title: hBD3 6hr BMDM rep2

city: Edinburgh

first: Graeme

middle: Richard

last: Grimes

address: Western General Hospital, Crewe Road

department: Human Genetics Unit

institute: University of Edinburgh, The Institute of Genetics and Cancer

description: hBD3 6hr BMDM rep2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation using LIMMA in R

source_name: Bone marrow derived macrophages

label_protocol: Amplified, biotinylated cRNA was synthesized using Illumina® TotalPrep Amplification Kit (Ambion, Austin, Texas)

growth_protocol: Bone marrow was flushed from femurs of Balb/c mice and incubated for 7-10 days in the presence of macrophage colony stimulating factor (M-CSF, 20ng/ml)

extract_protocol: RNA bee (AMS Biotechnology)

treatment_protocol: Macrophages at a concentration 5 x 10E5 cells per well (6 well plate) were incubated overnight in the absence of M-CSF. Cells were treated as described above, then incubated for 6 hour at 37 degrees.

value: Balb/c

value: Bone marrow derived macrophages

value: hBD3 5mg/ml

tag: time

value: 6 hours


title: Immunoprecipitated chromatin, antibody 1, replicate 1 Set 1

status: Public on Jan 01 2012

type: genomic

city: Newbury Park

first: Chetan

last: Deshpande

state: CA

address: One Amgen Center Dr

department: Molecular Sciences

country: USA

institute: Amgen Inc

description: 103007_251470610754_S01_CGH-v4_91_Amgen_082406.txt

hyb_protocol: The purified enriched and control DNA were hybridized to an Agilent 244K Human Promoter ChIP-on-chip Microarray Set (Agilent Technologies, Palo Alto, CA) using Maui AO (BioMicro Systems, Salt Lake City, UT). The microarrays were hybridized at 60º in a MAUI hybridization station on setting B (12spotMAUI) for 18 hours and then washed using Agilent aCGH wash buffers following the provided protocols.

scan_protocol: Microarrays were scanned using the Agilent DNA microarray scanner, and data were extracted from images using the Agilent Feature Extraction (version 9.5.1.1) software.

data_processing: The data were extracted using the Agilent Feature Extraction (version 9.5.1.1) software using the standard Agilent protocol with Lowess normalization.

molecule: genomic DNA

organism: Homo sapiens

source_name: Ramos cells, nonIP, control

label_protocol: 500ng of the control and ChIP-enriched genomic DNA was heat fragmented at 95C for 30’. The heat fragmented DNA was labeled using BioPrime DNA Labeling System (Invitrogen, Carlsbad, CA) with some modifications.

growth_protocol: Ramos cells were grown in RPMI supplemented with 10% fetal bovine serum, non-essential amino acids, and antibiotics.

extract_protocol: 2x10^8 cells were pelleted, washed with PBS, and lysed with hypotonic buffer on ice for 10 minutes to release the cytoplasm.  Nuclei were pelleted at 4 degrees C and lysed with ice-cold nuclear lysis buffer supplemented with protease inhibitor, on ice for 10 minutes.  Chromatin was sheared by sonication, using 5 pulses of 30 seconds each, separated by 1-minute rests.  DNA size was analyzed on a 2% agarose gel, and appeared as a smear ranging from 0.5-1 kb.

treatment_protocol: Untreated cells were used for chromatin isolation.

tag: cell type

value: Ramos germinal center B cells

value: Burkitt's lymphoma cell line

tag: antibody

source_name: Ramos cells, immunoprecipitataed, test

value: Ab1 = Cell Signaling #3826


title: hBD3 6hr BMDM rep3

type: RNA

country: United Kingdom

description: hBD3 6hr BMDM rep3

label: biotin

molecule: total RNA

organism: Mus musculus

tag: strain

tag: treatment


title: 14090082 - wt mannose 1 vs wt mannitol 1

city: Evry

first: Delphine

last: Gey

address: 2 rue Gaston Crémieux

department: URGV

country: France

institute: INRA

description: Diversification of the Molecular Mechanisms Involved in the Control of the Energetic Balance in Angiosperms

hyb_protocol: wt mannitol 1 Cy5 / wt mannose 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,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

source_name: wt mannitol 1

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) 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: whole plant - grown 5 days in MS/2 plus 0,3% glucose, 1 day in MS/2 without glucose and treatments 2% glucose, 2% mannose and 2% mannitol

extract_protocol: wt mannitol 1:13.56ug. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

tag: ecotype

tag: harvest date

source_name: wt mannose 1

extract_protocol: wt mannose 1:19.1ug. (Qiagen_RNeasy.pdf)


title: 14090075 - abi4 mannose 3 vs wt mannose 3

hyb_protocol: wt mannose 3 Cy5 / abi4 mannose 3 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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.

source_name: wt mannose 3

extract_protocol: wt mannose 3:19.04ug. (Qiagen_RNeasy.pdf)

source_name: abi4 mannose 3

extract_protocol: abi4 mannose 3:16.82ug. (Qiagen_RNeasy.pdf)


title: Immunoprecipitated chromatin, antibody 2, replicate 1 Set 1

description: 103007_251470610755_S01_CGH-v4_91_Amgen_082406.txt

value: Ab2 = EMD Biosciences #ST1099


title: Left ventricle_high-responder_training_4

city: TRONDHEIM

first: Anja

last: Bye

address: Olav Kyrres gt 9

country: Norway

institute: NTNU

description: .The laboratory animals included in this study consists of rats (N:NIH outbred rat stock) selectively breed for low and high response to exercise based on their change in maximal treadmill running capacity, as estimated before and after 8 weeks of exercise training.  This process has generated rat models with inherited differences for the adaptation component of aerobic capacity. The founder population, the N:NIH stock of rats, was developed in 1979 as a genetic resource of a heterogeneous population from the intentional outcross breeding of eight inbred strains, representing the broadest phylogenetic spectrum of laboratory rats available:  Maudsely Reactor (MR/N), Wistar (WN/N), Wistar Kyoto (WKY/N), Marshall 520 (M520), Fischer (F344), Ax C 9935 Irish (ACI), Brown Norway (BN/SsN), and Buffalo (BUF/N).  The resultant stock has wide genetic heterogeneity and is a superior choice as a starting population for artificial selection.

hyb_protocol: Samples were hybridized to Applied Biosystems Rat Genome Survey chips v.1.0. The samples were hybridised over two days. The biological groups were balanced between the two hybridisation batches and the samples randomly distributed within this format. Samples were analyzed by the Applied Biosystems 1700 Array Expression System.

data_processing: The data files from the AB 1700 Chemiluminescent Microarray Analyzer Software were processed using J-Express Pro v.2.8. The signal intensity values were extracted per spot, and all flagged and control spots were filtered out. Before compiled into an expression profile data matrix, all arrays were quantile normalized to be comparable. Genes with at most 20% missing values were allowed in the final dataset. The signal intensities in the dataset were further log transformed, and missing values were replaced using the method LSimpute Adaptive. The search for differentially expressed genes was performed both on a single gene and gene set level. Rank Product was used to look for differentially expressed genes on a gene by gene basis, while Gene Set Enrichment Analysis (GSEA) was used to look for sets of genes sharing common characteristics that were differentially expressed between the classes examined.

label: Biotin

organism: Rattus norvegicus

label_protocol: All samples were labeled at the same time and according to manufactures protocol

extract_protocol: Left ventricle tissue was snap-frozen in liquid nitrogen and stored at -80oC. RNA was isolated from the left ventricle (20 mg) with the mirVana RNA isolation kit (Ambion) according to the manufacturer's instructions. RNA integrity, purity and quantity were assessed by Bioanalyzer (Agilent Technologies, Santa Clara, US) and Nanodrop (NanoDrop Technologies, Baltimore, US). The concentration of total RNA was measured by Nanodrop with ultraviolet spectrophotometry at 260/280 nm. RNA quality was assessed by electrophoresis on Bioanalyzer chips (Agilent Technologies, Santa Clara, US). Only samples with a 260/280-ratio of more than 1.8, and RNA integrity number (RIN) value above 8 was analyzed.

tag: gender

value: female

tag: tissue

value: Left ventricle cardiac tissue

tag: age

value: 12 months

value: generation 7 of HRT (see description for additional details)


title: untreated 6hr BMDM rep3

description: untreated 6hr BMDM rep3


title: Left ventricle_high-responder_training_2

scan_protocol: Samples were analyzed by the Applied Biosystems 1700 Array Expression System.


title: EpCAM+ cells from DDC diet mouse

city: La Jolla

first: Roy

middle: M

last: Williams

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

hyb_protocol: As recommended by illumina

scan_protocol: As suggested by illumina using the illumina scanner

data_processing: Raw data filtered on P value for <0.05 with the remaining data normalised using the affy tools R bioconductor normalize.quantiles routine

label: streptavidin Cy3

source_name: EpCAM+ cells from DDC diet mouse

label_protocol: As suggested by illumina

growth_protocol: Generated DDB1F/F;Alb-Cre+/+ mouse, DDB1F/F;Mx1-Cre+/-. Oval cells (EpCAM positive cells) from these mouse models were compared with a conventional chemical injury model for oval cellsproliferation, mice treated with diet containing 3,5-diethoxycarbonyl-1,4-dihydro-collidine (DDC).

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Liver cells were isolated using a standard three-step protocol. Cells were centrifuged at least twice at 2000 rpm for 5 minutes and the pellets were suspended in ice-cold PBS containing 10% FBS and used as non-parenchymal cells. Cells were then incubated with fluorescence-conjugated EpCAM antibody in 3% BSA/PBS for 30 minutes on ice, sorted using FACSVantageSE DiVa.

value: mixed C57BL/6 x 129

value: mammary


title: Left ventricle_high-responder_training_1


title: 14090087 - wt mannose 2 vs abi4 mannose 2

hyb_protocol: abi4 mannose 2 Cy5 / wt mannose 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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.

source_name: abi4 mannose 2

extract_protocol: abi4 mannose 2:19.3ug. (Qiagen_RNeasy.pdf)

source_name: wt mannose 2

extract_protocol: wt mannose 2:9.8ug. (Qiagen_RNeasy.pdf)


title: 14090072 - abi4 mannose 2 vs wt mannose 2

hyb_protocol: wt mannose 2 Cy5 / abi4 mannose 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 14090071 - wt mannose 1 vs abi4 mannose 1

hyb_protocol: abi4 mannose 1 Cy5 / wt mannose 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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.

source_name: abi4 mannose 1

extract_protocol: abi4 mannose 1:6.15ug. (Qiagen_RNeasy.pdf)


title: Wild type hepatocytes

source_name: Hepatocytes from wild type mouse


title: Left ventricle_low-responder_sedentary_5

value: generation 7 of LRT (see description for additional details)


title: DDB1 mutant hepatocytes

source_name: Hepatocytes from DDB1F/F;Alb-Cre+/+


title: Left ventricle_low-responder_sedentary_4


title: Left ventricle_high-responder_sedentary_4


title: 14090070 - abi4 mannose 1 vs wt mannose 1

hyb_protocol: wt mannose 1 Cy5 / abi4 mannose 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: untreated 6hr BMDM rep2

description: untreated 6hr BMDM rep2


title: Left ventricle_low-responder_sedentary_3


title: hBD3 6hr BMDM rep1

description: hBD3 6hr BMDM rep1


title: 14090050 - wt glucose 2 vs abi4 glucose 2

hyb_protocol: abi4 glucose 2 Cy5 / wt glucose 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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.

source_name: abi4 glucose 2

extract_protocol: abi4 glucose 2:5.2ug. (Qiagen_RNeasy.pdf)

source_name: wt glucose 2

extract_protocol: wt glucose 2:17.84ug. (Qiagen_RNeasy.pdf)


title: untreated 6hr BMDM rep1

description: untreated 6hr BMDM rep1


title: 14090047 - abi4 glucose 1 vs wt glucose 1

hyb_protocol: wt glucose 1 Cy5 / abi4 glucose 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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.

source_name: wt glucose 1

extract_protocol: wt glucose 1:16.38ug. (Qiagen_RNeasy.pdf)

source_name: abi4 glucose 1

extract_protocol: abi4 glucose 1:12.57ug. (Qiagen_RNeasy.pdf)


title: 14090049 - abi4 glucose 2 vs wt glucose 2

hyb_protocol: wt glucose 2 Cy5 / abi4 glucose 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: KLA & hBD3 6hrs BMDM rep3

description: KLA & hBD3 6hrs BMDM rep3

source_name: Bone marrow derived macrophages

value: KLA & hBD3


title: KLA & hBD3 6hrs BMDM rep2

description: KLA & hBD3 6hrs BMDM rep2


title: Left ventricle_low-responder_sedentary_2


title: 14090079 - wt glucose 1 vs abi4 glucose 1

hyb_protocol: abi4 glucose 1 Cy5 / wt glucose 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: Left ventricle_low-responder_sedentary_1


title: 14090034 - wt mannitol 3 vs wt mannose 3

hyb_protocol: wt mannose 3 Cy5 / wt mannitol 3 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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.

source_name: wt mannitol 3

extract_protocol: wt mannitol 3:16.26ug. (Qiagen_RNeasy.pdf)


title: KLA 6hrs HBD3 rep2

description: KLA 6hrs HBD3 rep2

value: KLA 50ng/ml


title: KLA 6hrs HBD3 rep3

description: KLA 6hrs HBD3 rep3

value: Balb/c


title: Left ventricle_low-responder_training_3

source_name: Left ventricle_low-responder_training_3


title: Left ventricle_low-responder_training_5

source_name: Left ventricle_low-responder_training_5


title: Left ventricle_low-responder_training_4

source_name: Left ventricle_low-responder_training_4


title: Xoo PXO99 vs. PXO99A∆ax21 strain at 108 CFU/ml replicate3, counter dye swap

city: Davis

first: Malinee

last: Sriariyanun

address: 451 East Health Sciences Drive

department: Plant Pathology

institute: University of California, Davis

description: Biologiacl replicate3 of 3

hyb_protocol: Probes were resuspended in 28 ul of preheated 1X hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) at 42°C. To block non-specific hybridization, add 2 ul salmon sperm DNA (10 ug/ul) into the solution. Labeled probes were denatured by heating mixture at 95 °C for 3 mins and snap cool on ice for 30 seconds. Probed were applied into injector to hybridize with printed slides. Samples were hybridized for 16 hours (42°C in humidified water bath), sequentially washed with 42°C preheated low stringency wash buffer (2x SSC and 0.1% SDS) 5 minutes, then washed with high stringency wash buffer (0.1x SSC and 0.1% SDS) 5 minutes. Slides were transferred to 0.1x SSC buffer and agitated for 5 mins (2times) and dried under N2 (5 min, 30°C). Slides were kept under N2 until scanning.

scan_protocol: Hybridized microarray slides were imaged using a GenePix 4000B dual laser microarray scanner (Axon Instruments, USA) at 5 µm resolution. Slides were imaged using 100% laser power for both lasers (532 and 635 nm) and scanned twice using a high and low power of the scanner photomultiplicator settings (PMT).

data_processing: All images were processed using GenePix software (Axon Instruments, USA) for element identification and quantitation. We use LMgene packages and Bioconductor packages for R languages to extract data and normalized data from GPR files. The reference of LMgene is Rocke DM: Design and analysis of experiments with highthroughput biological assay data. Semin Cell Dev Biol 2004, 15(6):703-713. For GSM613754-65, low density is test, and high is reference. For GSM613766-83, PXO99∆ax21 is test, and PXO99 is reference.

organism: Xanthomonas oryzae pv. oryzae PXO99A

source_name: Total RNA from PXO99 cultured in PSB media labeled with Cyanine-5.

label_protocol: cDNA was generated by using SuperScriptTM III indirect cDNA labelling kit and following the manufacturer’s protocol (Invitrogen, Carlsbad, CA, U.S.A.). Twenty micrograms of high quality RNA was used as template. Generated cDNA was labelled with Cy3 and Cy5 reactive dye (GE Healthcare Piscataway, NJ)

growth_protocol: Cells were grown at 28 0C with shaking at 200 rpm, in nutrient-rich PSB media containing 10 g of peptone, 10 g of sucrose, 1 g of L-glutamic acid (monosodium salt). Bacterial cells were cultured in PSB media until OD600 is 0.5. Cells were diluted to 105 CFU/ml, and transferred to new PSB media. Cells were harvest and 106 CFU/ml and 108 CFU/ml for low and high cell density sample. Three separated cultures were used for each microarray studies

extract_protocol: A bacterial 1010-cells culture was harvested in a centrifuge tube and cell pellets were frozen in -80 0C immediately until RNA isolation. RNA was isolated using Trizol reagent (Invitrogen Corp.) and protocol is described in manufacturer manual. The RNA samples were treated with DNaseI (10 units, Promega Corp., Madison, WI, U.S.A.) for 30 mins at 37 0C, followed by column purification using RNeasy mini kit (Qiagen, Germantown, MD, U.S.A.). The quality of RNA was determined by gel electrophoresis on a 1% agarose gel and verified visually on a Nanodrop, or by Agilent 2100 Bioanalyzer (Agilent Technologies). The quantity of total RNA and mRNA were determined by measuring the absorbance at 260nm and 280nm. In addition, the level of protein contamination in the RNA was measured by using A260/A280 ratio.

tag: genotype/variation

value: wild type PXO99A

tag: culture condition

value: cultured in PSB

tag: density

value: 108 CFU/ml

source_name: Total RNA from PXO99∆ax21 cultured in PSB media labeled with Cyanine-5.


title: 14054618 - wt mannose 1 vs wt glucose 1

hyb_protocol: wt glucose 1 Cy5 / wt mannose 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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.

source_name: wt mannose 1


title: 14054619 - wt glucose 1 vs wt mannose 1

hyb_protocol: wt mannose 1 Cy5 / wt glucose 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: KLA 6hrs BMDM rep1

description: KLA  6hrs BMDM rep 1

hyb_protocol: Standard Illumina hybridization protocol

extract_protocol: RNA bee (AMS Biotechnology)

value: Bone marrow derived macrophages

value: 6 hours


title: 14090029 - wt mannitol 2 vs wt mannose 2

hyb_protocol: wt mannose 2 Cy5 / wt mannitol 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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.

source_name: wt mannitol 2

extract_protocol: wt mannitol 2:19.51ug. (Qiagen_RNeasy.pdf)


title: Xoo PXO99 vs. PXO99A∆ax21 strain at 108 CFU/ml replicate2, counter dye swap

description: Biologiacl replicate2 of 3


title: KLA & hBD3 6hrs BMDM rep1

description: KLA & hBD3 6hrs BMDM rep1


title: NIH3T3 KIT D54_SCF100ng/ml_imatinib mesilate 1µM

city: GENEVE

first: Séverine

last: TABONE-EGLINGER

address: 1 rue Michel Servet

country: Switzerland

institute: Centre Médical Universitaire

hyb_protocol: Ten micrograms of biotinylated cRNA was fragmented and hybridized onto Codelink® Whole Mouse Genome Bioarrays (GE/Amersham) for 18 hours at 37°C at 300 rpm in an incubator. The slides were washed and stained with streptavidin-cy5 (GE Healthcare) according to the manufacturer’s protocol.

scan_protocol: The slides were scanned using a Genepix® 4000B scanner (Axon, Union City, USA) and Genepix® software, with the laser set at 635 mm, the laser power at 100%, and the photomultiplier tube voltage at 60%.

data_processing: The scanned image files were analyzed using CodeLink® expression software, version 4.2 (GE Healthcare), which produces both a raw and normalized hybridization signal for each spot on the array. CodeLink® software was therefore used to normalize the raw hybridization signal on each array to the median of the array (median intensity is 1 after normalization) for better cross-array comparison. The threshold of detection was calculated using the normalized signal intensity of the 100 negative control samples in the array; spots with signal intensities below this threshold are referred to as “absent”.

source_name: NIH3T3 infected with KIT D54_24 hours incubated with SCF100ng/ml and imatinib mesilate 1µM

label_protocol: total RNA (100 ng) were amplified and biotin-labeled by in vitro transcription (IVT) with a MessageAmp™ II-Bacteria RNA Amplification Kit (Ambion/Applied Biosystem®). Before amplification, spikes of synthetic mRNA at different concentrations were added to all samples; these positive controls were used to ascertain the quality of the process.

growth_protocol: NIH3T3-infected cells were cultivated in DMEM with 10% newborn calf serum (Life Technologies®), 2% penicillin/streptomycin, and 50 ng/ml of CHO-SCF so that the growths of wild-type and mutant forms were equivalent. CHO-SCF was removed during starvation performed before the assays. Recombinant human SCF (rhSCF) used for the assays was purchased from R&D Systems®.

extract_protocol: Before RNA extraction, cells were detached following a classical trypsine protocol (Invitrogen®), washed two times in cold PBS (Invitrogen®) and finally freezed at -80°C without supernatant.    Total RNA of NIH3T3 cells were extracted according to the manufacturer’s protocol using TRIzol® method (Invitrogen®, Carlsbad, CA). RNA quality was controlled by spectophotometry using ND-1000 Nanodrop® and by microchips on Agilent bioanalyzer 2100 (Agilent® Technologies, Palo Alto, CA, USA).

treatment_protocol: For the experiment, the various NIH3T3 KIT expressing cell lines were seed at 1 million per 6 cm plate in complete medium without SCF and keep in this condition during one night (16 hours). Then, the cells were incubated for 24 hours with or without rhSCF and/or imatinib as indicated.

tag: cell line

tag: protein expressed

value: human KIT D54


title: NIH3T3 KIT WT/D6_SCF100ng/ml_imatinib mesilate 1µM

source_name: NIH3T3 infected with KIT WT/D6_24 hours incubated with SCF100ng/ml and imatinib mesilate 1µM

value: human KIT WT/D6


title: 14054346 - wt mannose 3 vs wt glucose 3

hyb_protocol: wt glucose 3 Cy5 / wt mannose 3 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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.

source_name: wt glucose 3

extract_protocol: wt glucose 3:17.19ug. (Qiagen_RNeasy.pdf)

source_name: wt mannose 3


title: Xoo PXO99 vs. PXO99A∆ax21 strain at 108 CFU/ml replicate2

description: Biologiacl replicate2 of 3


title: 14054347 - wt glucose 3 vs wt mannose 3

hyb_protocol: wt mannose 3 Cy5 / wt glucose 3 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: wt mannose 3:19.04ug. (Qiagen_RNeasy.pdf)


title: Xoo PXO99 vs. PXO99A∆ax21 strain at 108 CFU/ml replicate1, counter dye swap

description: Biologiacl replicate1 of 3


title: 14090030 - wt mannose 3 vs wt mannitol 3

hyb_protocol: wt mannitol 3 Cy5 / wt mannose 3 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: Xoo PXO99 vs. PXO99A∆ax21 strain at 108 CFU/ml replicate1

description: Biologiacl replicate1 of 3


title: 14090028 - wt mannose 2 vs wt mannitol 2

hyb_protocol: wt mannitol 2 Cy5 / wt mannose 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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.

source_name: wt mannose 2


title: Xoo PXO99 vs. PXO99A∆ax21 strain at 108 CFU/ml replicate3

description: Biologiacl replicate3 of 3


title: 14054345 - wt glucose 2 vs wt mannose 2

hyb_protocol: wt mannose 2 Cy5 / wt glucose 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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.

source_name: wt glucose 2


title: NIH3T3 KIT WT_SCF100ng/ml_imatinib mesilate 1µM

source_name: NIH3T3 infected with KIT WT-24 hours incubated with SCF100ng/ml and imatinib mesilate 1µM

value: human KIT WT


title: Xoo PXO99 vs. PXO99A∆ax21 strain at 107 CFU/ml replicate3, counter dye swap

description: Biologiacl replicate3 of 3

value: 107 CFU/ml


title: NIH3T3 MIGR_SCF100ng/ml_imatinib mesilate 1µM

source_name: NIH3T3 infected with empty vector (MIGR)_24 hours incubated with SCF100ng/ml and imatinib mesilate 1µM

value: empty vector


title: Left ventricle_low-responder_training_1

hyb_protocol: Samples were hybridized to Applied Biosystems Rat Genome Survey chips v.1.0. The samples were hybridised over two days. The biological groups were balanced between the two hybridisation batches and the samples randomly distributed within this format. Samples were analyzed by the Applied Biosystems 1700 Array Expression System.

source_name: Left ventricle_low-responder_training_1

value: female

value: Left ventricle cardiac tissue

value: 12 months


title: NIH3T3 KIT WT/D54_SCF100ng/ml_imatinib mesilate 1µM

source_name: NIH3T3 infected with KIT WT/D54_24 hours incubated with SCF100ng/ml and imatinib mesilate 1µM

value: human KIT WT/D54


title: 14054620 - wt mannose 2 vs wt glucose 2

hyb_protocol: wt glucose 2 Cy5 / wt mannose 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: NIH3T3 KIT WT/D54_without SCF or imatinib

source_name: NIH3T3 infected with KIT WT/D54_24 hours incubated with without SCF or imatinib


title: Xoo PXO99 vs. PXO99A∆ax21 strain at 107 CFU/ml replicate3

description: Biologiacl replicate3 of 3


title: NIH3T3 KIT WT/D6_without SCF or imatinib

source_name: NIH3T3 infected with KIT WT/D6_24 hours incubated with without SCF or imatinib


title: 14090102 - WT - D vs RNAi-bZIP9 - D

hyb_protocol: RNAi-bZIP9 - D Cy5 / WT - D Cy3 : 30pmol. (Hybridization_Protocol.txt) 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.

source_name: RNAi-bZIP9 - D

growth_protocol: whole plant - Seeds were grown for 7 days in 0.3% Glc MS/2 media at 22°C under continue light

extract_protocol: RNAi-bZIP9 - D:12.1ug. (Qiagen_RNeasy.pdf)

value: mutant (RNAi-bzip9)

source_name: WT - D

extract_protocol: WT - D:3.5ug. (Qiagen_RNeasy.pdf)


title: 14090100 - WT - C vs RNAi-bZIP9 - B

hyb_protocol: RNAi-bZIP9 - B Cy5 / WT - C Cy3 : 30pmol. (Hybridization_Protocol.txt) 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.

source_name: RNAi-bZIP9 - B

extract_protocol: RNAi-bZIP9 - B:9ug. (Qiagen_RNeasy.pdf)

source_name: WT - C

extract_protocol: WT - C:6.7ug. (Qiagen_RNeasy.pdf)


title: 14090101 - RNAi-bZIP9 - B vs WT - C

hyb_protocol: WT - C Cy5 / RNAi-bZIP9 - B Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: NIH3T3 KIT D6_SCF100ng/ml_imatinib mesilate 1µM

source_name: NIH3T3 infected with KIT D6_24 hours incubated with SCF100ng/ml and imatinib mesilate 1µM

value: human KIT D6


title: Xoo PXO99 vs. PXO99A∆ax21 strain at 107 CFU/ml replicate2

description: Biologiacl replicate2 of 3

source_name: Total RNA from PXO99∆ax21 cultured in PSB media labeled with Cyanine-5.

source_name: Total RNA from PXO99 cultured in PSB media labeled with Cyanine-5.


title: NIH3T3 KIT D54_without SCF or imatinib

source_name: NIH3T3 infected with KIT D54_24 hours incubated with without SCF or imatinib


title: 14090099 - RNAi-bZIP9 - A vs WT - B

hyb_protocol: WT - B Cy5 / RNAi-bZIP9 - A Cy3 : 30pmol. (Hybridization_Protocol.txt) 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.

source_name: WT - B

extract_protocol: WT - B:6.1ug. (Qiagen_RNeasy.pdf)

source_name: RNAi-bZIP9 - A

extract_protocol: RNAi-bZIP9 - A:10.9ug. (Qiagen_RNeasy.pdf)


title: NIH3T3 KIT D6_without SCF or imatinib

source_name: NIH3T3 infected with KIT D6_24 hours incubated with without SCF or imatinib


title: 14090103 - RNAi-bZIP9 - D vs WT - D

hyb_protocol: WT - D Cy5 / RNAi-bZIP9 - D Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 14090098 - WT - B vs RNAi-bZIP9 - A

hyb_protocol: RNAi-bZIP9 - A Cy5 / WT - B Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 14090105 - VP16-bZIP9 - 4 vs TDNA-bZIP9 - 4

hyb_protocol: TDNA-bZIP9 - 4 Cy5 / VP16-bZIP9 - 4 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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.

source_name: TDNA-bZIP9 - 4

extract_protocol: TDNA-bZIP9 - 4:9.5ug. (Qiagen_RNeasy.pdf)

value: mutant (TDNA-bzip9)

source_name: VP16-bZIP9 - 4

extract_protocol: VP16-bZIP9 - 4:13.7ug. (Qiagen_RNeasy.pdf)

value: mutant (VP16-bzip9)


title: NIH3T3 KIT WT/D54_SCF100ng/ml_imatinib mesilate 5µM

source_name: NIH3T3 infected with KIT WT/D54_24 hours incubated with SCF100ng/ml and imatinib mesilate 5µM


title: Xoo PXO99 vs. PXO99A∆ax21 strain at 106 CFU/ml replicate2, counter dye swap

description: Biologiacl replicate2 of 3

hyb_protocol: Probes were resuspended in 28 ul of preheated 1X hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) at 42°C. To block non-specific hybridization, add 2 ul salmon sperm DNA (10 ug/ul) into the solution. Labeled probes were denatured by heating mixture at 95 °C for 3 mins and snap cool on ice for 30 seconds. Probed were applied into injector to hybridize with printed slides. Samples were hybridized for 16 hours (42°C in humidified water bath), sequentially washed with 42°C preheated low stringency wash buffer (2x SSC and 0.1% SDS) 5 minutes, then washed with high stringency wash buffer (0.1x SSC and 0.1% SDS) 5 minutes. Slides were transferred to 0.1x SSC buffer and agitated for 5 mins (2times) and dried under N2 (5 min, 30°C). Slides were kept under N2 until scanning.

value: wild type PXO99A

value: cultured in PSB

value: 106 CFU/ml


title: 14090095 - VP16-bZIP9 - 3 vs TDNA-bZIP9 - 3

hyb_protocol: TDNA-bZIP9 - 3 Cy5 / VP16-bZIP9 - 3 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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.

source_name: TDNA-bZIP9 - 3

extract_protocol: TDNA-bZIP9 - 3:7.9ug. (Qiagen_RNeasy.pdf)

source_name: VP16-bZIP9 - 3

extract_protocol: VP16-bZIP9 - 3:9.4ug. (Qiagen_RNeasy.pdf)


title: Xoo PXO99 vs. PXO99A∆ax21 strain at 107 CFU/ml replicate2, counter dye swap

description: Biologiacl replicate2 of 3


title: Xoo PXO99 vs. PXO99A∆ax21 strain at 106 CFU/ml replicate3, counter dye swap

description: Biologiacl replicate3 of 3


title: Xoo PXO99 vs. PXO99A∆ax21 strain at 107 CFU/ml replicate1, counter dye swap

description: Biologiacl replicate1 of 3


title: NIH3T3 MIGR_without SCF or imatinib

hyb_protocol: Ten micrograms of biotinylated cRNA was fragmented and hybridized onto Codelink® Whole Mouse Genome Bioarrays (GE/Amersham) for 18 hours at 37°C at 300 rpm in an incubator. The slides were washed and stained with streptavidin-cy5 (GE Healthcare) according to the manufacturer’s protocol.

source_name: NIH3T3 infected with empty vector (MIGR)_24 hours incubated with without SCF or imatinib


title: 14090097 - TDNA-bZIP9 - 4 vs VP16-bZIP9 - 4

hyb_protocol: VP16-bZIP9 - 4 Cy5 / TDNA-bZIP9 - 4 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: NIH3T3 KIT WT_without SCF or imatinib

source_name: NIH3T3 infected with KIT WT_24 hours incubated with without SCF or imatinib


title: Xoo PXO99 vs. PXO99A∆ax21 strain at 106 CFU/ml replicate3

description: Biologiacl replicate3 of 3


title: NIH3T3 KIT WT/D6_SCF100ng/ml_imatinib mesilate 5µM

source_name: NIH3T3 infected with KIT WT/D6_24 hours incubated with SCF100ng/ml and imatinib mesilate 5µM


title: Xoo PXO99 vs. PXO99A∆ax21 strain at 107 CFU/ml replicate1

description: Biologiacl replicate1 of 3


title: 14090092 - TDNA-bZIP9 - 2 vs VP16-bZIP9 - 2

hyb_protocol: VP16-bZIP9 - 2 Cy5 / TDNA-bZIP9 - 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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.

source_name: VP16-bZIP9 - 2

extract_protocol: VP16-bZIP9 - 2:5.4ug. (Qiagen_RNeasy.pdf)

source_name: TDNA-bZIP9 - 2

extract_protocol: TDNA-bZIP9 - 2:10.9ug. (Qiagen_RNeasy.pdf)


title: Xoo PXO99 vs. PXO99A∆ax21 strain at 106 CFU/ml replicate1

description: Biologiacl replicate1 of 3

extract_protocol: A bacterial 1010-cells culture was harvested in a centrifuge tube and cell pellets were frozen in -80 0C immediately until RNA isolation. RNA was isolated using Trizol reagent (Invitrogen Corp.) and protocol is described in manufacturer manual. The RNA samples were treated with DNaseI (10 units, Promega Corp., Madison, WI, U.S.A.) for 30 mins at 37 0C, followed by column purification using RNeasy mini kit (Qiagen, Germantown, MD, U.S.A.). The quality of RNA was determined by gel electrophoresis on a 1% agarose gel and verified visually on a Nanodrop, or by Agilent 2100 Bioanalyzer (Agilent Technologies). The quantity of total RNA and mRNA were determined by measuring the absorbance at 260nm and 280nm. In addition, the level of protein contamination in the RNA was measured by using A260/A280 ratio.


title: NIH3T3 KIT D54_SCF100ng/ml_imatinib mesilate 5µM

source_name: NIH3T3 infected with KIT D54_24 hours incubated with SCF100ng/ml and imatinib mesilate 5µM


title: 14090091 - 35S-bZIP9 - 3 vs WT - 3

hyb_protocol: WT - 3 Cy5 / 35S-bZIP9 - 3 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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.

source_name: WT - 3

extract_protocol: WT - 3:5.9ug. (Qiagen_RNeasy.pdf)

extract_protocol: 35S-bZIP9 - 3:10.4ug. (Qiagen_RNeasy.pdf)

value: mutant (35S-bzip9)


title: Xoo PXO99A∆ax21 low density VS high density replicate3, counter dye swap

description: Biologiacl replicate3 of 3

source_name: Total RNA from PXO99∆ax21 high density cultured in PSB media labeled with Cyanine-5.

value: 108 CFU/ml

source_name: Total RNA from PXO99∆ax21 low density cultured in PSB media labeled with Cyanine-3.


title: NIH3T3 KIT D6_SCF100ng/ml_imatinib mesilate 5µM

source_name: NIH3T3 infected with KIT D6_24 hours incubated with SCF100ng/ml and imatinib mesilate 5µM

extract_protocol: Before RNA extraction, cells were detached following a classical trypsine protocol (Invitrogen®), washed two times in cold PBS (Invitrogen®) and finally freezed at -80°C without supernatant.    Total RNA of NIH3T3 cells were extracted according to the manufacturer’s protocol using TRIzol® method (Invitrogen®, Carlsbad, CA). RNA quality was controlled by spectophotometry using ND-1000 Nanodrop® and by microchips on Agilent bioanalyzer 2100 (Agilent® Technologies, Palo Alto, CA, USA).


title: 14090093 - VP16-bZIP9 - 2 vs TDNA-bZIP9 - 2

hyb_protocol: TDNA-bZIP9 - 2 Cy5 / VP16-bZIP9 - 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: Xoo PXO99A∆ax21 low density VS high density replicate3

description: Biologiacl replicate3 of 3

source_name: Total RNA from PXO99∆ax21 low density cultured in PSB media labeled with Cyanine-5.

source_name: Total RNA from PXO99∆ax21 high density cultured in PSB media labeled with Cyanine-3.


title: NIH3T3 KIT WT/D54_SCF100ng/ml

source_name: NIH3T3 infected with KIT WT/D54_24 hours incubated with SCF100ng/ml


title: Xoo PXO99 vs. PXO99A∆ax21 strain at 106 CFU/ml replicate2

description: Biologiacl replicate2 of 3

source_name: Total RNA from PXO99∆ax21 cultured in PSB media labeled with Cyanine-5.

source_name: Total RNA from PXO99 cultured in PSB media labeled with Cyanine-5.


title: 14090094 - TDNA-bZIP9 - 3 vs VP16-bZIP9 - 3

hyb_protocol: VP16-bZIP9 - 3 Cy5 / TDNA-bZIP9 - 3 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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.

source_name: TDNA-bZIP9 - 3


title: Xoo PXO99 vs. PXO99A∆ax21 strain at 106 CFU/ml replicate1, counter dye swap

description: Biologiacl replicate1 of 3


title: 14090090 - WT - 3 vs 35S-bZIP9 - 3

hyb_protocol: 35S-bZIP9 - 3 Cy5 / WT - 3 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: NIH3T3 MIGR_SCF100ng/ml_imatinib mesilate 5µM

source_name: NIH3T3 infected with empty vector (MIGR)_24 hours incubated with SCF100ng/ml and imatinib mesilate 5µM


title: NIH3T3 KIT WT/D6_SCF100ng/ml

source_name: NIH3T3 infected with KIT WT/D6_24 hours incubated with SCF100ng/ml

value: human KIT WT/D6


title: NIH3T3 KIT WT_SCF100ng/ml_imatinib mesilate 5µM

source_name: NIH3T3 infected with KIT WT_24 hours incubated with SCF100ng/ml and imatinib mesilate 5µM

value: human KIT WT


title: 14090086 - 35S-bZIP9 - 1 vs WT - 1

hyb_protocol: WT - 1 Cy5 / 35S-bZIP9 - 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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.

source_name: WT - 1

extract_protocol: WT - 1:11.4ug. (Qiagen_RNeasy.pdf)

extract_protocol: 35S-bZIP9 - 1:3.9ug. (Qiagen_RNeasy.pdf)


title: Xoo PXO99A∆ax21 low density VS high density replicate1, counter dye swap

description: Biologiacl replicate1 of 3


title: 14090089 - 35S-bZIP9 - 2 vs WT - 2

hyb_protocol: WT - 2 Cy5 / 35S-bZIP9 - 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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.

source_name: WT - 2

extract_protocol: WT - 2:5.1ug. (Qiagen_RNeasy.pdf)

extract_protocol: 35S-bZIP9 - 2:5.2ug. (Qiagen_RNeasy.pdf)


title: NIH3T3 KIT WT_SCF100ng/ml

source_name: NIH3T3 infected with KIT WT_24 hours incubated with SCF100ng/ml


title: Xoo PXO99A∆ax21 low density VS high density replicate2

description: Biologiacl replicate2 of 3


title: NIH3T3 KIT D6_SCF100ng/ml

source_name: NIH3T3 infected with KIT D6_24 hours incubated with SCF100ng/ml


title: Xoo PXO99A low density VS high density replicate3

description: Biologiacl replicate3 of 3

source_name: Total RNA from PXO99 low density cultured in PSB media labeled with Cyanine-5.

source_name: Total RNA from PXO99 high density cultured in PSB media labeled with Cyanine-3.


title: NIH3T3 MIGR_SCF100ng/ml

source_name: NIH3T3 infected with empty vector (MIGR)_24 hours incubated with SCF100ng/ml


title: Xoo PXO99A low density VS high density replicate3, counter dye swap

description: Biologiacl replicate3 of 3

source_name: Total RNA from PXO99 high density cultured in PSB media labeled with Cyanine-5.

source_name: Total RNA from PXO99 low density cultured in PSB media labeled with Cyanine-3.


title: Xoo PXO99A∆ax21 low density VS high density replicate1

description: Biologiacl replicate1 of 3

source_name: Total RNA from PXO99∆ax21 low density cultured in PSB media labeled with Cyanine-5.

source_name: Total RNA from PXO99∆ax21 high density cultured in PSB media labeled with Cyanine-3.


title: 14090088 - WT - 2 vs 35S-bZIP9 - 2

hyb_protocol: 35S-bZIP9 - 2 Cy5 / WT - 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: NIH3T3 KIT D54_SCF100ng/ml

source_name: NIH3T3 infected with KIT D54_24 hours incubated with SCF100ng/ml

value: human KIT D54


title: Xoo PXO99A∆ax21 low density VS high density replicate2, counter dye swap

description: Biologiacl replicate2 of 3

source_name: Total RNA from PXO99∆ax21 high density cultured in PSB media labeled with Cyanine-5.

source_name: Total RNA from PXO99∆ax21 low density cultured in PSB media labeled with Cyanine-3.


title: Xoo PXO99A low density VS high density replicate2

description: Biologiacl replicate2 of 3


title: Xoo PXO99A low density VS high density replicate2, counter dye swap

description: Biologiacl replicate2 of 3


title: Xoo PXO99A low density VS high density replicate1, counter dye swap

description: Biologiacl replicate1 of 3


title: 14090085 - WT - 1 vs 35S-bZIP9 - 1

hyb_protocol: 35S-bZIP9 - 1 Cy5 / WT - 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 13969729 - TDNAempty-2 vs bzip9-2

hyb_protocol: bzip9-2 Cy5 / TDNAempty-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: whole plant - 5 days in 0.3% Glc MS/2 under continue light; 1 day in MS/2 without Glc; treatments on the 7th day

extract_protocol: bzip9-2:7.8ug. (Qiagen_RNeasy.pdf)

value: mutant (bzip9 oe)

extract_protocol: TDNAempty-2:2ug. (Qiagen_RNeasy.pdf)

value: TDNAempty


title: 13969730 - bzip9-2 vs TDNAempty-2

hyb_protocol: TDNAempty-2 Cy5 / bzip9-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 13969727 - TDNAempty-1 vs bzip9-1

hyb_protocol: bzip9-1 Cy5 / TDNAempty-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: bzip9-1:11.7ug. (Qiagen_RNeasy.pdf)

extract_protocol: TDNAempty-1:7.6ug. (Qiagen_RNeasy.pdf)


title: 13969413 - bzip9-3 vs TDNAempty-3

hyb_protocol: TDNAempty-3 Cy5 / bzip9-3 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: TDNAempty-3:11.7ug. (Qiagen_RNeasy.pdf)

extract_protocol: bzip9-3:7.4ug. (Qiagen_RNeasy.pdf)


title: Xoo PXO99A low density VS high density replicate1

description: Biologiacl replicate1 of 3

hyb_protocol: Probes were resuspended in 28 ul of preheated 1X hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) at 42°C. To block non-specific hybridization, add 2 ul salmon sperm DNA (10 ug/ul) into the solution. Labeled probes were denatured by heating mixture at 95 °C for 3 mins and snap cool on ice for 30 seconds. Probed were applied into injector to hybridize with printed slides. Samples were hybridized for 16 hours (42°C in humidified water bath), sequentially washed with 42°C preheated low stringency wash buffer (2x SSC and 0.1% SDS) 5 minutes, then washed with high stringency wash buffer (0.1x SSC and 0.1% SDS) 5 minutes. Slides were transferred to 0.1x SSC buffer and agitated for 5 mins (2times) and dried under N2 (5 min, 30°C). Slides were kept under N2 until scanning.


title: Left ventricle_low-responder_training_2

hyb_protocol: Samples were hybridized to Applied Biosystems Rat Genome Survey chips v.1.0. The samples were hybridised over two days. The biological groups were balanced between the two hybridisation batches and the samples randomly distributed within this format. Samples were analyzed by the Applied Biosystems 1700 Array Expression System.

source_name: Left ventricle_low-responder_training_2

extract_protocol: Left ventricle tissue was snap-frozen in liquid nitrogen and stored at -80oC. RNA was isolated from the left ventricle (20 mg) with the mirVana RNA isolation kit (Ambion) according to the manufacturer's instructions. RNA integrity, purity and quantity were assessed by Bioanalyzer (Agilent Technologies, Santa Clara, US) and Nanodrop (NanoDrop Technologies, Baltimore, US). The concentration of total RNA was measured by Nanodrop with ultraviolet spectrophotometry at 260/280 nm. RNA quality was assessed by electrophoresis on Bioanalyzer chips (Agilent Technologies, Santa Clara, US). Only samples with a 260/280-ratio of more than 1.8, and RNA integrity number (RIN) value above 8 was analyzed.

value: female

value: Left ventricle cardiac tissue

value: generation 7 of LRT (see description for additional details)


title: 13969728 - bzip9-1 vs TDNAempty-1

hyb_protocol: TDNAempty-1 Cy5 / bzip9-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 13969731 - TDNAempty-3 vs bzip9-3

hyb_protocol: bzip9-3 Cy5 / TDNAempty-3 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 14119485 - prgH1 vs mock1

city: evry

first: edu

last: bueso

address: gaston cremieux

description: Transcriptomic analysis between Salmonella wt and differents mutants in type3 secretion system.

hyb_protocol: mock1 Cy5 / prgH1 Cy3 : 30pmol.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,460V,laser power 35%, Cy5:635nm,pmt voltage 460V,laser power 30%

growth_protocol: seedling - MS 22°C Long day

value: 2 week

tag: dev.stage (boyes et al. plant cell 2001)


title: 14119483 - mock1 vs prgH1

hyb_protocol: prgH1 Cy5 / mock1 Cy3 : 30pmol.


title: OsDIS1 Ovexpression plants_ drought conditions_rep1

city: Changsha

first: Joseph

last: Ning

state: Hunan

address: No.1 Nongda Road，Furong District

country: China

institute: Hunan Agricultural Univrsity

description:
D_OX 9-4-2_Log2NormSignal
251524111878_S01_GE1_105_Dec08_1_4.txt
Gene expression in OsDIS1 overexpression plants under drought conditions

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer's instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer's instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings，Dye channel: Green ,Scan resolution=5μm, PMT 100%，10% ，16bit.

data_processing: Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Oryza sativa

source_name: OsDIS1 overexpression rice leaves,drought conditions, replicate 1

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), followed the manufacturer's instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer's instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: The OsDIS1 overexpression 9-4-2 plants and the wild-type plants were cultured on 1/2 MS medium plus 3% sucrose for seven days. About half of the plants were sampled as the untreated control for RNA isolation, and the rest were transferred with 1/2 MS medium onto filter papers to induce drought stress. When the leaves of the OsDIS1 overexpression plants began to show drought stress phenotypes, we collected leaves for RNA isolation

value: OsDIS1 overexpression

tag: stress

value: drought

value: Leaves

value: Seven-day-old


title: 14119477 - mock2 vs prgH2

hyb_protocol: prgH2 Cy5 / mock2 Cy3 : 30pmol.