title: lactococcus lactis infected with phage c2 timepoint 35mins replicate 2

city: Utrecht

first: Aldert

last: Zomer

address: Yalelaan 1

department: Department of Infectious Diseases and Immunology,Faculty of Veterinary Medicine

institute: Utrecht University

hyb_protocol: Labelled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050).

scan_protocol: Following hybridization, all microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A).

data_processing: The scanning results were converted to data files with Agilent's Feature Extraction software (version 9.5). DNA microarray data was processed as previously described (Zomer et al., J. Bacteriol. November 2009 vol. 191 no. 22 7039-7049 ).

organism: Lactococcus cremoris subsp. cremoris UC509.9

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with c2, 35 minutes

label_protocol: Labelling was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable. For the purpose of the tiling arrays, to prevent spurious second strand synthesis occurring, 0.1 µg µl-1 of actinomycin D (Sigma) was added in addition of 1 µl RNAseout (Invitrogen, USA) validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77). For the purpose of the tiling arrays, to prevent spurious second strand synthesis occurring, 0.1 µg µl-1 of actinomycin D (Sigma) was added in addition of 1 µl RNAseout (Invitrogen, USA)

growth_protocol: L. lactis UC509.9 and was grown under static conditions in GM17 (M17 broth [Oxoid Ltd, Hampshire, U.K.] supplemented with 0.5 % D-glucose). Bacteriophages c2 and Tuc2009 were propagated on L. lactis UC509.9 as previously described and maintained at 4 °C. Bacteriophages were concentrated using 10 % polyethylene-glycol, as previously described. The Tuc2009-(re)lysogenised derivative of L. lactis UC509.9 is termed L. lactis UC509.

extract_protocol: RNA isolation and RNA quality control was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

treatment_protocol: At OD 0.13, the culture was split into two equal volumes. To one, phage (either C2 or Tuc2009) in TBT buffer (100 mM Tris pH 7.5, 100 mM NaCl, 10 mM MgCl2), was added to a final multiplicity of infection (MOI) of 5. To the other, acting as control, a corresponding amount of TBT buffer without phage was added. Samples (60 ml) were collected at 2, 5, 10, 15, 25, 35 and, in the case of Tuc2009 only, 45 min post infection (p.i.) by centrifugation ( Performed in a Thermo Scientific SL16R centrifuge using a 75003658 rotor at 5500 rpm for 1 min). Pellets were flash frozen in a -80 °C EtOH water bath. Samples were then maintained at -80 °C until further processing and analysis.

tag: infection

value: infected with c2, 35 minutes

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with mock, 35 minutes

value: infected with mock, 35 minutes


title: BCR-ABL-SNP_#01

status: Public on Jun 27 2013

type: genomic

city: Memphis

first: Charles

middle: G

last: Mullighan

state: TN

address: 262 Danny Thomas Place

department: Pathology

country: USA

institute: St Jude Children's Research Hospital

hyb_protocol: See Roche NimbleGen website and Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319. for details

scan_protocol: Scanning was performed using a GenePix 4000B scanner (Axon Instruments) as previously described in Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.

data_processing: Signal intensities at each HpaII amplifiable fragment were calculated as a robust (25% trimmed) mean of their component probe-level signal intensities. Any fragments found within the level of background MspI signal intensity, measured as 2.5 mean-absolute-differences (MAD) above the median of random probe signals, were categorized as failed. These failed loci therefore represent the population of fragments that did not amplify by PCR, whatever the biological (e.g. genomic deletions and other sequence errors) or experimental cause. On the other hand, Methylated loci were so designated when the level of HpaII signal intensity was similarly indistinguishable from background. PCR-amplifying fragments (those not flagged as either methylated or failed) were normalized using an intra-array quantile approach wherein HpaII/MspI ratios are aligned across density-dependent sliding windows of fragment size-sorted data (described in detail in Thompson et al, Bioinformatics 2008;24:1161-1167. Interarray normalization was performed independently for each channel using a quantile normalization, and after that the log(ratio) for each array was calculated as Log2 (HpaII signal) - Log2(MspI signal)

molecule: genomic DNA

organism: Homo sapiens

source_name: ALL Blast cells, MspI representation of genomic DNA

label_protocol: Random priming with 9-mers pre-labeled with either Cy3 or Cy5 according to manufacturer's instructions using the NimbleGen Dual-Color DNA Labeling Kit (cat # 05223547001)

extract_protocol: Representation of the genome generated by digestion with either MspI or HpaII and amplification by ligation-mediated PCR according to the HELP protocol (See B. Khulan, et al. Genome Res. 2006 Aug;16(8):1046-55)

tag: cell type

value: ALL Blast cells

tag: all blast cells from

value: tumor cells obtained at diagnosis in childhood ALL with BCR-ABL1 rearrangement

source_name: ALL Blast cells, HpaII representation of genomic DNA


title: BCR-ABL-SNP_#09


title: BCR-ABL-SNP_#21


title: Ba_10000_Aerosol_rep_2

city: Livermore

first: Kevin

last: McLoughlin

state: CA

address: PO Box 808

department: Global Security

institute: Lawrence Livermore National Laboratory

description: data used for Supplementary Table S6

hyb_protocol: DNA was hybridized to the census array using the NimbleGen hybridization kit.  Samples were allowed to hybridize for 17 hours and washed using the NimbleGen Wash Buffer Kit (Roche).

scan_protocol: Microarrays were scanned on an Axon GenePix 4000B 5 µm scanner (Molecular Devices, Sunnyvale, CA).

data_processing: Data was analyzed using NimbleScan software and custom software developed at Lawrence Livermore National Laboratory, CA, USA and  described in 'Gardner et al. A Micobial Detection Array (MDA) for Viral and Bacterial Detection. BMC Genomics 2010 Nov 25;11:668'. Additional stringency criteria were applied to exclude bacterial sequences and viruses having fewer than 20% of probes detected out of those expected. Probes were classified as detected if the intensity exceeded a threshold equal to the 99th percentile of intensities for negative control probes.

organism: Bacillus anthracis str. Ames

source_name: Aerosol filter sample spiked with B. anthracis DNA

label_protocol: B. anthracis-spiked samples were amplified using the REPLI-g Midi Kit (Qiagen, Gaithersburg, MD), intended to provide uniform whole genome amplification.  This kit was used according to the manufacturer’s instructions, allowing samples to amplify for 16 hours at 30°C. Amplified samples were purified using the Qiaquick PCR Purification Kit (Qiagen), and yielded 17.0 ± 1.8 µg amplified DNA for each sample. Amplified environmental DNA spiked with B. anthracis Ames genomic DNA was fluorescently labeled using the NimbleGen One-Color DNA Labeling Kit (Roche) according to the manufacturer’s recommended protocols.

extract_protocol: DNA was extracted from soil using the UltraClean Soil DNA Isolation Kit (MoBio, Carlsbad, CA) using the manufacturer’s alternative protocol for maximum yield.  Following extraction, 1 ng of each extracted DNA was used in a real-time PCR assay to test for inhibition.  All samples showed a high level of PCR inhibition and were reprocessed starting from Step 12 of the MoBio alternative protocol, intended to remove excess humic acid. For aerosol samples, primary sampling filters were obtained from BioWatch aerosol collection units (collected April 2009) from the National Capital Region Laboratory.  Filters were added to 30 mL 100 mM phosphate buffer (pH 7.4) containing 0.05% (v/v) Tween 80 and vortexed for 30 seconds followed by incubation on a rocking shaker for 15 minutes.  This agitation procedure was repeated three times.  The filters were removed from the tube and the remaining solution centrifuged at 3200 x g for 30 minutes at 4oC.  Following centrifugation, the supernatant was removed and discarded.  DNA purification was subsequently performed using the UltraClean Soil DNA Isolation Kit (MoBio).  DNA concentrations were measured using a Qubit fluorometer (Life Technologies, Grand Island, NY).

treatment_protocol: B. anthracis Ames DNA was acquired from the LLNL select agent laboratory and confirmed to be free of viable cells or spores by plating of 1/10 the total DNA volume on blood agar plates followed by incubation at 37°C for 72 hours.  DNA concentration was determined by measurement using a Qubit fluorometer and the number of femtograms/genome equivalent was determined based on GenBank chromosomal and plasmid genome sizes.  B. anthracis genomic DNA was added to nucleic acid extracted from the two environmental sources in six amounts (1, 10, 100, 1000, 10000, and 100000 genomic equivalents of B. anthracis DNA).  B. anthracis DNA was mixed with 100 pg of DNA extracted from aerosol filters or 1 ng DNA extracted from the combined Oakland and San Francisco soil extracts.

tag: ba copies

tag: background

value: Aerosol

tag: rep


title: BCR-ABL-SNP_#05


title: Ba_10000_Aerosol_rep_1

description: data used for Supplementary Table S6


title: lactococcus lactis infected with phage c2 timepoint 25mins replicate 2

type: RNA

country: Netherlands

molecule: total RNA

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with c2, 25 minutes

value: infected with c2, 25 minutes

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with mock, 25 minutes

value: infected with mock, 25 minutes


title: lactococcus lactis infected with phage c2 timepoint 15mins replicate 2

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with c2, 15 minutes

value: infected with c2, 15 minutes

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with mock, 15 minutes

value: infected with mock, 15 minutes


title: Ba_100000_Soil_rep_2

description: data used for Supplementary Table S6

source_name: Soil sample spiked with B. anthracis DNA

value: Soil


title: Cohort1-Prefrontal Cortex_Amphetamine (5 mg/kg) group_Sample 2

city: Seoul

first: Minsoo

last: Noh

address: 1 Gwanak-ro, Gwanak-gu

department: Pharmacy

country: South Korea

institute: Seoul National University

description: Co1-PFC_Amph 5_2

hyb_protocol: Hybridization was carried out using Affymetrix GeneChip Rat Genome 230 2.0 oligonucleotide arrays (Affymetrix, Santa Clara,CA, USA). The hybridized probe array was stained and washed with GeneChip hybridization, wash and stain kit using the Fluidics Station 450 (Affymetrix).

scan_protocol: The stained GeneChip probe array was scanned with a GeneChip Scanner 3000+7G (Affymetrix).

data_processing: The signal intensity of the gene expression level was calculated by the Expressin Console Software, Version 1.1 (Affymetrix) based on the MAS 5.0 algorithm.

label: biotin

organism: Rattus norvegicus

source_name: Prefrontal Cortex, Amphetamine

label_protocol: RNA was converted to cDNA and transcribed into cRNA in the presence of biotinylated ribonucleotides, according to standard Affymetrix protocols (Affymetrix ‘Expression Analysis Technical Manual’, #701021 Rev. 5).

growth_protocol: Male Wistar rats ( 4 weeks old) were obtained from Orient Bio Korea. The animals were housed in an environmentally-controlled animal room (temperature [22 ± 2°C] and humidity- [55 ± 5%], 12 hr/12 hr light/dark [6 AM-6 PM] cycle), in groups (during drug treatment and CPP experiments) and individually thereafter during self-administration tests. All experiments were performed in accordance with the Principles of Laboratory Animal Care (NIH) and the Animal Care and Use Guidelines of Sahmyook University, Korea.

extract_protocol: Total RNA was isolated using the Trizol reagent (Invitrogen, Carlsbad, CA, USA), according to the manufacturer's instructions.

treatment_protocol: Rats were acclimatized to their housing conditions prior to drug or saline administration. Drug treatment (twice daily, intraperitoneal [i.p.]) commenced when rats were 6 weeks old, and lasted for 7 days. Rats were divided into two groups: (cohort 1) 4 groups of rats (n=12 rats per group) given saline only (1 mg/kg, i.p.,”drug-naive” rats); and (cohort 2): 3 groups of rats given either methamphetamine, amphetamine or methylphenidate (5 mg/kg,i.p., “drug-pretreated”) prior to behavioral assays (Conditioned Place Preference [CPP] and Self-administration tests). During CPP tests, rats were conditioned with the psychostimulants at one of the following drugs and doses: Saline (Control group), 1.25 and 5 mg/kg, i.p. for stimulant-treated groups.

tag: strain

value: Wistar

tag: pretreatment drug & dose

value: saline

tag: cpp conditioning drug and dose

value: Amphetamine (5 mg/kg)

value: 0.1 mg/kg/infusion, Amphetamine

tag: tissue

value: Prefrontal Cortex


title: Cohort1-Prefrontal Cortex_Amphetamine (5 mg/kg) group_Sample 1

description: Co1-PFC_Amph 5_1


title: Cohort1-Prefrontal Cortex_Amphetamine (1.25 mg/kg) group_Sample 3

description: Co1-PFC_Amph 1.25_3

value: Amphetamine (1.25 mg/kg)


title: Ba_100000_Soil_rep_1

description: data used for Supplementary Table S6


title: lactococcus lactis infected with phage c2 timepoint 10mins replicate 2

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with c2, 10 minutes

value: infected with c2, 10 minutes

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with mock, 10 minutes

value: infected with mock, 10 minutes


title: lactococcus lactis infected with phage c2 timepoint 2mins replicate 2

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with c2, 2 minutes

value: infected with c2, 2 minutes

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with mock, 2 minutes

value: infected with mock, 2 minutes


title: BCR-ABL-SNP_#12

value: ALL Blast cells

value: tumor cells obtained at diagnosis in childhood ALL with BCR-ABL1 rearrangement


title: Cohort1-Prefrontal Cortex_Amphetamine (1.25 mg/kg) group_Sample 2

description: Co1-PFC_Amph 1.25_2


title: lactococcus lactis infected with phage c2 timepoint 25mins replicate 1

value: infected with c2, 25 minutes


title: Ba_100000_Aerosol_rep_2

description: data used for Supplementary Table S6

value: Aerosol


title: Cohort1-Prefrontal Cortex_Control group_Sample 5

source_name: Prefrontal Cortex, Saline (Control)

value: Saline

value: 0.1 ml/infusion, 0.9% Saline


title: MLL-SNP_#29

value: tumor cells obtained at diagnosis in childhood ALL with MLL rearrangement


title: Ba_100000_Aerosol_rep_1

description: data used for Supplementary Table S6


title: MLL-SNP_#05


title: lactococcus lactis infected with phage c2 timepoint 35mins replicate 1

value: infected with c2, 35 minutes

value: infected with mock, 35 minutes


title: Cohort1-Prefrontal Cortex_Control group_Sample 4

value: Wistar

value: saline


title: MLL-SNP_#04


title: Cohort1-Prefrontal Cortex_Amphetamine (1.25 mg/kg) group_Sample 1

description: Co1-PFC_Amph 1.25_1

value: 0.1 mg/kg/infusion, Amphetamine

value: Prefrontal Cortex


title: MLL-SNP_#17


title: lactococcus lactis infected with phage c2 timepoint 5mins replicate 2

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with c2, 5 minutes

value: infected with c2, 5 minutes

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with mock, 5 minutes

value: infected with mock, 5 minutes


title: BCR-ABL-SNP_#17


title: Cohort1-Prefrontal Cortex_Control group_Sample 3


title: MLL-SNP_#07


title: Cohort1-Prefrontal Cortex_Control group_Sample 1


title: lactococcus lactis infected with phage c2 timepoint 15mins replicate 1

value: infected with c2, 15 minutes

value: infected with mock, 15 minutes


title: lactococcus lactis infected with phage c2 timepoint 5mins replicate 1


title: lactococcus lactis infected with phage c2 timepoint 10mins replicate 1

value: infected with c2, 10 minutes

value: infected with mock, 10 minutes


title: MLL-SNP_#19

value: ALL Blast cells


title: Cohort1-Prefrontal Cortex_Control group_Sample 2


title: Ras shARF biological replicate 3

city: Saint Louis

first: Jason

middle: Dean

last: Weber

state: MO

address: 660 South Euclid Avenue

department: Internal Medicine

institute: Washington University

hyb_protocol: Following fragmentation with NuGen Encore Biotin Module, 2.5 ug of cDNA were hybridized on Gene 1.0 ST Array in the GeneChip Hybridization Oven 640 for 18 hr at 45C. GeneChip were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
Data were processed using Affymetrix Expression Console software. Gene level expression were summarized from the intensities and then normalized using the Robust Multiarray Analysis (RMA) algorithm.
probe group file: MoGene-1_0-st-v1.r4.pgf
meta-probeset file: MoGene-1_0-st-v1.r4.mps

label: Biotin

organism: Mus musculus

source_name: Fibroblasts

label_protocol: Biotinylated cDNA were prepared according to the standard NuGen WT-Ovation Pico RNA Amplification system from 50 ng total RNA.

growth_protocol: Cells were maintained in DMEM supplemented with 10% fetal bovine serum, 2mM glutamine, 0.1mM nonessential amino acids, 1mM sodium pyruvate, and 2ug/mL gentamicin

extract_protocol: Cells were harvested by trypsinization (0.05%) and washed twice with 1X PBS.  Total RNA was extracted using a Nucleospin RNA II Kit (Machery-Nagel)

tag: construct

value: shARF


title: MLL-SNP_#03

source_name: ALL Blast cells, MspI representation of genomic DNA


title: Ras shARF Biological replicate 1


title: Lactococcus lactis subsp. cremoris UC509.9 infected with tuc2009 timepoint 45mins replicate 2

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with tuc2009, 45 minutes

value: infected with tuc2009, 45 minutes

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with mock, 45 minutes

value: infected with mock, 45 minutes


title: lactococcus lactis infected with phage c2 timepoint 2mins replicate 1

value: infected with c2, 2 minutes

value: infected with mock, 2 minutes


title: SAM + Cocaine (M+C) 3

city: Tartu

first: Kaili

last: Anier

address: Ravila 19

country: Estonia

institute: University of Tartu

description:
SAMPLE 15
2 tissues were combined to a sample

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The raw data was analyzed with Illumina BeadStudio Gene Expression Module v3.3.7. Further data analysis was performed with R version 2.13.0 /Bioconductor software using lumi and limma packages.

source_name: SAM + Cocaine (M+C) 3, Mouse nucleus accumbens tissue

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA amplification Kit according to the manufacturer’s instructions using 750 ng of total RNA as a template (Ambion Inc, Austin, TX, USA).

extract_protocol: RNA was extracted from the  mouse NAc using Qiagen RNeasy mini kit in accordance with the prescribed protocol provided with the kit. RNA quantity and quality were assessed using the NanoDrop-1000 spectrophotometer and the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA).

treatment_protocol:
Mice were treated for 7 days intraperitoneally (i.p.) with sterile saline (0.1 mL/10 g body weight) or SAM (4520 mg/kg, 10 mM/kg) 20 minutes prior to cocaine hydrochloride administration (10 mg/kg, i.p.).
Animals (n = 17-22) were randomly assigned into one of the following treatment groups: (1) Saline + Saline “S+S”; (2) SAM + Saline “M+S”; (3) Saline + Cocaine “S+C” and (4) SAM + Cocaine “M+C”.
Locomotor activity was recorded for 90 minutes after the second injection days 1, 3, 5, and 7, and analyzed using VideoMot2 software. Mice were sacrificed 24 h after the end of the repeated treatment.

tag: gender

value: Male

tag: age

value: 5 months

tag: agent

value: SAM + Cocaine (M+C)

value: nucleus accumbens


title: Ras shARF biological replicate 2


title: SAM + Cocaine (M+C) 1

description:
SAMPLE 13
2 tissues were combined to a sample

source_name: SAM + Cocaine (M+C) 1, Mouse nucleus accumbens tissue


title: MLL-SNP_#15

value: tumor cells obtained at diagnosis in childhood ALL with MLL rearrangement

source_name: ALL Blast cells, HpaII representation of genomic DNA


title: SAM + Cocaine (M+C) 4

description:
SAMPLE 16
2 tissues were combined to a sample

source_name: SAM + Cocaine (M+C) 4, Mouse nucleus accumbens tissue


title: MLL-SNP_#02


title: Lactococcus lactis subsp. cremoris UC509.9 infected with tuc2009 timepoint 25mins replicate 2

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with tuc2009, 25 minutes

value: infected with tuc2009, 25 minutes

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with mock, 25 minutes

value: infected with mock, 25 minutes


title: Saline + Cocaine (S+C) 4

description:
SAMPLE 12
2 tissues were combined to a sample

source_name: Saline + Cocaine (S+C) 4, Mouse nucleus accumbens tissue

value: Saline + Cocaine (S+C)


title: Lactococcus lactis subsp. cremoris UC509.9 infected with tuc2009 timepoint 35mins replicate 2

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with tuc2009, 35 minutes

value: infected with tuc2009, 35 minutes

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with mock, 35 minutes

value: infected with mock, 35 minutes


title: SAM + Cocaine (M+C) 2

description:
SAMPLE 14
2 tissues were combined to a sample

source_name: SAM + Cocaine (M+C) 2, Mouse nucleus accumbens tissue


title: Ras Scr Biological replicate 2

value: shSCR


title: Ras Scr, Biological replicate 1


title: MLL-SNP_#06

value: ALL Blast cells


title: Ras Scr Biological replicate 3


title: MLL-SNP_#11


title: Lactococcus lactis subsp. cremoris UC509.9 infected with tuc2009 timepoint 10mins replicate 2

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with tuc2009, 10 minutes

value: infected with tuc2009, 10 minutes

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with mock, 10 minutes

value: infected with mock, 10 minutes


title: Lactococcus lactis subsp. cremoris UC509.9 infected with tuc2009 timepoint 15mins replicate 2

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with tuc2009, 15 minutes

value: infected with tuc2009, 15 minutes

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with mock, 15 minutes

value: infected with mock, 15 minutes


title: Saline + Cocaine (S+C) 3

description:
SAMPLE 11
2 tissues were combined to a sample

source_name: Saline + Cocaine (S+C) 3, Mouse nucleus accumbens tissue


title: MLL-SNP_#09

source_name: ALL Blast cells, MspI representation of genomic DNA


title: Saline + Cocaine (S+C) 2

description:
SAMPLE 10
2 tissues were combined to a sample

source_name: Saline + Cocaine (S+C) 2, Mouse nucleus accumbens tissue


title: Saline + Cocaine (S+C) 1

description:
SAMPLE 9
2 tissues were combined to a sample

source_name: Saline + Cocaine (S+C) 1, Mouse nucleus accumbens tissue


title: Lactococcus lactis subsp. cremoris UC509.9 infected with tuc2009 timepoint 5mins replicate 2

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with tuc2009, 5 minutes

value: infected with tuc2009, 5 minutes

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with mock, 5 minutes

value: infected with mock, 5 minutes


title: MLL-SNP_#16

source_name: ALL Blast cells, HpaII representation of genomic DNA


title: Saline + SAM (M+S) 4

description:
SAMPLE 8
2 tissues were combined to a sample

source_name: Saline + SAM (M+S) 4, Mouse nucleus accumbens tissue

value: Male

value: 5 months

value: Saline + SAM (M+S)


title: MLL-SNP_#01

value: tumor cells obtained at diagnosis in childhood ALL with MLL rearrangement


title: Lactococcus lactis subsp. cremoris UC509.9 infected with tuc2009 timepoint 0mins replicate 2

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with tuc2009, 0 minutes

value: infected with tuc2009, 0 minutes

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with mock, 0 minutes

value: infected with mock, 0 minutes


title: Lactococcus lactis subsp. cremoris UC509.9 infected with tuc2009 timepoint 2mins replicate 2

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with tuc2009, 2 minutes

value: infected with tuc2009, 2 minutes

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with mock, 2 minutes

value: infected with mock, 2 minutes


title: Saline + SAM (M+S) 3

description:
SAMPLE 7
2 tissues were combined to a sample

source_name: Saline + SAM (M+S) 3, Mouse nucleus accumbens tissue

value: nucleus accumbens


title: caffeine- 3

city: Camperdown

first: william

last: ritchie

state: NSW

address: Building 93

country: Australia

institute: centenary institute

hyb_protocol: Following fragmentation, samples were injected into Affymetrix array chips and hybridized at 45°C and 60 rpm for 17 hours in a hybridization oven (Affymetrix). GeneChips were stained and washed in the Affymetrix GeneChip Fluidic Station 450

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000 7G

data_processing: The data was analysed using R with the RUV procedure described in http://statistics.berkeley.edu/tech-reports/800 for scaling and normalization.

source_name: granulocytes not treated with caffeine

label_protocol: Biotinylated cDNA were prepared according to the Encore Biotin Module (Nugen) from 300 ng total RNA.

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

treatment_protocol: Cells were plated at a density of 3x105 cells per ml in two different tissue culture plates. The optimal concentration of caffeine (15 mM) was added to the culture medium for 4 hours before cells were washed twice with PBS. Actinomycin D (2 μg/ml) together with caffeine was then added into one plate whereas only actinomycin D was added to the other to block transcription of genes. After an additional 4 hours incubation, total RNA was collected and used for microarray analysis.

value: granulocytes


title: caffeine- 2


title: caffeine- 1


title: Lactococcus lactis subsp. cremoris UC509.9 infected with tuc2009 timepoint 45mins replicate 1

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with tuc2009, 45 minutes

value: infected with tuc2009, 45 minutes

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with mock, 45 minutes

value: infected with mock, 45 minutes


title: Saline + SAM (M+S) 2

description:
SAMPLE 6
2 tissues were combined to a sample

source_name: Saline + SAM (M+S) 2, Mouse nucleus accumbens tissue


title: MLL-SNP_#22

value: ALL Blast cells


title: Lactococcus lactis subsp. cremoris UC509.9 infected with tuc2009 timepoint 25mins replicate 1

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with tuc2009, 25 minutes

value: infected with tuc2009, 25 minutes

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with mock, 25 minutes

value: infected with mock, 25 minutes


title: MLL-SNP_#23

source_name: ALL Blast cells, MspI representation of genomic DNA


title: Saline + Saline (S+S) 4

description:
SAMPLE 4
2 tissues were combined to a sample

source_name: Saline + Saline (S+S) 4, Mouse nucleus accumbens tissue

value: Saline + Saline (S+S)


title: Saline + SAM (M+S) 1

description:
SAMPLE 5
2 tissues were combined to a sample

source_name: Saline + SAM (M+S) 1, Mouse nucleus accumbens tissue


title: caffeine+ 2

source_name: granulocytes treated with caffeine


title: Lactococcus lactis subsp. cremoris UC509.9 infected with tuc2009 timepoint 35mins replicate 1

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with tuc2009, 35 minutes

value: infected with tuc2009, 35 minutes

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with mock, 35 minutes

value: infected with mock, 35 minutes


title: Saline + Saline (S+S) 3

description:
SAMPLE 3
2 tissues were combined to a sample

source_name: Saline + Saline (S+S) 3, Mouse nucleus accumbens tissue

value: Male

value: 5 months


title: MLL-SNP_#10

value: tumor cells obtained at diagnosis in childhood ALL with MLL rearrangement

source_name: ALL Blast cells, HpaII representation of genomic DNA


title: caffeine+ 1


title: Lactococcus lactis subsp. cremoris UC509.9 infected with tuc2009 timepoint 15mins replicate 1

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with tuc2009, 15 minutes

value: infected with tuc2009, 15 minutes

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with mock, 15 minutes

value: infected with mock, 15 minutes


title: Lactococcus lactis subsp. cremoris UC509.9 infected with tuc2009 timepoint 10mins replicate 1

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with tuc2009, 10 minutes

value: infected with tuc2009, 10 minutes

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with mock, 10 minutes

value: infected with mock, 10 minutes


title: caffeine+ 3


title: Saline + Saline (S+S) 2

description:
SAMPLE 2
2 tissues were combined to a sample

source_name: Saline + Saline (S+S) 2, Mouse nucleus accumbens tissue

value: nucleus accumbens


title: MLL-SNP_#12


title: TEL-AML1-SNP_#84

value: tumor cells obtained at diagnosis in childhood ALL with ETV6-RUNX1 rearrangement


title: MLL-SNP_#18


title: TEL-AML1-SNP_#87


title: Lactococcus lactis subsp. cremoris UC509.9 infected with tuc2009 timepoint 5mins replicate 1

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with tuc2009, 5 minutes

value: infected with tuc2009, 5 minutes

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with mock, 5 minutes

value: infected with mock, 5 minutes


title: Lactococcus lactis subsp. cremoris UC509.9 infected with tuc2009 timepoint 0mins replicate 1

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with tuc2009, 0 minutes

value: infected with tuc2009, 0 minutes

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with mock, 0 minutes

value: infected with mock, 0 minutes


title: TEL-AML1-SNP_#85

source_name: ALL Blast cells, MspI representation of genomic DNA

value: ALL Blast cells


title: Lactococcus lactis subsp. cremoris UC509.9 infected with tuc2009 timepoint 2mins replicate 1

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with tuc2009, 2 minutes

value: infected with tuc2009, 2 minutes

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17 infected with mock, 2 minutes

value: infected with mock, 2 minutes


title: MLL-SNP_#08


title: Saline + Saline (S+S) 1

description:
SAMPLE 1
2 tissues were combined to a sample

source_name: Saline + Saline (S+S) 1, Mouse nucleus accumbens tissue

value: Saline + Saline (S+S)


title: Lactococcus lactis subsp. cremoris UC509.9 with tuc2009 in lysogenic state replicate 2

source_name: Lactococcus lactis subsp. cremoris UC509.9 with tuc2009 inserted in the genome grown in M17

value: tuc2009 in lysogenic state

source_name: Lactococcus lactis subsp. cremoris UC509.9 grown in M17


title: TEL-AML1-SNP_#25


title: Lactococcus lactis subsp. cremoris UC509.9 with tuc2009 in lysogenic state replicate 1


title: CD11b+Gr1- cell sample_3 (derived from IL17RC Knock out mouse)

city: South San Francisco

first: Zhaoshi

last: Jiang

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc

hyb_protocol: Agilent In Situ Hybridization Kit Plus was used where Cy-dye labeled control and test samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, the arrays were washed twice, dried and then scanned.

scan_protocol: Scanned on an Agilent scanner, images were processed using Agilent Feature Extraction software version 10.7.

data_processing: Agilent Feature Extraction software version 10.7 was used to create feature extraction files. The normal exponential convolution model was applied for the background correction, Loess and quantile were applied for within array and cross-array normalization. Gene differential expression was analyzed by the package of limma.

label_protocol: Samples were labeled by two-rounds of amplification using Ambion's MessageAmpII aRNA Amplification kit and Agilent's QuickAmp Labeling kit. For all samples, 750 ng of the labeled cRNA was fragmented and hybridized against Cy3-labeled Universal mouse reference (Stratagene, La Jolla, CA).

extract_protocol: Total RNA was isolated using Qiagen's RNAeasy kit following the manufacturer's instructions.  RNA quality was verified by running samples on an Agilent Bioanalyzer 2100.

treatment_protocol: Single cell suspension was prepared from tumors isolated from tumor bearing mice and the CD11b+Gr1+ and CD11b+Gr1- populations were labelled with anti-CD11b (Clone M1/70, eBiosciences) and anti-Gr1 (Clone RB6-8C5, eBiosciences) and purified by FACS sorting of live cells.

tag: sampleID

tag: strain/background

tag: experimentid

tag: genotype/variation

value: IL17RC Knock out

source_name: Universal mouse reference (UMR) from Stratagene

tag: reference

value: pooled mouse reference RNA


title: CD11b+Gr1- cell sample_5 (derived from IL17RC Knock out mouse)


title: CD11b+Gr1- cell sample_4 (derived from IL17RC Knock out mouse)


title: TEL-AML1-SNP_#58

tag: cell type

tag: all blast cells from

source_name: ALL Blast cells, HpaII representation of genomic DNA


title: CD11b+Gr1- cell sample_1 (derived from IL17RC Knock out mouse)


title: TEL-AML1-SNP_#76


title: TEL-AML1-SNP_#02


title: TEL-AML1-SNP_#13


title: TEL-AML1-SNP_#11


title: CD11b+Gr1- cell sample_4 (derived from wild type mouse)

value: wild type


title: CD11b+Gr1- cell sample_5 (derived from wild type mouse)


title: TEL-AML1-SNP_#36


title: TEL-AML1-SNP_#34


title: CD11b+Gr1- cell sample_2 (derived from wild type mouse)


title: CD11b+Gr1- cell sample_2 (derived from IL17RC Knock out mouse)


title: CD11b+Gr1- cell sample_3 (derived from wild type mouse)


title: Adult bone marrow HSCs/progenitors (Hmga2+/+), biological replicate 2

city: Vancouver

first: Connie

last: Eaves

state: BC

address: 675 West 10th Avenue

department: Terry Fox Laboratory

country: Canada

institute: BC Cancer Agency

description: Gene expression data from wild-type adult bone marrow HSCs/progenitors

hyb_protocol: Following fragmentation and labeling , 5 ug of cDNA were hybridized for 18 hr at 45C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000 7G System.

data_processing: All arrays were RMA normalized using the Bioconductor package 'xps' in R including the metacore probesets grouped by exon (this data linked as a supplementary table to GSE41758 as GSE41758_Data_by_Exon_IDs.txt.gz).

source_name: Adult bone marrow Lin-Sca1+cKit+ (Hmga2+/+)

label_protocol: An average of 50 ng total RNA was amplified using the Ovation Pico WTA System to yield an average of 9-10 ug cDNA (Ovation Pico WTA System User Guide, 2011, NuGen).  Afterwards, sense transcript cDNA was generated using the WT-Ovation Exon Module Version 1.0 protocol (WT-Ovation Exon Module User Guide, 2009-2010, NuGen). Fragmented and labeled single-stranded cDNA target were prepared according to the Encore Biotin Module protocol from 5 ug of ST-cDNA (Encore Biotin Module, 2009-2012, NuGen).

growth_protocol: Lin-Sca1+cKit+ cells from fresh tissues (E14.5 FL or adult bone marrow) were isolated by FACS

extract_protocol: RNA was isolated using the RNeasy Mini Spin Columns (QIAGEN) according to the manufacturer's instructions

value: Bone marrow

value: 8-12 weeks


title: TEL-AML1-SNP_#114


title: TEL-AML1-SNP_#78


title: CD11b+Gr1+ cell sample_5 (derived from IL17RC Knock out mouse)


title: CD11b+Gr1+ cell sample_2 (derived from IL17RC Knock out mouse)


title: Fetal liver HSCs/progenitors (Hmga2-/-), biological replicate 3

description: Gene expression data from Hmga2 knock-out E14.5 fetal liver HSCs/progenitors

source_name: E14.5 fetal liver Lin-Sca1+cKit+ (Hmga2-/-)

value: Fetal liver


title: CD11b+Gr1+ cell sample_4 (derived from IL17RC Knock out mouse)


title: TEL-AML1-SNP_#77


title: Fetal liver HSCs/progenitors (Hmga2+/+), biological replicate 3

description: Gene expression data from wild-type E14.5 fetal liver HSCs/progenitors

source_name: E14.5 fetal liver Lin-Sca1+cKit+ (Hmga2+/+)


title: Adult bone marrow HSCs/progenitors (Hmga2+/+), biological replicate 1


title: Fetal liver HSCs/progenitors (Hmga2+/+), biological replicate 2


title: CD11b+Gr1+ cell sample_3 (derived from IL17RC Kock out mouse)


title: TEL-AML1-SNP_#23


title: CD11b+Gr1+ cell sample_1 (derived from IL17RC Knock out mouse)


title: CD11b+Gr1+ cell sample_5 (derived from wild type mouse)


title: TEL-AML1-SNP_#05


title: CD11b+Gr1+ cell sample_2 (derived from wild type mouse)


title: CD11b+Gr1+ cell sample_3 (derived from wild type mouse)


title: TEL-AML1-SNP_#88


title: TEL-AML1-SNP_#14


title: TEL-AML1-SNP_#17


title: Fetal liver HSCs/progenitors (Hmga2+/+), biological replicate 1


title: CD11b+Gr1+ cell sample_4 (derived from wild type mouse)


title: Fetal liver HSCs/progenitors (Hmga2-/-), biological replicate 2


title: TEL-AML1-SNP_#18


title: CD11b+Gr1+ cell sample_1 (derived from wild type mouse)


title: M182S1 [RNA expression]

city: Quebec City

first: Frederic

last: Raymond

state: Quebec

address: 2440 Bd Hochelaga Suite 1710

department: École de nutrition

institute: Université Laval

hyb_protocol: The labeled and purified probes from L. donovani NFV-resistant and sensitive parasites were mixed with 200 μg/ml salmon sperm DNA (Agilent Technologies), 200 μg/ml yeast tRNA (Sigma-Aldrich, St-Louis, MO), 1X blocking agent buffer (Agilent Technologies) and 1 X hybridization buffer (Agilent Technologies). Mixed probes were denatured for 3 min at 95 ˚C followed by incubation at 37 ˚C for 30 minutes. Combined labeled probes were applied on the array under a lifterslip.  Hybridization was performed for 24 h at 65 ˚C using a hybridization oven. Slides were washed 5 min at room temperature in 0.5X SSC, 0.005% Triton-X102 with gentle agitation and subsequently washed 5 min in prewarmed 0.1X SSC, 0.005% Triton-X102 at room temperature with occasional stirring.

scan_protocol: The G2565CA microarray scanner (Agilent Technologies) was used to detect the fluorescent signal from microarray slides at a 5 μm resolution as previously described (Leprohon et al. 2009).

data_processing: GenePix Pro 6.0 software image analysis (Axon Instruments, Union City, CA) was used to quantify the fluorescence signal intensities of the microarray. Three different RNA or DNA preparations from Ld9518 NFV-resistant or sensitive amastigotes were analyzed including dye-swaps. Normalization and statistical analyses of microarray data were performed on R 2.2.1 software using the LIMMA (Linear models for microarray data) 2.7.3 package as previously described (Smyth and Speed 2003; Smyth 2004; Smyth et al. 2005). Background corrections were performed using the Edwards methods; the within array normalization was achieved by loss and between array normalization by the quantiles of A methods for each array (Yang et al. 2003). Multiple testing corrections were obtained using the false discovery rate method with a threshold p value of 0.05. Only stastistically significant genes with an absolute log ratio greater than 0.58 (log2 1.5) were considered as differentially expressed. GeneSpring GX 3.1 software was used for chromosome by chromosome analysis. Final results obtained after statistical analysis of all replicates are available on Series records [final_results.txt].

organism: Leishmania donovani

source_name: Wild-type

label_protocol: For each probe, 7 μg of RNA were converted to aminoallyl-dUTP incorporated cDNA using random hexamers (Roche Applied Science) and the Superscript III RNase H Reverse Transcriptase (Invitrogen) according to manufacturer’s recommendations. Unincorporated aminoallyl-dUTPs were removed from the labeled cDNA using ArrayIt columns. Thereafter, aminoallyl-dUTP incorporated cDNA were coupled to Alexa Fluor 555 or Alexa Fluor 647 (Invitrogen) according to manufacturer’s recommendations. Fluorescent cDNA probes were purified with ArrayIt columns.

growth_protocol: Axenically grown amastigotes of L. donovani field strain 9518 (Ld 9518) were maintained at 37 °C with 5% CO2 by weekly sub-passages in MAA/20 medium pH 5.6 in 25-cm2 flasks. MAA/20 consists of modified medium 199 (Gibco, Life Technologies, Burlington, ON, Canada) with Hank's salts, supplemented with 0.5% soybean trypto-casein (Pasteur Diagnostics, Marne la Coquette, France), 15 mM D glucose, 5 mM L-glutamine, 4 mM NaHCO3, 0.023 mM bovine hemin and 25 mM HEPES at a final pH of 5.6 and supplemented with 20% of fetal bovine serum (FBS). These axenic amastigotes show morphological, biochemical and biological characteristics similar to those of amastigotes isolated in vivo.

extract_protocol: Total RNA was isolated from 10exp8 amastigotes during the mid-log phase using the Illustra RNA Spin Mini kit (GE Healthcare) as described by the manufacturer. The RNA preparation was treated with TURBO DNase (Ambion, Austin, TX) to avoid any genomic DNA contamination. The quality and quantity of the RNA were measured using RNA 6000 Nano Assay chips on a Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Axenically grown amastigotes of L. donovani Ld 9518 were selected for NFV resistance as previously described (Kumar et al. 2010). Parasites displaying a resistance phenotype were maintained under a constant drug pressure (i.e. 25 µM) throughout our entire experimental procedures.

tag: strain background

value: NFV sensitive wild-type

value: amastigotes

source_name: Mutant 2

value: NFV resistant mutant


title: M182S2 [RNA expression]

source_name: Mutant 3


title: M181S2 [CGH]

source_name: Wild-type 2

label_protocol: For each probe 8 μg of digested genomic DNA were converted to fluorescently labeled DNA using Cy5- or Cy3- dCTP (Amersham, GE Healthcare, Piscataway, NJ), dNTP (Roche Applied Science, Laval, QC, Canada), random hexamers (Roche Applied Science) and the exo- Klenow DNA polymerase (NEB, Ipswich, MA). Fluorescent probes were then purified with ArrayIt coloumns (TeleChem International, Sunnyvale, CA).

extract_protocol: Genomic DNA was prepared from 10exp8 amastigotes using the DNAzol (Invitrogen, Life Technologies) according to manufacturer’s instructions. Genomic DNA was then sheared by passing the DNA preparation successively through 22G1 and 27G1/2 needles (Becton Dickinson, Franklin Lakes, NJ).  Fragmented DNA was then double digested with PvuII and MseI restriction enzymes. Digested and fragmented DNA was further purified using phenol-chloroform, followed by ethanol precipitation.


title: M182S3 [RNA expression]

source_name: Mutant

source_name: Wild-type 3


title: M181S3 [CGH]

source_name: Mutant 1


title: TEL-AML1-SNP_#20

source_name: ALL Blast cells, MspI representation of genomic DNA

value: tumor cells obtained at diagnosis in childhood ALL with ETV6-RUNX1 rearrangement


title: TEL-AML1-SNP_#27


title: TEL-AML1-SNP_#03


title: M181S1 [CGH]

source_name: Wild-type 1


title: Fetal liver HSCs/progenitors (Hmga2-/-), biological replicate 1


title: TEL-AML1-SNP_#19


title: Other-SNP_#116

value: B-precursor ALL with miscellaneous karyotype


title: TEL-AML1-SNP_#43


title: 14092692 - vcs Repet 1 vs Col-0 Repet 1

status: Public on Jun 26 2013

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: What are the endogenous RNA substrates co-regulated by RQC and PTGS pathways?

hyb_protocol: Col-0 Repet 1 Cy5 / vcs Repet 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

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

organism: Arabidopsis thaliana

source_name: Col-0 Repet 1

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

growth_protocol: aerial - Media=S-Medium Bouturage (Douchefa Biochemie) hygrometry=60%  Temperature=18C  Light=16 hours

extract_protocol: Col-0 Repet 1:20ug. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

tag: ecotype

value: columbia

value: wild type (control)

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

source_name: vcs Repet 1

extract_protocol: vcs Repet 1:10ug. (Qiagen_RNeasy.pdf)

value: mutant (vcs sail_1257h12)


title: 14092693 - Col-0 Repet 1 vs vcs Repet 1

hyb_protocol: vcs Repet 1 Cy5 / Col-0 Repet 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: 14092237 - Col-0 Repet 3  vs 35S:RTL2m 6.104 Repet 1

hyb_protocol: 35S:RTL2m 6.104 Repet 1 Cy5 / Col-0 Repet 3  Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 35S:RTL2m 6.104 Repet 1

extract_protocol: 35S:RTL2m 6.104 Repet 1:10ug. (Qiagen_RNeasy.pdf)

value: mutant (35s:RTL2m 6.104)

source_name: Col-0 Repet 3

extract_protocol: Col-0 Repet 3:20ug. (Qiagen_RNeasy.pdf)


title: 14092651 - xrn3 GABI Repet 1 vs Col-0 Repet 1

hyb_protocol: Col-0 Repet 1 Cy5 / xrn3 GABI Repet 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: xrn3 GABI Repet 1

extract_protocol: xrn3 GABI Repet 1:10ug. (Qiagen_RNeasy.pdf)

value: mutant (xrn3 gabi_417d11)


title: 14092685 - xrn4-6 Repet 1 vs Col-0 Repet 1

hyb_protocol: Col-0 Repet 1 Cy5 / xrn4-6 Repet 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: xrn4-6 Repet 1

extract_protocol: xrn4-6 Repet 1:10ug. (Qiagen_RNeasy.pdf)

value: mutant (xrn4-6 salk014209)


title: 14090083 - 35S:RTL2m 6.104 Repet 2 vs Col-0 Repet 4

hyb_protocol: Col-0 Repet 4 Cy5 / 35S:RTL2m 6.104 Repet 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col-0 Repet 4

extract_protocol: Col-0 Repet 4:20ug. (Qiagen_RNeasy.pdf)

source_name: 35S:RTL2m 6.104 Repet 2

extract_protocol: 35S:RTL2m 6.104 Repet 2:10ug. (Qiagen_RNeasy.pdf)


title: 14090055 - Col-0 Repet 4 vs 35S:RTL2m 6.104 Repet 2

hyb_protocol: 35S:RTL2m 6.104 Repet 2 Cy5 / Col-0 Repet 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: 14092691 - Col-0 Repet 1 vs xrn4 SAIL Repet 1

hyb_protocol: xrn4 SAIL Repet 1 Cy5 / Col-0 Repet 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: xrn4 SAIL Repet 1

extract_protocol: xrn4 SAIL Repet 1:10ug. (Qiagen_RNeasy.pdf)

value: mutant (xrn4 sail)


title: 14092645 - Col-0 Repet 1 vs xrn2-1 Repet 1

hyb_protocol: xrn2-1 Repet 1 Cy5 / Col-0 Repet 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: xrn2-1 Repet 1

extract_protocol: xrn2-1 Repet 1:10ug. (Qiagen_RNeasy.pdf)

value: mutant (xrn2-1 salk_041148)


title: 14092242 - xrn4-6 Repet 2 vs Col-0 Repet 2

hyb_protocol: Col-0 Repet 2 Cy5 / xrn4-6 Repet 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col-0 Repet 2

extract_protocol: Col-0 Repet 2:20ug. (Qiagen_RNeasy.pdf)

source_name: xrn4-6 Repet 2

extract_protocol: xrn4-6 Repet 2:10ug. (Qiagen_RNeasy.pdf)


title: 14092644 - xrn2-1 Repet 1 vs Col-0 Repet 1

hyb_protocol: Col-0 Repet 1 Cy5 / xrn2-1 Repet 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: 14092686 - Col-0 Repet 1 vs xrn4-6 Repet 1

hyb_protocol: xrn4-6 Repet 1 Cy5 / Col-0 Repet 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: 14092652 - Col-0 Repet 1 vs xrn3 GABI Repet 1

hyb_protocol: xrn3 GABI Repet 1 Cy5 / Col-0 Repet 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: 14092241 - Col-0 Repet 2 vs xrn3 GABI Repet 2

hyb_protocol: xrn3 GABI Repet 2 Cy5 / Col-0 Repet 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: xrn3 GABI Repet 2

extract_protocol: xrn3 GABI Repet 2:10ug. (Qiagen_RNeasy.pdf)


title: 14092687 - xrn4 SAIL Repet 1 vs Col-0 Repet 1

hyb_protocol: Col-0 Repet 1 Cy5 / xrn4 SAIL Repet 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: 14092238 - 35S:RTL2m 6.104 Repet 1 vs Col-0 Repet 3

hyb_protocol: Col-0 Repet 3  Cy5 / 35S:RTL2m 6.104 Repet 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: TEL-AML1-SNP_#38

hyb_protocol: See Roche NimbleGen website and Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319. for details

extract_protocol: Representation of the genome generated by digestion with either MspI or HpaII and amplification by ligation-mediated PCR according to the HELP protocol (See B. Khulan, et al. Genome Res. 2006 Aug;16(8):1046-55)

value: ALL Blast cells

source_name: ALL Blast cells, HpaII representation of genomic DNA


title: 14092234 - Col-0 Repet 4 vs 35S:RTL3.3.9 Repet 2

hyb_protocol: 35S:RTL3.3.9 Repet 2 Cy5 / Col-0 Repet 4 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 35S:RTL3.3.9 Repet 2

extract_protocol: 35S:RTL3.3.9 Repet 2:10ug. (Qiagen_RNeasy.pdf)

value: mutant (35s:RTL3.3.9)


title: CD11b+Gr1- cell sample_1 (derived from wild type mouse)

hyb_protocol: Agilent In Situ Hybridization Kit Plus was used where Cy-dye labeled control and test samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, the arrays were washed twice, dried and then scanned.

extract_protocol: Total RNA was isolated using Qiagen's RNAeasy kit following the manufacturer's instructions.  RNA quality was verified by running samples on an Agilent Bioanalyzer 2100.

value: wild type

source_name: Universal mouse reference (UMR) from Stratagene

value: pooled mouse reference RNA


title: 14092243 - Col-0 Repet 2 vs xrn4-6 Repet 2

hyb_protocol: xrn4-6 Repet 2 Cy5 / Col-0 Repet 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: 14090106 - Col-0 Repet 4 vs 35S:RTL1 Repet 2

hyb_protocol: 35S:RTL1 Repet 2 Cy5 / Col-0 Repet 4 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 35S:RTL1 Repet 2

extract_protocol: 35S:RTL1 Repet 2:10ug. (Qiagen_RNeasy.pdf)

value: mutant (35s:RTL1)


title: 14092240 - xrn3 GABI Repet 2 vs Col-0 Repet 2

hyb_protocol: Col-0 Repet 2 Cy5 / xrn3 GABI Repet 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: 14092648 - xrn3-3 Repet 1 vs Col-0 Repet 1

hyb_protocol: Col-0 Repet 1 Cy5 / xrn3-3 Repet 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: Col-0 Repet 1

extract_protocol: Col-0 Repet 1:20ug. (Qiagen_RNeasy.pdf)

source_name: xrn3-3 Repet 1

extract_protocol: xrn3-3 Repet 1:10ug. (Qiagen_RNeasy.pdf)

value: mutant (xrn3-3 sail1172c07)


title: 14092650 - Col-0 Repet 1 vs xrn3-3 Repet 1

hyb_protocol: xrn3-3 Repet 1 Cy5 / Col-0 Repet 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: 14092236 - 35S:RTL3.3.9 Repet 2 vs Col-0 Repet 4

hyb_protocol: Col-0 Repet 4 Cy5 / 35S:RTL3.3.9 Repet 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: 14090063 - Col-0 Repet 3  vs 35S:RTL1 Repet 1

hyb_protocol: 35S:RTL1 Repet 1 Cy5 / Col-0 Repet 3  Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 35S:RTL1 Repet 1

extract_protocol: 35S:RTL1 Repet 1:10ug. (Qiagen_RNeasy.pdf)


title: 14090107 - 35S:RTL1 Repet 2 vs Col-0 Repet 4

hyb_protocol: Col-0 Repet 4 Cy5 / 35S:RTL1 Repet 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: 14090069 - Col-0 Repet 3  vs 35S:RTL3.3.9 Repet 1

hyb_protocol: 35S:RTL3.3.9 Repet 1 Cy5 / Col-0 Repet 3  Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 35S:RTL3.3.9 Repet 1

extract_protocol: 35S:RTL3.3.9 Repet 1:10ug. (Qiagen_RNeasy.pdf)

source_name: Col-0 Repet 3

extract_protocol: Col-0 Repet 3:20ug. (Qiagen_RNeasy.pdf)


title: 14090104 - 35S:RTL3.3.9 Repet 1 vs Col-0 Repet 3

hyb_protocol: Col-0 Repet 3  Cy5 / 35S:RTL3.3.9 Repet 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: 14090064 - 35S:RTL1 Repet 1 vs Col-0 Repet 3

hyb_protocol: Col-0 Repet 3  Cy5 / 35S:RTL1 Repet 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: 14089828 - Col-0 Repet 1 vs 35S:RTL2.30.1.41 Repet 1

hyb_protocol: 35S:RTL2.30.1.41 Repet 1 Cy5 / Col-0 Repet 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 35S:RTL2.30.1.41 Repet 1:10ug. (Qiagen_RNeasy.pdf)


title: 14092247 - Col-0 Repet 2 vs xrn4 SAIL Repet 2

hyb_protocol: xrn4 SAIL Repet 2 Cy5 / Col-0 Repet 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: xrn4 SAIL Repet 2

extract_protocol: xrn4 SAIL Repet 2:10ug. (Qiagen_RNeasy.pdf)


title: 14089827 - 35S:RTL2.30.1.41 Repet 1 vs Col-0 Repet 1

hyb_protocol: Col-0 Repet 1 Cy5 / 35S:RTL2.30.1.41 Repet 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: 14089823 - Col-0 Repet 1 vs dcl-4-1 Repet 1

hyb_protocol: dcl-4-1 Repet 1 Cy5 / Col-0 Repet 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: dcl-4-1 Repet 1

extract_protocol: dcl-4-1 Repet 1:10ug. (Qiagen_RNeasy.pdf)


title: 14089824 - 35S:RTL2.11.1.18 Repet 1 vs Col-0 Repet 1

hyb_protocol: Col-0 Repet 1 Cy5 / 35S:RTL2.11.1.18 Repet 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 35S:RTL2.11.1.18 Repet 1:10ug. (Qiagen_RNeasy.pdf)


title: 14089822 - dcl-4-1 Repet 1 vs Col-0 Repet 1

hyb_protocol: Col-0 Repet 1 Cy5 / dcl-4-1 Repet 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: 14054617 - xrn4 SAIL Repet 2 vs Col-0 Repet 2

hyb_protocol: Col-0 Repet 2 Cy5 / xrn4 SAIL Repet 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: 14089820 - Col-0 Repet 1 vs cpb80 Repet 1

hyb_protocol: cpb80 Repet 1 Cy5 / Col-0 Repet 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: cpb80 Repet 1

extract_protocol: cpb80 Repet 1:10ug. (Qiagen_RNeasy.pdf)

value: mutant (cbp80 sail_1227_e07)


title: 14089826 - Col-0 Repet 1 vs 35S:RTL2.11.1.18 Repet 1

hyb_protocol: 35S:RTL2.11.1.18 Repet 1 Cy5 / Col-0 Repet 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.