title: MM.1S BMSCs control  card B

city: Boston

first: Diana

last: Cirstea

address: 44 Binney Street

institute: Dana-Farber Cancer Institute

description: Control/Test

data_processing: Relative quantification of miRNA expression was calculated with the 2−ΔΔCt Ct method using the ddCt program (Shannon McCormack Advanced Molecular Diagnostics Laboratory Research Services). The data was presented as log10 of the relative quantity of each miRNA. miRNAs with Ct values higher than 35 were excluded from the analysis. Normalization was carried out with the mean of RNU44 and RNU48.

label: FAM

source_name: MM.1S MM cell line

label_protocol: miRNA expression profiling was performed at Shannon McCormack Advanced Molecular Diagnostics Laboratory Research Services. TaqMan® Low-Density Array (TLDA) using human miRNA version 2.0A and version 3.0B cards (Applied Biosystems, Foster City, CA) were applied to examine the global change of miRNA expression levels in MM.1S cells when co-cultured with BMSCs with or without RGB-286638 treatment. A total of 756 mature miRNA updated in the Sanger miRBase v.15.0 were quantified according to the manufacturer's instructions. Briefly, total RNA was converted into cDNA using a single megaplex reverse transcriptase reaction. The megaplex reaction contained a specific stem-loop primer for each of the mature target microRNA's. The cDNA was subjected to a pre-amplification PCR. The diluted pre-amplification products served as substrates for TaqMan® quantitative PCR reactions.

growth_protocol: MM.1S MM cells were cultured in RPMI-1640 containing 10% fetal bovine serum (FBS; Sigma Chemical, St Louis, MO), 2 mM L-glutamine, 100 U/mL penicillin, and 100 g/mL streptomycin (GIBCO, Grand Island, NY). Generation of bone marrow stromal cells (BMSCs) was performed from BM specimens from MM patients obtained after appropriate IRB approved informed consent. Mononuclear cells (MNCs) separated by Ficoll-Hipaque density sedimentation were used to establish long-term BMSCs cultures. When an adherent cell monolayer had developed, cells were harvested in Hanks buffered saline solution containing 0.25% trypsin and 0.02% EDTA, washed, and collected by centrifugation.

extract_protocol: Total RNA was extracted from MM cell pellets, using mirVana miRNA Isolation Kit (Ambion, Inc) according to manufacturer’s protocol.

treatment_protocol: miRNA expression profiling was performed on MM.1S cells cultured 8 hours in control media or 50nM RGB-286638 with or without BMSCs.

value: MM.1S cells

tag: activation agent

value: cultured with MM patient-derived BMSCs

value: control media with MM patient-derived BMSCs

tag: time

value: 8 hours


title: Fam 3 Hybe

status: Public on Jun 02 2012

type: genomic

city: Seattle

first: Andy

last: Itsara

state: WA

address: Foege Building S-250, Box 355065, 3720 15th Ave NE

department: Genome Sciences

country: USA

institute: University of Washington School of Medicine

hyb_protocol: For array hybridization, 25 ng each of labeled test and reference DNA was then brought to 158 uL volume water. Subsequently, the labeled DNA was hybridized to a custom Agilent array following the Agilent hybridization protocol. Briefly, the recommended hybridization master mix for a 1X microarray was prepared and added to the labeled DNA followed by hybridization at 65°C on a rotator rack (20 rpm) for 72 hr. Array wash proceeded according to the manufacturer's protocol.

scan_protocol: Scanned on Agilent G2505C scanner Images were quantified using Agilent Feature Extraction Software (v 10.5.1.1).

data_processing: Feature extraction was carried out with Agilent Feature Extraction Software (v 10.5.1.1) according to the manufacturer's protocol with the exception of using probes on human chromosome 17 outside of 17q21.31 as the normalization set. The normalization set is specified in "chr17_60K_no17q21_TDT_06092010.txt".

molecule: genomic DNA

organism:
Homo sapiens
Mus musculus

source_name: Fam 3 proband

label_protocol: Sample labeling was achieved using Roche NimbleGen Dual-Color DNA Labeling kits following the manufacturer’s protocol but using half (500 ng) the input DNA without sonication and scaling the protocol appropriately.

growth_protocol:
Hybrid cell lines were cultured under selective pressure using the following medium: 86% DMEM, 1% 50X HAT supplement, 1% Geneticin, 1% Penicillin-Streptomycin, 1% MEM-NEAA (all Gibco), and 10% FBS (Irvine Scientific).
After electrofusion of Epstein-Barr Virus (EBV) cells with E2 cells, mouse/human hybrid colonies were observed at 18 days. Subsequently, 88 clones were selected for initial expansion and genotyping. Six A and six B chromosome 17 homologues were selected for additional subculture. At pass three, all 12 hybrid clones were tested for chromosome 17 by FISH. Based on the FISH results, two A and two B hybrid clones were selected and for confirmatory genotyping and all cases confirmed retention of the appropriate A or B genotype.

extract_protocol: Cells were dissociated using TrypLE EXpress (Gibco). Genomic DNA was extracted using standard techniques.

tag: chr17 homologue

value: B

tag: cell line

source_name: Fam 3 Mother


title: MM.1S RGB 8h card B

status: Public on Jun 01 2012

type: RNA

description: Test

molecule: total RNA

organism: Homo sapiens

tag: cell type

value: subjected to drug treatment

tag: treatment


title: MM.1S control card B

description: Control

value: cultured in control media

value: control media


title: IMR253

value: A

source_name: Fam 2 Mother


title: Fam 2 Hybe

source_name: Fam 2 proband


title: Control-rep3

city: Shanghai

first: Huang

last: Jianhua

address: Wulumuqi Middle Road

country: China

institute: Institute of Integrated Chinese and Western Medicine, Huashan Hospital, Fudan University

description: This sample is of normal control neural stem cells from brains of Kunming mouse at embryonic 14th day. It is the third of four control biological replicates used in this experiment, each from separate cultures and pregnant mouse.

hyb_protocol: Array hybridization using the NimbleGen Hybridization System.

scan_protocol: Array scanning using the Axon GenePix 4000B microarray scanner (Molecular Devices Corporation).

data_processing: Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization.

organism: Mus musculus

source_name: Neural stem cells from brains of Kunming mouse at embrynic 14 day

label_protocol: About 5 μg total RNA of each sample was used for labeling and array hybridization as the following steps: 1) Reverse transcription with by Invitrogen Superscript ds-cDNA synthesis kit; 2) ds-cDNA labeling with NimbleGen one-color DNA labeling kit.

growth_protocol: Mice embryos at embryonic day 14 (E14) were collected from timed-pregnant Kunming mice and placed in D-PBS (Invitrogen, CA, USA). The forebrain neuroepithelium was removed from embryos under a dissection microscope. The resultant tissue was dissociated by mechanical dissociation into a single cell suspension with a small-bore, fire-polished Pasteur pipette. The cells were filtered through a sterile nylon mesh and washed twice with a DMEM/F12 medium (Invitrogen, CA, USA) containing 100 units/ml penicillin and 100 µg/ml streptomycin. Numbers of viable cells were determined by staining with trypan blue. Neurosphere culture was initiated by seeding cells at a density of 1×105 to 2×105 viable cells/ml in the basal medium supplemented with 20 ng/ml human recombinant fibroblast growth factor-2 (hrFGF2, Invitrogen, CA, USA), 20 ng/ml human recombinant endothelial growth factor (hrEGF, Invitrogen, CA, USA) and Stempro NSC supplement (Invitrogen, CA, USA).

extract_protocol: Total RNA was isolated using the Qiagen RNeasy kit (Qiagen), in accordance with the manufacturer’s protocol.Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: Single neural stem cells were cultured in differentiaion medium containing no growth factors for 2 days. Then 10 nM oleanolic acid was added. Control neural stem cells received no treatment.48 h later, cells were harvested for extraction of total RNA.

tag: strain

value: Kunming

value: Control


title: Fam 1 Hybe

source_name: Fam 1 proband

source_name: Fam 1 Father


title: GS3-Mot1-FRB-b

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

hyb_protocol: Tecan HS4800 hybridization

scan_protocol: scanning of slides using Agilent G256BA Imagene feature extraction

data_processing: genes, no bg corr, dye corr

organism: Saccharomyces cerevisiae

label_protocol: robot amplification and labeling v1.0

extract_protocol: yeast RNA isolation for robotic amplification v1.0

tag: strain or line

tag: genotype/variation


title: Fish treated with 1500 µg/L Bisphenol A replicate 4

city: Singapore

first: Siew Hong

last: Lam

address: 14 Science Drive 4

department: Biological Sciences

country: Singapore

institute: National University of Singapore

description: Biological replicate 4 of 5: treated fish maintained in  1500 µg/L Bisphenol A

hyb_protocol: The respective paired Cy5- labeled cDNAs from control or treated sample and Cy3-labeled cDNAs from reference samples were co-hybridized on a single array at 42°C for 16 h in a hybridization chamber (MAUI, USA) on a glass array spotted with 22,776 zebrafish oligo probes.

scan_protocol: The arrays were scanned using the GenePix 4000B microarray scanner (Axon Instruments, USA) and the generated images with their fluorescence signal intensities were analyzed using GenePix Pro 4.0 image analysis software (Axon Instruments, USA).

data_processing: The data were global median normalized. Normalized ratio of means defined by CH1/CH2

organism: Danio rerio

source_name: whole fish 7 day post-fertilization

label_protocol: For fluorescence labeling of cDNAs, 10 µg of total RNA from the reference and experimental samples were reverse transcribed in the presence of Cy3-dUTP and Cy5-dUTP (Amersham Inc.), respectively. Reference RNA was obtained by pooling male and female whole adult total RNA at a ratio of 9:1 respectively. Labeled cDNA were concentrated, and resuspended in DIG EasyHyb (Roche Applied Science) buffer for hybridization.

growth_protocol: Zebrafish were maintained at room temperature (26°C + 1°C)

extract_protocol: Total RNA of tissue samples were extracted using Trizol reagent (Invitrogen) according to the manufacturers instructions.

treatment_protocol: Developing zebrafish were exposed to 500, 1500 and 4500 µg/L BPA for 7 days from 3 hour post-fertilization onwards groups of four zebrafishes. All control fish were maintained in egg water with 0.05% ethanol (vehicle).

tag: condition

value: Developing fish maintained in 1500 µg/L Bisphenol A

source_name: Whole Fish

tag: reference

value: Reference RNA was obtained by pooling 9:1 ratio of male and female total RNA extracted from whole adult wild-type zebrafish.


title: Control Fish Replicate2

description: Biological replicate 2 of 5: control fish maintained in egg water (with 0.05% ethanol as vehicle)

value: Developing fish maintained in egg water (with 0.05% ethanol as vehicle)


title: Fish treated with 500 µg/L Bisphenol A replicate 2

description: Biological replicate 2 of 5: treated fish maintained in  500 µg/L Bisphenol A

value: Developing fish maintained in 500 µg/L Bisphenol A


title: Fish treated with 500 µg/L Bisphenol A replicate 5

description: Biological replicate 5 of 5: treated fish maintained in  500 µg/L Bisphenol A


title: Control Fish Replicate5

description: Biological replicate 5 of 5: control fish maintained in egg water (with 0.05% ethanol as vehicle)


title: Fish treated with 1500 µg/L Bisphenol A replicate 2

description: Biological replicate 2 of 5: treated fish maintained in  1500 µg/L Bisphenol A


title: Fish treated with 1500 µg/L Bisphenol A replicate 1

description: Biological replicate 1 of 5: treated fish maintained in  1500 µg/L Bisphenol A


title: Tissue_EEC_14

city: Lublin

first: Anna

last: Torres

address: Jaczewskiego 4

department: Human Anatomy Department

country: Poland

institute: Medical University of Lublin

description:
50
Patients were observed for a maximum of 3 years after tissue collection. No relapse was noted in the study group. All patients were alive at the end of the observation period (observation censored in December 2010).
microRNA expression.

hyb_protocol: A mixture containing Cy3-labeled RNA, 18ul water, 4.5 ul 10x GE Blocking Agent and 22.5 ul 2x Hi-RPM Hybridization Buffer was incubated at 100°C for 5 minutes, immediately transferred to an ice bath for another 5 min and hybridized to Agilent Human miRNA microarray version 3 (G4470C) for 20 hours at 55°C in a SureHyb (Agilent) hybridization oven.  After hybridization, microarrays were washed 5 minutes at room temperature with GE Wash Buffer 1 (Agilent) and 5 minutes with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent G2565CA Microarray Scanner using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol:miRNA-v1_95_May07) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The raw data were normalized to the 75th percentile using the percentile shift normalization method (GeneSpring, Agilent). Before normalization, all data with values below 1 after being downloaded into GeneSpring were first converted to 1, and then the data were converted to logarithmic scale.

source_name: endometrioid endometrial cancer fresh frozen tissue

label_protocol: Cyanine-3 (Cy3) labeled RNA was prepared from 100ng RNA using the miRNA Complete Labeling and Hyb Kit (Agilent p/n 5190-0456) according to the manufacturer's instructions.

extract_protocol: RNA isolation from fresh frozen tissues was performed using the mirVANATM miRNA Isolation Kit (Ambion) and 40 to 80 mg of macrodissected tissue according to the manufacturer’s protocol. RNA was quantified using a Hellma Cell spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Concentration and purity of RNA were inspected using spectrophotometry (Biophotometer with Hellma TrayCell, Eppendorf) and RNA integrity was checked using the Bioanalyzer 2100 (Agilent) and Agilent RNA Nano kit. For RNA isolated from fresh frozen tissue, only samples with RIN≥ 6 were used in downstream applications.

treatment_protocol: Tissue samples were collected during surgery within 15 minutes of the removal of the uterus and immediately immersed in RNAlater (Ambion). After 24 hours incubation in RNAlater in 4°C, tissues were stored in -80°C until RNA extraction.

tag: tissue

value: endometrioid endometrial cancer (EEC)

tag: grade

tag: figo stage

value: >IA (IIIA)

tag: myometrial invasion

value: >=0.5 thickness

tag: relapse

value: no

tag: survival status

value: alive


title: Fish treated with 4500 µg/L Bisphenol A replicate 2

description: Biological replicate 2 of 5: treated fish maintained in  4500 µg/L Bisphenol A

value: Developing fish maintained in 4500 µg/L Bisphenol A


title: Fish treated with 500 µg/L Bisphenol A replicate 4

description: Biological replicate 4 of 5: treated fish maintained in  500 µg/L Bisphenol A


title: Control Fish Replicate3

description: Biological replicate 3 of 5: control fish maintained in egg water (with 0.05% ethanol as vehicle)


title: Tissue_EEC_13

description:
49
Patients were observed for a maximum of 3 years after tissue collection. No relapse was noted in the study group. All patients were alive at the end of the observation period (observation censored in December 2010).
microRNA expression.

value: IA

value: <0.5 thickness


title: Tissue_EEC_12

description:
1
Patients were observed for a maximum of 3 years after tissue collection. No relapse was noted in the study group. All patients were alive at the end of the observation period (observation censored in December 2010).
microRNA expression.

value: >IA (IB)


title: Tissue_EEC_17

description:
83
Patients were observed for a maximum of 3 years after tissue collection. No relapse was noted in the study group. All patients were alive at the end of the observation period (observation censored in December 2010).
microRNA expression.

value: >IA (IIIB)


title: Tissue_EEC_18

description:
90
Patients were observed for a maximum of 3 years after tissue collection. No relapse was noted in the study group. All patients were alive at the end of the observation period (observation censored in December 2010).
microRNA expression.


title: Tissue_EEC_16

description:
70
Patients were observed for a maximum of 3 years after tissue collection. No relapse was noted in the study group. All patients were alive at the end of the observation period (observation censored in December 2010).
microRNA expression.


title: Tissue_EEC_15

description:
59
Patients were observed for a maximum of 3 years after tissue collection. No relapse was noted in the study group. All patients were alive at the end of the observation period (observation censored in December 2010).
microRNA expression.


title: Tissue_NE_4

description:
93
microRNA expression.

source_name: normal endometrium fresh frozen tissue

value: normal endometrium


title: Fish treated with 4500 µg/L Bisphenol A replicate 3

description: Biological replicate 3 of 5: treated fish maintained in  4500 µg/L Bisphenol A


title: Control Fish Replicate4

description: Biological replicate 4 of 5: control fish maintained in egg water (with 0.05% ethanol as vehicle)


title: Fish treated with 500 µg/L Bisphenol A replicate 3

description: Biological replicate 3 of 5: treated fish maintained in  500 µg/L Bisphenol A


title: Fish treated with 4500 µg/L Bisphenol A replicate 1

description: Biological replicate 1 of 5: treated fish maintained in  4500 µg/L Bisphenol A


title: Control Fish Replicate1

description: Biological replicate 1 of 5: control fish maintained in egg water (with 0.05% ethanol as vehicle)


title: Fish treated with 500 µg/L Bisphenol A replicate 1

description: Biological replicate 1 of 5: treated fish maintained in  500 µg/L Bisphenol A


title: Tissue_EEC_11

description:
88
Patients were observed for a maximum of 3 years after tissue collection. No relapse was noted in the study group. All patients were alive at the end of the observation period (observation censored in December 2010).
microRNA expression.


title: Tissue_EEC_9

description:
15
Patients were observed for a maximum of 3 years after tissue collection. No relapse was noted in the study group. All patients were alive at the end of the observation period (observation censored in December 2010).
microRNA expression.


title: Tissue_EEC_10

description:
69
Patients were observed for a maximum of 3 years after tissue collection. No relapse was noted in the study group. All patients were alive at the end of the observation period (observation censored in December 2010).
microRNA expression.


title: Tissue_NE_2

description:
31
microRNA expression.


title: Tissue_NE_1

description:
14
microRNA expression.


title: Tissue_EEC_7

description:
81
Patients were observed for a maximum of 3 years after tissue collection. No relapse was noted in the study group. All patients were alive at the end of the observation period (observation censored in December 2010).
microRNA expression.


title: Tissue_NE_3

description:
34
microRNA expression.


title: Tissue_EEC_8

description:
91
Patients were observed for a maximum of 3 years after tissue collection. No relapse was noted in the study group. All patients were alive at the end of the observation period (observation censored in December 2010).
microRNA expression.


title: Tissue_EEC_3

description:
68
Patients were observed for a maximum of 3 years after tissue collection. No relapse was noted in the study group. All patients were alive at the end of the observation period (observation censored in December 2010).
microRNA expression.

value: >IA (IIIC1)


title: Tissue_EEC_2

description:
57
Patients were observed for a maximum of 3 years after tissue collection. No relapse was noted in the study group. All patients were alive at the end of the observation period (observation censored in December 2010).
microRNA expression.


title: Tissue_EEC_5

description:
78
Patients were observed for a maximum of 3 years after tissue collection. No relapse was noted in the study group. All patients were alive at the end of the observation period (observation censored in December 2010).
microRNA expression.


title: Tissue_EEC_6

description:
79
Patients were observed for a maximum of 3 years after tissue collection. No relapse was noted in the study group. All patients were alive at the end of the observation period (observation censored in December 2010).
microRNA expression.


title: Fish treated with 4500 µg/L Bisphenol A replicate 4

description: Biological replicate 4 of 5: treated fish maintained in  4500 µg/L Bisphenol A


title: Tissue_EEC_4

description:
73
Patients were observed for a maximum of 3 years after tissue collection. No relapse was noted in the study group. All patients were alive at the end of the observation period (observation censored in December 2010).
microRNA expression.


title: Tissue_EEC_1

description:
43
Patients were observed for a maximum of 3 years after tissue collection. No relapse was noted in the study group. All patients were alive at the end of the observation period (observation censored in December 2010).
microRNA expression.


title: 13969423 - wt2 vs Ovexoxi1-2

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Analysis of the overexpression of the Oxi1

hyb_protocol: Ovexoxi1-2 Cy5 / wt2 Cy3 : 30pmol.

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

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: rosette - pots 70% 23°C

tag: ecotype

tag: age

value: overexpression of the Oxi1

value: wild type


title: Fish treated with 1500 µg/L Bisphenol A replicate 3

description: Biological replicate 3 of 5: treated fish maintained in  1500 µg/L Bisphenol A

value: Developing fish maintained in 1500 µg/L Bisphenol A

value: Reference RNA was obtained by pooling 9:1 ratio of male and female total RNA extracted from whole adult wild-type zebrafish.


title: 13969422 - Ovexoxi1-1 vs wt1

hyb_protocol: wt1 Cy5 / Ovexoxi1-1 Cy3 : 30pmol.

extract_protocol: Ovexoxi1-1:10ug. (Qiagen_RNeasy.pdf)


title: 14228096 - E2 vs no_E2

city: Evry

first: Delphine

last: Gey

address: 2 rue Gaston Crémieux

description: Identify genes involved in somatic embryogenesis

hyb_protocol: no_E2 Cy5 / E2 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: no_E2: non-meristemoid cells from the same calli

growth_protocol: callus - 10h light/20°C/70%humidity middle:Bouturage+µ1-3/2 After 18 days: First day: enzymatic digestion (16h / 24°C) then put the Protoplaste suspension at 20°C. Jour30:middle + cytokinine 60 days:microcals are transfered on a regeneration middle(5UM de Thidiazuron).

treatment_protocol: no treatment

value: wassilewskija

source_name: E2: clusters of meristemoid cells, microdissected from calli

value: clusters of meristemoid cells


title: 14162672 - no_E1 vs E1

hyb_protocol: E1 Cy5 / no_E1 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: E1: clusters of meristemoid cells, microdissected from calli

extract_protocol: E1:20ng. (Qiagen_RNeasy.pdf)

tag: harvest date

source_name: no_E1: non-meristemoid cells from the same calli

extract_protocol: no_E1:5ng. (Qiagen_RNeasy.pdf)


title: 14228095 - no_E2 vs E2

hyb_protocol: E2 Cy5 / no_E2 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.

value: non-meristemoid cells from the same calli


title: 14120007 - E3 vs no_E3

hyb_protocol: no_E3 Cy5 / E3 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: no_E3: non-meristemoid cells from the same calli

extract_protocol: no_E3:5ng. (Qiagen_RNeasy.pdf)

source_name: E3: clusters of meristemoid cells, microdissected from calli

extract_protocol: E3:5ng. (Qiagen_RNeasy.pdf)


title: 14163075 - E4 vs no_E4

hyb_protocol: no_E4 Cy5 / E4 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: no_E4: non-meristemoid cells from the same calli

source_name: E4: clusters of meristemoid cells, microdissected from calli

extract_protocol: E4:5ng. (Qiagen_RNeasy.pdf)


title: 14120010 - no_E2 vs E2

extract_protocol: E2:5ng. (Qiagen_RNeasy.pdf)

extract_protocol: no_E2:5ng. (Qiagen_RNeasy.pdf)


title: 14162671 - E1 vs no_E1

hyb_protocol: no_E1 Cy5 / E1 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: 14120009 - E2 vs no_E2


title: 14228094 - E1 vs no_E1


title: 14227731 - wt hollow 2 vs wt teeth 2

description: CUC2 is expressed in meristem. It permits to create organs boundaries. It is also expressed in leave margins. Is there a mecanism meristem like in leave margins?

hyb_protocol: wt_teeth_2 Cy5 / wt_hollow_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: aerial - x

value: columbia

value: 15 day

tag: genotype

value: leaf teeth

value: leaf hollow


title: 13969311 - no_E4 vs E4

hyb_protocol: E4 Cy5 / no_E4 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.

tag: cell type


title: 14227646 - wt teeth 2 vs wt hollow 2

hyb_protocol: wt_hollow_2 Cy5 / wt_teeth_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.

value: leaf margin


title: 14249146 - wt hollow 4 vs wt teeth 4

hyb_protocol: wt_teeth_4 Cy5 / wt_hollow_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: 14120008 - no_E3 vs E3

hyb_protocol: E3 Cy5 / no_E3 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: 14249183 - cuc2 margin 4 vs wt margin 4

hyb_protocol: wt_4 Cy5 / cuc2_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: 14228093 - no_E1 vs E1


title: 13969321 - µD2 vs no µD2

description: Transcriptome bias induce by protocols used in microdissection

hyb_protocol: no_µD2 Cy5 / µD2 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: flower - CF JO

extract_protocol: Qiagen RNeasy

treatment_protocol: Name:Microdissection - technical - microdissection,microdissection:.

value: flower

tag: treatment

value: no microdissection

value: microdissection


title: 14227235 - E3 vs no_E3


title: 14227234 - no_E3 vs E3


title: 14249147 - wt teeth 4 vs wt hollow 4

hyb_protocol: wt_hollow_4 Cy5 / wt_teeth_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: 14249182 - wt margin 4 vs cuc2 margin 4

hyb_protocol: cuc2_4 Cy5 / wt_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: 14227645 - cuc2 margin 3 vs wt margin 3

hyb_protocol: wt_3 Cy5 / cuc2_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: 13969326 - no µD1 vs µD1

hyb_protocol: µD1 Cy5 / no_µD1 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: 14227644 - wt margin 3 vs cuc2 margin 3

hyb_protocol: cuc2_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: 13969320 - no µD2 vs µD2

hyb_protocol: µD2 Cy5 / no_µD2 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: 14227642 - wt hollow 3 vs wt teeth 3

hyb_protocol: wt_teeth_3 Cy5 / wt_hollow_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: 13969454 - Ovexoxi1-2 vs wt2

hyb_protocol: wt2 Cy5 / Ovexoxi1-2 Cy3 : 30pmol.


title: 13969327 - µD1 vs no µD1

hyb_protocol: no_µD1 Cy5 / µD1 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: 14227643 - wt teeth 3 vs wt hollow 3

hyb_protocol: wt_hollow_3 Cy5 / wt_teeth_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: 14227639 - cuc2 margin 1 vs wt margin 1

hyb_protocol: wt_1 Cy5 / cuc2_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: 13969421 - wt1 vs Ovexoxi1-1

hyb_protocol: Ovexoxi1-1 Cy5 / wt1 Cy3 : 30pmol.


title: 14227641 - cuc2 margin 2 vs wt margin 2

hyb_protocol: wt_2 Cy5 / cuc2_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: 14227640 - wt margin 2 vs cuc2 margin 2

hyb_protocol: cuc2_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: 14227259 - 2j10h2iP _1 vs 1j10h2iP _1 MSgluc+2iP 2 d and 10 hr vs. MSgluc+2iP 1 d and 10 hr

description: Study of the moleculars mecanism during transdifferenciation of Root ApicalMeristem to Shoot Apical Meristem

hyb_protocol: 1j10h2iP _1 Cy5 / 2j10h2iP _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.

growth_protocol: roots - germination and growth on MS10+NPA (5 days) transfert on MS10+ANA during 1 day and 18 hours transfert on MSgluc+2iP during 1 days and 10 hours

value: roots

growth_protocol: roots - germination and growth on MS10+NPA (5 days) transfert on MS10+ANA during 1 day and 18 hours transfert on MSgluc+2iP during 2 days and 10 hours


title: 14227730 - wt teeth 1 vs wt hollow 1

hyb_protocol: wt_hollow_1 Cy5 / wt_teeth_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: MM.1S BMSCs RGB 8h  card B

description: Test

source_name: MM.1S MM cell line

value: MM.1S cells

tag: activation agent

value: cultured with MM patient-derived BMSCs and subjected to drug treatment

value: RGB-286638 (50 nM) with MM patient-derived BMSCs

tag: time

value: 8 hours


title: 14227258 - 1j10h2iP _1 vs 2j10h2iP _1 MSgluc+2iP 2 d and 10 hr vs. MSgluc+2iP 1 d and 10 hr

hyb_protocol: 2j10h2iP _1 Cy5 / 1j10h2iP _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.

value: germination and growth on MS10+NPA (5 days) transfert on MS10+ANA during 1 day and 18 hours transfert on MSgluc+2iP during 2 days and 10 hours

value: germination and growth on MS10+NPA (5 days) transfert on MS10+ANA during 1 day and 18 hours transfert on MSgluc+2iP during 1 days and 10 hours


title: 14227257 - 1j10h2iP _1 vs 6h2iP _1 MSgluc+2iP 1 d and 10 hr vs. Sgluc+2iP 6 hr

hyb_protocol: 6h2iP _1 Cy5 / 1j10h2iP _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.

growth_protocol: roots - germination and growth on MS10+NPA (5 days) transfert on MS10+ANA during 1 day and 18 hours transfert on MSgluc+2iP during 6 hours


title: 14227250 - 1j10h2iP _2 vs 2j10h2iP _2 MSgluc+2iP 2 d and 10 hr vs. MSgluc+2iP 1 d and 10 hr

hyb_protocol: 2j10h2iP _2 Cy5 / 1j10h2iP _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: 14227251 - 2j10h2iP _2 vs 1j10h2iP _2 MSgluc+2iP 2 d and 10 hr vs. MSgluc+2iP 1 d and 10 hr

hyb_protocol: 1j10h2iP _2 Cy5 / 2j10h2iP _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: 14227638 - wt margin 1 vs cuc2 margin 1

hyb_protocol: cuc2_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.

value: wild type


title: 14227252 - wt hollow 1 vs wt teeth 1

hyb_protocol: wt_teeth_1 Cy5 / wt_hollow_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: 14227249 - 1j10h2iP _2 vs 6h2iP _2 MSgluc+2iP 1 d and 10 hr vs. Sgluc+2iP 6 hr

hyb_protocol: 6h2iP _2 Cy5 / 1j10h2iP _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.

value: germination and growth on MS10+NPA (5 days) transfert on MS10+ANA during 1 day and 18 hours transfert on MSgluc+2iP during 6 hours


title: 14227246 - 1j18h ANA_2 vs 6h2iP _2 MSgluc+2iP 6 hr vs. baseline

hyb_protocol: 6h2iP _2 Cy5 / 1j18h ANA_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.

value: columbia

source_name: 1j18h ANA_2

growth_protocol: roots - germination and growth on MS10+NPA (5 days) transfert on MS10+ANA during 1 day and 18 hours


title: 14227255 - 6h2iP _1 vs 1j18h ANA_1 MSgluc+2iP 6 hr vs. baseline

hyb_protocol: 1j18h ANA_1 Cy5 / 6h2iP _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: 1j18h ANA_1

value: germination and growth on MS10+NPA (5 days) transfert on MS10+ANA during 1 day and 18 hours


title: Peripheral blood derived erythroid progenitors - biological replicate 2

city: Belgrade

first: Vladan

middle: Predrag

last: Cokic

address: Dr Subotica 4

country: Serbia

institute: Institute for Medical Research

description: Biological replicate 2 of 3. Erythroid progenitor cells, untreated, harvested at day 6 of erythroid liquide culture

hyb_protocol: For hybridization, 36 μl hybridization mixture [26 μl cDNA mixture, 1 μl (10 μg) COT-1 DNA, 1 μl (8-10 μg) poly(dA), 1 μl yeast tRNA (4 μg), 6 μl 20X SSC and 1 μl 10% SDS] was pre-heated at 100oC for 2 minutes and cooled for 1 minute. Total volume of probe was added on the array and covered with cover slip. Slides are placed in hybridization chamber and 20µl water was added to the slide, and incubated overnight at 65oC.  Slides were then washed for 2 minutes each in 2X SSC, 1X SSC and 0.1X SSC and spin-dried.

scan_protocol: Microarray slides were scanned in both Cy3 (532nm) and Cy5 (635nm) channels using Axon GenePix 4000B scanner (Axon Instruments, Inc., Foster City, CA) with a 10-micron resolution. Scanned microarray images were exported as TIFF files to GenePix Pro 3.0 software for image analysis. The raw images were collected at 16-bit/pixel resolutions with 0 to 65,535 count dynamic range.

data_processing: We have used the normalization method (Linear & Lowess) to normalize the data and then the Welch T test (comparison mean for single group test). For advanced data analysis, data files (in gpr format) and image (in jpeg format) were imported into mAdb (microarray database), and analyzed by software tools provided by National Institutes Health Center for Information Technology. The gene list was copied and analyzed in Ingenuity for functional characterization. Ingenuity Pathways Analysis is a software application that enables identification of the biological mechanisms, pathways and functions most relevant to the genes of interest [www.ingenuity.com]. Each microarray experiment was globally normalized to make the median value of the log2-ratio equal to zero. The normalization process corrects for dye bias, photo multiplier tube voltage imbalance, and variations between channels in the amounts of the labeled cDNA probes hybridized. The data files representing the differentially expressed genes were then created.

source_name: Peripheral blood

label_protocol: Labeled cDNA probes were produced: 5 μg of tRNA was incubated at 70oC for 5 minutes along with 1 μl of aminoallyl-oligo dT primer and quickly chilled for 3 minutes. Then, 2 μl 10X first strand buffer, 1.5 μl SSII enzyme (Stratagene, La Jolla, CA), 1.5 μl 20X aminoallyl dUTP and 2 μl of 0.1M DTT were added and incubated for 90 minutes at 42oC. After incubation, volume of the reaction mixture was raised to 60 μl with 40 μl of DEPC water. cDNA was purified by the MinElute column (Qiagen). 300 μl of Binding buffer PB was added to the coupled cDNA, and the mixture applied to the MinElute column, and centrifuged for 1minute at 10.000 rpm.  After discharging the flow-through, 600 μl of washing buffer PE was added to the column, and centrifuged for 1 minute at 10.000 rpm. The flow-through was discharged and the washing repeated. Then the columns were placed into a fresh eppendorf tube and 15 μl elution buffer added to the membrane, incubated for 1 minute at room temperature, centrifuged for 1 minute at 10.000 rpm and probe collected. The probe was dried in speed-vac for 16 minutes. Finally, 5 μl of 2X coupling buffer and 5 μl Cy3 and Cy5 dye (GE Healthcare Bio-Sciences Corp., Piscataway, NJ) were mixed into the control (huURNA) and experimental cDNAs (huES cell-derived) respectively and incubated at room temperature in dark for 90 minutes. After incubation, the volume was raised to 60 μl by 50 μl DEPC water and then cDNA was purified by the MinElute column and eluted with 13 μl elution buffer by centrifugation.

growth_protocol: For erythroid differentiation, hematopoietic CD34+ progenitor cells were resuspended in medium, which contained 30% FBS, 2 mmol/L glutamine, 100 U/ml penicillin, 100 ug/ml streptomycin, 1% deionized BSA, 10 mmol/L beta-mercaptoethanol, 1 mmol/L dexamethasone, 33 ug/ml holo-transferrin, 10 ng/ml SCF, 1 ng/ml IL-3 and 1 ng/ml GM-CSF (Sigma, St. Louis, MO), and 1 U/ml human recombinant EPO (Amgen Inc, Thousand Oaks, CA).

extract_protocol: we used the RNeasy protocol for isolation of total RNA (tRNA) from erythroid progenitor cells (Qiagen, Valencia, CA) according to the manufacturer's instructions

treatment_protocol: After 6 days of erythropoietin treatment and incubation at 37°C (5% CO2, 95% humidity)

value: Erythroid progenitor cells 100% CD71+

tag: cell origin

value: Peripheral blood

source_name: Total human universal RNA (HuURNA)

tag: sample source

value: isolated from a collection of adult human tissues to represent a broad range of expressed genes from both male and female donors (BD Biosciences, Palo Alto, CA)

tag: sample type

value: Total human universal RNA (HuURNA)


title: Cord blood derived erythroid progenitors - biological replicate 3

description: Biological replicate 3 of 3. Erythroid progenitor cells, untreated, harvested at day 6 of erythroid liquide culture

source_name: Cord blood

value: Cord blood


title: Peripheral blood derived erythroid progenitors - biological replicate 1

description: Biological replicate 1 of 2. Erythroid progenitor cells, untreated, harvested at day 6 of erythroid liquide culture


title: 14227253 - 1j18h ANA_1 vs 6h2iP _1 MSgluc+2iP 6 hr vs. baseline

hyb_protocol: 6h2iP _1 Cy5 / 1j18h ANA_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.

tag: tissue


title: Cord blood derived erythroid progenitors - biological replicate 2


title: Peripheral blood derived erythroid progenitors - biological replicate 3


title: Bone marrow derived erythroid progenitors - biological replicate 1

source_name: Bone marrow

value: Bone marrow


title: Bone marrow derived erythroid progenitors - biological replicate 2


title: 14227248 - 6h2iP _2 vs 1j10h2iP _2 MSgluc+2iP 1 d and 10 hr vs. Sgluc+2iP 6 hr

hyb_protocol: 1j10h2iP _2 Cy5 / 6h2iP _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.

value: roots


title: 14227256 - 6h2iP _1 vs 1j10h2iP _1 MSgluc+2iP 1 d and 10 hr vs. Sgluc+2iP 6 hr

hyb_protocol: 1j10h2iP _1 Cy5 / 6h2iP _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: Cord blood derived erythroid progenitors - biological replicate 1

description: Biological replicate 1 of 3. Erythroid progenitor cells, untreated, harvested at day 6 of erythroid liquide culture


title: MM.1S BMSCs RGB 8h  card A

description: Test

value: MM.1S cells


title: Bone marrow derived erythroid progenitors - biological replicate 3


title: 14227247 - 6h2iP _2 vs 1j18h ANA_2 MSgluc+2iP 6 hr vs. baseline

hyb_protocol: 1j18h ANA_2 Cy5 / 6h2iP _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: Fetal liver derived erythroid progenitors - biological replicate 2

description: Biological replicate 2 of 2. Erythroid progenitor cells, untreated, harvested at day 6 of erythroid liquide culture

source_name: Fetal liver

value: Fetal liver


title: Fetal liver derived erythroid progenitors - biological replicate 1


title: MM.1S control card A

description: Control

value: cultured in control media

value: control media


title: MM.1S RGB 8h card A

description: Test

value: subjected to drug treatment

value: 8 hours


title: ABI3_ChIP 3/2, membrane B [070420ABI3]

city: Gatersleben

first: Gudrun

last: Moenke

address: Corrensstr. 3

country: Germany

institute: IPK

description:
070420ABI3
Raw data file: 070420_B_ABI3.txt
ChIP technical replicate of biol. replicate 3
Hybridization on membrane B

hyb_protocol: Arrays were prehybridized for 1h at 65°C in Church buffer (0,5M sodium phosphate, pH7,2, 7% SDS, 1% BSA, 1mM EDTA, 10µg/ml sheared salmon sperm DNA) per cm2 of membrane in a rotating thermal oven. Labelled probes were added and hybridization continued for 4 days. Membranes were washed twice in 0,2x SSC, 0,1% SDS for 20 min at 65°C and then placed on a moist Whatman paper, wrapped in Saran wrap and exposed to a Fuji image plate for 10 days in a lead chamber.

scan_protocol: Signals were detected using a FLA 3000 phosphoimager at 50µm resolution and 16 bit grey scale (Fuji). Spot intensities were obtained by aligning the pre-defined spotting pattern using ArrayVision software (GE Healthcare).

data_processing: Five ABI3 ChIP-chip experiments (three biological and two technical replicates) were performed, each consisting of a pair of hybridisations with amplified input chromatin and immuno-precipitated chromatin. For normalization, the median of log2 transformed signal intensities of each hybridisation was centred at zero. Quantile normalization (Bolstad et al. 2003) was applied separately to datasets of input and immuno-precipitated chromatin. Duplicated spotting of each amplicon on the arrays provided an internal quality control, which was used to exclude all signals with a difference of normalized log2 intensities larger than one between the two spots (1.56% of all signals). Missing values were again substituted by the mean of normalized log2 intensities from other hybridisations of the same kind, chromatin or immuno-precipitated chromatin, if the signal was excluded in no more than two hybridisations. Finally, the mean of normalized log2 intensities from both spots of each amplicon was calculated and the mean values of hybridisations with input chromatin were subtracted from the mean values of hybridizations with immuno-precipitated chromatin, resulting in log2 enrichment factors for most (> 99.85%) of the spotted amplicons in all five experiments.

source_name: Chromatin fragments precipitated with anti-ABI3 antibody, seeds

label_protocol: Labelled probes were obtained by combining three parallel random priming reactions using the Megaprime Kit (GE Healthcare, Uppsala, Sweden), 1ng amplified chromatin, and 50µCi [α-33P]dCTP per reaction.

growth_protocol: Arabidopsis plants were grown on soil, with a 16 h light/ 8 h dark cycle

extract_protocol: Chromatin was isolated from unripe seeds of Arabidopsis thaliana Col-0, harvested 11-13 days after pollination. Cross-linking was done with 1% formaldehyde  for 20 min under vacuum, terminated by addition of glycine with a final concentration of 125 mM. Seeds were Potter-homogenized, filtered and the nuclei collected by centrifugation. Nuclear membranes were dissolved with detergents and  the chromatin was collected by high speed centrifugation. Chromatin was fragmented to an average size of 500 bp by ultra sonic treatment.   10 µg chromatin were combined with 2 µg anti-ABI3 antibody. The antibody-chromatin complex was captured by protein A coated magnetic beads (Invitrogen). After different washings the TF-DNA complex was eluted from the beads at 65°C for 15 min using 1% SDS. Eluates were incubated overnight at 65°C to reverse the cross-links. DNA  fragments were purified using a QIAquick PCR Purification Kit (Qiagen) and their concentration was determined with a NanoDrop 3300 (Thermo Fisher Scientific) fluorescence spectrophotometer. An aliquot (0.5 µg) of non-immunoprecipitated chromatin served as input control.   DNA fragments were blunted and ligated  with the  adapters oJW102  and oJW103 (Young lab:jura.wi.mit.edu/young_public/hESregulation/ChIP.html).  Adapter-ligated fragments were amplified using oJW102 as sole primer.

value: seed

tag: developmental stage according to boyes et al. (2004)

tag: chip antibody

value: anti-ABI3 Antibody


title: Input 3/2, membrane B [070420Chr]

description:
070420Chr
Raw data file: 070420_B_CHR.txt
control technical replicate of biol. replicate 3
Hybridization on membrane B

source_name: Control (input) non-immunoprecipitated chromatin fragments, seeds

value: no


title: Input 3/1 membrane B [070223Chr]

description:
070223Chr
Raw data file: 070223_B_CHR.txt
control biol.replicate 3
Hybridization on membrane B


title: ABI3_ChIP 3/1, membrane B [070223ABI3]

description:
070223ABI3
Raw data file: 070223_B_ABI3.txt
ChIP biol.replicate 3
Hybridization on membrane B


title: MM.1S BMSCs control  card A

description: Control/Test

extract_protocol: Total RNA was extracted from MM cell pellets, using mirVana miRNA Isolation Kit (Ambion, Inc) according to manufacturer’s protocol.

value: cultured with MM patient-derived BMSCs

value: control media with MM patient-derived BMSCs


title: Input 2/2, membrane B [070427Chr]

description:
070427Chr
Raw data file: 070427_B_CHR.txt
control technical replicate of biol. replicate 2
Hybridization on membrane B


title: Input 2/1, membrane B [070222Chr]

description:
070222Chr
Raw data file: 070222_B_CHR.txt
control biol. replicate 2
Hybridization on membrane B


title: ABI3_ChIP 1, membrane B [061220ABI3]

description:
061220ABI3
Raw data file: 061220_B_ABI3.txt
ChIP biol. replicate 1
Hybridization on membrane B


title: ABI3_ChIP 2/1, membrane B [070222ABI3]

description:
070222ABI3
Raw data file: 070222_B_ABI3.txt
ChIP biol. replicate 2
Hybridization on membrane B


title: Input 1, membrane B [061220Chr]

description:
061220Chr
Raw data file: 061220_B_CHR.txt
control biol. replicate 1
Hybridization on membrane B


title: Mycobacterium avium subspecies paratuberculosis-Acid-NO treated

city: Amherst

first: Andrea

last: Cossu

state: MA

address: 102 Holdsworth way

department: Department of Food Science

institute: University of Massachusetts, Amherst

description: 4 Technical (spot) replicates. Mycobacterium avium subspecies paratuberculosis, Acid-NO treated.

hyb_protocol: Hybridization was performed following the Recommended Sample Preparation and Hybridization Protocol drawn-up by the MYcroarrays® Company (Biodiscovery LLC) with some modifications. 220µl of hybridization solution (66µl of 20X SSPE (3M NaCl, 20mM EDTA, 118.2mM NaH2PO4, 81.8mM Na2HPO4), 10% formamide, 0.01mg/ml BSA, 0.01% Tween-20, 1mM DTT, 1% manufacturer control oligos, 10µg of each target coupled-aRNA, RNAse-free water to final volume) was prepared and pre-warmed at 56°C. Hybridizations were carried out in a water bath at 55°C for 18h with OneArray Sealed Hybridization Chambers (PhalanxBio Inc., Palo Alto, CA, USA). After incubation, slides were washed twice with SSPE 1X- 0.1mM DTT for 2 min followed by a 30 sec final wash with 0.25 X SSPE – 0.1mM DTT, dried with air-spray and immediately scanned.

scan_protocol: Scans were carried out with the Gene Pix AXON 4200A instrument (Axon Instruments) at 5-um resolution with full dynamic range of signal intensities at 1 – 65.000 in two-colour red/green mode (635nm and 532 nm filters).

data_processing:
The intensities of the two dyes for each spot were quantified using the Gene Pix 6.0 Software and calculated as the mean of median intensity of each replicate spot for each gene. Total array intensity was used to normalize spot signal intensities with the ratio-mean based algorithm option. Subtraction of local feature background median was achieved as default. Negative corrected intensities were set to 10.
A change of 2-fold in the intensities with a p-value < 0.05 was considered significant for a differential gene expression. Data were transformed in normalized log2 ratio (Alexa Fluor dye 555/647) representing MAP exp/MAP k-.

label: Alexa Fluor 555

organism: Mycobacterium avium subsp. paratuberculosis

source_name: Mycobacterium avium subspecies paratuberculosis acid-NO treated

label_protocol: Forty µg samples of amplified RNA (aRNA)  were labelled with either Alexa Fluor dye 647 or 555  purchased from Invitrogen, USA, following manufacturer's protocol. Purification of coupled aRNA was performed by RNeasy purification system (Qiagen) and incorporation of dye was evaluated using the Nanodrop spectrophotometer. Before hybridization, coupled aRNA was fragmented using the RNA fragmentation reagents (Ambion, Inc) following the manufacturer's protocol.

growth_protocol: MAP1515 (ATCC 43015) was cultured in Middlebrook 7H9 medium (Sigma-Aldrich, MO, USA) supplemented with 0.2% glycerol (Sigma-Aldrich, MO, USA), 0.05% Tween 80 (Sigma-Aldrich, MO, USA) and 10% v/v albumin dextrose catalase (ADC, Sigma-Aldrich, MO, USA), 2 mg/L of Mycobactin J (MicJ, Allied Monitors, Fayette, MO, USA) were also added. Cells were grown in 25 cm2 vented tissue culture flasks (T25) positioned up-right at 37°C before stress treatment.

extract_protocol: tot-RNA extracted with the RiboPure-Bacteria Kit (Ambion, Inc). Mycobacterial cells were re-suspended in 350µl of RNAwiz solution and transferred to a 0.5ml RNAse-free skirted screw-cap microcentrifuge tube containing 250µl of 0.1mm ice-cold Zirconia Beads. Tubes were immediately processed in the RiboLyser RNA Lysing Machine (RiboLyser FP120-HY-230, Hybaid) for 3 cycles (30s at speed 6.5 with 1 min of cooling interval between each bead beating step). Remaining steps were performed according to the manufacturer’s instructions. All RNA samples were treated with Dnase I (Ambion, Inc)  and  purified by RNeasy column (Qiagen). RNA yield and purity was evaluated with the Nanodrop spectrophotometer (NanoDrop1000, Thermo Scientific) and RNA quality was examined by Denaturing Gel Electrophoresis. We carried out three independent experiments on three different flasks. Good quality RNA samples obtained from each pellet were then pooled together and used for microarray experiments to get an average of three separate experiments. mRNA was obtained by using the MICROBExpress Bacterial mRNA Purification Kit (Ambion) and was lineary amplified bu using the MessageAmp II Bacterial Kit (Ambion, Inc)

treatment_protocol: Mid log-phase cells were treated with a 7H9/ADC/Tw80/MicJ buffered pH 5.3 medium with a final concentration of 5 mM of sodium nitrite (NaNO2) (Sigma) and exposed to the stress for 3 hours at 37°C. Cells were harvested by centrifugation at 5800 x g for 15min at 4°C and re-suspended in RNA later solution (Sigma). Pellets were then incubated overnight at 4°C and stored at -80°C until RNA extraction.

tag: bacterial cells

tag: strain

label: Alexa Fluor 647

source_name: Mycobacterium avium subspecies paratuberculosis control untreated

growth_protocol: MAP1515 (ATCC 43015) was cultured in Middlebrook 7H9 medium (Sigma-Aldrich, MO, USA) supplemented with  0.2% glycerol (Sigma-Aldrich, MO, USA), 0.05% Tween 80 (Sigma-Aldrich, MO, USA), 10% v/v albumin dextrose catalase (ADC, Sigma-Aldrich, MO, USA) and 2 mg/L of Mycobactin J (MicJ, Allied Monitors, Fayette, MO, USA)  in 25 cm2 vented tissue culture flasks (T25) positioned up-right at 37°C until mid-log phase.

treatment_protocol: Mid log-phase cells were grown in 7H9/ADC/Tw80/MicJ medium for 3h at 37°C. Cells were harvested by centrifugation at 5800 x g for 15min at 4°C and re-suspended in RNA later solution (Sigma). Pellets were then incubated overnight at 4°C and stored at -80°C until RNA extraction.