title: 34K_Blk_F_6hr_200_4


title: 34K_Blk_F_6hr_200_3

status: Public on Nov 29 2008

type: RNA

city: Durham

first: Holly

middle: Kloos

last: Dressman

state: NC

address: 101 Science Drive

department: Institute for Genome Sciences and Policy

country: USA

institute: Duke University Medical Center

scan_protocol: scan according to Axon GenePix 4000B recommendations

data_processing: Genespring GX 7.3 (Agilent Technologies) was used to perform initial data filtering in which spots whose signal intensities below 70 in either the Cy3 or Cy5 channel were removed.  For each analysis, only those samples in that analysis were used in the filtering process.  To compare data from previously published results, we only used those probes that mapped to each other across the Human Operon version 3.0 and version 4.0 arrays.  To then account for missing values, PAM software (http://www-stat.stanford.edu/ tibs/PAM/) was used to impute missing values.  k-nearest neighbor was used where missing values were imputed using a k-nearest neighbor average in gene space.  In the analysis approach in which all samples were included, lowess normalization of the data followed by batch effect removal using 2-way mixed model ANOVA (Partek Incorporated) was performed.

molecule: total RNA

organism: Mus musculus

source_name: 34K, Blk, Female, 6hr, 200

extract_protocol: Briefly, 5 x 106 MNCs were pelleted and total RNA was isolated using the RNAeasy minispin column

treatment_protocol: 200 cGy of total body irradiation

tag: Array

tag: Strain

value: Blk

tag: Gender

value: Female

tag: Time

tag: Agent

value: Radiation

tag: Dosage

source_name: Stratagene Universal Mouse reference

treatment_protocol: no treatment

tag: Stratagene Universal Mouse reference


title: Pre Chemotherapy patient_91A

description: Pre Chemotherapy patient_91A

organism: Homo sapiens

source_name: Mononuclear cells, Pre Chemo patient

tag: Mononuclear cells, Pre Chemo patient

source_name: Stratagene Universal Human reference

tag: Stratagene Universal Human reference


title: 36K_Blk_F_24hr_50_8

source_name: 36K, Blk, Female, 24hr, 50

treatment_protocol: 50 cGy of total body irradiation


title: Post Irradiation patient_83B

description: Post Irradiation patient_83B

source_name: Mononuclear cells, Post Irradiation patient

treatment_protocol: 150-200 cGy of total body irradiation


title: 36K_Blk_F_24hr_50_5


title: 36K_Blk_F_24hr_50_3


title: 34K_Blk_F_6hr_200_1


title: Post Irradiation patient_80B

description: Post Irradiation patient_80B

tag: Mononuclear cells, Post Irradiation patient


title: Post Irradiation patient_79B

description: Post Irradiation patient_79B


title: Pre Chemotherapy patient_94A

description: Pre Chemotherapy patient_94A


title: 34K_Blk_M_24hr_50_1

source_name: 34K, Blk, Male, 24hr, 50

value: Male


title: Post Irradiation patient_78B

description: Post Irradiation patient_78B


title: 34K_Blk_M_6hr_50_4

source_name: 34K, Blk, Male, 6hr, 50


title: 34K_Blk_M_24hr_50_5


title: 34K_Blk_F_6hr_50_6

source_name: 34K, Blk, Female, 6hr, 50


title: 34K_Blk_M_24hr_50_7


title: 34K_Blk_M_6hr_50_2


title: 34K_Blk_M_6hr_50_3


title: 36K_Blk_F_24hr_50_1


title: 34K_Blk_F_6hr_50_7


title: 34K_Blk_M_24hr_50_3


title: 34K_Blk_M_24hr_50_2


title: Post Irradiation patient_77B

description: Post Irradiation patient_77B


title: 36K_Blk_F_24hr_50_6


title: 36K_Blk_M_7day_50_4

source_name: 36K, Blk, Male, 7day, 50


title: 36K_Blk_M_7day_50_5


title: Post Irradiation patient_76B

description: Post Irradiation patient_76B


title: 36K_Blk_F_24hr_50_4


title: Post Irradiation patient_75B

description: Post Irradiation patient_75B


title: 36K_Blk_M_7day_50_3


title: 34K_Blk_F_6hr_50_4


title: 36K_Blk_M_6hr_50_2

source_name: 36K, Blk, Male, 6hr, 50


title: 36K_Blk_M_6hr_50_3


title: 34K_Blk_F_6hr_50_3


title: Post Irradiation patient_70B

description: Post Irradiation patient_70B


title: Pre Irradiation patient_77A

description: Pre Irradiation patient_77A

source_name: Mononuclear cells, Pre Irradiation patient

treatment_protocol: no IR treatment


title: Pre Irradiation patient_78A

description: Pre Irradiation patient_78A

tag: Mononuclear cells, Pre Irradiation patient


title: 34K_Balbc_F_6hr_50_2

source_name: 34K, Balbc, Female, 6hr, 50

value: Balbc


title: 34K_Blk_M_0hr_control_7

source_name: 34K, Blk, Male, 0hr, control

value: control


title: 36K_Blk_F_24hr_200_4

source_name: 36K, Blk, Female, 24hr, 200


title: Post Irradiation patient_62B

description: Post Irradiation patient_62B


title: 34K_Blk_M_0hr_control_5


title: 36K_Blk_F_24hr_200_3


title: Post Irradiation patient_64B

description: Post Irradiation patient_64B


title: Pre Irradiation patient_83A

description: Pre Irradiation patient_83A


title: 36K_Blk_M_0hr_control_18

source_name: 36K, Blk, Male, 0hr, control


title: 34K_Balbc_F_6hr_50_5


title: 34K_Balbc_F_6hr_50_7


title: 36K_Blk_F_0hr_control_8

source_name: 36K, Blk, Female, 0hr, control


title: 34K_Balbc_F_6hr_50_4


title: Pre Irradiation patient_76A

description: Pre Irradiation patient_76A


title: 34K_Blk_M_0hr_control_4


title: 34K_Balbc_F_6hr_50_3


title: 34K_Blk_F_6hr_50_2


title: 36K_Blk_F_0hr_control_7


title: Pre Irradiation patient_68A2

description: Pre Irradiation patient_68A2


title: 34K_Blk_F_6hr_50_1


title: 34K_Blk_F_6hr_50_5


title: 34K_Balbc_F_6hr_50_6


title: 36K_Blk_F_0hr_control_6


title: 36K_Blk_M_0hr_control_17


title: 34K_Blk_M_0hr_control_13


title: 34K_Blk_M_0hr_control_15


title: 34K_Blk_M_0hr_control_3


title: 34K_Blk_M_0hr_control_14


title: 36K_Blk_F_0hr_control_9


title: 34K_Balbc_F_6hr_50_9


title: Pre Irradiation patient_64A

description: Pre Irradiation patient_64A


title: 36K_Blk_M_0hr_control_16


title: Pre Irradiation patient_62A

description: Pre Irradiation patient_62A


title: 34K_Blk_M_0hr_control_9


title: 36K_Blk_F_0hr_control_5


title: 34K_Blk_M_0hr_control_1


title: 34K_Blk_M_0hr_control_10


title: 34K_Balbc_F_6hr_50_8


title: 34K_Balbc_F_6hr_50_1


title: 36K_Blk_F_0hr_control_3


title: 34K_Blk_M_0hr_control_11


title: 34K_Blk_F_0hr_control_24

source_name: 34K, Blk, Female, 0hr, control


title: 34K_Blk_M_0hr_control_12

source_name: Stratagene Universal Mouse reference


title: 34K_Blk_F_0hr_control_25


title: 34K_Blk_M_0hr_control_2


title: 34K_Blk_F_0hr_control_22


title: 36K_Blk_F_0hr_control_18


title: 34K_Blk_F_0hr_control_23


title: 34K_Blk_F_0hr_control_20


title: 36K_Blk_F_0hr_control_17


title: 34K_Blk_F_0hr_control_21


title: 34K_Balbc_F_0hr_control_6

source_name: 34K, Balbc, Female, 0hr, control


title: 34K_Balbc_F_0hr_control_5


title: 34K_Balbc_F_0hr_control_9


title: 34K_Balbc_F_0hr_control_8


title: 36K_Blk_F_0hr_control_4


title: 34K_Balbc_F_0hr_control_7


title: 34K_Blk_F_0hr_control_19


title: 36K_Blk_F_0hr_control_15


title: 34K_Balbc_F_0hr_control_3


title: 34K_Balbc_F_0hr_control_10


title: 34K_Balbc_F_0hr_control_4


title: 36K_Blk_F_0hr_control_11


title: 36K_Blk_F_0hr_control_12


title: 36K_Blk_F_0hr_control_1


title: 34K_Balbc_F_0hr_control_1


title: 36K_Blk_F_0hr_control_16


title: 36K_Blk_F_0hr_control_13


title: 36K_Blk_F_0hr_control_10


title: 34K_Balbc_F_0hr_control_2


title: 36K_Blk_F_0hr_control_14


title: 13690411 - Bl-1_LMV_2 vs Bl-1_Mock_2

status: Public on Oct 20 2008

city: Evry

first: Frederique

last: Bitton

address: 2 rue Gaston Cremieux

country: France

institute: INRA

description: Common and specific genes deregulated in response to various potyviruses in different Arabidopsis genetic backgrounds.

hyb_protocol: Bl-1_Mock_2 Cy5 / Bl-1_LMV_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 6.0, Cy3:pmt voltage 532nm,500V,laser power 30%, Cy5:635nm,pmt voltage 500V,laser power 30%

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

organism: Arabidopsis thaliana

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

growth_protocol: leaf - S2 greenhouse	 Medi : Klassmann soil, substrat 4	 hygrometry : low	 Temperature : 20°C to 33 °C, cooling when 24 °C	 Light : from 7h to 20 h, less than 70 W/m2

extract_protocol: Bl-1_Mock_2:30ug. Lyse cells or tissue (clear the lysate with the NucleoSpin® RNA Filter Strips) Add 300 µl RA1 +3 µl ß-me Pipette up and down 10-15 times to mix and resuspend genomic DNA that might have precipitated during the RA4 addition. Add 300 µl RA4 Transfer crude lysates to NucleoSpin® RNA Binding Strips Bind RNA to silica membrane of the NucleoSpin® RNA Binding Strips Apply vacuum : 200 mbar2 1 min Desalt silica membrane by washing with 500 µl RA3 Apply vacuum : 200 mbar2 3 min DNase incubation : add 30 µl DNase reaction mixture and incubate at room temperature 15 min Wash silica membrane : add 500 µl RA2, 800 µl RA3, 500 µl RA4 Apply vacuum : 200 mbar2 1 min each step Remove MN Wash Plate Dry NucleoSpin® RNA Binding Module : Apply vacuum : maximum vacuum 10 min Dry the outlets of the NucleoSpin® RNA Binding strips by placing it on a Paper Sheet Elute highly pure total RNA : add 75 µl RNasefree water incubate 2 min Apply vacuum : 500 mbar2 1 min

treatment_protocol: Name:Mock - control buffer - control,potyvirus:time 7day . Two to three Arabidopsis leaves are inoculated with grinded plant juice (not infected). Two days after the first one, a second inoculation is realised. Seven days after inoculation, inoculated leaves are collected.

tag: Arabidopsis thaliana ( bologna-1 )  - dev.stage (Boyes et al. Plant Cell 2001):boyes 1.06

extract_protocol: Bl-1_LMV_2:30ug. Lyse cells or tissue (clear the lysate with the NucleoSpin® RNA Filter Strips) Add 300 µl RA1 +3 µl ß-me Pipette up and down 10-15 times to mix and resuspend genomic DNA that might have precipitated during the RA4 addition. Add 300 µl RA4 Transfer crude lysates to NucleoSpin® RNA Binding Strips Bind RNA to silica membrane of the NucleoSpin® RNA Binding Strips Apply vacuum : 200 mbar2 1 min Desalt silica membrane by washing with 500 µl RA3 Apply vacuum : 200 mbar2 3 min DNase incubation : add 30 µl DNase reaction mixture and incubate at room temperature 15 min Wash silica membrane : add 500 µl RA2, 800 µl RA3, 500 µl RA4 Apply vacuum : 200 mbar2 1 min each step Remove MN Wash Plate Dry NucleoSpin® RNA Binding Module : Apply vacuum : maximum vacuum 10 min Dry the outlets of the NucleoSpin® RNA Binding strips by placing it on a Paper Sheet Elute highly pure total RNA : add 75 µl RNasefree water incubate 2 min Apply vacuum : 500 mbar2 1 min

treatment_protocol: Name:LMV - pathogen - pathogen infection,potyvirus:time 7day . LMV viruses are multiplied on susceptible hosts. For a ten plants inoculation, 1g of fresh infected plant is grinded in a mortar in a 3 volume inoculation buffer with carborandum. Two to three Arabidopsis leaves are inoculated with grinded infected plant juice. Two days after the first one, a second inoculation is realised. Seven days after inoculation, inoculated leaves are collected.


title: 13690414 - Col_Mock_2 vs Col_LMV_2

hyb_protocol: Col_LMV_2 Cy5 / Col_Mock_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Col_LMV_2:30ug. Lyse cells or tissue (clear the lysate with the NucleoSpin® RNA Filter Strips) Add 300 µl RA1 +3 µl ß-me Pipette up and down 10-15 times to mix and resuspend genomic DNA that might have precipitated during the RA4 addition. Add 300 µl RA4 Transfer crude lysates to NucleoSpin® RNA Binding Strips Bind RNA to silica membrane of the NucleoSpin® RNA Binding Strips Apply vacuum : 200 mbar2 1 min Desalt silica membrane by washing with 500 µl RA3 Apply vacuum : 200 mbar2 3 min DNase incubation : add 30 µl DNase reaction mixture and incubate at room temperature 15 min Wash silica membrane : add 500 µl RA2, 800 µl RA3, 500 µl RA4 Apply vacuum : 200 mbar2 1 min each step Remove MN Wash Plate Dry NucleoSpin® RNA Binding Module : Apply vacuum : maximum vacuum 10 min Dry the outlets of the NucleoSpin® RNA Binding strips by placing it on a Paper Sheet Elute highly pure total RNA : add 75 µl RNasefree water incubate 2 min Apply vacuum : 500 mbar2 1 min

tag: Arabidopsis thaliana (col-0)  - dev.stage (Boyes et al. Plant Cell 2001):boyes 1.06

extract_protocol: Col_Mock_2:30ug. Lyse cells or tissue (clear the lysate with the NucleoSpin® RNA Filter Strips) Add 300 µl RA1 +3 µl ß-me Pipette up and down 10-15 times to mix and resuspend genomic DNA that might have precipitated during the RA4 addition. Add 300 µl RA4 Transfer crude lysates to NucleoSpin® RNA Binding Strips Bind RNA to silica membrane of the NucleoSpin® RNA Binding Strips Apply vacuum : 200 mbar2 1 min Desalt silica membrane by washing with 500 µl RA3 Apply vacuum : 200 mbar2 3 min DNase incubation : add 30 µl DNase reaction mixture and incubate at room temperature 15 min Wash silica membrane : add 500 µl RA2, 800 µl RA3, 500 µl RA4 Apply vacuum : 200 mbar2 1 min each step Remove MN Wash Plate Dry NucleoSpin® RNA Binding Module : Apply vacuum : maximum vacuum 10 min Dry the outlets of the NucleoSpin® RNA Binding strips by placing it on a Paper Sheet Elute highly pure total RNA : add 75 µl RNasefree water incubate 2 min Apply vacuum : 500 mbar2 1 min


title: 13690857 - Bl-1_LMV_1 vs Bl-1_Mock_1

hyb_protocol: Bl-1_Mock_1 Cy5 / Bl-1_LMV_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Bl-1_Mock_1:30ug. Lyse cells or tissue (clear the lysate with the NucleoSpin® RNA Filter Strips) Add 300 µl RA1 +3 µl ß-me Pipette up and down 10-15 times to mix and resuspend genomic DNA that might have precipitated during the RA4 addition. Add 300 µl RA4 Transfer crude lysates to NucleoSpin® RNA Binding Strips Bind RNA to silica membrane of the NucleoSpin® RNA Binding Strips Apply vacuum : 200 mbar2 1 min Desalt silica membrane by washing with 500 µl RA3 Apply vacuum : 200 mbar2 3 min DNase incubation : add 30 µl DNase reaction mixture and incubate at room temperature 15 min Wash silica membrane : add 500 µl RA2, 800 µl RA3, 500 µl RA4 Apply vacuum : 200 mbar2 1 min each step Remove MN Wash Plate Dry NucleoSpin® RNA Binding Module : Apply vacuum : maximum vacuum 10 min Dry the outlets of the NucleoSpin® RNA Binding strips by placing it on a Paper Sheet Elute highly pure total RNA : add 75 µl RNasefree water incubate 2 min Apply vacuum : 500 mbar2 1 min

extract_protocol: Bl-1_LMV_1:30ug. Lyse cells or tissue (clear the lysate with the NucleoSpin® RNA Filter Strips) Add 300 µl RA1 +3 µl ß-me Pipette up and down 10-15 times to mix and resuspend genomic DNA that might have precipitated during the RA4 addition. Add 300 µl RA4 Transfer crude lysates to NucleoSpin® RNA Binding Strips Bind RNA to silica membrane of the NucleoSpin® RNA Binding Strips Apply vacuum : 200 mbar2 1 min Desalt silica membrane by washing with 500 µl RA3 Apply vacuum : 200 mbar2 3 min DNase incubation : add 30 µl DNase reaction mixture and incubate at room temperature 15 min Wash silica membrane : add 500 µl RA2, 800 µl RA3, 500 µl RA4 Apply vacuum : 200 mbar2 1 min each step Remove MN Wash Plate Dry NucleoSpin® RNA Binding Module : Apply vacuum : maximum vacuum 10 min Dry the outlets of the NucleoSpin® RNA Binding strips by placing it on a Paper Sheet Elute highly pure total RNA : add 75 µl RNasefree water incubate 2 min Apply vacuum : 500 mbar2 1 min


title: 13690932 - CvI_Mock_1 vs CvI_LMV_1

hyb_protocol: CvI_LMV_1 Cy5 / CvI_Mock_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: CvI_LMV_1:30ug. Lyse cells or tissue (clear the lysate with the NucleoSpin® RNA Filter Strips) Add 300 µl RA1 +3 µl ß-me Pipette up and down 10-15 times to mix and resuspend genomic DNA that might have precipitated during the RA4 addition. Add 300 µl RA4 Transfer crude lysates to NucleoSpin® RNA Binding Strips Bind RNA to silica membrane of the NucleoSpin® RNA Binding Strips Apply vacuum : 200 mbar2 1 min Desalt silica membrane by washing with 500 µl RA3 Apply vacuum : 200 mbar2 3 min DNase incubation : add 30 µl DNase reaction mixture and incubate at room temperature 15 min Wash silica membrane : add 500 µl RA2, 800 µl RA3, 500 µl RA4 Apply vacuum : 200 mbar2 1 min each step Remove MN Wash Plate Dry NucleoSpin® RNA Binding Module : Apply vacuum : maximum vacuum 10 min Dry the outlets of the NucleoSpin® RNA Binding strips by placing it on a Paper Sheet Elute highly pure total RNA : add 75 µl RNasefree water incubate 2 min Apply vacuum : 500 mbar2 1 min

tag: Arabidopsis thaliana (cape verde islands)  - dev.stage (Boyes et al. Plant Cell 2001):boyes 1.06

extract_protocol: CvI_Mock_1:30ug. Lyse cells or tissue (clear the lysate with the NucleoSpin® RNA Filter Strips) Add 300 µl RA1 +3 µl ß-me Pipette up and down 10-15 times to mix and resuspend genomic DNA that might have precipitated during the RA4 addition. Add 300 µl RA4 Transfer crude lysates to NucleoSpin® RNA Binding Strips Bind RNA to silica membrane of the NucleoSpin® RNA Binding Strips Apply vacuum : 200 mbar2 1 min Desalt silica membrane by washing with 500 µl RA3 Apply vacuum : 200 mbar2 3 min DNase incubation : add 30 µl DNase reaction mixture and incubate at room temperature 15 min Wash silica membrane : add 500 µl RA2, 800 µl RA3, 500 µl RA4 Apply vacuum : 200 mbar2 1 min each step Remove MN Wash Plate Dry NucleoSpin® RNA Binding Module : Apply vacuum : maximum vacuum 10 min Dry the outlets of the NucleoSpin® RNA Binding strips by placing it on a Paper Sheet Elute highly pure total RNA : add 75 µl RNasefree water incubate 2 min Apply vacuum : 500 mbar2 1 min


title: 13690856 - Bl-1_Mock_1 vs Bl-1_LMV_1

hyb_protocol: Bl-1_LMV_1 Cy5 / Bl-1_Mock_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13690935 - CvI_LMV_2 vs CvI_Mock_2

hyb_protocol: CvI_Mock_2 Cy5 / CvI_LMV_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: CvI_Mock_2:30ug. Lyse cells or tissue (clear the lysate with the NucleoSpin® RNA Filter Strips) Add 300 µl RA1 +3 µl ß-me Pipette up and down 10-15 times to mix and resuspend genomic DNA that might have precipitated during the RA4 addition. Add 300 µl RA4 Transfer crude lysates to NucleoSpin® RNA Binding Strips Bind RNA to silica membrane of the NucleoSpin® RNA Binding Strips Apply vacuum : 200 mbar2 1 min Desalt silica membrane by washing with 500 µl RA3 Apply vacuum : 200 mbar2 3 min DNase incubation : add 30 µl DNase reaction mixture and incubate at room temperature 15 min Wash silica membrane : add 500 µl RA2, 800 µl RA3, 500 µl RA4 Apply vacuum : 200 mbar2 1 min each step Remove MN Wash Plate Dry NucleoSpin® RNA Binding Module : Apply vacuum : maximum vacuum 10 min Dry the outlets of the NucleoSpin® RNA Binding strips by placing it on a Paper Sheet Elute highly pure total RNA : add 75 µl RNasefree water incubate 2 min Apply vacuum : 500 mbar2 1 min

extract_protocol: CvI_LMV_2:30ug. Lyse cells or tissue (clear the lysate with the NucleoSpin® RNA Filter Strips) Add 300 µl RA1 +3 µl ß-me Pipette up and down 10-15 times to mix and resuspend genomic DNA that might have precipitated during the RA4 addition. Add 300 µl RA4 Transfer crude lysates to NucleoSpin® RNA Binding Strips Bind RNA to silica membrane of the NucleoSpin® RNA Binding Strips Apply vacuum : 200 mbar2 1 min Desalt silica membrane by washing with 500 µl RA3 Apply vacuum : 200 mbar2 3 min DNase incubation : add 30 µl DNase reaction mixture and incubate at room temperature 15 min Wash silica membrane : add 500 µl RA2, 800 µl RA3, 500 µl RA4 Apply vacuum : 200 mbar2 1 min each step Remove MN Wash Plate Dry NucleoSpin® RNA Binding Module : Apply vacuum : maximum vacuum 10 min Dry the outlets of the NucleoSpin® RNA Binding strips by placing it on a Paper Sheet Elute highly pure total RNA : add 75 µl RNasefree water incubate 2 min Apply vacuum : 500 mbar2 1 min


title: 13690933 - CvI_LMV_1 vs CvI_Mock_1

hyb_protocol: CvI_Mock_1 Cy5 / CvI_LMV_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688145 - Col_LMV_1 vs Col_Mock_1

hyb_protocol: Col_Mock_1 Cy5 / Col_LMV_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

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

extract_protocol: Col_Mock_1:30ug. Lyse cells or tissue (clear the lysate with the NucleoSpin® RNA Filter Strips) Add 300 µl RA1 +3 µl ß-me Pipette up and down 10-15 times to mix and resuspend genomic DNA that might have precipitated during the RA4 addition. Add 300 µl RA4 Transfer crude lysates to NucleoSpin® RNA Binding Strips Bind RNA to silica membrane of the NucleoSpin® RNA Binding Strips Apply vacuum : 200 mbar2 1 min Desalt silica membrane by washing with 500 µl RA3 Apply vacuum : 200 mbar2 3 min DNase incubation : add 30 µl DNase reaction mixture and incubate at room temperature 15 min Wash silica membrane : add 500 µl RA2, 800 µl RA3, 500 µl RA4 Apply vacuum : 200 mbar2 1 min each step Remove MN Wash Plate Dry NucleoSpin® RNA Binding Module : Apply vacuum : maximum vacuum 10 min Dry the outlets of the NucleoSpin® RNA Binding strips by placing it on a Paper Sheet Elute highly pure total RNA : add 75 µl RNasefree water incubate 2 min Apply vacuum : 500 mbar2 1 min

extract_protocol: Col_LMV_1:30ug. Lyse cells or tissue (clear the lysate with the NucleoSpin® RNA Filter Strips) Add 300 µl RA1 +3 µl ß-me Pipette up and down 10-15 times to mix and resuspend genomic DNA that might have precipitated during the RA4 addition. Add 300 µl RA4 Transfer crude lysates to NucleoSpin® RNA Binding Strips Bind RNA to silica membrane of the NucleoSpin® RNA Binding Strips Apply vacuum : 200 mbar2 1 min Desalt silica membrane by washing with 500 µl RA3 Apply vacuum : 200 mbar2 3 min DNase incubation : add 30 µl DNase reaction mixture and incubate at room temperature 15 min Wash silica membrane : add 500 µl RA2, 800 µl RA3, 500 µl RA4 Apply vacuum : 200 mbar2 1 min each step Remove MN Wash Plate Dry NucleoSpin® RNA Binding Module : Apply vacuum : maximum vacuum 10 min Dry the outlets of the NucleoSpin® RNA Binding strips by placing it on a Paper Sheet Elute highly pure total RNA : add 75 µl RNasefree water incubate 2 min Apply vacuum : 500 mbar2 1 min


title: 13688144 - Col_Mock_1 vs Col_LMV_1

hyb_protocol: Col_LMV_1 Cy5 / Col_Mock_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13690855 - Ler_LMV-2 vs Ler-mock-2

hyb_protocol: Ler-mock-2 Cy5 / Ler_LMV-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: leaf - S2 greenhouse	 Medium : Klassmann soil, substrat 4	 hygrometry : low	 Temperature : 20°C to 33 °C, cooling when 24 °C	 Light : 7h to 20 h, less than 70 W/m2

extract_protocol: Ler-mock-2:100mg. Lyse cells or tissue (clear the lysate with the NucleoSpin® RNA Filter Strips) Add 300 µl RA1 +3 µl ß-me Pipette up and down 10-15 times to mix and resuspend genomic DNA that might have precipitated during the RA4 addition. Add 300 µl RA4 Transfer crude lysates to NucleoSpin® RNA Binding Strips Bind RNA to silica membrane of the NucleoSpin® RNA Binding Strips Apply vacuum : 200 mbar2 1 min Desalt silica membrane by washing with 500 µl RA3 Apply vacuum : 200 mbar2 3 min DNase incubation : add 30 µl DNase reaction mixture and incubate at room temperature 15 min Wash silica membrane : add 500 µl RA2, 800 µl RA3, 500 µl RA4 Apply vacuum : 200 mbar2 1 min each step Remove MN Wash Plate Dry NucleoSpin® RNA Binding Module : Apply vacuum : maximum vacuum 10 min Dry the outlets of the NucleoSpin® RNA Binding strips by placing it on a Paper Sheet Elute highly pure total RNA : add 75 µl RNasefree water incubate 2 min Apply vacuum : 500 mbar2 1 min

tag: Arabidopsis thaliana (landsberg erecta)  - dev.stage (Boyes et al. Plant Cell 2001):boyes 1.06

extract_protocol: Ler_LMV-2:100mg. Lyse cells or tissue (clear the lysate with the NucleoSpin® RNA Filter Strips) Add 300 µl RA1 +3 µl ß-me Pipette up and down 10-15 times to mix and resuspend genomic DNA that might have precipitated during the RA4 addition. Add 300 µl RA4 Transfer crude lysates to NucleoSpin® RNA Binding Strips Bind RNA to silica membrane of the NucleoSpin® RNA Binding Strips Apply vacuum : 200 mbar2 1 min Desalt silica membrane by washing with 500 µl RA3 Apply vacuum : 200 mbar2 3 min DNase incubation : add 30 µl DNase reaction mixture and incubate at room temperature 15 min Wash silica membrane : add 500 µl RA2, 800 µl RA3, 500 µl RA4 Apply vacuum : 200 mbar2 1 min each step Remove MN Wash Plate Dry NucleoSpin® RNA Binding Module : Apply vacuum : maximum vacuum 10 min Dry the outlets of the NucleoSpin® RNA Binding strips by placing it on a Paper Sheet Elute highly pure total RNA : add 75 µl RNasefree water incubate 2 min Apply vacuum : 500 mbar2 1 min


title: 13690852 - Ler_LMV-1 vs Ler-mock-1

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

extract_protocol: Ler-mock-1:100mg. Lyse cells or tissue (clear the lysate with the NucleoSpin® RNA Filter Strips) Add 300 µl RA1 +3 µl ß-me Pipette up and down 10-15 times to mix and resuspend genomic DNA that might have precipitated during the RA4 addition. Add 300 µl RA4 Transfer crude lysates to NucleoSpin® RNA Binding Strips Bind RNA to silica membrane of the NucleoSpin® RNA Binding Strips Apply vacuum : 200 mbar2 1 min Desalt silica membrane by washing with 500 µl RA3 Apply vacuum : 200 mbar2 3 min DNase incubation : add 30 µl DNase reaction mixture and incubate at room temperature 15 min Wash silica membrane : add 500 µl RA2, 800 µl RA3, 500 µl RA4 Apply vacuum : 200 mbar2 1 min each step Remove MN Wash Plate Dry NucleoSpin® RNA Binding Module : Apply vacuum : maximum vacuum 10 min Dry the outlets of the NucleoSpin® RNA Binding strips by placing it on a Paper Sheet Elute highly pure total RNA : add 75 µl RNasefree water incubate 2 min Apply vacuum : 500 mbar2 1 min

extract_protocol: Ler_LMV-1:100mg. Lyse cells or tissue (clear the lysate with the NucleoSpin® RNA Filter Strips) Add 300 µl RA1 +3 µl ß-me Pipette up and down 10-15 times to mix and resuspend genomic DNA that might have precipitated during the RA4 addition. Add 300 µl RA4 Transfer crude lysates to NucleoSpin® RNA Binding Strips Bind RNA to silica membrane of the NucleoSpin® RNA Binding Strips Apply vacuum : 200 mbar2 1 min Desalt silica membrane by washing with 500 µl RA3 Apply vacuum : 200 mbar2 3 min DNase incubation : add 30 µl DNase reaction mixture and incubate at room temperature 15 min Wash silica membrane : add 500 µl RA2, 800 µl RA3, 500 µl RA4 Apply vacuum : 200 mbar2 1 min each step Remove MN Wash Plate Dry NucleoSpin® RNA Binding Module : Apply vacuum : maximum vacuum 10 min Dry the outlets of the NucleoSpin® RNA Binding strips by placing it on a Paper Sheet Elute highly pure total RNA : add 75 µl RNasefree water incubate 2 min Apply vacuum : 500 mbar2 1 min


title: 13690854 - Ler-mock-2 vs Ler_LMV-2

hyb_protocol: Ler_LMV-2 Cy5 / Ler-mock-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13690843 - Ler-mock-1 vs Ler_TEV-1

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

extract_protocol: Ler_TEV-1:100mg. Lyse cells or tissue (clear the lysate with the NucleoSpin® RNA Filter Strips) Add 300 µl RA1 +3 µl ß-me Pipette up and down 10-15 times to mix and resuspend genomic DNA that might have precipitated during the RA4 addition. Add 300 µl RA4 Transfer crude lysates to NucleoSpin® RNA Binding Strips Bind RNA to silica membrane of the NucleoSpin® RNA Binding Strips Apply vacuum : 200 mbar2 1 min Desalt silica membrane by washing with 500 µl RA3 Apply vacuum : 200 mbar2 3 min DNase incubation : add 30 µl DNase reaction mixture and incubate at room temperature 15 min Wash silica membrane : add 500 µl RA2, 800 µl RA3, 500 µl RA4 Apply vacuum : 200 mbar2 1 min each step Remove MN Wash Plate Dry NucleoSpin® RNA Binding Module : Apply vacuum : maximum vacuum 10 min Dry the outlets of the NucleoSpin® RNA Binding strips by placing it on a Paper Sheet Elute highly pure total RNA : add 75 µl RNasefree water incubate 2 min Apply vacuum : 500 mbar2 1 min

treatment_protocol: Name:TEV - pathogen - pathogen infection,potyvirus:time 7day . TEV viruses are multiplied on susceptible hosts. For a ten plants inoculation, 1g of fresh infected plant is grinded in a mortar in a 3 volume inoculation buffer with carborandum. Two to three Arabidopsis leaves are inoculated with grinded infected plant juice. Two days after the first one, a second inoculation is realised. Seven days after inoculation, inoculated leaves are collected.


title: 13690844 - Ler_TEV-1 vs Ler-mock-1

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


title: 13690847 - Ler-PPV-Mock-1 vs Ler-PPV-1

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

growth_protocol: leaf - High confinement greenhouse	 Medium : Klassmann soil, substrat 4 + agrofino	 hygrometry : 70%	 Temperature : 15°C night, 20°C day	 Light : from 7h to 20 h

extract_protocol: Ler-PPV-1:100mg. Lyse cells or tissue (clear the lysate with the NucleoSpin® RNA Filter Strips) Add 300 µl RA1 +3 µl ß-me Pipette up and down 10-15 times to mix and resuspend genomic DNA that might have precipitated during the RA4 addition. Add 300 µl RA4 Transfer crude lysates to NucleoSpin® RNA Binding Strips Bind RNA to silica membrane of the NucleoSpin® RNA Binding Strips Apply vacuum : 200 mbar2 1 min Desalt silica membrane by washing with 500 µl RA3 Apply vacuum : 200 mbar2 3 min DNase incubation : add 30 µl DNase reaction mixture and incubate at room temperature 15 min Wash silica membrane : add 500 µl RA2, 800 µl RA3, 500 µl RA4 Apply vacuum : 200 mbar2 1 min each step Remove MN Wash Plate Dry NucleoSpin® RNA Binding Module : Apply vacuum : maximum vacuum 10 min Dry the outlets of the NucleoSpin® RNA Binding strips by placing it on a Paper Sheet Elute highly pure total RNA : add 75 µl RNasefree water incubate 2 min Apply vacuum : 500 mbar2 1 min

treatment_protocol: Name:PPV - pathogen - pathogen infection,potyvirus:time 7day . PPV viruses are multiplied on susceptible hosts. For a ten plants inoculation, 1g of fresh infected plant is grinded in a mortar in a 3 volume inoculation buffer with carborandum. Two to three Arabidopsis leaves are inoculated with grinded infected plant juice. Two days after the first one, a second inoculation is realised. Seven days after inoculation, inoculated leaves are collected.

extract_protocol: Ler-PPV-Mock-1:100mg. Lyse cells or tissue (clear the lysate with the NucleoSpin® RNA Filter Strips) Add 300 µl RA1 +3 µl ß-me Pipette up and down 10-15 times to mix and resuspend genomic DNA that might have precipitated during the RA4 addition. Add 300 µl RA4 Transfer crude lysates to NucleoSpin® RNA Binding Strips Bind RNA to silica membrane of the NucleoSpin® RNA Binding Strips Apply vacuum : 200 mbar2 1 min Desalt silica membrane by washing with 500 µl RA3 Apply vacuum : 200 mbar2 3 min DNase incubation : add 30 µl DNase reaction mixture and incubate at room temperature 15 min Wash silica membrane : add 500 µl RA2, 800 µl RA3, 500 µl RA4 Apply vacuum : 200 mbar2 1 min each step Remove MN Wash Plate Dry NucleoSpin® RNA Binding Module : Apply vacuum : maximum vacuum 10 min Dry the outlets of the NucleoSpin® RNA Binding strips by placing it on a Paper Sheet Elute highly pure total RNA : add 75 µl RNasefree water incubate 2 min Apply vacuum : 500 mbar2 1 min


title: 36K_Blk_F_0hr_control_2

extract_protocol: Briefly, 5 x 106 MNCs were pelleted and total RNA was isolated using the RNAeasy minispin column


title: 13690845 - Ler-mock-2 vs Ler_TEV-2

hyb_protocol: Ler_TEV-2 Cy5 / Ler-mock-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Ler_TEV-2:100mg. Lyse cells or tissue (clear the lysate with the NucleoSpin® RNA Filter Strips) Add 300 µl RA1 +3 µl ß-me Pipette up and down 10-15 times to mix and resuspend genomic DNA that might have precipitated during the RA4 addition. Add 300 µl RA4 Transfer crude lysates to NucleoSpin® RNA Binding Strips Bind RNA to silica membrane of the NucleoSpin® RNA Binding Strips Apply vacuum : 200 mbar2 1 min Desalt silica membrane by washing with 500 µl RA3 Apply vacuum : 200 mbar2 3 min DNase incubation : add 30 µl DNase reaction mixture and incubate at room temperature 15 min Wash silica membrane : add 500 µl RA2, 800 µl RA3, 500 µl RA4 Apply vacuum : 200 mbar2 1 min each step Remove MN Wash Plate Dry NucleoSpin® RNA Binding Module : Apply vacuum : maximum vacuum 10 min Dry the outlets of the NucleoSpin® RNA Binding strips by placing it on a Paper Sheet Elute highly pure total RNA : add 75 µl RNasefree water incubate 2 min Apply vacuum : 500 mbar2 1 min


title: 13690410 - Bl-1_Mock_2 vs Bl-1_LMV_2

hyb_protocol: Bl-1_LMV_2 Cy5 / Bl-1_Mock_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Bl-1_LMV_2:30ug. Lyse cells or tissue (clear the lysate with the NucleoSpin® RNA Filter Strips) Add 300 µl RA1 +3 µl ß-me Pipette up and down 10-15 times to mix and resuspend genomic DNA that might have precipitated during the RA4 addition. Add 300 µl RA4 Transfer crude lysates to NucleoSpin® RNA Binding Strips Bind RNA to silica membrane of the NucleoSpin® RNA Binding Strips Apply vacuum : 200 mbar2 1 min Desalt silica membrane by washing with 500 µl RA3 Apply vacuum : 200 mbar2 3 min DNase incubation : add 30 µl DNase reaction mixture and incubate at room temperature 15 min Wash silica membrane : add 500 µl RA2, 800 µl RA3, 500 µl RA4 Apply vacuum : 200 mbar2 1 min each step Remove MN Wash Plate Dry NucleoSpin® RNA Binding Module : Apply vacuum : maximum vacuum 10 min Dry the outlets of the NucleoSpin® RNA Binding strips by placing it on a Paper Sheet Elute highly pure total RNA : add 75 µl RNasefree water incubate 2 min Apply vacuum : 500 mbar2 1 min

extract_protocol: Bl-1_Mock_2:30ug. Lyse cells or tissue (clear the lysate with the NucleoSpin® RNA Filter Strips) Add 300 µl RA1 +3 µl ß-me Pipette up and down 10-15 times to mix and resuspend genomic DNA that might have precipitated during the RA4 addition. Add 300 µl RA4 Transfer crude lysates to NucleoSpin® RNA Binding Strips Bind RNA to silica membrane of the NucleoSpin® RNA Binding Strips Apply vacuum : 200 mbar2 1 min Desalt silica membrane by washing with 500 µl RA3 Apply vacuum : 200 mbar2 3 min DNase incubation : add 30 µl DNase reaction mixture and incubate at room temperature 15 min Wash silica membrane : add 500 µl RA2, 800 µl RA3, 500 µl RA4 Apply vacuum : 200 mbar2 1 min each step Remove MN Wash Plate Dry NucleoSpin® RNA Binding Module : Apply vacuum : maximum vacuum 10 min Dry the outlets of the NucleoSpin® RNA Binding strips by placing it on a Paper Sheet Elute highly pure total RNA : add 75 µl RNasefree water incubate 2 min Apply vacuum : 500 mbar2 1 min


title: 13690851 - Ler-mock-1 vs Ler_LMV-1

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


title: 13690849 - Ler-PPV-Mock-2 vs Ler-PPV-2

hyb_protocol: Ler-PPV-2 Cy5 / Ler-PPV-Mock-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Ler-PPV-2:100mg. Lyse cells or tissue (clear the lysate with the NucleoSpin® RNA Filter Strips) Add 300 µl RA1 +3 µl ß-me Pipette up and down 10-15 times to mix and resuspend genomic DNA that might have precipitated during the RA4 addition. Add 300 µl RA4 Transfer crude lysates to NucleoSpin® RNA Binding Strips Bind RNA to silica membrane of the NucleoSpin® RNA Binding Strips Apply vacuum : 200 mbar2 1 min Desalt silica membrane by washing with 500 µl RA3 Apply vacuum : 200 mbar2 3 min DNase incubation : add 30 µl DNase reaction mixture and incubate at room temperature 15 min Wash silica membrane : add 500 µl RA2, 800 µl RA3, 500 µl RA4 Apply vacuum : 200 mbar2 1 min each step Remove MN Wash Plate Dry NucleoSpin® RNA Binding Module : Apply vacuum : maximum vacuum 10 min Dry the outlets of the NucleoSpin® RNA Binding strips by placing it on a Paper Sheet Elute highly pure total RNA : add 75 µl RNasefree water incubate 2 min Apply vacuum : 500 mbar2 1 min

extract_protocol: Ler-PPV-Mock-2:100mg. Lyse cells or tissue (clear the lysate with the NucleoSpin® RNA Filter Strips) Add 300 µl RA1 +3 µl ß-me Pipette up and down 10-15 times to mix and resuspend genomic DNA that might have precipitated during the RA4 addition. Add 300 µl RA4 Transfer crude lysates to NucleoSpin® RNA Binding Strips Bind RNA to silica membrane of the NucleoSpin® RNA Binding Strips Apply vacuum : 200 mbar2 1 min Desalt silica membrane by washing with 500 µl RA3 Apply vacuum : 200 mbar2 3 min DNase incubation : add 30 µl DNase reaction mixture and incubate at room temperature 15 min Wash silica membrane : add 500 µl RA2, 800 µl RA3, 500 µl RA4 Apply vacuum : 200 mbar2 1 min each step Remove MN Wash Plate Dry NucleoSpin® RNA Binding Module : Apply vacuum : maximum vacuum 10 min Dry the outlets of the NucleoSpin® RNA Binding strips by placing it on a Paper Sheet Elute highly pure total RNA : add 75 µl RNasefree water incubate 2 min Apply vacuum : 500 mbar2 1 min


title: 13690846 - Ler_TEV-2 vs Ler-mock-2

hyb_protocol: Ler-mock-2 Cy5 / Ler_TEV-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13690848 - Ler-PPV-1 vs Ler-PPV-Mock-1

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


title: FL CD34+CD38+ cells, biological replicate 1

status: Public on Sep 10 2008

city: Leiden

first: Arnolda

last: de Nooij-van Dalen

address: Albinusdreef 2

department: Hematology

country: Netherlands

institute: LUMC

description: Gene expression data from CD34+CD38- cells isolated from normal human Bone Marrow

hyb_protocol: following fragmentation 10 ug cRNA was hybridized at 45 C for 16 hours with constant rotation at 60 rpm

scan_protocol: Scanning was performed as described in the GeneChip Expression Analysis technical manual

data_processing: The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.

label: biotin

source_name: fetal liver

label_protocol: biotinylated cRNA

extract_protocol: Rneasy colums (Qiagen)

tag: CD34+CD38+ cells


title: 13690934 - CvI_Mock_2 vs CvI_LMV_2

hyb_protocol: CvI_LMV_2 Cy5 / CvI_Mock_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: CvI_LMV_2:30ug. Lyse cells or tissue (clear the lysate with the NucleoSpin® RNA Filter Strips) Add 300 µl RA1 +3 µl ß-me Pipette up and down 10-15 times to mix and resuspend genomic DNA that might have precipitated during the RA4 addition. Add 300 µl RA4 Transfer crude lysates to NucleoSpin® RNA Binding Strips Bind RNA to silica membrane of the NucleoSpin® RNA Binding Strips Apply vacuum : 200 mbar2 1 min Desalt silica membrane by washing with 500 µl RA3 Apply vacuum : 200 mbar2 3 min DNase incubation : add 30 µl DNase reaction mixture and incubate at room temperature 15 min Wash silica membrane : add 500 µl RA2, 800 µl RA3, 500 µl RA4 Apply vacuum : 200 mbar2 1 min each step Remove MN Wash Plate Dry NucleoSpin® RNA Binding Module : Apply vacuum : maximum vacuum 10 min Dry the outlets of the NucleoSpin® RNA Binding strips by placing it on a Paper Sheet Elute highly pure total RNA : add 75 µl RNasefree water incubate 2 min Apply vacuum : 500 mbar2 1 min

extract_protocol: CvI_Mock_2:30ug. Lyse cells or tissue (clear the lysate with the NucleoSpin® RNA Filter Strips) Add 300 µl RA1 +3 µl ß-me Pipette up and down 10-15 times to mix and resuspend genomic DNA that might have precipitated during the RA4 addition. Add 300 µl RA4 Transfer crude lysates to NucleoSpin® RNA Binding Strips Bind RNA to silica membrane of the NucleoSpin® RNA Binding Strips Apply vacuum : 200 mbar2 1 min Desalt silica membrane by washing with 500 µl RA3 Apply vacuum : 200 mbar2 3 min DNase incubation : add 30 µl DNase reaction mixture and incubate at room temperature 15 min Wash silica membrane : add 500 µl RA2, 800 µl RA3, 500 µl RA4 Apply vacuum : 200 mbar2 1 min each step Remove MN Wash Plate Dry NucleoSpin® RNA Binding Module : Apply vacuum : maximum vacuum 10 min Dry the outlets of the NucleoSpin® RNA Binding strips by placing it on a Paper Sheet Elute highly pure total RNA : add 75 µl RNasefree water incubate 2 min Apply vacuum : 500 mbar2 1 min


title: 13690850 - Ler-PPV-2 vs Ler-PPV-Mock-2

hyb_protocol: Ler-PPV-Mock-2 Cy5 / Ler-PPV-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: FL CD34+CD38- cells, biological replicate 1

tag: CD34+CD38- cells


title: FL CD34+CD38+ cells, biological replicate 2


title: UCB CD34+CD38+ cells, biological replicate 2

source_name: umbilical cord blood


title: FL CD34+CD38- cells, biological replicate 2


title: UCB CD34+CD38+ cells, biological replicate 1


title: 13690416 - Col_LMV_2 vs Col_Mock_2

hyb_protocol: Col_Mock_2 Cy5 / Col_LMV_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Col_Mock_2:30ug. Lyse cells or tissue (clear the lysate with the NucleoSpin® RNA Filter Strips) Add 300 µl RA1 +3 µl ß-me Pipette up and down 10-15 times to mix and resuspend genomic DNA that might have precipitated during the RA4 addition. Add 300 µl RA4 Transfer crude lysates to NucleoSpin® RNA Binding Strips Bind RNA to silica membrane of the NucleoSpin® RNA Binding Strips Apply vacuum : 200 mbar2 1 min Desalt silica membrane by washing with 500 µl RA3 Apply vacuum : 200 mbar2 3 min DNase incubation : add 30 µl DNase reaction mixture and incubate at room temperature 15 min Wash silica membrane : add 500 µl RA2, 800 µl RA3, 500 µl RA4 Apply vacuum : 200 mbar2 1 min each step Remove MN Wash Plate Dry NucleoSpin® RNA Binding Module : Apply vacuum : maximum vacuum 10 min Dry the outlets of the NucleoSpin® RNA Binding strips by placing it on a Paper Sheet Elute highly pure total RNA : add 75 µl RNasefree water incubate 2 min Apply vacuum : 500 mbar2 1 min

extract_protocol: Col_LMV_2:30ug. Lyse cells or tissue (clear the lysate with the NucleoSpin® RNA Filter Strips) Add 300 µl RA1 +3 µl ß-me Pipette up and down 10-15 times to mix and resuspend genomic DNA that might have precipitated during the RA4 addition. Add 300 µl RA4 Transfer crude lysates to NucleoSpin® RNA Binding Strips Bind RNA to silica membrane of the NucleoSpin® RNA Binding Strips Apply vacuum : 200 mbar2 1 min Desalt silica membrane by washing with 500 µl RA3 Apply vacuum : 200 mbar2 3 min DNase incubation : add 30 µl DNase reaction mixture and incubate at room temperature 15 min Wash silica membrane : add 500 µl RA2, 800 µl RA3, 500 µl RA4 Apply vacuum : 200 mbar2 1 min each step Remove MN Wash Plate Dry NucleoSpin® RNA Binding Module : Apply vacuum : maximum vacuum 10 min Dry the outlets of the NucleoSpin® RNA Binding strips by placing it on a Paper Sheet Elute highly pure total RNA : add 75 µl RNasefree water incubate 2 min Apply vacuum : 500 mbar2 1 min


title: mPB CD34+CD38+ cells, biological replicate 2

source_name: mobilized peripheral blood


title: BM CD34+CD38- cells, biological replicate 1

source_name: Bone Marrow


title: UCB CD34+CD38- cells, biological replicate 1


title: mPB CD34+CD38- cells, biological replicate 2


title: mPB CD34+CD38- cells, biological replicate 1


title: mPB CD34+CD38+ cells, biological replicate 1


title: BM CD34+CD38+ cells, biological replicate 1


title: UCB CD34+CD38- cells, biological replicate 2


title: Culture rejuvenated leaf 3/4 gr12 vs. Leaf 9 L9112 (Slide6_H)

status: Public on Sep 01 2008

city: Ames

first: Patrick

middle: S.

last: Schnable

state: IA

address: 2035B Roy J Carver Co-Lab

institute: Iowa State University

description: Maize seedlings were grown under controlled conditions and were harvested when target leaf was at plastochron 6 (P6; a length greater than 4 mm, but less than 6 mm).  Total RNA was isolated from 6 replication pools of approximately 24 P6-staged leaf primordia for leaf 4 or 9 from seed-derived plants or leaf 3 or 4 from culture-derived plantlets using Trizol reagent (Invitrogen, Carlbad, CA) with slight modifications to manufacturer’s protocol.  Thirty micrograms of  total RNA were labeled as describe in the “cDNA Microarray Hybridization”file at Schnable Lab website (Iowa State University).  Each sample was labeled with Cy dye and hybridized to the (GPL3578, GPL3021 or GPL1996) platform.

hyb_protocol: Fluorescent targets were hybridized as described in the “cDNA Microarray Hybridization” file at Schnable Lab website (Iowa State University).

scan_protocol: Scan protocol Each microarray chip (18 total) was scanned a minimum of six times by increasing laser power and PMT gain settings using a ScanArray 5000 (Packard, Meriden, CT).  This scanning method was adopted from Skibbe and colleagues (2006).  Two scans from each chip were selected based on the median value of the natural log of the signal median for all spots on the slide.

data_processing: The lowess normalization method of Dudoit and colleagues (2002) was applied to the log of background-corrected raw signal intensities (signal intensity minus the median background intensity) to remove signal-intensity-dependent dye effects from each slide.  lowess normalization was performed separately for each slide to avoid introducing dependence among the independent biological replications. The normalized data for each slide/dye combination were mean centered (each individual value associated with a particular slide/dye combination minus the average value associated with a particular slide/dye combination) so that expression measures would be comparable across all 18 slides.  The lowess normalized data from each scan was used for a mixed linear model analysis (Wolfinger et al., 2001).

organism: Zea mays

source_name: Developing leaf

label_protocol: Fluorescent cDNA targets were synthesized and hybridized as described at Schnable Lab website (Iowa State University).   Labeled targets containing a minimum of 3000 picomoles of cDNA, 50 picomoles of Cy dye, and more than one dy molecule per 50 (100) bases of Cy3 (Cy5) were used for hybridizations.

extract_protocol: Total RNA extraction with Trizol (Invitrogen, Carlsbad, CA) with minor modifications to manufacturer’s instructions

tag: Genotype:	F1 hybrid between W23 and stock 924A

tag: Tissue

value: Leaf primordia

tag: Dev stage

value: Plastochron 6

tag: Sample name

value: Culture rejuvenated leaf 3/4 gr12

tag: Tissue:		Leaf primordia

tag: Dev stage:	Plastochron 6

tag: Sample name:	Leaf 9 L9112


title: Leaf 9 L9824d vs. Leaf 4 L4116d (Slide16_H)

value: Leaf 9 L9824d

tag: Sample name:	Leaf 4 L4116d


title: Leaf 9 L9106 vs. Leaf 4 L4302 (Slide1_H)

value: Leaf 9 L9106

tag: Sample name:	Leaf 4 L4302


title: Leaf 4 L4116a vs. Culture rejuvenated leaf 3/4 g8 (Slide8_H)

value: Leaf 4 L4116a

tag: Sample name:	Culture rejuvenated leaf 3/4 g8


title: Culture rejuvenated leaf 3/4 g10 vs. Leaf 9 L9824d (Slide18_H)

value: Culture rejuvenated leaf 3/4 g10

tag: Sample name:	Leaf 9 L9824d


title: Leaf 9 L9824c vs. Leaf 4 L4116c (Slide13_H)

value: Leaf 9 L9824c

tag: Sample name:	Leaf 4 L4116c


title: Culture rejuvenated leaf 3/4 g11 vs. Leaf 9 L9824b (Slide12_H)

value: Culture rejuvenated leaf 3/4 g11

tag: Sample name:	Leaf 9 L9824b


title: Leaf 9 L9824b vs. Leaf 4 L4114 (Slide10_H)

value: Leaf 9 L9824b

tag: Sample name:	Leaf 4 L4114


title: Leaf 4 L4106 vs. Culture rejuvenated leaf 3/4 gr12 (Slide5_H)

value: Leaf 4 L4106

tag: Sample name:	Culture rejuvenated leaf 3/4 gr12


title: Culture rejuvenated leaf 3/4 g8 vs. Leaf 9 L9824a (Slide9_H)

value: Culture rejuvenated leaf 3/4 g8

tag: Sample name:	Leaf 9 L9824a


title: Leaf 4 L4116d vs. Culture rejuvenated leaf 3/4 g10 (Slide17_H)

value: Leaf 4 L4116d

tag: Sample name:	Culture rejuvenated leaf 3/4 g10


title: Leaf 4 L4116c vs. Culture rejuvenated leaf 3/4 g9 (Slide14_H)

tag: Genotype:	F1 hybrid between W23 and stock 924A

value: Leaf 4 L4116c

tag: Sample name:	Culture rejuvenated leaf 3/4 g9


title: Leaf 9 L9112 vs. Leaf 4 L4106 (Slide4_H)

tag: Tissue

tag: Dev stage

value: Leaf 9 L9112

tag: Sample name:	Leaf 4 L4106


title: Leaf 4 L4114 vs. Culture rejuvenated leaf 3/4 g11 (Slide11_H)

tag: Sample name

value: Leaf 4 L4114

tag: Tissue:		Leaf primordia

tag: Dev stage:	Plastochron 6

tag: Sample name:	Culture rejuvenated leaf 3/4 g11


title: Culture rejuvenated leaf 3/4 g10 vs. Leaf 9 L9824d (Slide18_L)


title: Leaf 9 L9824c vs. Leaf 4 L4116c (Slide13_L)


title: Culture rejuvenated leaf 3/4 g9 vs. Leaf 9 L9824c (Slide15_L)

value: Culture rejuvenated leaf 3/4 g9

tag: Sample name:	Leaf 9 L9824c


title: Leaf 4 L4116c vs. Culture rejuvenated leaf 3/4 g9 (Slide14_L)

value: Leaf primordia


title: Leaf 4 L4116d vs. Culture rejuvenated leaf 3/4 g10 (Slide17_L)

value: Plastochron 6


title: Culture rejuvenated leaf 3/4 g11 vs. Leaf 9 L9824b (Slide12_L)


title: Leaf 9 L9824a vs. Leaf 4 L4116a (Slide7_H)

value: Leaf 9 L9824a

tag: Sample name:	Leaf 4 L4116a


title: Culture rejuvenated leaf 3/4 gr1-5 vs. Leaf 9 L9106 (Slide3_H)

value: Culture rejuvenated leaf 3/4 gr1-5

tag: Sample name:	Leaf 9 L9106


title: Leaf 4 L4302 vs. Culture rejuvenated leaf 3/4 gr1-5 (Slide2_H)

value: Leaf 4 L4302

tag: Sample name:	Culture rejuvenated leaf 3/4 gr1-5


title: Culture rejuvenated leaf 3/4 g8 vs. Leaf 9 L9824a (Slide9_L)


title: Leaf 9 L9824d vs. Leaf 4 L4116d (Slide16_L)

value: Leaf 9 L9824d

tag: Sample name:	Leaf 4 L4116d


title: Leaf 9 L9824a vs. Leaf 4 L4116a (Slide7_L)


title: HeLa_TMPyP4 Treatment_48hrs_Dyeswap2

status: Public on Aug 25 2008

city: Delhi

first: Anjali

last: Verma

state: Delhi

address: Mall road

department: Structural Biology and Genome Informatics Division

country: India

institute: Institute of Genomics and Integrative Biology

description: HeLa S3 cells were grown in Dulbecco's modified eagle medium (DMEM), 3.7 g/L sodium bicarbonate, 90%; fetal bovine serum, 10%. Cells were washed twice with 1X PBS before RNA isolation.

hyb_protocol: Hybridization was done in DigEasy hybridization buffer (Roche). To prevent non-specific hybridizations single stranded DNA from salmon testes and yeast transfer RNA were used. Hybridizations were performed at 37ºC for 16hrs.

scan_protocol: Slides were scanned at 10um resolution with Genepix pro 6.0 scanner using two different lasers, for Cy5 (635nm) and for Cy3 (532 nm).

data_processing: GenePixPro 6.0, Data was normalized so that the mean of the ratio of medians (635/532) of all features is equal to 1 using software Acuity 4.0 (Molecular Devices).The data (normalized values) is expressed as log2 ratio.  Within sample normalization (not across samples) was performed. After normalization, the data was filtered to include only those elements which contained only a small percentage (< 3) of saturated pixels, were not flagged bad or found absent (flags = 0), had relatively uniform intensity and uniform background (Rgn R2 (635/532) = 0.6) and were detectable above background (SNR = 3).

label: Cy5, control

source_name: HeLa S3 cell culture

label_protocol: Labeling was done with the help of cRNA target synthesis and labeling kit provided by Roche, as per manufacturer protocol.

growth_protocol: Cells were grown in 25cm2 canted flasks in the presence of air, 95%, 5% CO2 at 37ºC. The cells were grown in Dulbecco's modified eagle medium (DMEM), 3.7 g/L sodium bicarbonate, 90%; fetal bovine serum, 10%. After treatments the cells were grown in minimum exposure to light

extract_protocol: Total RNA was isolated with Trizol reagent as per manufacturer protocol(SIGMA).

treatment_protocol: Cells were grown to 50% confluency before TMPyP4 treatments (100 uM final concentration in complete medium), in minimum exposure to light

tag: HeLa S3 cell line is a subclone of HeLa cells which is derived from cervix cancer epithelial cells (ADENOCARCINOMA)

label: Cy3, treated


title: Leaf 4 L4106 vs. Culture rejuvenated leaf 3/4 gr12 (Slide5_L)

tag: Sample name:	Culture rejuvenated leaf 3/4 gr12


title: 13685573 - 77CY_2 vs WT_2

status: Public on Aug 13 2008

city: Evry Cedex

first: Agnes

last: Yu

address: 2 rue Gaston Cremieux CP 5708

department: URGV

description: Transcriptome analysis of Myb77 knock out mutant line or of Myb77fragment overxpressing transgenic line.

hyb_protocol: WT_2 Cy5 / 77CY_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

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

growth_protocol: plantlet - media : 1/2 MS medium, 3% sucrose, 0.8% agar temperature : 22°C daylight; 20°C at night light : 12 hours of daylight, full lamp illumination (4 of 9W tube lamps)

tag: Arabidopsis thaliana (columbia)  - harvest date:10-06-07

tag: Arabidopsis thaliana (columbia)  mutant (overexpression_of_MYB77_fragment) - harvest date:10-06-07


title: Leaf 4 L4302 vs. Culture rejuvenated leaf 3/4 gr1-5 (Slide2_L)

tag: Genotype:	F1 hybrid between W23 and stock 924A


title: Leaf 9 L9106 vs. Leaf 4 L4302 (Slide1_L)

tag: Tissue

value: Leaf 9 L9106

tag: Sample name:	Leaf 4 L4302


title: 13685568 - WT_1 vs 77KO_1

hyb_protocol: 77KO_1 Cy5 / WT_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: Arabidopsis thaliana (columbia)  mutant (KO_MYB77_gene) - harvest date:09-06-07

tag: Arabidopsis thaliana (columbia)  - harvest date:09-06-07


title: Leaf 9 L9112 vs. Leaf 4 L4106 (Slide4_L)

tag: Dev stage

tag: Sample name

tag: Tissue:		Leaf primordia

tag: Sample name:	Leaf 4 L4106


title: 13685572 - WT_2 vs 77KO_2

hyb_protocol: 77KO_2 Cy5 / WT_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: Arabidopsis thaliana (columbia)  mutant (KO_MYB77_gene) - harvest date:10-06-07


title: 13685570 - WT_1 vs 77CY_1

hyb_protocol: 77CY_1 Cy5 / WT_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: Arabidopsis thaliana (columbia)  mutant (overexpression_of_MYB77_fragment) - harvest date:09-06-07


title: 13685574 - WT_2 vs 77CY_2

hyb_protocol: 77CY_2 Cy5 / WT_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Culture rejuvenated leaf 3/4 g9 vs. Leaf 9 L9824c (Slide15_H)

tag: Dev stage:	Plastochron 6

tag: Sample name:	Leaf 9 L9824c


title: 13685571 - 77KO_2 vs WT_2

hyb_protocol: WT_2 Cy5 / 77KO_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Culture rejuvenated leaf 3/4 gr12 vs. Leaf 9 L9112 (Slide6_L)

value: Culture rejuvenated leaf 3/4 gr12

tag: Sample name:	Leaf 9 L9112


title: 13685569 - 77CY_1 vs WT_1

hyb_protocol: WT_1 Cy5 / 77CY_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Leaf 9 L9824b vs. Leaf 4 L4114 (Slide10_L)

tag: Sample name:	Leaf 4 L4114


title: HeLa_TMPyP4 Treatment_48hrs_Dyeswap1

tag: HeLa S3 cell line is a subclone of HeLa cells which is derived from cervix cancer epithelial cells (ADENOCARCINOMA)


title: Leaf 4 L4114 vs. Culture rejuvenated leaf 3/4 g11 (Slide11_L)

tag: Sample name:	Culture rejuvenated leaf 3/4 g11


title: E2_Gonad_4

status: Public on Aug 01 2008

city: Ocean SPrings

first: Joe

last: Griffitt

state: MS

address: 703 East BEach Drive

department: Coastal Sciences

institute: University of Southern Mississippi

description: Biological replicate 4 of 4: E2-exposed gonad

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

data_processing: Microarray image processing and data pre-processing were performed using Agilent's Feature Extraction software v 9.5.  The intensity of each spot was summarized by the median pixel intensity.  A log2 transformed signal ratio between the experimental (Cy5) channel and the reference (Cy3) channel was calculated for each spot, followed by within-array lowess transformation and between array scale normalization on median intensities (Zahurak et al., 2007).   Probes that did not hybridize were removed from consideration.

organism: Micropterus salmoides

source_name: LMB E2-treated gonad

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

extract_protocol: Trizol

treatment_protocol: LMB exposed to E2 or vehicle control for 48 hours.

tag: RNA from individual fish

source_name: reference pool

treatment_protocol: no treatement

tag: The reference sample consisted of equal amounts of RNA from female and male tissues (liver and gonad).


title: 13685567 - 77KO_1 vs WT_1

hyb_protocol: WT_1 Cy5 / 77KO_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: HeLa_TMPyP4 Treatment_48hrs_Replicate2

label: Cy3, control

label: Cy5, treated


title: HeLa_TMPyP4 Treatment_48hrs_Replicate1


title: Leaf 4 L4116a vs. Culture rejuvenated leaf 3/4 g8 (Slide8_L)

tag: Genotype:	F1 hybrid between W23 and stock 924A

tag: Tissue

value: Leaf 4 L4116a

tag: Sample name:	Culture rejuvenated leaf 3/4 g8


title: E2_Liver_1

description: Biological replicate 1 of 4: E2-exposed liver

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

source_name: LMB E2-treated liver


title: CTRL_Gonad_4

description: Biological replicate 4 of 4: control gonad

source_name: LMB control gonad


title: E2_Liver_2

description: Biological replicate 2 of 4: E2-exposed liver


title: E2_Liver_4

description: Biological replicate 4 of 4: E2-exposed liver


title: E2_Gonad_3

description: Biological replicate 3 of 4: E2-exposed gonad


title: E2_Liver_3

description: Biological replicate 3 of 4: E2-exposed liver


title: CTRL_Liver_1

description: Biological replicate 1 of 4: control liver

source_name: LMB control liver


title: CTRL_Liver_2

description: Biological replicate 2 of 4: control liver


title: Culture rejuvenated leaf 3/4 gr1-5 vs. Leaf 9 L9106 (Slide3_L)

tag: Dev stage

tag: Sample name:	Leaf 9 L9106


title: CTRL_Liver_4

description: Biological replicate 4 of 4: control liver


title: E2_Gonad_2

description: Biological replicate 2 of 4: E2-exposed gonad


title: CTRL_Gonad_2

description: Biological replicate 2 of 4: control gonad


title: CTRL_Liver_3

description: Biological replicate 3 of 4: control liver


title: CTRL_Gonad_3

description: Biological replicate 3 of 4: control gonad


title: E2_Gonad_1


title: CTRL_Gonad_1

description: Biological replicate 1 of 4: control gonad


title: Macroscopically without findings T-cells_mouse_nr8996

status: Public on Jul 15 2008

type: genomic

city: Heidelberg

first: Hendrik

last: Reuter

department: Moleculare Genetics B060

country: Germany

institute: DKFZ

hyb_protocol: labeled DNA was hybridised for 40h following manufactureres instructions (Mouse Genome CGH Microarray Kit 244A).

scan_protocol: hybridised arrays were scanned using an DNA microarray scanner from Agilent Technologies, Santa Clara, USA,

data_processing: scanned images were processed applying Feature Extraction Software v9.1 and CGH Analytics 3.4.27 software, Agilent Technologies, Santa Clara, USA,

molecule: genomic DNA

source_name: Atm deficient thymocytes

label_protocol: genomic DNA was restricted with AluI and RsaI and Klenowlabeled with Cy5, Cy3 resp. following manufactureres instructions (Mouse Genome CGH Microarray Kit 244A).

growth_protocol: mice were bred in DKFZ animal facility, DKFZ, Heidelberg, Germany

extract_protocol: Total DNA was extracted using Ceasiumchloride density ultracentrifugation (PMID: 15880582).

treatment_protocol: mice were not treated. Deseased mice were sacrificed by cervical dislocation or CO2 atmosphere.

tag: macroscopically without findings

tag: 129S6 SvEvTac_Atmtm1Awb

source_name: Wildtype thymocytes

tag: 129S6 SvEvTac


title: Isolated thymic lymphocytes from thymus of Atm knock out mouse 7066

description:
Total RNA was extracted using Ceasiumchloride density ultracentrifugation (PMID: 15880582).
2µg total RNA was amplified and labeled using TAcKLE Protocol (PMID: 15718295).

hyb_protocol: aRNA produced by T7 amplification was reversely transcribed and subsequently labeled using Klenow fragment and Cy-dUTPs. Hybridization was carried out at 37 °C in UltraHyb buffer (Ambion) on a GeneTAC hybridization station (Genomic Solutions).

scan_protocol: hybridised arrays were scanned using an DNA microarray scanner from Agilent Technologies, Santa Clara, USA, applying Feature Extraction Software v9.1 and GenePix Pro 5.0 software

data_processing: spot replicates were averaged. Spots not recognized by the image analysis software "GenePix Pro 5.0" (Axon Instruments) were excluded from the calculations. Raw fluorescence intensities were normalized applying the variance stabilization method (W. Huber et al., Bioinformatics 18 Suppl. 1, 2002). To eliminate low quality data, the data points were ranked according to spot homogeneity, as assayed by the ratio of median to mean fluorescence intensity, the ratio of spot to local background intensity and the standard deviation of the log2 ratios between spot replicates. Those data points ranked among the lower 20% were removed from the data set. Genes that could not be quantified in more than 33% of all experiments of the experimental series after filtering were excluded as well.

label: Cy3, Cy5

source_name: 2µg total RNA from mouse thymocytes

label_protocol: see description

extract_protocol: see description

tag: Atm knock out thymocytes

source_name: 2µg Universal Mouse Reference RNA (Stratagene #740100)

tag: Universal Mouse Reference RNA (Stratagene #740100), pooled from 11 mouse cell lines representing distinct tissues


title: Macroscopically without findings T-cells_mouse_nr8992


title: Macroscopically without findings T-cells_mouse_nr13592


title: Macroscopically without findings T-cells_mouse_nr13571


title: Macroscopically without findings T-cells_mouse_nr8983


title: Macroscopically without findings T-cells_mouse_nr11065


title: T-cell lymphoma T-cells_mouse_nr11044

tag: T-cell lymphoma


title: T-cell lymphoma T-cells_mouse_nr341


title: Isolated thymic lymphocytes from thymus of Atm knock out mouse 278


title: Isolated thymic lymphocytes from thymus of Atm knock out mouse 412


title: Isolated thymic lymphocytes from thymic lymphoma of Atm knock out mouse 11044

tag: Atm knock out thymocytes T-cell lymphoma


title: Isolated thymic lymphocytes from thymus of Atm knock out mouse 8992


title: Isolated thymic lymphocytes from wildtype mouse 10295

tag: wildtype-thymocytes


title: Macroscopically without findings T-cells_mouse_nr11045


title: T-cell lymphoma T-cells_mouse_nr8997


title: T-cell lymphoma T-cells_mouse_nr11088


title: Isolated thymic lymphocytes from wildtype mouse 11051

tag: 2µg Universal Mouse Reference RNA (Stratagene #740100)


title: Macroscopically without findings T-cells_mouse_nr8986


title: T-cell lymphoma T-cells_mouse_nr374


title: Macroscopically without findings T-cells_mouse_nr412


title: Isolated thymic lymphocytes from thymus of Atm knock out mouse 11045


title: T-cell lymphoma T-cells_mouse_nr294


title: T-cell lymphoma T-cells_mouse_nr7070


title: Macroscopically without findings T-cells_mouse_nr278bei


title: T-cell lymphoma T-cells_mouse_nr11052


title: Macroscopically without findings T-cells_mouse_nr380


title: Macroscopically without findings T-cells_mouse_nr7069


title: Macroscopically without findings T-cells_mouse_nr387


title: Isolated thymic lymphocytes from thymus of Atm knock out mouse 387


title: Macroscopically without findings T-cells_mouse_nr410


title: Isolated thymic lymphocytes from wildtype mouse 9006


title: Isolated thymic lymphocytes from thymus of Atm knock out mouse 5933


title: Isolated thymic lymphocytes from thymic lymphoma of Atm knock out mouse 11088b