1 000 min R1

tag: Schizosaccharomyces pombe asynchronized (Asyn) cells of chk1 mutant (OD600 was around 0.25) treated with 8 mM Hydroxyurea (HU+) for 0 min.


title: SP HU+ Asyn chk1 010 min R2

tag: Schizosaccharomyces pombe asynchronized (Asyn) cells of chk1 mutant treated with 8 mM Hydroxyurea (HU+) for 10 min.


title: SP HU+ Asyn chk1 000 min R2


title: SP HU+ Asyn chk1 030 min R1

tag: Schizosaccharomyces pombe asynchronized (Asyn) cells of chk1 mutant treated with 8 mM Hydroxyurea (HU+) for 30 min.


title: SP HU+ Asyn chk1 010 min R3


title: SP HU+ Asyn chk1 000 min R3


title: SP HU+ Asyn chk1 030 min R3


title: SP HU+ Asyn cds1 120 min R1

tag: Schizosaccharomyces pombe asynchronized (Asyn) cells of cds1 mutant treated with 8 mM Hydroxyurea (HU+) for 120 min.


title: SP HU+ Asyn cds1 120 min R3


title: SP HU+ Asyn cds1 060 min R1

tag: Schizosaccharomyces pombe asynchronized (Asyn) cells of cds1 mutant treated with 8 mM Hydroxyurea (HU+) for 60 min.


title: SP HU+ Asyn chk1 010 min R1


title: SP HU+ Asyn chk1 030 min R2


title: SP HU+ Asyn cds1 120 min R2


title: SP HU+ Asyn cds1 060 min R3


title: SP HU+ Asyn cds1 030 min R3

tag: Schizosaccharomyces pombe asynchronized (Asyn) cells of cds1 mutant treated with 8 mM Hydroxyurea (HU+) for 30 min.


title: SP HU+ Asyn cds1 030 min R1


title: SP HU+ Asyn cds1 010 min R2

tag: Schizosaccharomyces pombe asynchronized (Asyn) cells of cds1 mutant treated with 8 mM Hydroxyurea (HU+) for 10 min.


title: SP HU+ Asyn cds1 010 min R3


title: SP HU+ Asyn cds1 000 min R2

tag: Schizosaccharomyces pombe asynchronized (Asyn) cells of cds1 mutant (OD600 was around 0.25) treated with 8 mM Hydroxyurea (HU+) for 0 min.


title: SP HU+ Asyn cds1 060 min R2


title: SP HU+ Asyn cds1 000 min R3


title: SP HU+ Asyn cds1 030 min R2


title: SP HU+ Asyn rad3 120 min R1

tag: Schizosaccharomyces pombe asynchronized (Asyn) cells of rad3 mutant treated with 8 mM Hydroxyurea (HU+) for 120 min.


title: SP HU+ Asyn cds1 000 min R1


title: SP HU+ Asyn cds1 010 min R1


title: SP HU+ Asyn chk1 060 min R3


title: SP HU+ Asyn rad3 120 min R3


title: SP HU+ Asyn rad3 060 min R3

tag: Schizosaccharomyces pombe asynchronized (Asyn) cells of rad3 mutant treated with 8 mM Hydroxyurea (HU+) for 60 min.


title: SP HU+ Asyn rad3 030 min R2

tag: Schizosaccharomyces pombe asynchronized (Asyn) cells of rad3 mutant treated with 8 mM Hydroxyurea (HU+) for 30 min.


title: SP HU+ Asyn rad3 060 min R2


title: SP HU+ Asyn rad3 060 min R1


title: SP HU+ Asyn rad3 010 min R3

tag: Schizosaccharomyces pombe asynchronized (Asyn) cells of rad3 mutant treated with 8 mM Hydroxyurea (HU+) for 10 min.


title: SP HU+ Asyn rad3 000 min R3

tag: Schizosaccharomyces pombe asynchronized (Asyn) cells of rad3 mutant (OD600 was around 0.25) treated with 8 mM Hydroxyurea (HU+) for 0 min.

tag: Reference RNA was obtained by pooling equal amount of total RNA extracted from Schizosaccharomyces pombe mid-log phase cells (OD600 was around 0.3) growing at 30 degree centigrade without supplement with HU.


title: SP HU+ Asyn rad3 010 min R2


title: SP HU+ Asyn rad3 000 min R1


title: SP HU+ Asyn WT 120 min R3

tag: Schizosaccharomyces pombe asynchronized (Asyn) cells of wildtype (WT) treated with 8 mM Hydroxyurea (HU+) for 120 min.


title: SP HU+ Asyn rad3 030 min R1


title: SP HU+ Asyn rad3 010 min R1


title: SP HU+ Asyn WT 120 min R1


title: SP HU+ Asyn rad3 000 min R2


title: SP HU+ Asyn rad3 030 min R3


title: SP HU+ Asyn WT 010 min R3

tag: Schizosaccharomyces pombe asynchronized (Asyn) cells of wildtype (WT) treated with 8 mM Hydroxyurea (HU+) for 10 min.


title: SP HU+ Asyn WT 120 min R2


title: SP HU+ Asyn WT 030 min R3

tag: Schizosaccharomyces pombe asynchronized (Asyn) cells of wildtype (WT) treated with 8 mM Hydroxyurea (HU+) for 30 min.


title: SP HU+ Asyn WT 010 min R1


title: SP HU+ Asyn WT 010 min R2


title: SP HU+ Asyn WT 060 min R2

tag: Schizosaccharomyces pombe asynchronized (Asyn) cells of wildtype (WT) treated with 8 mM Hydroxyurea (HU+) for 60 min.


title: SP HU+ Asyn WT 060 min R1


title: PHx72h-2 (72h post partial hepatectomy)

status: Public on Dec 13 2007

city: Taipei

first: Ann-Ping

last: Tsou

address: 155, Li-Nong St., Sec.2

department: Inst. Biotechnology in Medicine

country: Taiwan

institute: National Yang-Ming University

description: Tissue

data_processing: The arrays were scanned using an Affimetrix GeneChip scanner 3000. The resulting image data was captured and converted to digital output using GeneChip Operating Software v.1.1.1. The absolute results (*.chp) from different experiments (probe arrays of the same type) that are scaled to the same target signal using the All Probe Sets scaling option (scaling factor, 500) may be directly compared. Parameter: Alpha1=0.05, Alpha2=0.065, Tau=0.015.

label: Biotin

organism: Mus musculus

source_name: mouse liver

tag: Adult C57/BLJ6 male Mouse


title: PHx8h-2 (8h post partial hepatectomy)

description: Tissue


title: SP HU+ Asyn WT 030 min R2


title: PHx12h-1 (12h post partial hepatectomy)

description: Tissue


title: NY1DD Sickle Cell Mouse brains, MOR treated, 10mins. 825 SCMOR3

city: Minneapolis

first: Ajay

last: Yekkirala

state: MN

address: 308 Harvard St 8-120

institute: University of Minnesota

description: All info provided.

hyb_protocol: 1) Resuspend dried labeled cDNAs in 7.8ul water 2) Add remaining reagents for Hyb cocktail and mix by pipetting. 3) Heat the probe preparation at 95-100 degrees for 2 minutes. Boiling denatures the sample and makes it accessible for hybridization. 4) Snap cool on ice for 1-3 minutes. 5) Pulse the tubes in the centrifuge to pull down condensation 6) Clean lifterslips with soap and water, then Acetone and dry with Kimwipes. Make sure there are no debris on the array before laying down lifterslip. Place lifterslip on array using either fingers or forceps with dull white strips touching the glass. This creates a platform which allows even distribution of the hybridization solution across the array. Slowly pipette the probe under one corner of the slip until the entire array surface is covered. 7) Put 10-20ul 3XSSC at each little divot at the ends of the Hyb chamber. This is to ensure a constant humidity in the chamber during hybridizations. If the 3XSSC is not applied, the array will dry out. 8) Tightly screw down lid of Hyb chamber and carefully place in incubator. Take caution to keep array completely flat during transfer and hybridizations. 9) Allow hybridization to run for at least 5 hours but not more than 16 hours, in the dark at 42C.

scan_protocol: 1) Prepare wash solutions in glass slide dishes 2) Carefully remove array from incubator or water bath, making sure to keep chamber level. Unscrew chamber and remove array. 3) Keep array level and submerge in 2XSSC to get the lifterslip to fall off. Once submerged tilt array and gently dump off coverslip. It may be necessary to lightly swish array under solution to dislodge the slip. 4) Once slip is off and lying on bottom of slide dish, put array in a slide rack and transfer to the first wash solution. Do not allow the chips to dry out at any point during the washes. 5) Wash hybs. a) 2X SSC, 0.1% SDS (4ml 10%SDS per 400ml) at 37 or 550C for 3 minutes with no agitation b) 2X SSC, RT Let sit 3 minutes in solution then dip up and down 10 times. c) 0.2X SSC RT Let sit 3 minutes in solution then dip up and down 10 times 6) Immediately dry array in room temperature table top centrifuge at 500 rpm for 6 min.

data_processing: Scanned image was processed using the GenePix Pro (Axon Laboratories) software and RAW values were calculated. The data was then updated in the GeneSpring Software (Agilent Tech.) and lowess normalizations were used on all the raw data.

label_protocol: SuperScript Direct labeling system (Invitogen, Cat#: L1015-01) was used and manufacturer's protocol was followed.

extract_protocol:
1) Homogenize brain in 500 microL of TRIzol in a 1.5mL tube with a pestle. Dilute with 500microL.
2)Incubate for 5 mins at RT.
3) Add 200 microL chloroform and vortex. Incubate for 2-3mins and centrifuge at 12000 x g for 15 mins.
4) Transfer upper aqueous portion to a clean tube and precipitate RNA byadding 500 microL of isopropanol. Incubate for 10 mins at RT and centrifuge at 12000 x g for 15 mins.
5) Wash pellet in 75% EtOH and dry pellet for 5-10 mins.
6) Dissolve RNA in 40 microL RNase free water.

tag: Strain:NY1DD Sickle Cell Mice

tag: Gender

value: Male

tag: Age

value: 9 wks

tag: Drug

value: Morphine for 10 mins.

source_name: NY1DD Sickle Cell Mouse brains, Saline treated control, 10mins.

value: Saline for 10 mins.


title: mL-2 (normal mouse liver)

description: Tissue


title: SP HU+ Asyn WT 000 min R3

tag: Schizosaccharomyces pombe asynchronized (Asyn) cells of wildtype (WT) (OD600 was around 0.25) treated with 8 mM Hydroxyurea (HU+) for 0 min.


title: SP HU+ Asyn WT 060 min R3


title: C57BL/6J wild-type mouse brains, MOR treated, 10mins. 916 WTMOR 1

description: All info provided.

tag: Strain:C57BL/6J Mice

source_name: C57BL/6J wild-type mouse brains, saline treated, 10mins.

tag: Strain:C57BL/6J wild-type mice


title: SP HU+ Asyn WT 030 min R1


title: PHx12h-2 (12h post partial hepatectomy)

description: Tissue


title: SP HU+ Asyn WT 000 min R1


title: SP HU+ Asyn WT 000 min R2


title: PHx36h-2 (36h post partial hepatectomy)

description: Tissue


title: C57BL/6J wild-type mouse brains, MOR treated, 10mins. 916 WTMOR 2

description: All info provided.


title: PHx4h-1 (4h post partial hepatectomy)

description: Tissue


title: SP HU+ Asyn rad3 120 min R2

tag: Schizosaccharomyces pombe asynchronized (Asyn) cells of rad3 mutant treated with 8 mM Hydroxyurea (HU+) for 120 min.


title: PHx48h-1 (48h post partial hepatectomy)

description: Tissue


title: PHx36h-1 (36h post partial hepatectomy)

description: Tissue


title: PHx8h-1 (8h post partial hepatectomy)

description: Tissue


title: adult head_AA22_experimenttimtemp

status: Public on Dec 07 2007

city: Southampton

first: Herman

last: Wijnen

state: Hampshire

address: Life Sciences Building 85 - Highfield Campus

department: Centre for Biological Sciences

country: United Kingdom

institute: University of Southampton

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Bioconductor Robust Multi-array Average

label: biotin

organism: Drosophila melanogaster

source_name: adult head

label_protocol: Approximately 25 µg of total RNA was processed to produce biotinylated cRNA targets.

growth_protocol: initially 25 C DD, then 12-hr 18 C/12-hr 25 C thermocycle in constant darkness

extract_protocol: Flies were immediately frozen on dry ice. Approximately 100-200 heads were isolated on sieves after breaking the frozen flies

treatment_protocol: 25 C DD (after 12-hr 18 C/12-hr 25 C thermocycle in constant darkness)

tag: y w; tim01 stock


title: mL-1 (normal mouse liver)

description: Tissue


title: PHx4h-2 (4h post partial hepatectomy)

description: Tissue


title: C57BL/6J wild-type mouse brains, MOR treated, 10mins. 925 WTMOR3

description: All info provided.


title: adult head_AA18_experimenttimtemp


title: NY1DD Sickle Cell Mouse brains, MOR treated, 10mins. 823 SCMOR2

description: All info provided.

source_name: NY1DD Sickle Cell Mouse brains,Saline treated control, 10mins.


title: adult head_CA22_experimenttimtemp

treatment_protocol: 12-hr 18 C/12-hr 25 C thermocycle in constant darkness


title: adult head_AA10_experimenttimtemp


title: adult head_CA14_experimenttimtemp


title: adult head_AA30_experimentcnbwtemp

tag: cn bw stock


title: adult head_AA42_experimentcnbwtemp


title: adult head_CA6_experimenttimtemp


title: adult head_AA2_experimenttimtemp


title: adult head_AA34_experimentcnbwtemp


title: adult head_CA18_experimenttimtemp


title: adult head_AA38_experimentcnbwtemp


title: adult head_AA14_experimenttimtemp


title: PHx48h-2 (48h post partial hepatectomy)

description: Tissue


title: adult head_AA6_experimenttimtemp


title: adult head_AA46_experimentcnbwtemp


title: adult head_CA2_experimenttimtemp


title: adult head_AA26_experimentcnbwtemp


title: PHx72h-1 (72h post partial hepatectomy)

description: Tissue


title: adult head_CA10_experimenttimtemp


title: adult head_AA22_experimentcnbwtemp


title: adult head_AA14_experimentcnbwtemp


title: adult head_AA18_experimentcnbwtemp


title: adult head_AA10_experimentcnbwtemp


title: adult head_AA2_experimentcnbwtemp


title: adult head_CA14_experimentywtemp2

tag: y w stock


title: adult head_AA6_experimentcnbwtemp


title: adult head_AA14_experimentywtemp2


title: NY1DD Sickle Cell Mouse brains, MOR treated, 10mins. 819 SCMOR1

description: All info provided.


title: adult head_AA22_experimentywtemp2


title: adult head_AA10_experimentywtemp2


title: adult head_CA22_experimentywtemp2


title: adult head_AA6_experimentywtemp1

treatment_protocol: 25 C in constant darkness (after 12-hr 18 C/12-hr 25 C thermocycle in constant darkness)


title: adult head_CA2_experimentywtemp2


title: adult head_CA10_experimentywtemp2


title: adult head_CA6_experimentywtemp1

status: Public on Dec 05 2007


title: adult head_AA2_experimentywtemp2


title: adult head_CA6_experimentywtemp2


title: adult head_AA18_experimentywtemp2


title: adult head_AA14_experimentywtemp1


title: adult head_AA18_experimentywtemp1


title: adult head_AA6_experimentywtemp2


title: adult head_CA14_experimentywtemp1


title: adult head_AA10_experimentywtemp1


title: adult head_AA2_experimentywtemp1


title: adult head_CA10_experimentywtemp1


title: adult head_CA18_experimentywtemp2


title: adult head_CA2_experimentywtemp1

tag: y w stock adult head


title: A549_Cisplatin_rep2

status: Public on Dec 01 2007

city: Leicester

first: Gabriela

middle: M.

last: Almeida

address: Biocentre, University Road

department: Cancer Studies and Molecular Medicine

institute: University of Leicester

hyb_protocol: Fragmented cRNA was added to hybridisation buffer (100 mM 2-Morpholinoethanesulfonic acid (MES), 1 M [Na+], 20 mM EDTA, 0.01% Tween 20) with 0.1 mg/ml herring sperm DNA (Promega, Southampton, UK), 0.5 mg/ml acetylated bovine serum albumin (BSA) (Invitrogen, Paisley, UK). The hybridisation buffer was spiked with 50 pM control oligonucleotide B2 and the eukaryotic cRNA controls bioB, bioC, bioD and cre (1.5, 5, 25 and 100 pM respectively), all controls were from the GeneChip Eukaryotic Hybridisation Control Kit (Affymetrix, Santa Clara, California, USA). The hybridisation mixture was heated to 99 °C for 5 minutes, cooled to 45 °C for 5 minutes and centrifuged at 14,000 × g for 5 minutes to remove any insoluble material from the hybridisation mixture. Each hybridisation mixture containing 10 µg of fragmented biotin-labelled cRNA was hybridised to a pre-wetted (with hybridisation buffer) GeneChip Human Genome Focus (HG-Focus) array (Affymetrix, Santa Clara, California, USA) for 16 hours at 45 °C with permanent rotation at 60 rpm in a Hybridisation Oven 640 (Affymetrix, Santa Clara, California, USA). Probe array washing and staining were performed according to specific Gene Chip protocols (Affymetrix, Santa Clara, California, USA) in the Fluidics Station 400 (Affymetrix, Santa Clara, California, USA). Briefly, HG-Focus arrays were washed in a non-stringent wash buffer containing 6× SSPE (0.9 M NaCl, 0.06 M NaH2PO4, 0.006 M EDTA) (Cambrex, Berkshire, UK) and 0.01% Tween-20 at 25 °C, then with a stringent buffer containing 100 mM MES, 0.1 M [Na+], 0.01% Tween-20 at 50 °C. Following this wash, the probe arrays were stained with a solution containing 10 µg/ml of streptavidin-phycoerythrin (SAPE) conjugate (Invitrogen, Paisley, UK) dissolved in a buffer containing 100 mM MES, 1 M [Na+], 0.05% Tween 20 and 2 mg/ml acetylated BSA (Invitrogen, Paisley, UK). Following staining, the probe arrays were exposed to 3 µg/ml goat biotinylated anti-streptavidin antibody (Vector laboratories, Peterborough, UK) in a buffer as above containing 0.1 mg/ml normal goat IgG (Sigma, Poole, UK) and 2 mg/ml acetylated BSA (Invitrogen, Paisley, UK). Finally, the probe arrays were re-stained with SAPE as described above.

scan_protocol: Probe arrays were scanned twice at 570 nm using a GeneArray laser scanner (Agilent Technologies, Palo Alto, California, USA) and the fluorescence intensity of the scanned image registered in CEL intensity files.

data_processing: DNA-Chip Analyser (dChip) software (Li and Wong 2001 PNAS, 98:31) was used to automatically select probes, detect outliers/artefacts, normalise the fluorescence intensity over multiple arrays and calculate model-based expression values from CEL intensity files.

organism: Homo sapiens

source_name: A549 human adenocarcinoma cell line, cisplatin-treated

label_protocol:
The SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen, Paisley, UK) was used to convert the mRNA in the T-RNA samples into ds-cDNA by reverse transcription with an oligo-dT primer. Initially, first strand cDNA was formed in a reaction containing 15 g of T-RNA and 100 pmol of T7-oligo (dT) primer (5’ – GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG - (dT)24 – 3’) (Proligo, France). This mixture was incubated at 70 °C for 10 minutes and quickly chilled on ice for 5 minutes, after which the following reagents were added: first strand reaction buffer [50 mM Tris-HCl (pH 8.3) 75 mM KCl, 3 mM MgCl2], 10 mM dithiothreitol (DTT) and 500 µM each dNTP. Tubes were placed at 42 °C for 2 minutes to equilibrate the temperature prior to the addition of Superscript II reverse transcriptase (400 U) and further incubated for 1 hour at 42 °C. The second strand cDNA synthesis was performed by adding, to the solution containing the first strand cDNA, 200 µM each dNTP, 10 U of E. coli DNA ligase, 40 U of E. coli DNA polymerase I, 2 U of E. coli RNase H and second strand reaction buffer [20 mM Tris-HCl (pH 6.9), 90 mM KCl, 4.6 MgCl2, 0.15 mM beta–NAD+, 10 mM (NH4)2SO4]. The reaction was incubated for 2 hours at 16 °C. Following this incubation, 10 U of T4 DNA polymerase were added and incubated for 5 minutes at 16 °C. The reaction was stopped by the addition of 31.25 mM EDTA. The resulting ds-cDNA was extracted against an equal volume of phenol:chloroform:isoamyl alcohol (25:24:1) (Sigma, Poole, UK) using phase lock gels (Eppendorf, Cambridge, UK) and centrifuging at 12,000 × g for 2 minutes. The ds-cDNA was then precipitated from the aqueous phase by the addition of 0.5 volumes of 7.5 M ammonium acetate (Sigma, Poole, UK) and 2.5 volumes of absolute ethanol (Sigma, Poole, UK), using Pellet Paint (Novagen, Nottingham, UK) as a carrier. Pellet was washed in ethanol, dried and resuspended in an appropriate volume of RNase/DNase-free water (Sigma, Poole, UK).
Synthesis of biotin labelled cRNA was performed by in vitro transcription using the BioArray HighYield RNA Transcript Labelling kit (ENZO, Farmingdale, USA), according to the manufacturer’s instructions. Briefly, ds-cDNA synthesised from above was used as template, and T7 RNA polymerase was added to perform the in vitro transcription reaction from the T7 RNA polymerase promoter in the template. Biotin-labelled ribonucleotides (Bio-CTP, Bio-UTP) were included in the reaction along with non-labelled ribonucleotides (ATP, GTP, CTP, UTP) to produce biotin-labelled cRNA molecules. The reaction was incubated at 37 °C for 5 hours. This step was followed by cRNA cleanup with RNeasy Mini columns according to the manufacturer’s specifications (Qiagen, Crawley, UK). Quantification and purity assessment of cRNA was performed in a spectrophotometer by measuring the absorbance at 260 and 280 nm and the adjusted cRNA yield calculated taking into account the carryover of unlabelled T-RNA by the following formula: adjusted cRNA yield = RNAm – (T-RNAi)(y), where RNAm is the amount of cRNA measured after the IVT reaction, T-RNAi is the starting amount of T-RNA and y is the fraction of cDNA used in the IVT reaction. Size distribution of the labelled transcripts was investigated in the Agilent 2100 Bioanalyzer using the Eukaryote Total RNA Nano assay (Agilent Technologies, Palo Alto, California, USA). The appropriate amount of cRNA (13 µg) was fragmented in a buffer containing 40 mM Tris-acetate (pH 8.1), 100 mM KOAc and 30 mM MgOAc for 35 minutes at 94 °C. An aliquot, containing at least 1 µg of cRNA, of each fragmented sample was analysed in a 1% agarose gel electrophoresis to confirm fragmentation efficiency.

growth_protocol: Cells were grown as a monolayer in RPMI 1640 media containing L-glutamine with 10% FCS, in the absence of antibiotics, in an incubator at 37 ºC with 5% CO2. Cells were passaged twice a week by trypsin/EDTA (0.05% trypsin, 0.7 mM EDTA) treatment. Cells were tested and confirmed to be free of mycoplasma contamination.

extract_protocol: After the 10 hour incubation post-cisplatin treatment, T-RNA was extracted by using TRIzol Reagent (Invitrogen, Paisley, UK), according to the manufacturer’s instructions. All additional reagents used were of molecular biology grade and purchased from Sigma (Poole, UK). Briefly, cells were lysed directly in the culture dish with 1 ml TRIzol Reagent and the resulting cell lysate passed several times through a pipette to achieve homogenisation. The homogenised samples were incubated in microcentrifuge tubes at room temperature for 5 minutes to permit the complete dissociation of nucleoprotein complexes. 200 µl of chloroform were added to each homogenised sample, tubes shaken vigorously by hand for 15 seconds and incubated at room temperature for 2 to 3 minutes. Samples were centrifuged at 12,000 × g for 15 minutes at 4 °C, after which the aqueous phase was transferred to a fresh tube. RNA was precipitated from the aqueous phase by mixing with 0.5 ml isopropyl alcohol. Samples were incubated at room temperature for 10 minutes and centrifuged at 12,000 × g for 10 minutes at 4 °C. Supernatant was removed and RNA pellet washed once with 1 ml of 75% ethanol. Samples were mixed by vortexing and centrifuged at 7,500 × g for 5 minutes at 4 ºC. At the end of the procedure, the RNA pellet was briefly air-dried for 5 to 10 minutes after which RNA was dissolved in an appropriate volume of RNase/DNase-free water, pre-warmed to 60 ºC, by passing the solution a few times through a pipette tip, and incubating for 10 minutes at 55 to 60 ºC. T-RNA concentration was determined by measuring the absorbance of a 1:100 diluted solution at 260 nm in a GeneQuant II RNA/DNA calculator spectrophotometer (Pharmacia Biotech, Cambridge, UK), assuming that if A260 = 1, the content equals 40 µg/ml of RNA. RNA purity was assessed by the ratio A260/A280. T-RNA integrity was investigated in the Agilent 2100 Bioanalyzer, by assessing size distribution of the T-RNA using the Eukaryote Total RNA Nano assay (Agilent Technologies, Palo Alto, California, USA), according to the manufacturer’s specifications.

treatment_protocol: Cells were seeded at a density of 1x106 per 10 cm Petri dish 24 hours before treatment. Cells were then incubated with 8 ml of a freshly prepared cisplatin solution of 50 µM at 37 ºC for 1 hour. At the end of the 1-hour incubation, the media was removed, cells washed twice in warm PBS, and incubated in drug-free media at 37 ºC for 10 hours.

tag: A549 non-small cell lung cancer (NSCLC) cell line


title: A549_Control_rep3

source_name: A549 human adenocarcinoma cell line, control

treatment_protocol: Cells were seeded at a density of 1x106 per 10 cm Petri dish 24 hours before treatment. Cells were then incubated with 8 ml of regular growth media at 37 ºC for 1 hour. At the end of the 1-hour incubation, the media was removed, cells washed twice in warm PBS, and incubated in drug-free media at 37 ºC for 10 hours.


title: A549_Cisplatin_rep1


title: A549_Control_rep2


title: A549_control_rep1

label_protocol:
The SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen, Paisley, UK) was used to convert the mRNA in the T-RNA samples into ds-cDNA by reverse transcription with an oligo-dT primer. Initially, first strand cDNA was formed in a reaction containing 15 µg of T-RNA and 100 pmol of T7-oligo (dT) primer (5’ – GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG - (dT)24 – 3’) (Proligo, France). This mixture was incubated at 70 °C for 10 minutes and quickly chilled on ice for 5 minutes, after which the following reagents were added: first strand reaction buffer [50 mM Tris-HCl (pH 8.3) 75 mM KCl, 3 mM MgCl2], 10 mM dithiothreitol (DTT) and 500 µM each dNTP. Tubes were placed at 42 °C for 2 minutes to equilibrate the temperature prior to the addition of Superscript II reverse transcriptase (400 U) and further incubated for 1 hour at 42 °C. The second strand cDNA synthesis was performed by adding, to the solution containing the first strand cDNA, 200 µM each dNTP, 10 U of E. coli DNA ligase, 40 U of E. coli DNA polymerase I, 2 U of E. coli RNase H and second strand reaction buffer [20 mM Tris-HCl (pH 6.9), 90 mM KCl, 4.6 MgCl2, 0.15 mM beta–NAD+, 10 mM (NH4)2SO4]. The reaction was incubated for 2 hours at 16 °C. Following this incubation, 10 U of T4 DNA polymerase were added and incubated for 5 minutes at 16 °C. The reaction was stopped by the addition of 31.25 mM EDTA. The resulting ds-cDNA was extracted against an equal volume of phenol:chloroform:isoamyl alcohol (25:24:1) (Sigma, Poole, UK) using phase lock gels (Eppendorf, Cambridge, UK) and centrifuging at 12,000 × g for 2 minutes. The ds-cDNA was then precipitated from the aqueous phase by the addition of 0.5 volumes of 7.5 M ammonium acetate (Sigma, Poole, UK) and 2.5 volumes of absolute ethanol (Sigma, Poole, UK), using Pellet Paint (Novagen, Nottingham, UK) as a carrier. Pellet was washed in ethanol, dried and resuspended in an appropriate volume of RNase/DNase-free water (Sigma, Poole, UK).
Synthesis of biotin labelled cRNA was performed by in vitro transcription using the BioArray HighYield RNA Transcript Labelling kit (ENZO, Farmingdale, USA), according to the manufacturer’s instructions. Briefly, ds-cDNA synthesised from above was used as template, and T7 RNA polymerase was added to perform the in vitro transcription reaction from the T7 RNA polymerase promoter in the template. Biotin-labelled ribonucleotides (Bio-CTP, Bio-UTP) were included in the reaction along with non-labelled ribonucleotides (ATP, GTP, CTP, UTP) to produce biotin-labelled cRNA molecules. The reaction was incubated at 37 °C for 5 hours. This step was followed by cRNA cleanup with RNeasy Mini columns according to the manufacturer’s specifications (Qiagen, Crawley, UK). Quantification and purity assessment of cRNA was performed in a spectrophotometer by measuring the absorbance at 260 and 280 nm and the adjusted cRNA yield calculated taking into account the carryover of unlabelled T-RNA by the following formula: adjusted cRNA yield = RNAm – (T-RNAi)(y), where RNAm is the amount of cRNA measured after the IVT reaction, T-RNAi is the starting amount of T-RNA and y is the fraction of cDNA used in the IVT reaction. Size distribution of the labelled transcripts was investigated in the Agilent 2100 Bioanalyzer using the Eukaryote Total RNA Nano assay (Agilent Technologies, Palo Alto, California, USA). The appropriate amount of cRNA (13 µg) was fragmented in a buffer containing 40 mM Tris-acetate (pH 8.1), 100 mM KOAc and 30 mM MgOAc for 35 minutes at 94 °C. An aliquot, containing at least 1 µg of cRNA, of each fragmented sample was analysed in a 1% agarose gel electrophoresis to confirm fragmentation efficiency.


title: adult head_CA22_experimentywtemp1


title: Vitis aestivalis 'Norton ' mock inoculated at 48 h post inoculation	60

status: Public on Nov 29 2007

city: Mountain Grove

first: Wenping

last: Qiu

state: MO

address: 9740 Red Spring Road

department: Agriculture

institute: Missouri State University

description: Gene expression data from V. aestivalis 'Norton ' at 0 hour post mock inoculation

hyb_protocol: cRNA was cleaned up by the Affymetrix sample cleanup module which in included in the One-Cycle Target Labeling kit. Fifteen ug of cRNA at concentration of 1.301ug/ul were used for hybridization. Prior to hybridization, cRNA was heated at 94ºC for 35 min, and was fragmented to 35 to 200 nucleotides.  After adding hybridization buffer to the fragmented samples, hybridization cocktails were boiled for 5 min, incubated for 5 min at 45ºC, then centrifuged for 5 minutes prior to loading per standard one-cycle protocol. Hybridization took place in an Affy hybridization oven model 640, for 16h at 45ºC. All washing took place on the fluidics station (as per the recommended fluidics protocol) with non-stringent wash buffer (6X SSPE and 0.01% Tween-20) and Stringent wash buffer (100mM MES, 0.1M NaCl, 0.01% Tween-20). Fluorescence was amplified by first adding streptavidin-phycoerythrin (SAPE) stain, then adding a biotinylated antibody (anti-streptavidin) solution, followed by another SAPE staining (as per standard one-cycle protocol). The fluidics protocol Midi_Euk2v3 was used (as per V. vinifera microarray package insert) on fluidics station model 450.

scan_protocol: Affymetrix Scanner 3000 7G was used to collect at resolution of 1.56um with emission filter at a wavelength of 570nm and excitation wavelength of 532nm.

data_processing: Raw intensity data were processed using the GeneChip Operating Software Version 1.2 (GCOS 1.2; Affymetrix, 2001). Background correction and expression value calculation were performed as described by Affymetrix (2002). Normalization was done by global scaling, with a target intensity value of 150 (Affymetrix, 2001). Probe sets with missing values were deleted across all replicates and species to allow comparisons among datasets

organism: Vitis aestivalis

source_name: The 10 randomly collected V. aestivalis 'Norton ' leaves at 48 hour after mock inoculation

label_protocol: The cDNA synthesis and antisense cRNA amplification/biotin labeling was performed using the One-Cycle Target Labeling Kit (Catalog number: 900493, Affymetrix, Santa Clara, California)

growth_protocol: 14 hours day/10 hours night. Light intensity: 500 umol m-2.  Light source: high pressure sodium and metal halide. Temperature: 25°C.  Relative humidity: 85%.

extract_protocol: Total RNA was extracted from each replicate sample individually. The leaves were ground in liquid nitrogen and homogenized in extraction buffer (2% Hexadecyltrimethyl Ammonium Bromide 1%  sodium dodecyl sulfate, 2.5M NaCl, 0.5M Tris, 50mM EDTA, 5% beta-mercaptoethanol, and 3% polyvinyl poly-pyrrolidone. Following a 30-min incubation at -80°C, the samples were thawed and centrifuged. The supernatant was supplemented with 1/30 volume of 3 M sodium acetate (pH5.2) and 1/10 volume of ethanol, incubated on ice and centrifuged three times at 7000g, 30 min 4 ºC, each time transferring the supernatant into a clean tube. The supernatant was supplemented with 1/9 volume of 3 M sodium acetate (pH5.2) and iso-propanol to a final concentration of 33%. Following 60-min incubation at -20°C, the RNA was collected by centrifugation at 12,000g, 30 min, 4 ºC. The RNA was then supplemented with 1/3 volume of 8 M LiCl and incubated overnight at 4 °C. RNA was then collected by centrifugation at 12,000g, 30 min, 4 ºC, washed with 75% ethanol, and resuspended in 40 ul DEPC water.  Ten micrograms of total RNA were treated with Turbo DNase I (Ambion) and purified with RNA purification kit (Qiagen) according to manufacturer’s instructions.

treatment_protocol: third or forth leaves were mock inoculated

tag: Fully-expanded leaves at the third or fourth position from the top of each shoot were used for treatment


title: Vitis aestivalis 'Norton ' mock inoculated at 8 h post inoculation	63

source_name: The 10 randomly collected V. aestivalis 'Norton ' leaves at 8 hour after mock inoculation


title: Vitis aestivalis 'Norton ' mock inoculated at 0 h post inoculation	67

source_name: The 10 randomly collected V. aestivalis 'Norton ' leaves at 0 hour after mock inoculation


title: Vitis aestivalis 'Norton ' mock inoculateds at 4 h post inoculation	62

source_name: The 10 randomly collected V. aestivalis 'Norton ' leaves at 4 hour after mock inoculation


title: Vitis aestivalis 'Norton ' mock inoculated at 12 h post inoculation	64

source_name: The 10 randomly collected V. aestivalis 'Norton ' leaves at 12 hour after mock inoculation


title: Vitis aestivalis 'Norton ' mock inoculated at 12 h post inoculation	58


title: Vitis aestivalis 'Norton ' mock inoculated at 4 h post inoculation	68


title: Vitis aestivalis 'Norton ' mock inoculated at 24 h post inoculation	65

source_name: The 10 randomly collected V. aestivalis 'Norton ' leaves at 24 hour after mock inoculation


title: Vitis aestivalis 'Norton ' mock inoculated at 24 h post inoculation	71


title: Vitis aestivalis 'Norton ' mock inoculated at 24 h post inoculation	59

source_name: The 10 randomly collected V. aestivalis 'Norton ' leaves at 24 hour after after mock inoculation

treatment_protocol: third or forth leaveswere mock inoculated


title: Vitis aestivalis 'Norton ' mock inoculated at 8 h post inoculation	69


title: Vitis aestivalis 'Norton ' mock inoculated at 12 h post inoculation	70


title: Vitis aestivalis 'Norton ' mock inoculated at 48 h post inoculation	66


title: adult head_CA18_experimentywtemp1


title: Vitis aestivalis 'Norton ' infected w/ powdery mildew (Erysiphe necator) conidiospores 48 h post inoculation	54

description: Gene expression data from V. aestivalis 'Norton ' at 0 hour post inoculation of E. necator conidiospores

source_name: The 10 randomly collected V. aestivalis 'Norton ' leaves at 48 hour after inoculation with E. necator conidiospores

treatment_protocol: third or forth leaves were inocualted with E. necator conidiospores by touching 10 day-old powdery mildew colonies directly onto the target leaves


title: Vitis aestivalis 'Norton ' mock inoculated at 0 h post inoculation	61


title: Vitis aestivalis 'Norton ' mock inoculated at 48 h post inoculation	72


title: Vitis aestivalis 'Norton ' infected w/ powdery mildew (Erysiphe necator) conidiospores 4 h post inoculation	50

source_name: The 10 randomly collected V. aestivalis 'Norton ' leaves at 4 hour after inoculation with E. necator conidiospores


title: Vitis aestivalis 'Norton ' mock inoculated at 0 h post inoculation	55


title: Vitis aestivalis 'Norton ' infected w/ powdery mildew (Erysiphe necator) conidiospores 24 h post inoculation	53

source_name: The 10 randomly collected V. aestivalis 'Norton ' leaves at 24 hour after inoculation with E. necator conidiospores


title: Vitis aestivalis 'Norton ' infected w/ powdery mildew (Erysiphe necator) conidiospores 8 h post inoculation	51

source_name: The 10 randomly collected V. aestivalis 'Norton ' leaves at 8 hour after inoculation with E. necator conidiospores


title: Vitis aestivalis 'Norton ' infected w/ powdery mildew (Erysiphe necator) conidiospores 48 h post inoculation	48


title: Vitis aestivalis 'Norton ' infected w/ powdery mildew (Erysiphe necator) conidiospores 12 h post inoculation	40

source_name: The 10 randomly collected V. aestivalis 'Norton ' leaves at 12 hour after inoculation with E. necator conidiospores


title: A549_Cisplatin_rep3


title: 56272 H3_1/Input_1

type: genomic

first: Jorja

last: Henikoff

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: Histones were identically tagged at their N-termini with biotin ligase recognition peptide (BLRP) (de Boer, E. et al. Proc Natl Acad Sci U S A 100, 7480-5 (2003), and Beckett, D. et al. Protein Sci 8, 921-9 (1999)) and expressed together with E. coli biotin ligase in Drosophila S2 cells. Nuclei were prepared as described (McKittrick, E., et al., Proc. Natl. Acad. Sci. USA 101, 1525-1530 (2004).), and treated with micrococcal nuclease (MNase) to digest chromatin to yield mostly mononucleosomes. Chromatin was extracted (input) using a modification of the procedure of Blower, M.D., et al. (Developmental Cell 2, 319-330 (2002)). Biotinylated histone-containing nucleosome particles (pull-down) were purified and DNA was extracted from both input and pull-down fraction for microarray analysis. DNA from input (3 ug) and pull-down (4 ug) was provided to NimbleGen Systems for differential labelling by random priming with Cy3- or Cy5 and hybridization to oligonucleotide arrays.  For each experiment, input and pull-down channel signal intensities and scaled log2(ratios) were provided by NimbleGen Systems.

hyb_protocol: Hybridization protocol provided and performed by NimbleGen (http://www.nimblegen.com/product s/chip/index.html). Set MAUI hybridization unit to 42 deg C and allow time for the temperatu re to stabilize. Based on the A_260 measurement, combine 13 micrograms each of the Test and Reference Samples into a single 1.5 ml microcentrifuge tube. Protect tube from light during handling to prevent photobleaching of the light-sensitive Cy dyes. Dry the combined contents  in a Speed-Vac on low heat. Resuspend the sample in 10.9microliter VWR water and vortex to completely dissolve the sample. Spin the tube down briefly to collect the contents in the bo ttom. Using the NimbleGen Array Reuse Kit, add the following to the resuspended sample: 19.5  microliter 2X Hybridization Buffer, 7.8 microliter Hybridization Component A, 0.4 microlite r Cy3 CPK6 50mer Oligo (50nM), 0.4 microliter Cy5 CPK6 50mer Oligo (100nM). CPK6 oligos are included in the hybridization as controls that hybridize to alignment features on the Nimble Gen arrays. They are required for proper extraction of array data from the scanned image. Mi x the tube briefly then spin down to collect the contents in the bottom and place at 95 deg C for 5 minutes. Immediately transfer the tube to the MAUI 42 deg C sample block and hold at  this temperature until you are are ready for sample loading. Place the MAUI Mixer SL Hybridization Chamber on the array using the provided assembly/disas sembly jig and carefully follow MAUI setup instructions. Use the braying tool to remove all air bubbles from the adhesive gasket around the outside of the hybridization chamber. Put th e array and hybridization chamber on the MAUI and allow 30 seconds for the chips to come up to temperature. Load the sample using the pipet supplied with the MAUI Station and following  manufacturer instructions. During the loading, a small amount (3-7 microliter) of the sampl e may flow out of the outlet port. Confirm that there are no bubbles in the chamber. If ther e are, very gently massage any bubbles to either of the ends, away from the center of the ar ray. Avoid applying too much pressure since this will force liquid out of the ports. Place t he loaded array into one of the four MAUI bays and let equilibrate for 30 seconds. Wipe off any sample leakage at the ports with a Kim-Wipe, and adhere MAUI stickers to both ports. Clo se the bay clamp and select mix mode B. Hold down the mix button to start mixing. Confirm th at the mixing is in progress before closing the cover. Hybridize the sample 16-20 hours. Prior to removing the array from the MAUI Hybridization Station, prepare the following solut ions. You will need two 250ml dishes of Wash I, and one each for Wash II and Wash III. One d ish for Wash I should be shallow and be wide enough to accomodate the array and mixer loaded  in the MAUI assembly/dissassembly jig. The lid from a 1000 microliter pipet tip box works w ell. Also, the buffer in the first Wash I dish should be heated to 42 deg C to help soften t he adhesive on the hybridization chamber; this will help prevent braking the array. Place th e remaining three wash solutions in 300 microliter Tissue-Tek slide staining dishes. Wash I:  225 ml VWR Water, 25ml 10X Wash Buffer I, 25microliter 1M DTT. Wash II: 225ml VWR Water, 25 ml 10X Wash Buffer II, 25microliter 1M DTT. Wash III: 225ml VWR Water, 25microliter 10X Wash  Buffer III, 25microliter 1M DTT. Remove chip from MAUI Hybridization Station, load it back into the MAUI assembly/disassembly jig, and immerse in the shallow 250ml Wash I at 42 deg C.  Peel the hybridization chamber off very slowly to prevent the slide from cracking. Do not l et the surface of the slide dry out at any point during washing. While the chip is submerged , carefully peel off the mixer. Gently agitate the chip in Wash I for 10-15 seconds. Transfe r the slide into a slide rack in the second dish of Wash I and incubate 2 minutes with agita tion. Transfer to Wash II and incubate 1 minute with agitation. Rock the disk to move the wa sh over the tops of the arrays. Transfer to Wash III and incubate for 15 sec with agitation.  Remove array and spin dry in array-drying unit for 1 minute. Store the dried array in a dar k desiccator.

scan_protocol: Sample scan protocol provided and performed by NimbleGen (http://www.nimblegen.com/products/ chip/index.html). Axon Scanner (model 4000B). Turn on the power of the scanner. The switch i s on the back right hand side. Launch GenePix Software 10 minutes before scanning to allow l asers to warm. Open the scanner door and open the side carriage. Place chip in carriage so t hat array is face down and barcode end is closest to you. Move the black lever on the left s ide of the carriage left until the array is lying flat in the carriage. Release the lever so  that the arry is pushed over gently to the right side of the carriage and held firmly. Clos e the carriage (you should hear a click) and slide the scanner door shut. Open the hardware settings. Select the following settings for scanning: Wavelength (532=Cy3, 635=Cy5). Set the  532 laser PMT Gain to 650 and the 635 laser PMT Gain to 750. Power=100%. Pixel Size=5m. Lin es to average=1. Focus position=0micrometer. Select Image/Ratio to view both channels simult aneously. Perform a preview scan by clicking on the fast-forward icon. Stop scan once the fu ll arry is in view by pressing the stop icon. Switch to zoom mode by clicking on the array i mage and pressing Z. Click and drag the mouse on the area in which you want to zoom. Center the image of the entire array area within the viewing window. Under Tools on the left side o f the screen, click the Scan Area icon. Click and drag to define a box that bounds the visib ile array area. The box dimensions should be stretched to create a box just slightly larger than the array area. It is critical to include all of the corner probes within the scan imag e. Scan chip by clicking the play icon. While scanning, set the zoom level to view the whole im age and adjust the brightness and contrast of the displayed image to eliminate visible satur ation. Based on the appearance of the array features, adjust the PMT setting as appropriate.  The features should be mostly yellow. If your features are mostly green, either decrease th e 532 PMT or raise the 635 PMT. If the features are mostly red or orange, either raise the 5 32 PMT or decrease the 635 PMT. Zoom the view to a region scanned under the most recent PMT settings and click on the Histogram tab at the top of the left side of the screen to check g lobal intensity of the features. On the top left side of the screen make sure you have the 5 32 and 635 wavelength boxes checked so both wavelength histograms are displayed. Make sure t he Log Axis box is checked. You want the red and green curves to be as close as possible to one another. If the red curve is above the green, lower the red PMT setting or raise the gre en PMT setting. You want the curve to have 1e-5 normalized counts at the 65,000 intensity le vel (saturation). This means that you have about 1% of the features saturated. The position of the two curves on top of each other is more important than hitting the 1% saturation mark .  The histogram only graphs the area of the image that is viewable in the screen on the ima ge tab. If the histogram is no longer changing then either the chip is done scanning or the area that you can see on the image screen has been scanned. After the PMT settings are prope rly adjusted, stop the current scan, do not save this image. Restart the scan under the new settings and wait until the scan has completed. Save the images. Make sure you save both the  532nm and 635nm images as separate single image tif files.

data_processing: Log base 2 (56272_635/56272_532) ratios were bi-weight mean centered

molecule: genomic DNA

source_name: Chromatin affinity-purified DNA with tagged histone H3 from Drosophila S2 cells

label_protocol:
Sample labeling protocol provided and performed by NimbleGen (http://www.nimblegen.com/produ
cts/chip/index.html). Prepare the following three solutions: 50X dNTP Mix, Random 9mer Buffe
r, 10X TE.  Dilute Cy5 dye-labeled 9mers to 1 O.D./42 microliter Random 9mer Buffer. Aliquot
 to 40 microliter individual reaction volumes in 0.2 milliliter thin-walled PCR tubes and st
ore at -20 degrees C. Assemble the following components in a 0.2 milliliter thin-walled PCR
tube: 1 microgram LM-PCR Sample and 40 microliter Cy5-9mer Primers. Heat denature samples in
 thermocycler at 98 degrees C for 10 minutes. Quick chill in ice water bath. Snap-chilling s
tep after denaturation is critical for efficiency labeling. Add the following: 10 microliter
s 50X dNTPmix, 8 microliters VWR deionized water, 2 microliters Kienow (50 U/microliter). Do
 not vortex after addition of Kienow. Mix well by pipetting 10 times. Spin down at low RPM t
o force contents to bottom of tube. Incubate at 37 degrees C for 2 hours in a thermocycler p
rotected from light. Stop the reaction by addition of EDTA: 10 microliter Stop Solution (0.5
 M EDTA). Transfer the reaction to a 1.5 milliliter tube. Precipitate the labeled samples by
 adding NaCl and isopropanol to each tube as indicated: 11.5 microliter 5M NaCl, 110 microli
ter Isopropanol. Vortex briefly after addition of 5M NaCl prior to addition of isopropanol.
Vortex. Incubate 10 minutes at room temperature in the dark. Centrifuge at maximum speed for
 10 minutes. Remove supernatant with pipette. Rinse pellet with 500 microliter 80% ice-cold
ethanol. Dislodge pellet from tube wall. Centrifuge at maximum speed for 2 minutes. Remove s
upernatant with pipette. Speed-Vac on low heat for 5 minutes until dry, protected from light
. Store labeled samples at -20 degrees C, protected from light. Rehydrate dried pellets in 2
5 microliter VWR deionized water. Spin tubes down briefly prior to opening. Vortex for 30 se
conds and quick spin to collect contents at bottom of tube. Continue to vortex or let site i
n the dark at room temp until the pellet is completely rehydrated, then vortex again and qui
ckly spin. Measure the A_260 in each sample. It is important to consume as little sample as
possible when performing this measurement. Typical yields range from 10 to 30 micrograms per
 reaction.

source_name: Input DNA

label_protocol:
Sample labeling protocol provided and performed by NimbleGen (http://www.nimblegen.com/produ
cts/chip/index.html). Prepare the following three solutions: 50X dNTP Mix, Random 9mer Buffe
r, 10X TE.  Dilute Cy3 dye-labeled 9mers to 1 O.D./42 microliter Random 9mer Buffer. Aliquot
 to 40 microliter individual reaction volumes in 0.2 milliliter thin-walled PCR tubes and st
ore at -20 degrees C. Assemble the following components in a 0.2 milliliter thin-walled PCR
tube: 1 microgram LM-PCR Sample and 40 microliter Cy3-9mer Primers. Heat denature samples in
 thermocycler at 98 degrees C for 10 minutes. Quick chill in ice water bath. Snap-chilling s
tep after denaturation is critical for efficiency labeling. Add the following: 10 microliter
s 50X dNTPmix, 8 microliters VWR deionized water, 2 microliters Kienow (50 U/microliter). Do
 not vortex after addition of Kienow. Mix well by pipetting 10 times. Spin down at low RPM t
o force contents to bottom of tube. Incubate at 37 degrees C for 2 hours in a thermocycler p
rotected from light. Stop the reaction by addition of EDTA: 10 microliter Stop Solution (0.5
 M EDTA). Transfer the reaction to a 1.5 milliliter tube. Precipitate the labeled samples by
 adding NaCl and isopropanol to each tube as indicated: 11.5 microliter 5M NaCl, 110 microli
ter Isopropanol. Vortex briefly after addition of 5M NaCl prior to addition of isopropanol.
Vortex. Incubate 10 minutes at room temperature in the dark. Centrifuge at maximum speed for
 10 minutes. Remove supernatant with pipette. Rinse pellet with 500 microliter 80% ice-cold
ethanol. Dislodge pellet from tube wall. Centrifuge at maximum speed for 2 minutes. Remove s
upernatant with pipette. Speed-Vac on low heat for 5 minutes until dry, protected from light
. Store labeled samples at -20 degrees C, protected from light. Rehydrate dried pellets in 2
5 microliter VWR deionized water. Spin tubes down briefly prior to opening. Vortex for 30 se
conds and quick spin to collect contents at bottom of tube. Continue to vortex or let site i
n the dark at room temp until the pellet is completely rehydrated, then vortex again and qui
ckly spin. Measure the A_260 in each sample. It is important to consume as little sample as
possible when performing this measurement. Typical yields range from 10 to 30 micrograms per
 reaction.

tag: Input DNA


title: Vitis aestivalis 'Norton ' mock inoculated at 8 h post inoculation	57


title: Vitis aestivalis 'Norton ' infected w/ powdery mildew (Erysiphe necator) conidiospores 0 h post inoculation	43

source_name: The 10 randomly collected V. aestivalis 'Norton ' leaves at 0 hour after inoculation with E. necator conidiospores


title: Vitis aestivalis 'Norton ' infected w/ powdery mildew (Erysiphe necator) conidiospores 48 h post inoculation	42


title: Vitis aestivalis 'Norton ' infected w/ powdery mildew (Erysiphe necator) conidiospores 8 h post inoculation	45


title: Vitis aestivalis 'Norton ' infected w/ powdery mildew (Erysiphe necator) conidiospores 12 h post inoculation	52


title: Vitis aestivalis 'Norton ' infected w/ powdery mildew (Erysiphe necator) conidiospores 8 h post inoculation	39


title: Vitis aestivalis 'Norton ' infected w/ powdery mildew (Erysiphe necator) conidiospores 12 h post inoculation	46


title: Vitis aestivalis 'Norton ' infected w/ powdery mildew (Erysiphe necator) conidiospores 24 h post inoculation	41


title: Vitis aestivalis 'Norton ' infected w/ powdery mildew (Erysiphe necator) conidiospores 0 h post inoculation	37


title: Vitis aestivalis 'Norton ' infected w/ powdery mildew (Erysiphe necator) conidiospores 0 h post inoculation	49


title: Vitis vinifera 'Cabernet sauvignon' mock inoculated at 12 h post inoculation	34

description: Gene expression data from V. vinifera 'Cabernet Sauvignon' at 0 hour post mock inoculation

organism: Vitis vinifera

source_name: The 10 randomly collected V. vinifera 'Cabernet Sauvignon' leaves at 12 hour after mock inoculation


title: 58788 H33FL_1/INPUT_2

data_processing: Log base 2 (58788_635/58788_532) ratios were bi-weight mean centered

source_name: Chromatin affinity-purified DNA with tagged histone H3.3 region from Drosophila S2 cells

label_protocol:
Sample labeling protocol provided and performed by NimbleGen (http://www.nimblegen.com/produ
cts/chip/index.html). Prepare the following three solutions: 50X dNTP Mix, Random 9mer Buffe
r, 10X TE.  Dilute Cy5 dye-labeled 9mers to 1 O.D./42 microliter Random 9mer Buffer. Aliquot
 to 40 microliter individual reaction volumes in 0.2 milliliter thin-walled PCR tubes and st
ore at -20 degrees C. Assemble the following components in a 0.2 milliliter thin-walled PCR
tube: 1 microgram LM-PCR Sample and 40 microliter Cy5-9mer Primers. Heat denature samples in
 thermocycler at 98 degrees C for 10 minutes. Quick chill in ice water bath. Snap-chilling s
tep after denaturation is critical for efficiency labeling. Add the following: 10 microliter
s 50X dNTPmix, 8 microliters VWR deionized water, 2 microliters Kienow (50 U/microliter). Do
 not vortex after addition of Kienow. Mix well by pipetting 10 times. Spin down at low RPM t
o force contents to bottom of tube. Incubate at 37 degrees C for 2 hours in a thermocycler p
rotected from light. Stop the reaction by addition of EDTA: 10 microliter Stop Solution (0.5
 M EDTA). Transfer the reaction to a 1.5 milliliter tube. Precipitate the labeled samples by
 adding NaCl and isopropanol to each tube as indicated: 11.5 microliter 5M NaCl, 110 microli
ter Isopropanol. Vortex briefly after addition of 5M NaCl prior to addition of isopropanol.
Vortex. Incubate 10 minutes at room temperature in the dark. Centrifuge at maximum speed for
 10 minutes. Remove supernatant with pipette. Rinse pellet with 500 microliter 80% ice-cold
ethanol. Dislodge pellet from tube wall. Centrifuge at maximum speed for 2 minutes. Remove s
upernatant with pipette. Speed-Vac on low heat for 5 minutes until dry, protected from light
. Store labeled samples at -20 degrees C, protected from light. Rehydrate dried pellets in 2
5 microliter VWR deionized water. Spin tubes down briefly prior to opening. Vortex for 30 se
conds and quick spin to collect contents at bottom of tube. Continue to vortex or let site i
n the dark at room temp until the pellet is completely rehydrated, then vortex again and qui
ckly spin. Measure the A_260 in each sample. It is important to consume as little sample as
possible when performing this measurement. Typical yields range from 10 to 30 micrograms per
 reaction.
Sample labeling protocol provided and performed by NimbleGen (http://www.nimblegen.com/produ
cts/chip/index.html). Prepare the following three solutions: 50X dNTP Mix, Random 9mer Buffe
r, 10X TE.  Dilute Cy3 dye-labeled 9mers to 1 O.D./42 microliter Random 9mer Buffer. Aliquot
 to 40 microliter individual reaction volumes in 0.2 milliliter thin-walled PCR tubes and st
ore at -20 degrees C. Assemble the following components in a 0.2 milliliter thin-walled PCR
tube: 1 microgram LM-PCR Sample and 40 microliter Cy3-9mer Primers. Heat denature samples in
 thermocycler at 98 degrees C for 10 minutes. Quick chill in ice water bath. Snap-chilling s
tep after denaturation is critical for efficiency labeling. Add the following: 10 microliter
s 50X dNTPmix, 8 microliters VWR deionized water, 2 microliters Kienow (50 U/microliter). Do
 not vortex after addition of Kienow. Mix well by pipetting 10 times. Spin down at low RPM t
o force contents to bottom of tube. Incubate at 37 degrees C for 2 hours in a thermocycler p
rotected from light. Stop the reaction by addition of EDTA: 10 microliter Stop Solution (0.5
 M EDTA). Transfer the reaction to a 1.5 milliliter tube. Precipitate the labeled samples by
 adding NaCl and isopropanol to each tube as indicated: 11.5 microliter 5M NaCl, 110 microli
ter Isopropanol. Vortex briefly after addition of 5M NaCl prior to addition of isopropanol.
Vortex. Incubate 10 minutes at room temperature in the dark. Centrifuge at maximum speed for
 10 minutes. Remove supernatant with pipette. Rinse pellet with 500 microliter 80% ice-cold
ethanol. Dislodge pellet from tube wall. Centrifuge at maximum speed for 2 minutes. Remove s
upernatant with pipette. Speed-Vac on low heat for 5 minutes until dry, protected from light
. Store labeled samples at -20 degrees C, protected from light. Rehydrate dried pellets in 2
5 microliter VWR deionized water. Spin tubes down briefly prior to opening. Vortex for 30 se
conds and quick spin to collect contents at bottom of tube. Continue to vortex or let site i
n the dark at room temp until the pellet is completely rehydrated, then vortex again and qui
ckly spin. Measure the A_260 in each sample. It is important to consume as little sample as
possible when performing this measurement. Typical yields range from 10 to 30 micrograms per
 reaction.

extract_protocol: Histones were identically tagged at their N-termini with biotin ligase recognition peptide (BLRP) (de Boer, E. et al. Proc Natl Acad Sci U S A 100, 7480-5 (2003), and Beckett, D. et al. Protein Sci 8, 921-9 (1999)) and expressed together with E. coli biotin ligase in Drosophila S2 cells. Nuclei were prepared as described (McKittrick, E., et al., Proc. Natl. Acad. Sci. USA 101, 1525-1530 (2004).), and treated with micrococcal nuclease (MNase) to digest chromatin to yield mostly mononucleosomes. Chromatin was extracted (input) using a modification of the procedure of Blower, M.D., et al. (Developmental Cell 2, 319-330 (2002)). Biotinylated histone-containing nucleosome particles (pull-down) were purified and DNA was extracted from both input and pull-down fraction for microarray analysis. DNA from input (3 ug) and pull-down (4 ug) was provided to NimbleGen Systems for differential labelling by random priming with Cy3- or Cy5 and hybridization to oligonucleotide arrays.  For each experiment, input and pull-down channel signal intensities and scaled log2(ratios) were provided by NimbleGen Systems.


title: Vitis vinifera 'Cabernet sauvignon' mock inoculated at 8 h post inoculation	33

source_name: The 10 randomly collected V. vinifera 'Cabernet Sauvignon' leaves at 8 hour after mock inoculation


title: Vitis vinifera 'Cabernet sauvignon' mock inoculated at 24 h post inoculation	35

source_name: The 10 randomly collected V. vinifera 'Cabernet Sauvignon' leaves at 24 hour after mock inoculation


title: Vitis vinifera 'Cabernet sauvignon' mock inoculated at 48 h post inoculation	36

source_name: The 10 randomly collected V. vinifera 'Cabernet Sauvignon' leaves at 48 hour after mock inoculation


title: Vitis aestivalis 'Norton ' infected w/ powdery mildew (Erysiphe necator) conidiospores 4 h post inoculation	38


title: 58588 H3_1/Input_1

data_processing: Log base 2 (58588_635/58588_532) ratios were bi-weight mean centered

label_protocol:
Sample labeling protocol provided and performed by NimbleGen (http://www.nimblegen.com/produ
cts/chip/index.html). Prepare the following three solutions: 50X dNTP Mix, Random 9mer Buffe
r, 10X TE.  Dilute Cy3 dye-labeled 9mers to 1 O.D./42 microliter Random 9mer Buffer. Aliquot
 to 40 microliter individual reaction volumes in 0.2 milliliter thin-walled PCR tubes and st
ore at -20 degrees C. Assemble the following components in a 0.2 milliliter thin-walled PCR
tube: 1 microgram LM-PCR Sample and 40 microliter Cy3-9mer Primers. Heat denature samples in
 thermocycler at 98 degrees C for 10 minutes. Quick chill in ice water bath. Snap-chilling s
tep after denaturation is critical for efficiency labeling. Add the following: 10 microliter
s 50X dNTPmix, 8 microliters VWR deionized water, 2 microliters Kienow (50 U/microliter). Do
 not vortex after addition of Kienow. Mix well by pipetting 10 times. Spin down at low RPM t
o force contents to bottom of tube. Incubate at 37 degrees C for 2 hours in a thermocycler p
rotected from light. Stop the reaction by addition of EDTA: 10 microliter Stop Solution (0.5
 M EDTA). Transfer the reaction to a 1.5 milliliter tube. Precipitate the labeled samples by
 adding NaCl and isopropanol to each tube as indicated: 11.5 microliter 5M NaCl, 110 microli
ter Isopropanol. Vortex briefly after addition of 5M NaCl prior to addition of isopropanol.
Vortex. Incubate 10 minutes at room temperature in the dark. Centrifuge at maximum speed for
 10 minutes. Remove supernatant with pipette. Rinse pellet with 500 microliter 80% ice-cold
ethanol. Dislodge pellet from tube wall. Centrifuge at maximum speed for 2 minutes. Remove s
upernatant with pipette. Speed-Vac on low heat for 5 minutes until dry, protected from light
. Store labeled samples at -20 degrees C, protected from light. Rehydrate dried pellets in 2
5 microliter VWR deionized water. Spin tubes down briefly prior to opening. Vortex for 30 se
conds and quick spin to collect contents at bottom of tube. Continue to vortex or let site i
n the dark at room temp until the pellet is completely rehydrated, then vortex again and qui
ckly spin. Measure the A_260 in each sample. It is important to consume as little sample as
possible when performing this measurement. Typical yields range from 10 to 30 micrograms per
 reaction.
Hybridization protocol provided and performed by NimbleGen (http://www.nimblegen.com/product
s/chip/index.html). Set MAUI hybridization unit to 42 deg C and allow time for the temperatu
re to stabilize. Based on the A_260 measurement, combine 13 micrograms each of the Test and
Reference Samples into a single 1.5 ml microcentrifuge tube. Protect tube from light during
handling to prevent photobleaching of the light-sensitive Cy dyes. Dry the combined contents
 in a Speed-Vac on low heat. Resuspend the sample in 10.9microliter VWR water and vortex to
completely dissolve the sample. Spin the tube down briefly to collect the contents in the bo
ttom. Using the NimbleGen Array Reuse Kit, add the following to the resuspended sample: 19.5
 microliter 2X Hybridization Buffer, 7.8 microliter Hybridization Component A, 0.4 microlite
r Cy3 CPK6 50mer Oligo (50nM), 0.4 microliter Cy5 CPK6 50mer Oligo (100nM). CPK6 oligos are
included in the hybridization as controls that hybridize to alignment features on the Nimble
Gen arrays. They are required for proper extraction of array data from the scanned image. Mi
x the tube briefly then spin down to collect the contents in the bottom and place at 95 deg
C for 5 minutes. Immediately transfer the tube to the MAUI 42 deg C sample block and hold at
 this temperature until you are are ready for sample loading.
Place the MAUI Mixer SL Hybridization Chamber on the array using the provided assembly/disas
sembly jig and carefully follow MAUI setup instructions. Use the braying tool to remove all
air bubbles from the adhesive gasket around the outside of the hybridization chamber. Put th
e array and hybridization chamber on the MAUI and allow 30 seconds for the chips to come up
to temperature. Load the sample using the pipet supplied with the MAUI Station and following
 manufacturer instructions. During the loading, a small amount (3-7 microliter) of the sampl
e may flow out of the outlet port. Confirm that there are no bubbles in the chamber. If ther
e are, very gently massage any bubbles to either of the ends, away from the center of the ar
ray. Avoid applying too much pressure since this will force liquid out of the ports. Place t
he loaded array into one of the four MAUI bays and let equilibrate for 30 seconds. Wipe off
any sample leakage at the ports with a Kim-Wipe, and adhere MAUI stickers to both ports. Clo
se the bay clamp and select mix mode B. Hold down the mix button to start mixing. Confirm th
at the mixing is in progress before closing the cover. Hybridize the sample 16-20 hours.
Prior to removing the array from the MAUI Hybridization Station, prepare the following solut
ions. You will need two 250ml dishes of Wash I, and one each for Wash II and Wash III. One d
ish for Wash I should be shallow and be wide enough to accomodate the array and mixer loaded
 in the MAUI assembly/dissassembly jig. The lid from a 1000 microliter pipet tip box works w
ell. Also, the buffer in the first Wash I dish should be heated to 42 deg C to help soften t
he adhesive on the hybridization chamber; this will help prevent braking the array. Place th
e remaining three wash solutions in 300 microliter Tissue-Tek slide staining dishes. Wash I:
 225 ml VWR Water, 25ml 10X Wash Buffer I, 25microliter 1M DTT. Wash II: 225ml VWR Water, 25
ml 10X Wash Buffer II, 25microliter 1M DTT. Wash III: 225ml VWR Water, 25microliter 10X Wash
 Buffer III, 25microliter 1M DTT. Remove chip from MAUI Hybridization Station, load it back
into the MAUI assembly/disassembly jig, and immerse in the shallow 250ml Wash I at 42 deg C.
 Peel the hybridization chamber off very slowly to prevent the slide from cracking. Do not l
et the surface of the slide dry out at any point during washing. While the chip is submerged
, carefully peel off the mixer. Gently agitate the chip in Wash I for 10-15 seconds. Transfe
r the slide into a slide rack in the second dish of Wash I and incubate 2 minutes with agita
tion. Transfer to Wash II and incubate 1 minute with agitation. Rock the disk to move the wa
sh over the tops of the arrays. Transfer to Wash III and incubate for 15 sec with agitation.
 Remove array and spin dry in array-drying unit for 1 minute. Store the dried array in a dar
k desiccator.

extract_protocol:
Histones were identically tagged at their N-termini with biotin ligase recognition peptide (BLRP) (de Boer, E. et al. Proc Natl Acad Sci U S A 100, 7480-5 (2003), and Beckett, D. et al. Protein Sci 8, 921-9 (1999)) and expressed together with E. coli biotin ligase in Drosophila S2 cells. Nuclei were prepared as described (McKittrick, E., et al., Proc. Natl. Acad. Sci. USA 101, 1525-1530 (2004).), and treated with micrococcal nuclease (MNase) to digest chromatin to yield mostly mononucleosomes. Chromatin was extracted (input) using a modification of the procedure of Blower, M.D., et al. (Developmental Cell 2, 319-330 (2002)). Biotinylated histone-containing nucleosome particles (pull-down) were purified and DNA was extracted from both input and pull-down fraction for microarray analysis. DNA from input (3 ug) and pull-down (4 ug) was provided to NimbleGen Systems for differential labelling by random priming with Cy3- or Cy5 and hybridization to oligonucleotide arrays.  For each experiment, input and pull-down channel signal intensities and scaled log2(ratios) were provided by NimbleGen Systems.Sample labeling protocol provided and performed by NimbleGen (http://www.nimblegen.com/produ
cts/chip/index.html). Prepare the following three solutions: 50X dNTP Mix, Random 9mer Buffe
r, 10X TE.  Dilute Cy3 dye-labeled 9mers to 1 O.D./42 microliter Random 9mer Buffer. Aliquot
 to 40 microliter individual reaction volumes in 0.2 milliliter thin-walled PCR tubes and st
ore at -20 degrees C. Assemble the following components in a 0.2 milliliter thin-walled PCR
tube: 1 microgram LM-PCR Sample and 40 microliter Cy3-9mer Primers. Heat denature samples in
 thermocycler at 98 degrees C for 10 minutes. Quick chill in ice water bath. Snap-chilling s
tep after denaturation is critical for efficiency labeling. Add the following: 10 microliter
s 50X dNTPmix, 8 microliters VWR deionized water, 2 microliters Kienow (50 U/microliter). Do
 not vortex after addition of Kienow. Mix well by pipetting 10 times. Spin down at low RPM t
o force contents to bottom of tube. Incubate at 37 degrees C for 2 hours in a thermocycler p
rotected from light. Stop the reaction by addition of EDTA: 10 microliter Stop Solution (0.5
 M EDTA). Transfer the reaction to a 1.5 milliliter tube. Precipitate the labeled samples by
 adding NaCl and isopropanol to each tube as indicated: 11.5 microliter 5M NaCl, 110 microli
ter Isopropanol. Vortex briefly after addition of 5M NaCl prior to addition of isopropanol.
Vortex. Incubate 10 minutes at room temperature in the dark. Centrifuge at maximum speed for
 10 minutes. Remove supernatant with pipette. Rinse pellet with 500 microliter 80% ice-cold
ethanol. Dislodge pellet from tube wall. Centrifuge at maximum speed for 2 minutes. Remove s
upernatant with pipette. Speed-Vac on low heat for 5 minutes until dry, protected from light
. Store labeled samples at -20 degrees C, protected from light. Rehydrate dried pellets in 2
5 microliter VWR deionized water. Spin tubes down briefly prior to opening. Vortex for 30 se
conds and quick spin to collect contents at bottom of tube. Continue to vortex or let site i
n the dark at room temp until the pellet is completely rehydrated, then vortex again and qui
ckly spin. Measure the A_260 in each sample. It is important to consume as little sample as
possible when performing this measurement. Typical yields range from 10 to 30 micrograms per
 reaction.

tag: Chromatin affinity-purified DNA with tagged histone H3 from Drosophila S2 cells


title: Vitis vinifera 'Cabernet sauvignon' mock inoculated at 0 h post inoculation	31

source_name: The 10 randomly collected V. vinifera 'Cabernet Sauvignon' leaves at 0 hour after mock inoculation


title: Vitis vinifera 'Cabernet sauvignon' mock inoculated at 4 h post inoculation	32

source_name: The 10 randomly collected V. vinifera 'Cabernet Sauvignon' leaves at 4 hour after mock inoculation


title: Vitis vinifera 'Cabernet sauvignon' mock inoculated at 48 h post inoculation	30


title: Vitis vinifera 'Cabernet sauvignon' infected w/ powdery mildew (Erysiphe necator) conidiospores 48 h post inoculation	18

description: Gene expression data from V. vinifera 'Cabernet Sauvignon' at 0 hour post inoculation of E. necator conidiospores

source_name: The 10 randomly collected V. vinifera 'Cabernet Sauvignon' leaves at 48 hour after inoculation with E. necator conidiospores


title: Vitis vinifera 'Cabernet sauvignon' mock inoculated at 4 h post inoculation	20


title: Vitis vinifera 'Cabernet sauvignon' mock inoculateds at 4 h post inoculation	26


title: Vitis vinifera 'Cabernet sauvignon' mock inoculated at 0 h post inoculation	25


title: Vitis aestivalis 'Norton ' infected w/ powdery mildew (Erysiphe necator) conidiospores 24 h post inoculation	47


title: Vitis vinifera 'Cabernet sauvignon' mock inoculated at 24 h post inoculation	29


title: Vitis vinifera 'Cabernet sauvignon' infected w/ powdery mildew (Erysiphe necator) conidiospores 24 h post inoculation	11

source_name: The 10 randomly collected V. vinifera 'Cabernet Sauvignon' leaves at 24 hour after inoculation with E. necator conidiospores


title: Vitis vinifera 'Cabernet sauvignon' mock inoculated at 24 h post inoculation	23

source_name: The 10 randomly collected V. vinifera 'Cabernet Sauvignon' leaves at 24 hour after after mock inoculation


title: Vitis vinifera 'Cabernet sauvignon' mock inoculated at 0 h post inoculation	19


title: Vitis vinifera 'Cabernet sauvignon' mock inoculated at 12 h post inoculation	22


title: Vitis vinifera 'Cabernet sauvignon' infected w/ powdery mildew (Erysiphe necator) conidiospores 4 h post inoculation	14

source_name: The 10 randomly collected V. vinifera 'Cabernet Sauvignon' leaves at 4 hour after inoculation with E. necator conidiospores


title: Vitis vinifera 'Cabernet sauvignon' infected w/ powdery mildew (Erysiphe necator) conidiospores 12 h post inoculation	10

source_name: The 10 randomly collected V. vinifera 'Cabernet Sauvignon' leaves at 12 hour after inoculation with E. necator conidiospores


title: Vitis vinifera 'Cabernet sauvignon' mock inoculated at 8 h post inoculation	27


title: Vitis vinifera 'Cabernet sauvignon' mock inoculated at 8 h post inoculation	21


title: Vitis vinifera 'Cabernet sauvignon' infected w/ powdery mildew (Erysiphe necator) conidiospores 48 h post inoculation	12


title: Vitis vinifera 'Cabernet sauvignon' infected w/ powdery mildew (Erysiphe necator) conidiospores 12 h post inoculation	16


title: Vitis vinifera 'Cabernet sauvignon' mock inoculated at 48 h post inoculation	24


title: Vitis vinifera 'Cabernet sauvignon' infected w/ powdery mildew (Erysiphe necator) conidiospores 8 h post inoculation	15

source_name: The 10 randomly collected V. vinifera 'Cabernet Sauvignon' leaves at 8 hour after inoculation with E. necator conidiospores


title: Vitis vinifera 'Cabernet sauvignon' mock inoculated at 12 h post inoculation	28


title: Vitis vinifera 'Cabernet sauvignon' infected w/ powdery mildew (Erysiphe necator) conidiospores 0 h post inoculation	13

source_name: The 10 randomly collected V. vinifera 'Cabernet Sauvignon' leaves at 0 hour after inoculation with E. necator conidiospores


title: Vitis vinifera 'Cabernet sauvignon' infected w/ powdery mildew (Erysiphe necator) conidiospores 24 h post inoculation	17


title: Vitis vinifera 'Cabernet sauvignon' infected w/ powdery mildew (Erysiphe necator) conidiospores 8 h post inoculation	9


title: Vitis vinifera 'Cabernet sauvignon' infected w/ powdery mildew (Erysiphe necator) conidiospores 4 h post inoculation	8


title: Vitis aestivalis 'Norton ' mock inoculated at 4 h post inoculation	56

source_name: The 10 randomly collected V. aestivalis 'Norton ' leaves at 4 hour after mock inoculation


title: Vitis vinifera 'Cabernet sauvignon' infected w/ powdery mildew (Erysiphe necator) conidiospores 48 h post inoculation	6


title: Vitis vinifera 'Cabernet sauvignon' infected w/ powdery mildew (Erysiphe necator) conidiospores 0 h post inoculation	7