title: 739BLV + LPS

status: Public on Oct 16 2008

city: Beltsville

first: Robert

last: Li

address: Barc East

department: Animal & Natural Resources Institute

institute: USDA

description: Peripheral Blood Mononuclear Cells from BLV positive Cattle treated with LPS in vitro for 2h

hyb_protocol: The microarrays were prehybridized with 1 MES hybridization buffer (100 mM 2-morpholinoethanesulfonic acid, 1.0 M Na, 20 mM EDTA, 0.01% Tween 20), 40 g of herring sperm DNA, and 200 g of acetylated bovine serum albumin (BSA) at 45°C for 15 min followed by hybridization with 10 g of denatured and fragmented cRNA per microarray at 45°C for 16–20 h with constant rotation. After hybridization, the microarrays were immediately washed extensively with nonstringent buffer (6 SSPE, 0.01% Tween 20) at room temperature followed by a stringent wash (100 mM MES salt and free acid solution, 0.1 M Na, 0.01% Tween 20) at 45°C. After the final rinse with the nonstringent buffer, the microarrays were stained with 1 stain buffer (100 mM MES, 1 M Na, 0.05% Tween 20, 50 mg/ml BSA, and 1 mg/ml Cy3-streptavidin) at room temperature for 25 min. The stain buffer was removed, and the microarrays were rinsed once more with nonstringent buffer. The microarrays were immediately dried under a stream of argon gas and scanned using an Axon GenePix 4000B scanner (Molecular Devices, Union City, CA) at 5-m resolution.

scan_protocol: Scanned using an Axon GenePix 4000B scanner (Molecular Devices, Union City, CA) at 5-m resolution.

data_processing: Quantile Normalization method

source_name: Bovine Peripheral Blood Mononuclear Cells Stimulated by LPS (739 BLV+)

label_protocol: Biotin-labeled cRNA was generated in a two-step procedure. Initially, first-strand cDNAs were synthesized from 4.0 g of total RNA using 1.0 unit of SuperScript II RT (Invitrogen, Carlsbad, CA) in the presence of 100 pmol T7 promoter Oligo dT primer. After secondstrand synthesis, the DNA was purified with a DNA Clean and Concentrator-5 kit (Zymo Research, Orange, CA). The purified double- stranded cDNA was transcribed into cRNA using the MEGAscript in vitro transcription kit (Ambion). The in vitro transcription reaction was carried out in a total volume of 23.0 l consisting of 3.0 l of double-stranded cDNA, 2.3 l of 10 Ambion reaction buffer, 2.3 l of 10 Ambion T7 enzyme mix, and 15.4 l of NTP labeling mix (7.5 mM ATP, 7.5 mM GTP, 5.625 mM UTP, 5.625 mM CTP, 1.875 mM biotin-16-UTP, and 1.875 mM biotin-11-CTP). The in vitro transcription reaction was incubated at 37°C for [1]16 h in a thermocycler. The cRNA was purified with an RNeasy Mini kit (Qiagen). Generally, 40–60 g of cRNA were synthesized using 4.0 g of input total RNA. The size range of the cRNA, expected to be between 300 and 3,000 bp with the maximum intensity centered at least 1,000 bp, was verified by Agilent Bioanalyzer analysis. The biotinylated cRNA was fragmented to 50-200 bp.

extract_protocol: Trizol followed by Qiagen RNeasy

tag: Beef cattle between 6 and 10 years old


title: 722BLV + PBS

type: RNA

middle: W

state: MD

country: USA

description: Peripheral Bllod Mononuclear Cells from BLV positive cattle treated with PBS in vitro for 2h

data_processing: quantile normalization method

molecule: total RNA

organism: Bos taurus

source_name: Bovine Peripheral Blood Mononuclear Cells Stimulated by PBS (722BLV-)

tag: beef cattle (female) between 6 to 10 years old


title: 717BLV + PBS

description: Peripheral Blood Mononuclear Cells from BLV positive Cattle treated with PBS in vitro for 2h

source_name: Bovine Peripheral Blood Mononuclear Cells Stimulated by PBS (717 BLV-)

tag: Beef cattle (female) between 6 and 10 years old


title: Decapped mRNAs during Arabidopsis Early Flower Development - 5 day, set1

status: Public on Oct 10 2008

type: mixed

city: Pasadena

first: Yuling

last: Jiao

state: CA

address: 1200 E California Blvd

department: Biology

institute: California Institute of Technology

description: Plants were grown on a soil:vermiculite:perlite mixture under constant illumination at 20°C. Immediately after the onset of bolting, the inflorescences of 35S:AP1-GR ap1 cal plants were treated with a solution containing 1 μM dexamethasone (Sigma-Aldrich, St. Louis, MO, USA), 0.01% (v/v) ethanol, and 0.015% (v/v) Silwet L-77. For each time point, tissue from ~25 plants was collected using jewelers forceps. Tissue was removed as close to the surface of the inflorescence as possible to ensure an enrichment of meristematic cells.

hyb_protocol: Dye-labeled antisense RNA was hybridized to microarrays using a MAUI hybridization system (BioMicro Systems, Salt Lake City, UT, USA) as previously described (Wellmer et al. (2006) PLoS Genetics 2, e117). Specifically, hybridizations were done as follows: dye-labeled antisense RNA preparations were dried down and the resulting pellets were re-suspended in 5 ul 10 mM EDTA and 45 ul SlideHyb Buffer #1 (Ambion, Austin, Texas, United States) and hybridized for 14 h to microarrays at 48C using a MAUI hybridization system (BioMicro Systems, Salt Lake City, Utah, United States) according to the manufacturer's instructions.

scan_protocol: Microarrays were scanned and the data acquired with an Axon GenePix 4200A scanner using GenePix v5.0 analysis software.

data_processing: Data were processed in eCADS (Dabney and Storey (2007) Genome Biol. 8, R44).

molecule: other

organism: Arabidopsis thaliana

source_name: decapped mRNA from early developing flower tissues

extract_protocol: Decapped mRNA was isolated from poly(A)+ mRNA using a modified RLM-RACE protocol.

tag: Material was derived from inflorescences of synchronized 35S:AP1-GR ap1 cal plants.

molecule: polyA RNA

source_name: total mRNA from early developing flower tissues

label_protocol: protocol Dye-labeled antisense RNA was previously described (Wellmer et al. (2006) PLoS Genetics 2, e117). In brief, first and second strand cDNA was synthesized using a poly(A)-primer with a T7 promoter sequence. Then, in vitro transcription was performed using the Megascript T7 kit (Ambion, Austin, TX). For the oligonucleotide array, dye molecules were coupled to the amplified RNA, and the dye-labeled RNA was fragmented before hybridization.

extract_protocol: PolyA RNA was isolated using the Micro-FastTrack 2.0 mRNA isolation kit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.


title: 731BLV + PBS

source_name: Bovine Peripheral Blood Mononuclear Cells Stimulated by PBS (731BLV-)

tag: Beef Cattle (female) between 6 and 10 years old


title: 708BLV + LPS

source_name: Bovine Peripheral Blood Mononuclear Cells Stimulated by LPS (708 BLV + **)


title: Decapped mRNAs during Arabidopsis Early Flower Development - 4 day, set3

label_protocol: In brief, first and second strand cDNA was synthesized using a poly(A)-primer with a T7 promoter sequence. Then, in vitro transcription was performed using the Megascript T7 kit (Ambion, Austin, TX). For the oligonucleotide array, dye molecules were coupled to the amplified RNA, and the dye-labeled RNA was fragmented before hybridization.


title: zSP2

city: Shinjuku-ku

first: Isao

last: Kobayashi

state: Tokyo

address: 35 Shinanoma-chi

department: Cell Differentiation

country: Japan

institute: Keio University

description: Lymphoid cells (FS-low, SS-low) from zebrafish kidney were subdivided into the SP and MP population (referred to as "zSP" and "zMP") based on the Hoechst fluorescence intensity.

hyb_protocol: Following fragmentation, 10 microg of cRNA was hybridized for 16 hr at 45C on GeneChip Zebrafish Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Expression values were calculated by RMA algorithm using the affy package of Bioconductor (http://www.bioconductor.org/).

label: Biotin

organism: Danio rerio

source_name: Adult zebrafish kidney

label_protocol: Biotinylated cRNA was generated by 2 round of in vitro transcription (IVT) using MessageAmp II aRNA Amplification Kit (Applyied Biosystems).

extract_protocol: Cells were sorted into lysis buffer directly, and total RNAs were extracted using Absolutely RNA Nanoprep Kit (Stratagene) according to manufacturer's instructions.

tag: Wild type


title: 723BLV + LPS

source_name: Bovine Peripheral Blood Mononuclear Cells Stimulated by LPS (723 BLV+)


title: 744BLV + PBS

description: Peripheral Blood Mononuclear Cells from BLV Positive Cattle treated with PBS in vitro for 2h

data_processing: Quantile normalization method

source_name: Bovine Peripheral Blood Mononuclear Cells Stimulated by PBS (744BLV-)

tag: Beef cattle (female) between 6 to 10 years old


title: zSP1


title: Decapped mRNAs during Arabidopsis Early Flower Development - 5 day, set3


title: 742BLV + PBS

source_name: Bovine Peripheral Blood Mononuclear Cells Stimulated by PBS (742 BLV-)


title: Decapped mRNAs during Arabidopsis Early Flower Development - 5 day, set2


title: Decapped mRNAs during Arabidopsis Early Flower Development - 4 day, set2


title: Decapped mRNAs during Arabidopsis Early Flower Development - 3 day, set1


title: Decapped mRNAs during Arabidopsis Early Flower Development - 4 day, set4


title: 741BLV + LPS

source_name: Bovine Peripheral Blood Mononuclear Cells Stimulated by LPS (741 BLV+)


title: Decapped mRNAs during Arabidopsis Early Flower Development - 3 day, set3


title: zMP2


title: Decapped mRNAs during Arabidopsis Early Flower Development - 3 day, set2


title: 708BLV + LPS

source_name: Bovine Peripheral Blood Mononuclear Cells Stimulated by LPS (708 BLV+)


title: Decapped mRNAs during Arabidopsis Early Flower Development - 3 day, set4


title: Decapped mRNAs during Arabidopsis Early Flower Development - 2 day, set4


title: Decapped mRNAs during Arabidopsis Early Flower Development - 5 day, set4


title: zMP1


title: Decapped mRNAs during Arabidopsis Early Flower Development - 4 day, set1


title: Decapped mRNAs during Arabidopsis Early Flower Development - 2 day, set2


title: Decapped mRNAs during Arabidopsis Early Flower Development - 2 day, set1


title: Decapped mRNAs during Arabidopsis Early Flower Development - 1 day, set1


title: Decapped mRNAs during Arabidopsis Early Flower Development - 1 day, set3


title: Decapped mRNAs during Arabidopsis Early Flower Development - 2 day, set3


title: Decapped mRNAs during Arabidopsis Early Flower Development - 0 day, set4


title: Decapped mRNAs during Arabidopsis Early Flower Development - 1 day, set4


title: liver_restricted_9076_d-14

status: Public on Oct 01 2008

first: Erin

middle: E

last: Connor

address: 10300 Baltimore Avenue

department: Animal and Natural Resources Institute

institute: USDA-ARS, BARC

description: microarray hybridization was performed in two separate batches. Therefore, principal component analysis was performed to inspect overall variation, and the largest component of variation segregated the samples into two distinct groups corresponding to the hybridization batch of the samples. This technical artifact was minimized by adjusting the within batch median of each gene to zero.

hyb_protocol: Single channel hybridization according to NimbleGen

scan_protocol: at 5-uM resolution

source_name: liver biopsy, restricted, day -14

label_protocol: Incorporation according to NimbleGen

growth_protocol: Twelve Black Angus steers (Wye cross) averaging 211+/-3 kg body weight and 248+/-5 d of age were used in the study. Animals were fed a total mixed ration of 88% corn silage and 12% soybean meal, supplemented with mineral mix (Mag Choice, Renaissance Nutrition, Inc., Roaring Spring, PA) throughout the experimental period (20 wks). The mean (+/-SE) dry matter percentage of the diet was 33.8 (+/-0.2). Mean (+/-SE) analytical values (dry matter basis) were 1.07 (+/-0.01) Mcal/kg ME gain, 13.7 (+/-0.2)% CP, 33.6 (+/-0.3)% NDF, 21.5(+/-0.4)% ADF, 0.50 (+/-.0.01)% Ca and 0.40 (+/-0.01)% P.

extract_protocol: Total RNA was isolated from liver samples using TRIZOL Reagent (Invitrogen Corp., Carlsbad, CA). Samples were DNase-treated using the TURBO DNA-free kit (Ambion, Inc., Austin, TX) according to manufacturer's instructions, followed by column purification using the RNeasy Mini Kit (Qiagen, Valencia, CA).

treatment_protocol: Steers were assigned randomly to one of two treatment groups, control or feed-restricted, and housed indoors in individual pens. Steers were acclimated to their pens for 5 d prior to starting the experimental treatments. Feed was offered once daily between 0630 and 0930 and orts from the previous day's feeding were collected and weighed to estimate actual intake. Control animals were fed ad libitum throughout the 20-wk experimental period. Feed-restricted steers were offered 60-70% of intake of control animals for 12 wks to target a limited rate of gain of approximately 0.5 kg/d. Restricted steers were then fed ad libitum for the remaining 8 wks of the experiment (realimentation period). During the first 3 d of realimentation, feed offered to both treatment groups was divided into two equal rations to gradually adjust restricted animals to full intake. Water was offered ad libitum throughout the experimental period. Approximately 200 mg of liver tissue was collected from each steer by needle biopsy using a Tru-Cut biopsy needle at -14, +1, +14 d relative to realimentation. Liver samples were immediately frozen in liquid nitrogen and stored at -80C until RNA isolation.

tag: Black Angus steer (Wye cross); liver biopsy, day -14 relative to realimentation


title: Decapped mRNAs during Arabidopsis Early Flower Development - 0 day, set3


title: liver_restricted_8973_d+1

source_name: liver biopsy, restricted, day +1

tag: Black Angus steer (Wye cross); liver biopsy, day +1 relative to realimentation


title: Decapped mRNAs during Arabidopsis Early Flower Development - 0 day, set2


title: liver_control_9028_d-14

source_name: liver biopsy, control, day -14


title: liver_control_9062_d-14


title: Decapped mRNAs during Arabidopsis Early Flower Development - 0 day, set1


title: liver_control_9036_d+1

source_name: liver biopsy, control, day +1


title: liver_restricted_8955_d-14


title: liver_restricted_8973_d+14

source_name: liver biopsy, restricted, day +14

tag: Black Angus steer (Wye cross); liver biopsy, day +14 relative to realimentation


title: liver_control_9062_d+14

source_name: liver biopsy, control, day +14


title: wild with calcium treatment vs crzA mutant with calcium treatment

status: Public on Oct 03 2008

city: Sendai

first: Daisuke

last: Hagiwara

state: Miyagi

address: 6-6-10 Aoba Aramaki

department: New Industry Creation Hatchery Center

institute: Tohoku university

description: Gene expression was considered to be significantly higher or lower whenever the spot intensity changed by at least 2-fold in all four replicates.

hyb_protocol: DNA microarray slides were hybridized in a Slide Booster (Advalytix) at 42ºC overnight (16-18 h). Then, the slides were washed twice in wash buffers (first in a buffer containing 2×SSC and 0.1 % SDS for 15 min, then in a buffer containing 1×SSC and 0.1% SDS for 5 min at room temperature. Finally, the slides were rinsed with 0.2×SSC at room temperature for 5 min and dried by centrifugation.

scan_protocol: The slides were scanned using GenePix4000B scanner (Molecular Devices).

data_processing: The resulting TIFF images were imported into GenePix Pro and fluorescent intensity of spots were calculated for each of the Cy3 and Cy5 channels. Global normalization was applied to  analysis. Following normalization, spots whose Cy3 or Cy5 intensity was less than 0 were removed from the data set (the exceptional case was that intensity of the other channel was more than 100). The dye-swap replicates and in-slide replicates were subjected to all analyses. Finally, gene expression ratios (channel 2/channel 1) were calculated for each replicates.

organism: Aspergillus nidulans

source_name: wild with calcium treatment

label_protocol: Cy3- and Cy5-labeled cDNA probes were prepared using the Amersham CyScribe Post-Labelling Kit (GE Healthcare). Initially, amino allyl-dUTP (AA-dUTP) was incorporated into cDNA in a reverse transcriptase reaction, in which 1 μg mRNA was used as the template for each sample. The AAdUTP-modified cDNA samples were labeled with Cy3 or Cy5 using CyDye NHS-esters, resulting in Cy3- or Cy5-labeled cDNA probes. The Cy3 and Cy5 probes were purified using the CyScribe GFX Purification Kit (GE Healthcare) and evaporator-dried. Samples were then dissolved in 28 μL of hybridization buffer (50% formamide, 5×SSC, 0.1% SDS, 0.6 μg/μL Salmon Sperm DNA).

growth_protocol: 10 8 conidia of starains were inoculated into 100 ml of standard A. nidulans minimal media, Czapek-Dox (CD) medium (adjusted pH 6.5 with KOH) containing appropriate requirements and cultured for 18 hours in a rotated shaker (160 rpm) at 37ºC. After this, the culture was added by 3.33 ml of 1.5 M CaCl2 solution (final concentration, 50 mM) and continued to culture. After 15min, mycelia were harvested, frozen in liquid nitrogen, ground to a powder, and used for RNA preparation.

extract_protocol: Total RNA was purified using the Qiagen RNeasy plant mini kit according to the manufacturer's instructions (QIAGEN).

tag: Strain

tag: genotype

value: (biA1, pyrG89, wA3, argB2, pyroA4, argB+)

source_name: crzA mutant with calcium treatment

value: crzA mutant (BPU1)

value: (biA1, pyrG89, wA3, argB2, pyroA4, crzA::argB)


title: wild with calcium treatment vs crzA mutant with calcium treatment (dye-swap)


title: wild without calcium treatment vs wild with calcium treatment

source_name: wild without calcium treatment


title: wild without calcium treatment vs wild with calcium treatment (dye-swap)


title: liver_restricted_8955_d+14


title: liver_restricted_8955_d+1


title: liver_control_9028_d+14


title: liver_control_9028_d+1


title: liver_control_9036_d-14


title: liver_control_9036_d+14


title: liver_restricted_8973_d-14


title: liver_control_9062_d+1

hyb_protocol: single channel


title: liver_control_9070_d+14

tag: Black Angus steer (Wye cross); liver biopsy, day + 14 relative to realimentation


title: liver_restricted_9067_d+1

tag: Black Angus steer (Wye cross); liver biopsy, day + 1 relative to realimentation


title: liver_control_9070_d-14


title: liver_restricted_9076_d+1


title: liver_control_9073_d+14


title: liver_restricted_9067_d-14

tag: Black Angus steer (Wye cross); liver biopsy, day - 14 relative to realimentation


title: liver_restricted_9064_d+14


title: liver_restricted_9054_d-14


title: liver_control_9088_d-14


title: carcinomatous component

type: genomic

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description: 500 ng of the carcinomatous component of a salivary gland carcinosarcoma has been hybridized to a 4x44k oligo array

hyb_protocol: hybridizations were performed according to the manufacturer's instructions (Agilent Technologies)

scan_protocol: Microarray Scanner G2565AB (Agilent Technologies), default settings

data_processing: Spots were quantified in Feature Extraction software version 9.1 (Agilent Technologies) using default settings.

molecule: genomic DNA

organism: Homo sapiens

source_name: carcinomatous component of a carcinosarcoma

label_protocol: according to standard protocol ENZO BioArray™ CGH Labeling System (Farmingdale, NY, USA)

extract_protocol: standard phenol/chloroform extraction

tag: FFPE material, described in Vekony et al, Oral Oncology 2008 in press

tag: carcinomatous component macrodissected

source_name: reference DNA

extract_protocol: as described in Wilting et al, J Pathol, volume 209, p 220-30

tag: Pooled DNA from the blood of 10 normal male individuals


title: liver_restricted_9054_d+1


title: liver_restricted_9054_d+14


title: liver_control_9088_d+1


title: liver_control_9073_d-14

extract_protocol: Total RNA was isolated from liver samples using TRIZOL Reagent (Invitrogen Corp., Carlsbad, CA). Samples were DNase-treated using the TURBO DNA-free kit (Ambion, Inc., Austin, TX) according to manufacturer’s instructions, followed by column purification using the RNeasy Mini Kit (Qiagen, Valencia, CA).

treatment_protocol: Steers were assigned randomly to one of two treatment groups, control or feed-restricted, and housed indoors in individual pens. Steers were acclimated to their pens for 5 d prior to starting the experimental treatments. Feed was offered once daily between 0630 and 0930 and orts from the previous day’s feeding were collected and weighed to estimate actual intake. Control animals were fed ad libitum throughout the 20-wk experimental period. Feed-restricted steers were offered 60-70% of intake of control animals for 12 wks to target a limited rate of gain of approximately 0.5 kg/d. Restricted steers were then fed ad libitum for the remaining 8 wks of the experiment (realimentation period). During the first 3 d of realimentation, feed offered to both treatment groups was divided into two equal rations to gradually adjust restricted animals to full intake. Water was offered ad libitum throughout the experimental period. Approximately 200 mg of liver tissue was collected from each steer by needle biopsy using a Tru-Cut biopsy needle at -14, +1, +14 d relative to realimentation. Liver samples were immediately frozen in liquid nitrogen and stored at -80C until RNA isolation.


title: liver_restricted_9076_d+14


title: liver_restricted_9067_d+14


title: liver_restricted_9064_d-14


title: sarcomatous component

description: 500 ng of the sarcomatous component of a salivary gland carcinosarcoma has been hybridized to a 4x44k oligo array

hyb_protocol: hybridisations were performed according to the manufacturer's instructions (Agilent Technologies)

source_name: sarcomatous compartment of carcinosarcoma

tag: mesenchymal component of a salivary gland carcinosarcoma


title: liver_control_9073_d+1


title: liver_control_9070_d+1

tag: Black Angus steer (Wye cross); liver biopsy, day + 1 relative to realimentation,


title: liver_control_9088_d+14


title: liver_restricted_9064_d+1


title: VUMC_myo_carc_11 (1)

description: For preparation of the hybridization mixture 50 µl of Cy3-labeled test DNA, 50 µl of Cy5-labeled reference DNA and 100 µg Human Cot-1 DNA (Invitrogen) were mixed and precipitated using 0.1 volume of 3 M NaAc pH 5.2 and 2.5 volume of ice-cold absolute ethanol. After mixing by inversion the DNA was collected by centrifugation for 30 min at 20,000 g and 4°C, the supernatant aspirated and the pellet air-dried for approximately 5-10 min. The pellet was then dissolved in 13 µl water and 26 µl 20% SDS taking care to prevent foam formation. After incubating at room temperature for 15 min 91 µl of Master mix (14.3 % (w/v) dextran sulphate (USB), 71% (v/v) formamide (Invitrogen), 2.9 X SSC pH 7.0 (Sigma)) was added and gently mixed. The hybridization solution was then incubated at 73°C for 10 min to denature the DNA and subsequently at 37°C for 60 min to allow the Cot-1 DNA to block repetitive sequences. Hybridization and washing was done automatically using a GeneTAC/HybArray12 hybstation (Genomic Solutions / Perkin Elmer). Hybridization was for 38 h at 37°C. Subsequently slides were washed 6 cycles (flow for 10 s, hold for 20 s) with 50% (v/v) formamide, 2X SSC, 2 cycles with phosphate-buffer (0.1 M Na2HPO4/NaH2PO4, pH 8.0, 0.1% (v/v) Igepal CA630 (Sigma)), 2 cycles with 0.2 X SSC (Sigma) and 2 cycles with 0.1 X SSC. Slides were then taken out of the hybstation and briefly rinsed in 0.01 X SSC, dried by centrifugation for 3 min at 1000 g and scanned using a Microarray Scanner G2565AB (Agilent Technologies).

scan_protocol: Microarray Scanner G2505B (Agilent Technologies), default settings

source_name: myoepithelial carcinoma

label_protocol: according to standard protocol of ENZO BioArray™ CGH Labeling System (Farmingdale, NY, USA)

extract_protocol: standard phenol/chloroform procedure, described by Vekony et al, Clin Cancer Res 2007

tag: primary myoepithelial carcinoma of salivary glands, female, FFPE material

label_protocol: as CH1, CY5 instead of Cy3

tag: normal DNA pooled from the blood of ten healthy males


title: Decapped mRNAs during Arabidopsis Early Flower Development - 1 day, set2

source_name: decapped mRNA from early developing flower tissues

tag: Material was derived from inflorescences of synchronized 35S:AP1-GR ap1 cal plants.

source_name: total mRNA from early developing flower tissues


title: CLL746_DE751 (85K)

city: Cold Spring Harbor

first: Vladimir

last: Grubor

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description: This was done in colour reversal and this is the primary experiment.

hyb_protocol: Hybridizations consisted of 35 uL of hybridization solution (37% formamide, 4x SSC, 0.1%SDS, and labeled DNA). Samples were denatured in an MJ Research Tetrad (Bio-Rad, Hercules, CA) at 95 degrees C for 5 min, and then pre-annealed at 37 degrees C for no more than 30 min. The solution was then applied to the microarray and hybridized under a coverslip in an oven at 42 degrees C for 14 to 16 h. Thereafter, slides were washed 1 min in 0.2% SDS/0.2x SSC, 30 sec in 0.2x SSC, and 30 sec in 0.05x SSC. Slides were dried by centrifugation and scanned immediately.

scan_protocol: Scanned on an Axon GenePix 4000B scanner using a pixel size of 5 um. Microarrays were scanned and gridded using GenePix Pro 4.0 software (MDS Analytical Technologies, Toronto, Canada) and data were imported into S-Plus 2000 analysis software (Insightful, Seattle, WA).

data_processing: The data were normalized using a lowess curve-fitting algorithm, followed by a local normalization (previously described in Hicks et al.). After placement in genome order, the mean of log ratios was computed for color reversal experiments for each sample. Segmentation was performed on the above-described data. Segments are defined as non-overlapping, genomic regions where copy number has changed. Our segmentation method is based on the minimization of the square-sum of differences between log-ratios and means (squared deviation) over segments larger than 6 probes in size. Initially, the segmenter searches for breakpoints that might be boundaries of segments. The first known breakpoint on a given chromosome is its first probe. For a given breakpoint, a 100-probe window to its right is selected. The sum of squared deviations of the flanking probes is calculated for each probe within this window. A probe whose squared deviation value produces a local minimum with respect to its neighbors, and is below a threshold of 95% of the square deviation within a window, is accepted as a new, known breakpoint. Whenever a probe is found below the threshold in the newly defined region, the segmenter recursively breaks said region into two pieces until it cannot find any further breakpoints therein. If no breakpoints are found, the 100- probe window is shifted by half its size and this procedure continues until a chromosome end is reached. Initial segments are constructed using found breakpoints. Each segment and its neighbors are validated for significance by the Kolmogorov-Smirnov (K-S) algorithm. If the p-value of compared segments is less than 10-5, then said segment is accepted as real. If not, the segments are merged. The segmenter also reports statistics such as mean, standard deviation, and median for each segment.

source_name: PMN fraction gDNA labelled with Cyanine-5 (red).

label_protocol: Briefly, complexity-reduced representations,consisting of small (200-1200 bp) fragments were amplified by adapter-mediated PCR of genomic DNA. DNA samples (2 ug) werelabeled either with Cy5-dCTP or Cy3-dCTP using Amersham-Pharmacia MegaPrimelabeling kit (Amersham Biosciences, Piscataway, NJ), and competitively hybridized to each other on the same slide. Each sample genome was analyzed in duplicate, swappingthe Cy5 and Cy3 dyes with the control (i.e. "colour reversal")

extract_protocol: Gentra Puregene gDNA extraction kit

tag: Tissue

value: Purified PMNs

source_name: B-Cell fraction gDNA labelled with Cyanine-3(green).

label_protocol: Briefly, complexity-reduced representations,consisting of small (200-1200 bp) fragments were amplified by adapter-mediated PCR of genomic DNA. DNA samples (2 ug) were labeled either with Cy5-dCTP or Cy3-dCTP using Amersham-Pharmacia MegaPrimelabeling kit (Amersham Biosciences, Piscataway, NJ), and competitively hybridized toeach other on the same slide. Each sample genome was analyzed in duplicate, swappingthe Cy5 and Cy3 dyes with the control (i.e. "colour reversal")

value: Purified Leukaemic B-cells


title: CLL873_DE755 (85K)


title: CLL875_DE760 (85K)

source_name: B-Cell fraction gDNA labelled with Cyanine-5 (red).

source_name: PMN fraction gDNA labelled with Cyanine-3(green).


title: CLL746_DE752 (85K)


title: CLL875_DE759 (85K)


title: CLL824_LH0385 (385K)

label_protocol: Briefly, complexity-reduced representations,consisting of small (150-400 bp) fragments were amplified by adapter-mediated PCR of genomic DNA. DNA samples (2 ug) werelabeled either with Cy5-dCTP or Cy3-dCTP using Amersham-Pharmacia MegaPrimelabeling kit (Amersham Biosciences, Piscataway, NJ), and competitively hybridized to each other on the same slide. Each sample genome was analyzed in duplicate, swappingthe Cy5 and Cy3 dyes with the control (i.e. "colour reversal")

label_protocol: Briefly, complexity-reduced representations,consisting of small (150-400 bp) fragments were amplified by adapter-mediated PCR of genomic DNA. DNA samples (2 ug) were labeled either with Cy5-dCTP or Cy3-dCTP using Amersham-Pharmacia MegaPrimelabeling kit (Amersham Biosciences, Piscataway, NJ), and competitively hybridized toeach other on the same slide. Each sample genome was analyzed in duplicate, swappingthe Cy5 and Cy3 dyes with the control (i.e. "colour reversal")


title: CLL821_LH0381 (385K)


title: CLL361_LH0370 (385K)


title: CLL873_DE756 (85K)


title: CLL931_JT5441 (385K)


title: CLL361_LH0369 (385K)


title: CLL824_LH0386 (385K)


title: CLL687_KC0001 (385K)


title: CLL609_DE747 (85K)


title: CLL875_JT5439 (385K)


title: CLL821_LH0382 (385K)


title: CLL100_LH0366 (385K)


title: CLL625_JT5438 (385K)


title: CLL562_LH0373 (385K)


title: CLL875_JT5440 (385K)


title: CLL665_LH0358 (385K)


title: CLL609_DE748 (85K)


title: CLL665_LH0357 (385K)


title: CLL813_LH0361 (385K)


title: CLL931_JT5442 (385K)


title: CLL100_LH0365 (385K)


title: CLL562_LH0374 (385K)


title: CLL625_DE744 (85K)


title: CLL625_DE743 (85K)


title: CLL813_LH0362 (385K)


title: CLL452_JT5436 (385K)


title: CLL687_KC0002 (385K)


title: CLL625_JT5437 (385K)


title: CLL253_JT3264 (385K)


title: CLL283_DE739 (85K)


title: CLL283_DE740 (85K)


title: CLL280_JT3260 (385K)


title: CLL253_JT3263 (385K)


title: CLL864_DE731 (85K)


title: CLL849_DE727 (85K)


title: CLL849_DE728 (85K)


title: CLL452_JT5435 (385K)


title: CLL864_DE732 (85K)


title: P.chabaudi_HPI072_C4-258

city: San Francisco

first: Sajeev

last: Batra

institute: UCSF

description: P.chabaudi hours post infection 072 ( C4-258 )

hyb_protocol: Cy5 labeled sample was hybridized to the MEEBO array in 3x SSC at 65C 48 hours.

scan_protocol: MEEBO arrays were scanned with an Axon 4000B scanner (Axon Instruments, Union City, CA, USA) and gridded using the bundled GenePix 6.0 software.

data_processing: Spot analysis was performed with GenePix v6.0 and stored in a relational database (Acuity).

organism: Mus musculus

label_protocol: RNA extracted from the samples was amplified using Amino Allyl MessageAmp II aRNA kit from Ambion. The amplified material was then coupled to Cy5.

extract_protocol: Ambion Mouse RiboPure-Blood RNA Isolation kit

tag: Mus musculus female mice 8 weeks old C57/bl6

tag: Amplified RNA from whole blood

source_name: amplified mouse universal reference RNA (Stratagene) doped with pooled amplified sample RNA


title: CLL845_DE720 (85K)


title: CLL280_JT3259 (385K)


title: Uninfected_HPI048_C4-257

description: Uninfected hours post infection 048 ( C4-257 )

tag: amplified mouse universal reference RNA (Stratagene) doped with pooled amplified sample RNA


title: CLL845_DE719 (85K)


title: CLL582_GQ136 (385K)


title: CLL582_GQ137 (385K)


title: CLL849_GQ124 (385K)


title: CLL864_GQ128 (385K)


title: Uninfected_HPI024_C4-256

description: Uninfected hours post infection 024 ( C4-256 )


title: CLL355_GQ133 (385K)


title: CLL845_GQ121 (385K)


title: CLL280_DE707 (85K)


title: CLL355_GQ132 (385K)


title: Uninfected_HPI040_C4-246

description: Uninfected hours post infection 040 ( C4-246 )


title: CLL864_GQ129 (385K)


title: CLL845_GQ120 (385K)


title: CLL849_GQ125 (385K)


title: Uninfected_HPI032_C4-245

description: Uninfected hours post infection 032 ( C4-245 )


title: CLL280_DE708 (85K)


title: CLL377_GQ105 (385K)


title: CLL631_GQ101 (385K)


title: CLL395_GQ109 (385K)


title: CLL631_GQ100 (385K)


title: CLL395_GQ108 (385K)


title: Uninfected_HPI032_C4-244

description: Uninfected hours post infection 032 ( C4-244 )


title: CLL813_DE704 (85K)


title: CLL813_DE703 (85K)


title: P.chabaudi_HPI016_C4-242

description: P.chabaudi hours post infection 016 ( C4-242 )


title: P.chabaudi_HPI008_C4-241

description: P.chabaudi hours post infection 008 ( C4-241 )


title: CLL377_GQ104 (385K)


title: CLL972_DE976 (385K)


title: CLL957_DE971 (385K)


title: Uninfected_HPI072_C4-240

description: Uninfected hours post infection 072 ( C4-240 )


title: CLL972_DE975 (385K)


title: P.chabaudi_HPI072_C4-239

description: P.chabaudi hours post infection 072 ( C4-239 )


title: CLL955_DE964 (385K)


title: CLL956_DE968 (385K)


title: CLL678_DE699 (85K)


title: CLL955_DE963 (385K)


title: CLL678_DE700 (85K)


title: CLL957_DE972 (385K)


title: Uninfected_HPI064_C4-237

description: Uninfected hours post infection 064 ( C4-237 )


title: CLL515_DE687 (85K)


title: CLL100_DE684 (85K)


title: CLL515_DE688 (85K)


title: CLL100_DE683 (85K)


title: CLL954_DE959 (385K)


title: P.chabaudi_HPI064_C4-235

description: P.chabaudi hours post infection 064 ( C4-235 )


title: CLL956_DE967 (385K)


title: CLL562_DE679 (85K)


title: CLL947_DE947 (385K)


title: CLL937_DE932 (385K)


title: CLL948_DE952 (385K)


title: P.chabaudi_HPI064_C4-234

description: P.chabaudi hours post infection 064 ( C4-234 )


title: CLL949_DE956 (385K)


title: Uninfected_HPI064_C4-236

description: Uninfected hours post infection 064 ( C4-236 )


title: CLL939_DE935 (385K)


title: CLL562_DE680 (85K)


title: CLL954_DE960 (385K)


title: CLL948_DE951 (385K)


title: CLL937_DE931 (385K)


title: CLL936_DE927 (385K)


title: CLL939_DE936 (385K)


title: P.chabaudi_HPI056_C4-232

description: P.chabaudi hours post infection 056 ( C4-232 )


title: Uninfected_HPI056_C4-233

description: Uninfected hours post infection 056 ( C4-233 )


title: CLL824_DE675 (85K)

description: This was done in colour reversal and this is the primary experiment.


title: CLL824_DE676 (85K)


title: CLL947_DE948 (385K)


title: CLL936_DE928 (385K)


title: Uninfected_HPI048_C4-231

description: Uninfected hours post infection 048 ( C4-231 )


title: P.chabaudi_HPI048_C4-229

description: P.chabaudi hours post infection 048 ( C4-229 )


title: CLL680_DE920 (385K)


title: CLL680_DE919 (385K)


title: CLL698_DE923 (385K)


title: Uninfected_HPI040_C4-228

description: Uninfected hours post infection 040 ( C4-228 )


title: CLL821_DE672 (85K)


title: P.chabaudi_HPI040_C4-226

description: P.chabaudi hours post infection 040 ( C4-226 )


title: CLL253_DE667 (85K)


title: P.chabaudi_HPI032_C4-224

description: P.chabaudi hours post infection 032 ( C4-224 )


title: CLL949_DE955 (385K)


title: CLL698_DE924 (385K)


title: CLL253_DE668 (85K)


title: CLL821_DE671 (85K)


title: CLL816_DE663 (85K)


title: CLL463_DE912 (385K)


title: Uninfected_HPI024_C4-221

description: Uninfected hours post infection 024 ( C4-221 )


title: P.chabaudi_HPI024_C4-218

description: P.chabaudi hours post infection 024 ( C4-218 )


title: CLL816_DE664 (85K)


title: CLL361_DE660 (85K)


title: CLL584_DE916 (385K)


title: CLL237_DE908 (385K)


title: Uninfected_HPI016_C4-216

description: Uninfected hours post infection 016 ( C4-216 )


title: CLL361_DE659 (85K)


title: CLL237_DE907 (385K)


title: CLL649_DE903 (385K)


title: Uninfected_HPI008_C4-213

description: Uninfected hours post infection 008 ( C4-213 )


title: CLL649_DE904 (385K)


title: CLL665_DE632 (85K)


title: Uninfected_HPI008_C4-212

description: Uninfected hours post infection 008 ( C4-212 )


title: CLL335_DE899 (385K)


title: CLL665_DE631 (85K)


title: CLL746_DE891 (385K)


title: CLL609_DE888 (385K)


title: P.chabaudi_HPI008_C4-210

description: P.chabaudi hours post infection 008 ( C4-210 )


title: CLL922_DE884 (385K)


title: CLL920_DE879 (385K)


title: CLL609_DE887 (385K)


title: Uninfected_HPI000_C4-209

description: Uninfected hours post infection 000 ( C4-209 )


title: CLL664_DE628 (85K)


title: CLL922_DE883 (385K)


title: CLL746_DE892 (385K)


title: CLL920_DE880 (385K)


title: CLL335_DE900 (385K)


title: CLL664_DE627 (85K)


title: CLL831_DE876 (385K)


title: CLL584_DE915 (385K)


title: CLL831_DE875 (385K)


title: Uninfected_HPI000_C4-208

description: Uninfected hours post infection 000 ( C4-208 )


title: CLL611_DE623 (85K)


title: CLL444_DE872 (385K)


title: P.chabaudi_HPI000_C4-206

description: P.chabaudi hours post infection 000 ( C4-206 )


title: CLL444_DE871 (385K)


title: P.chabaudi_HPI000_C4-207

description: P.chabaudi hours post infection 000 ( C4-207 )


title: CLL321_DE867 (385K)


title: CLL611_DE624 (85K)


title: CLL321_DE619 (85K)


title: CLL463_DE911 (385K)


title: P.chabaudi_HPI032_C4-199

description: P.chabaudi hours post infection 032 ( C4-199 )


title: CLL614_DE864 (385K)

description: This was done in colour reversal and this is the primary experiment.


title: Uninfected_HPI016_C4-198

description: Uninfected hours post infection 016 ( C4-198 )


title: CLL334_DE859 (385K)


title: CLL321_DE868 (385K)


title: Uninfected_HPI072_C4-197

description: Uninfected hours post infection 072 ( C4-197 )


title: CLL687_DE595 (85K)


title: CLL921_DE855 (385K)


title: CLL321_DE620 (85K)


title: CLL873_DE851 (385K)


title: CLL189_DE584 (85K)


title: CLL614_DE863 (385K)


title: CLL334_DE860 (385K)


title: CLL873_DE852 (385K)


title: CLL189_DE583 (85K)


title: CLL921_DE856 (385K)


title: CLL283_DE848 (385K)


title: CLL687_DE596 (85K)


title: NK_cells_Mock-infected_72h_d6-130

source_name: Amplified RNA from whole blood

tag: Mus musculus female mice, 8 weeks old, strain C57/bl6

source_name: Amplified mouse universal reference RNA (Stratagene) doped with pooled amplified sample RNA


title: P.chabaudi_HPI016_C4-195

description: P.chabaudi hours post infection 016 ( C4-195 )


title: NK_cells_Mock-infected_72h_d6-131

tag: Amplified mouse universal reference RNA (Stratagene) doped with pooled amplified sample RNA


title: NK_cells_P._chabaudi-infected_72h_d6-132


title: Blood_Mock-infected_72h_d6-125


title: Control2_against_P6RG612-2 Bionta

city: Seibersdorf

first: Friederike

last: Trognitz

state: NÖ

address: Seibersdorf

department: Health & Environment

country: Austria

institute: AIT Austrian Institute of Technology GmbH

description: Biological replicate 2 out of 2

hyb_protocol: The labeled targets were mixed in equal amounts, concentrated to 20 µl and mixed with 20 µl 4x hybridization mix (GE Health Bioscience) and 40 µl of formamide. The mix was spread to the blocked microarray which was covered by a lifter slip (Erie Scientific). The hybridization was done overnight at 42°C in a hybridization chamber (Camlab; Cambridge UK). After hybridization the slides were washed in 1xSSC, 0.1% SDS for 15 min at 50°C, then with 0.1xSSC, 0.1% SDS for 10 min at room temperature and finally twice with 0.2xSSC for 5 min at room temperature.

scan_protocol: Microarray images were acquired on a Tecan LS 200 Scanner (Tecan Austria GmbH, Austria) using the AGC mode.

data_processing: Quantitation of signals was done using GenePix® Pro 6.0 software (Axon Instruments, Foster City, US, California). .

organism: Solanum tuberosum

source_name: Bionta

label_protocol: For labeling of the targets the protocol for template-switching PCR ( Petalidis et al. 2003) was applied. In brief, 500 ng of total RNA was transcribed to cDNA using the SMART cDNA synthesis kit (Takara, Clontech) in combination with 10 pmol 3'SMART CDS primer IIA (5' -AAGCAGTGGTATCAACGCAGAGTAC-T30VN-3') and 10 pm of template switching primer [5'-d(AAGCAGTGGTATCAACGCAGAGTACGC)r(GGG)-3'. For the following long distance PCR 2 µl of the cDNA were used together with 10 µl 10x Advantage 2 PCR Buffer (Takara, Clontech), 2 µl 10 mM dNTPs, 4 µl 10 pmol PCR primer (5'-AAGCAGTGGTATCAACGCAGAGT-3') and 2 µl Advantage 2 polymerase mix (Takara, Clontech) in a total volume of 100 µl following the cycle conditions described by Petalidis et al. (2003) with 21 cycles. Amplicons were cleaned using the QIAquick PCR purification system (Qiagen) and concentrations were measured using the Nanodrop photometer prior of the labeling. For the labeling the BioPrime® Array CGH Genomic Labeling System (Invitrogen) using Cy3™-dCTP or Cy35-dCTP (GE Healthcare) was applied according to the specifications of the manufacturer.

growth_protocol: Two potato cultivars, Russet Burbank and Bionta, were grown in in-vitro, pathogen free. Nodal explants were produced from full developed in vitro plants.   Two bacteria strains PsJN and P6RG6-12 were grown overnight in PBS medium. The PBS medium alone was used for control inoculation.

extract_protocol: For each treatment three plants were collected and pooled to reduce the biological variation. For each treatment the experiment was conducted two times. From the pools of each treatment RNA was isolated according to a modified method of Chang et al. (1993).  In brief, 1 g of plant material was ground to fine powder and transferred into 15 ml extraction buffer (2% CTAB, 2% PVP K 40, 100 mM Tris-HCl pH 8.0, 25 mM EDTA, 2 M NaCl, 2.67% ß-mercaptoethanol) and pre-warmed to 65°C. After thorough mixing and incubation for 10 min the homogenate was extracted twice with an equal volume of chloroform:isoamyl alcohol (24:1) by vortexing and centrifugation for 20 min at 5000 rpm. The supernatant was transferred to a fresh tube containing 15 ml 10 M LiCl and precipitated overnight at 4°C. The next day the tubes were centrifuged at 4°C for 30 min at 10000 rpm, and the pellet was dissolved in pre-warmed 700 µl SSTE buffer (1 M NaCl, 0.5 % SDS, 10 mM Tris-HCl, pH 8.0, 1 mM EDTA) and incubated for 5 minutes at 60°C. Then 700 µl chloroform-isoamylalcohol (24:1) was added and centrifuged for 10 min at room temperature. The supernatant was transferred to a fresh tube containing 1.2µl ethanol. The RNA was precipitated for 1 hour at -80°C and then centrifuged at 4°C for 30 min at 10 000 rpm. The pellet was washed with 70% ethanol and the dry pellet was re-suspended in 100 µl RNase free water

treatment_protocol: For the in vitro inoculation of explants, bacterial inoculum was prepared according to Conn et al. (1997). In brief, from an overnight culture in nutrient broth bacterial cells were collected and resuspended in PBS buffer to obtain 108 cfu/ml. Nodal explants were immersed in the bacterial solution for 15 sec and then placed in the test tubes containing MS medium (Murashige & Skoog (1962) supplemented with 0.8% agar and 1% saccarose. Control plantlets were inoculated with PBS buffer. For the gene expression experiments plants were collected after 18 days of inoculation

tag: control


title: P6RG612-1_against_control1 Bionta

description: Biological replicate 1 out of 2


title: CLL189_DE788 (385K)


title: CLL664_DE780 (385K)


title: P.chabaudi_HPI024_C4-196

description: P.chabaudi hours post infection 024 ( C4-196 )


title: Blood_P._chabaudi-infected_72h_d6-126


title: Blood_P._chabaudi-infected_72h_d6-127


title: NK_cells_P._chabaudi-infected_72h_d6-134


title: NK_cells_P._chabaudi-infected_72h_d6-133


title: CLL189_DE787 (385K)


title: CLL816_DE844 (385K)


title: NK_cells_Mock-infected_72h_d6-129


title: Blood_Mock-infected_72h_d6-124


title: CLL816_DE843 (385K)


title: CLL678_DE784 (385K)


title: Control1_against_P6RG612-1 Bionta

description: Biological replicate 2 out of 2


title: Control_2_against_PsJN-AHL2 Bionta

description: Biological replicate 2 out of 2

tag: PsJN AHLmutant treated


title: Control1_against_PsJN-AHL1 Bionta

description: Biological replicate 1 out of 2


title: Control2_against_PsJN2 Bionta

description: Biological replicate 1 out of 2

tag: PsJN


title: PsJN-AHL2_against_control2 Bionta

description: Biological replicate 2 out of 2

tag: PsJN AHLmutant


title: Control1_against_PsJN1 Bionta

description: Biological replicate 1 out of 2


title: CLL283_DE847 (385K)


title: VUMC_myo_11

description: For preparation of the hybridization mixture 50 µl of Cy3-labeled test DNA, 50 µl of Cy5-labeled reference DNA and 100 µg Human Cot-1 DNA (Invitrogen) were mixed and precipitated using 0.1 volume of 3 M NaAc pH 5.2 and 2.5 volume of ice-cold absolute ethanol. After mixing by inversion the DNA was collected by centrifugation for 30 min at 20,000 g and 4°C, the supernatant aspirated and the pellet air-dried for approximately 5-10 min. The pellet was then dissolved in 13 µl water and 26 µl 20% SDS taking care to prevent foam formation. After incubating at room temperature for 15 min 91 µl of Master mix (14.3 % (w/v) dextran sulphate (USB), 71% (v/v) formamide (Invitrogen), 2.9 X SSC pH 7.0 (Sigma)) was added and gently mixed. The hybridization solution was then incubated at 73°C for 10 min to denature the DNA and subsequently at 37°C for 60 min to allow the Cot-1 DNA to block repetitive sequences. Hybridization and washing was done automatically using a GeneTAC/HybArray12 hybstation (Genomic Solutions / Perkin Elmer). Hybridization was for 38 h at 37°C. Subsequently slides were washed 6 cycles (flow for 10 s, hold for 20 s) with 50% (v/v) formamide, 2X SSC, 2 cycles with phosphate-buffer (0.1 M Na2HPO4/NaH2PO4, pH 8.0, 0.1% (v/v) Igepal CA630 (Sigma)), 2 cycles with 0.2 X SSC (Sigma) and 2 cycles with 0.1 X SSC. Slides were then taken out of the hybstation and briefly rinsed in 0.01 X SSC, dried by centrifugation for 3 min at 1000 g and scanned using a Microarray Scanner G2565AB (Agilent Technologies).

hyb_protocol: Hybridization protocol available via www.vumc.nl/microarrays Also described in Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192 no prehyb solution used

data_processing: Spot analysis and quality control was fully automated using BlueFuse version 3.4 (BlueGnome, Cambridge, UK). Spots were excluded when the quality flag was less than 1, the Confidence value less than 0.3 when stdev was larger than 0.2 or when no chromosomal mapping information was available. Log2ratio’s of spots that were not excluded after quality flagging and mapping were normalized to their median value.

source_name: myoepithelioma

label_protocol: according to snijders et al., 2001

tag: primary myoepithelioma of the submandibular salivary glands, FFPE material, spindle cell morphology, female, 39 years, no recurrence or metastasis

label_protocol: According to snijders et al., 2001

extract_protocol: DNAzol (Invitrogen) according to manufacturer's protocol


title: PsJN-AHL1_against_control1 Bionta

description: Biological replicate 1 out of 2


title: VUMC_myo_12

tag: primary myoepithelioma of the parotid salivary glands, FFPE material, spindle cell morphology, male, 67 years, no recurrence or metastasis

tag: normal DNA pooled from the blood of ten healthy females


title: VUMC_myo_14

tag: primary myoepithelioma of the parotid salivary glands, FFPE material, plasmacytoid cell morphology, male, 59 years, no recurrence or metastasis


title: VUMC_myo_10

tag: primary myoepithelioma of the parotid salivary glands, FFPE material, spindle cell morphology, female, 62 years, no recurrence or metastasis


title: VUMC_myo_7

tag: primary myoepithelioma from the parapharynx, FFPE material, spindle cell morphology, female, 61 years, no recurrence or metastasis

tag: normal DNA pooled from the blood of ten healthy males


title: VUMC_myo_13

tag: primary myoepithelioma of the parotid salivary glands, FFPE material, epithelioid cell morphology, male, 58 years, no recurrence or metastasis


title: VUMC_myo_9

tag: primary myoepithelioma of the parotid salivary glands, FFPE material, spindle cell morphology, male, 40 years, no recurrences or metastasis


title: VUMC_myo_8

tag: primary myoepithelioma of the parotid salivary gland, FFPE material, spindle cell morphology, male, 49 years, no recurrence or metastasis


title: PsJN1_against_control1 Bionta

description: Biological replicate 1 out of 2


title: VUMC_myo_6

tag: primary myoepithelioma from the parotid salivary glands, FFPE material, epithelioid morphology, female, 65 years, no recurrence or metastasis


title: PsJN-AHL1_control1 Russet Burbank

description: Biological replicate 1 out of 2

source_name: Russet Burbank


title: VUMC_myo_3

tag: primary myoepithelioma of the parotid salivary glands, epithelioid morphology, female, 75 years old, no recurrence or metastasis, FFPE material


title: P6RG6-12_2_against_control2 Bionta

description: Biological replicate 2 out of 2


title: VUMC_myo_2

tag: primary myoepithelioma of the parotid salivary glands, spindle cell morphology, female, 43 years, no recurrence or metastasis, FFPE material


title: PsJN1_control1 Russet Burbank

description: Biological replicate 1 out of 2

tag: control


title: Control2_P6RG612-2 Russet Burbank

description: Biological replicate 2 out of 2


title: Control_2_PsJN-AHL2 Russet Burbank

description: Biological replicate 2 out of 2

tag: PsJN AHLmutant treated


title: VUMC_myo_4

tag: primary myoepithelioma of the parapharynx, spindle cell morphology, female, 69 years, FFPE material, no recurrence or metastasis


title: Control2_PsJN2 Russet Burbank

description: Biological replicate 2 out of 2

tag: PsJN


title: VUMC_myo_1

tag: primary myoepithelioma of the parotid salivary glands, FFPE material, spindle cell morphology, female, 57 years old, no recidive or metastasis


title: VUMC_myo_5

tag: primary myoepithelioma of the submandibular salivary glands, spindle cell morphology, male, 69 years, no recurrence or metastasis, FFPE material


title: PsJN-AHL2against_control2 Russet Burbank

description: Biological replicate 2 out of 2

tag: PsJN AHLmutant


title: VUMC_myo_carc_3

tag: primary myoepithelial carcinoma of the parotid salivary gland, FFPE material, spindle cell morphology, male, 39 years, no recidive or metastasis

tag: normal DNA pooled from the blood of ten healthy females


title: PsJN2_against_control2 Bionta

description: Biological replicate 2 out of 2


title: P6RG6-12_1_cotrol1 Russet Burbank

description: Biological replicate 1 out of 2


title: VUMC_myo_carc_2

tag: primary myoepithelial carcinoma of the parotid salivary gland, male, 55 years, FFPE material, spindle cell morphology, no recidive, no information about metastasis


title: PsJN2_against_control2 Russet Burbank

description: Biological replicate 2 out of 2


title: P6RG6-12_2_against_control2 Russet Burbank

description: Biological replicate 2 out of 3


title: Control_1_PsJN1 Burbank

description: Biological replicate 1 out of 2


title: CLL515_DE767 (385K)

tag: Tissue


title: CLL515_DE768 (385K)


title: Control_1_2_PsJN-AHL1 Russet Burbank

description: Biological replicate 1 out of 2


title: Control_1_1_against_PsJN1 Russet Burbank

description: Biological replicate 1 out of 2

tag: PsJN treated


title: VUMC_myo_carc_6

data_processing: Spot analysis and quality control was fully automated using BlueFuse version 3.4 (BlueGnome, Cambridge, UK). Spots were excluded when the quality flag was less than 1, the Confidence value less than 0.3, stdev was more than 0.2 or when no chromosomal mapping information was available. Log2ratio’s of spots that were not excluded after quality flagging and mapping were normalized to their median value.

label_protocol: according to snijders at al, 2001

extract_protocol: standard phenol/chlorophorm extraction

tag: primary myoepithelial carcinoma of the salivary glands, FFPE material, spindle cell morphology, female

label_protocol: accroding to snijders at al, 2001

tag: normal DNA pooled from the blood of ten healthy males


title: VUMC_myo_carc_10

tag: primary myoepithelial carcinoma of the salivary glands, plasmacytoid morphology, female, FFPE material


title: Control1_against_P6RG612-1 Russet Burbank

description: Biological replicate 3 out of 3


title: CLL678_DE783 (385K)


title: VUMC_myo_carc_5

data_processing: Spot analysis and quality control was fully automated using BlueFuse version 3.4 (BlueGnome, Cambridge, UK). Spots were excluded when the quality flag was less than 1, the Confidence value less than 0.3, when stdev was larger than 0.2 or when no chromosomal mapping information was available. Log2ratio’s of spots that were not excluded after quality flagging and mapping were normalized to their median value

label_protocol: according to snijders et al, 2001

tag: primary myoepithelial carcinoma of the salivary glands, FFPE material, male, epithelioid morphology


title: CLL664_DE779 (385K)


title: Control_1_1_against_PsJN-AHL1 Russet Burbank

description: Biological replicate 1 out of 2


title: CLL611_DE772 (385K)


title: VUMC_myo_carc_9

tag: primary myoepithelial carcinoma of the parotid salivary gland, FFPE material, clear cell morphology, female, 80 years


title: VUMC_myo_carc_11 (2)

extract_protocol: standard phenol/chloroform extraction, described by Vekony et al, clin cancer res 2007


title: VUMC_myo_carc_7

tag: primary myoepithelial carcinoma of the salivary glands, FFPE material, plasmacytoid morphology, male


title: CLL611_DE771 (385K)


title: VUMC_myo_15

tag: primary myoepithelioma of the parotid salivary glands, FFPE material, epithelioid morphology, female, 70 years, no recurrence or metastasis


title: VUMC_myo_carc_12

tag: primary myoepithelial carcinoma of the salivary glands, FFPE material, male


title: RKO_HSF1siRNA_6hHNE_REP2

city: Nashville

first: Aaron

middle: Thomas

last: Jacobs

state: TN

address: 23rd Ave. @ Pierce Ave.

department: Biochemistry

institute: Vanderbilt University

description: Cells transfected with Stealth HSF1 siRNA (5'CGGAUUCAGGGAAGCAGCUGGUGCA) and subsequently treated for 6 hours with 50 uM HNE in vehicle 0.5% DMSO, in DMEM Media containing 10% FBS

hyb_protocol: Hybridization performed according to standard Affymetrix protocols

scan_protocol: Scanned on Affymetrix GeneChip Scanner 3000 7G

data_processing: Data processed using Affymetrix Expression Console software using default RMA parameters, log2 scale

source_name: RKO cells transfected with HSF1 Stealth siRNA treated 6 h with 50 uM HNE in DMSO 0.5% final

label_protocol: First Strand and Second Strand synthesis, followed by 2 rounds of SPIA amplification to generate cDNA was performed using WT-Ovation™ FFPE System V2 (Nugen Catalog#3400-60, Lot#801142-A). Fragmentaion and Biotinylation were completed using FL-Ovation™ cDNA Biotin Module V2 (Nugen Catalog# 4200, lot#709151-F)

extract_protocol: Cells from 10 cm plates were scraped and pelleted by centrifugation, followed by resuspension in 1 ml Trizol, incubation for 5 in at room temp, and addition of 200 ul CHCl3 with vigorous shaking by hand. After centrifugation 10 min 14,000 rpm, aqueous phase combined with equal volume of 70% EtOH, and subsequent cleanup on Qiagen RNeasy kit (Catalog# 74104)

tag: RKO colon carcinoma cells (ATCC #CRL-2577), cultured in DMEM (Invitrogen Catalog#10569) containing 10% FBS (Atlas Biologicals)


title: RKO_HSF1siRNA_6hHNE_REP3


title: VUMC_myo_carc_1

tag: myoepithelial carcinoma of the parotid salivary gland, FFPE material, male, 32 years, no recurrence, no information about metastasis, plasmacytoid morphology


title: VUMC_my_carc_4

tag: primary myoepithelial carcinoma in the oral cavity, FFPE material, female, 60 years, spindle cell morphology, no recurrence or metastasis


title: VUMC_myo_carc_8

tag: primary myoepithelial carcinoma of the salivary glands, FFPE material, plasmacytoid morphology, female


title: RKO_HSF1siRNA_6hDMSO_REP2

description: Cells transfected with Stealth HSF1 siRNA (5'CGGAUUCAGGGAAGCAGCUGGUGCA) and subsequently treated for 6 hours with vehicle 0.5% DMSO in DMEM Media containing 10% FBS

source_name: RKO cells transfected with HSF1 Stealth siRNA treated 6 h with DMSO 0.5%


title: RKO_HSF1siRNA_6hDMSO_REP1


title: RKO_HSF1siRNA_6hDMSO_REP3


title: RKO_NEGsiRNA_6hHNE_REP3

description: Cells transfected with Stealth Negative Control siRNA (Invitrogen Catalog# 12935-300) and subsequently treated for 6 hours with 50 uM HNE in 0.5% DMSO final, in DMEM Media containing 10% FBS

source_name: RKO cells transfected with NEG Stealth siRNA treated 6 h with 50 uM HNE in DMSO 0.5% final


title: RKO_NEGsiRNA_6hDMSO_REP2

description: Cells transfected with Stealth Negative Control siRNA (Invitrogen Catalog# 12935-300) and subsequently treated for 6 hours with 0.5% DMSO in DMEM Media containing 10% FBS

source_name: RKO cells transfected with NEG Stealth siRNA treated 6 h with vehicle DMSO 0.5%


title: A673 cells treated with control siRNA, biological rep1

city: Berlin

first: Guenther

middle: HS

last: Richter

address: Augustenburger Platz 1

department: Department of Pediatrics, Division of Oncology and Hematology

country: Germany

institute: Charité - Universitätsmedizin Berlin

description: A673 cells were treated for 24 hours either with 100 nM Trichostatin A (TSA) or 0.01% DMSO. In siRNA experiments A673 cells were resuspended in medium containing 5 nM siRNA and transfection reagent and incubated for 48 hours. RNA from cells under such treatment was isolated with Trizol and subjected to microarray analysis onto human U133A microarray following the Affymetrix protocol.

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: Microarray Suite 5.0 was used with the data and for normalization by scaling all probe sets to 500.

label: biotin, streptavidin-phycoerytrin

source_name: A673 cell line, a human EWS/FLI translocated Ewing tumor cell line

label_protocol: A total of 10 µg RNA from each sample was used to prepare biotinylated target cRNA as previously described (Staege MS, Hutter C, Neumann I, et al. DNA microarrays reveal relationship of Ewing family tumors to both endothelial and fetal neural crest-derived cells and define novel targets. Cancer Res 2004;64:8213-21). A detailed protocol is available at www.affymetrix.com.

growth_protocol: Cells were cultivated in RPMI 1640 medium containing 10 % FCS with additional 1 % penicillin/streptomycin in a humidified atmosphere at 37 °C and 5 % CO2.

extract_protocol: At 80 % confluency of the cells, total RNA was prepared with acid phenol/chloroform extraction (TRIzol, Invitrogen; Karlsruhe, Germany) followed by purification with RNeasy Mini Kit (Qiagen; Hilden, Germany) according to the manufacturer’s instructions and was quantified spectro-photometrically. The quality of the purified RNA was assessed by agarose gel analysis.

treatment_protocol: A673 cells were treated for 24 hours either with 100 nM Trichostatin A (TSA) or 0.01% DMSO. In siRNA experiments A673 cells were resuspended in medium containing 5 nM siRNA and transfection reagent and incubated for 48 hours. RNA from cells under such treatment was isolated.

tag: treated A673 Ewing tumor cell line


title: RKO_NEGsiRNA_6hDMSO_REP1


title: RKO_NEGsiRNA_6hHNE_REP2


title: RKO_HSF1siRNA_6hHNE_REP1


title: A673 cells treated with DMSO, biological rep1


title: RKO_NEGsiRNA_6hDMSO_REP3


title: Small RNA SBS signatures: mutant mop1-1

type: MPSS

city: Davis

first: Blake

middle: C.

last: Meyers

address: 451 Health Sciences Dr.

department: UC Davis Genome Center

institute: University of California - Davis

description: This library was derived from maize variety K55.  Immature ears were harvested from plants grown outdoors in Tuscon, AZ.  The material was harvested from plants 68 days after germination, with the floral tissue including young tassels 2-3 cm long.  Total RNA was isolated using a standard TRIZOL-based method and the small RNA libraries were generated as described by Lu et al. (Methods 2007, 43:110), followed by sequencing with Illumina's SBS method. The adapter sequences were removed, and the abundance of each distinct small RNA was determined.

data_processing: Small RNA molecules were sequenced using Illumina's SBS technology (Genome Analyzer 1).  Potential 3' adapter sequence was trimmed off from the signatures and only the signautres longer than equal to 15 nt were kept for analysis.  Since the maize genomic sequence and annotation have not yet been completed, we were not able identify the complete set of genome-matching small RNAs nor those that match to regulatory RNAs.  We normalized the expression level of all small RNAs in the set to 5 million (TP5M), which is close the number of total small RNA signautres sequenced.  Note that we used Illumina's first generation Genome Analyzer and the pipeline for SBS sequencing.

organism: Zea mays

source_name: mutant mop1-1

extract_protocol: Trizol

tag: Maize variety K55

tag: Immature ears harvested 68 days after germination

tag: Maize mop1-1 (MEDIATOR OF PARAMUTATION1) mutant. Ortholog of the Arabidopsis RDR2 gene.


title: A673 cells treated with ezh2 siRNA-validated


title: A673 cells treated with TSA, biological rep1


title: stable control replicate 2

first: Don

last: Ganem

address: 513 Parnassus Ave

department: G.W. Hooper

institute: University of California, San Francisco

description: stable BJAB control cell line. Biological replicate 2 of 2.

hyb_protocol: Samples were prepared with Gene Expression Hybridization Kit (Agilent) and placed in Agilent microarray hybridization chambers and rack. Hybridization occurred for 17 hr. at 65°.

scan_protocol: Scanned on Axon Genepix 4000B scanner. Images were processed with Agilent Feature Extraction Software v9.1.1.

data_processing: Linear LOWESS normalization was used. Default Agilent normalization was employed within Genespring GX. In detail, Each gene's measured intensity was divided by its control channel value in each sample; if the control channel was below 0 then 0 was used instead. If the control channel and the signal channel were both below 0 then no data was reported.  Each measurement was divided by the 50.0th percentile of all measurements in that sample.   The percentile was calculated using only genes marked present.    Each gene was divided by the median of its measurements in all samples. If the median of the raw values was below 0 then each measurement for that gene was divided by 0 if the numerator was above 0, otherwise the measurement was thrown out.

source_name: Stratagene Universal Reference RNA

label_protocol: 500 ng of total RNA was labeled using Low RNA Input Fluor Linear Amp Kit PLUS (Agilent).

growth_protocol: Cells were split to 2x10^5 cells per ml every 48 hr.

extract_protocol: Cells were harvested with RNA-bee (Tel-test). RNA integrity was assayed using a Bioanalyzer 2100 (Agilent) and quantitated with a ND1000 spectrophotometer (Nanodrop).

treatment_protocol: BJAB and BCBL-1 cells were electroporated with siPORT system (Ambion) at 30 nM for mimics and 100 nM for inhibitors (RNA harvested 48 and 72 hr. after transfection, respectively)

tag: Pooled cell line RNA

source_name: stable BJAB cell line

tag: transduced with retrovirus


title: transfected anti-K5 replicate 1

description: BCBL-1 cells transfected with inhibitor anti-K5. Biological replicate 1 of 1.

source_name: transfected BCBL-1 cells

tag: 72 hr. post transfection


title: SFO Control 5

city: Bristol

first: DAVID

last: MURPHY

state: AVON

address: Whitson Street

department: Medicine and Dentistry

country: United Kingdom

institute: University of Bristol

description: Sample represents the Subfornical organ from 5 untreated SD animals

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: GCOS version 1.2

label: Amino allyl UTP (biotin)

organism: Rattus norvegicus

source_name: SFO Control

label_protocol: MessegeAmp II aRNA amplification kit (Ambion). Protocol available at http://ambion.com/catalog/CatNum.php?1753

extract_protocol: Tissue was dissected in an RNase free manner and stored in RNAlater (Ambion) at -20C for no more than 1 month. Homogenisation in QIAzol was conducted mechanically and the aqueous phase separated using a PLG (Eppendorf). RNA was further purified using RNeasy Minelute cleanup kit (Qiagen). RNA quality was confirmed using nanodrop and bioanylizer 2100 (Agilent)

tag: Strain

value: Sprague Dawley

tag: Gender

value: Male

tag: Age

value: 10-12 weeks

tag: Tissue

value: Subfornical Organ


title: A673 cells treated with ezh2 siRNA no.2, biological rep2


title: A673 cells treated with control siRNA, biological rep2

growth_protocol: Cells were cultivated in RPMI 1640 medium containing 10 % FCS with additional 1 % penicillin/streptomycin in a humidified atmosphere at 37 °C and 5 % CO2

tag: treated A673 Ewing tumor cell line derived from muscle tissue


title: SFO Control 4


title: A673 cells treated with ezh2 siRNA no.2, biological rep1


title: A673 cells treated with DMSO, biological rep2

tag: treated A673 Ewing Tumor cell line derived from muscle tissue


title: stable miR-K1-K5 replicate 1

description: stable BJAB cell line expressing miR-K1-K5. Biological replicate 1 of 2.


title: Small RNA SBS signatures: wild-type

data_processing: Small RNA molecules were sequenced using Illumina's SBS technology (Genome Analyzer 1).  A total of 5,640,318 (3,640,512 distinct) SBS reads of 27 nt were obtained from the wild-type sample.  Potential 3' adaptor sequence was trimmed off from the signatures and only the signautres longer than equal to 15 nt (3,355,880 distinct) were kept for analysis.  Since the maize genomic sequence and annotation have not yet been completed, we were not able identify the complete set of genome-matching small RNAs nor those that match to regulatory RNAs.  We normalized the expression level of all small RNAs in the set to 5 million (TP5M), which is close the number of total small RNA signautres sequenced.  Note that we used Illumina's first generation Genome Analyzer and the pipeline for SBS sequencing.

source_name: wild-type

tag: Wild-type


title: RKO_NEGsiRNA_6hHNE_REP1

tag: RKO colon carcinoma cells (ATCC #CRL-2577), cultured in DMEM (Invitrogen Catalog#10569) containing 10% FBS (Atlas Biologicals)


title: transfected miR-K5 replicate 1

description: BJAB cells transfected with miR-K5. Biological replicate 1 of 2.

source_name: transfected BJAB cells

tag: 48 hr. post transfection


title: stable control replicate 1

description: stable BJAB control cell line. Biological replicate 1 of 2.


title: transfected miR-neg replicate 1

description: BJAB cells transfected with miR-neg. Biological replicate 1 of 2.


title: transfected miR-K5 replicate 2

description: BJAB cells transfected with miR-K5. Biological replicate 2 of 2.


title: stable miR-K1-K5 replicate 2

description: stable BJAB cell line expressing miR-K1-K5. Biological replicate 2 of 2.


title: A673 cells treated with TSA, biological rep2


title: SFO Control 1


title: SFO Control 3


title: SFO Water deprivation 2

description: Sample represents the Subfornical organ from 5 water deprived SD animals

source_name: SFO Water deprivation


title: SFO Control 2


title: SFO Water deprivation 4


title: Regulation of the RPE (retinal pigment epithelium) transcriptome by the neural retina (E14CM-SER-SER-1)

status: Public on Sep 30 2008

city: New Haven

first: Lawrence

middle: J

last: Rizzolo

state: CT

address: 333 Cedar St

department: Dept of Surgery

institute: Yale University

hyb_protocol: standard

scan_protocol: standard

data_processing: signal value generated from global scaling

label: biotin-U

organism: Gallus gallus

source_name: retinal pigment epithelium

label_protocol: affymetrix 3'-amplification ivt

extract_protocol: RNeasy Protect^ kit (Qiagen)

tag: E14 RPE in basal medium supplemented with 2% fetal bovine serum and retinal conditioned medium


title: transfected miR-neg replicate 2

description: BJAB cells transfected with miR-neg. Biological replicate 2 of 2.


title: Regulation of the RPE (retinal pigment epithelium) transcriptome by the neural retina (E14CM-SER-SER-3)


title: Regulation of the RPE (retinal pigment epithelium) transcriptome by the neural retina (E14SF3-1)

tag: E14 RPE in basal medium


title: SFO Food deprivation 4

description: Sample represents the Subfornical organ from 5 food deprived SD animals

source_name: SFO Food deprivation

treatment_protocol: Animal was food deprived for 48 hours


title: Regulation of the RPE (retinal pigment epithelium) transcriptome by the neural retina (E14SF3-SER-2)

label: biotin-UTP

tag: E14 RPE in basal medium supplemented with 2% fetal bovine serum


title: Regulation of the RPE (retinal pigment epithelium) transcriptome by the neural retina (E7CM-SER-SER-3)

tag: E7 RPE in basal medium supplemented with 2% fetal bovine serum and retinal conditioned medium


title: SFO Food deprivation 3


title: SFO Food deprivation 5


title: SFO Food deprivation 2


title: Regulation of the RPE (retinal pigment epithelium) transcriptome by the neural retina (E14RCSF3-2)

tag: E14 RPE in basal medium supplemented with retinal conditioned medium


title: SFO Water deprivation 3


title: Regulation of the RPE (retinal pigment epithelium) transcriptome by the neural retina (E14SF3-2)


title: SFO Water deprivation 1


title: SFO Water deprivation 5


title: transfected anti-neg replicate 1

description: BCBL-1 cells transfected with control inhibitor anti-neg. Biological replicate 1 of 1.

tag: Pooled cell line RNA


title: Regulation of the RPE (retinal pigment epithelium) transcriptome by the neural retina (E14RCSF3-3)


title: Regulation of the RPE (retinal pigment epithelium) transcriptome by the neural retina (E7RCSF3-3)

tag: E7 RPE in basal medium supplemented with retinal conditioned medium


title: Regulation of the RPE (retinal pigment epithelium) transcriptome by the neural retina (E14SF3-SER-3)


title: Regulation of the RPE (retinal pigment epithelium) transcriptome by the neural retina (E14CM-SER-SER-2)


title: Regulation of the RPE (retinal pigment epithelium) transcriptome by the neural retina (E14SF3-3)


title: Regulation of the RPE (retinal pigment epithelium) transcriptome by the neural retina (E14RCSF3-1)


title: SFO Food deprivation 1


title: Regulation of the RPE (retinal pigment epithelium) transcriptome by the neural retina (E7RCSF3-2)


title: Regulation of the RPE (retinal pigment epithelium) transcriptome by the neural retina (E14SF3-SER-1)


title: Regulation of the RPE (retinal pigment epithelium) transcriptome by the neural retina (E7RCSF3-1)


title: Regulation of the RPE (retinal pigment epithelium) transcriptome by the neural retina (E7SF3-SER-3)

source_name: Retinal Pigment Epithelium

tag: E7 RPE in basal medium supplemented with 2% fetal bovine serum


title: Regulation of the RPE (retinal pigment epithelium) transcriptome by the neural retina (E7CM-SER-SER-2)


title: Empty PC12 1 days (PC12_1_1_1)

status: Public on Sep 29 2008

city: Leiden

first: Peter

last: 't Hoen

address: PO Box 9600

department: Center for Human and Clinical Genetics

institute: Leiden University Medical Center

description: Gene expression data from PC12 cells stably transfected with a doxycylin-inducible exon1 huntingtin fragment with normal-sized or elongated glutamine stretch

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Non-background corrected average intensities across all replicate beads (obtained from Beadstudio) were normalized with vsn

label: biotin

source_name: PC12 cell culture

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: RNA was isolated from one 9 cm petriddish

extract_protocol: RNA was isolated with the RNeasy kit

treatment_protocol: Cells were treated with 1ug /ml doxycylin for the indicated number of days

tag: Empty PC13

tag: Time after induction

value: 1 days


title: Empty PC12 5 days (PC12_5_2_2)

tag: Empty PC17

value: 5 days


title: Empty PC12 0 days (PC12_0_1_1)

tag: Empty PC12

value: 0 days


title: Construct Q23 Line 5 1 days (Q23_1_5_2)

tag: Construct

value: Q23, Line 5


title: Empty PC12 1 days (PC12_1_2_2)

tag: Empty PC16


title: Empty PC12 5 days (PC12_5_1_1)

tag: Empty PC14


title: Regulation of the RPE (retinal pigment epithelium) transcriptome by the neural retina (E7SF3-Ser-1)


title: Empty PC12 0 days (PC12_0_2_2)

tag: Empty PC15


title: Construct Q74 Line 4 1 days (Q74_1_4_2)

value: Q74, Line 4


title: Construct Q74 Line 4 5 days (Q74_5_4_2)


title: Construct Q74 Line 6 1 days (Q74_1_6_2)

value: Q74, Line 6


title: Construct Q74 Line 6 0 days (Q74_0_6_2)


title: Construct Q74 Line 6 5 days (Q74_5_6_1)


title: Construct Q23 Line 1 0 days (Q23_0_1_2)

value: Q23, Line 1


title: Regulation of the RPE ( retinal pigment epithelium) transcriptome by the neural retina (E7SF3-1)

tag: E7 cells in basal media


title: Construct Q74 Line 4 0 days (Q74_0_4_2)


title: Construct Q23 Line 5 0 days (Q23_0_5_2)


title: Regulation of the RPE (retinal pigment epithelium) transcriptome by the neural retina (E7CM-SER-SER-1)


title: Construct Q74 Line 6 5 days (Q74_5_6_2)


title: Regulation of the RPE (retinal pigment epithelium) transcriptome by the neural retina (E7SF3-2)


title: Construct Q74 Line 6 1 days (Q74_1_6_1)


title: Construct Q23 Line 1 1 days (Q23_1_1_2)


title: Construct Q23 Line 1 5 days (Q23_5_1_2)


title: Regulation of the RPE (retinal pigment epithelium) transcriptome by the neural retina (E7SF3-3)


title: Regulation of the RPE (retinal pigment epithelium) transcriptome by the neural retina (E7SF3-Ser-2)


title: Construct Q74 Line 6 0 days (Q74_0_6_1)


title: Construct Q74 Line 4 5 days (Q74_5_4_1)


title: 13420177 - DGPP_set2 vs Control_set2

status: Public on Sep 27 2008

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: The specific plant phosphorylated form of phosphatidic acid (PA), diacyglycerol pyrophosphate (DGPP), was recently shown to be a second messenger in abscisic acid (ABA) signaling. The aim of the project is to identify among the set of ABA-regulated genes the ones also regulated by DGPP and/or PA.

hyb_protocol: Control set2 Cy5 / DGPP 18:1 300(u)M set2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 520V,laser power 100%

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.

source_name: Control, set2

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

growth_protocol: cell culture - Media Jouanneau and Peaud-Lenokl, 1967 hygrometry=non relevant			 Temperature=22°C			 Light=40umol photons s-1 m-2

extract_protocol: Control set2:14.85ug.

treatment_protocol: no treatment

tag: Arabidopsis thaliana (Columbia)

tag: Age

value: 3 days

source_name: DGPP 18:1 300uM, set2

treatment_protocol: Name:DGPP 18:1 - compound based treatment - compound addition,dgpp 18:1:quantity 300000mM time 3hour . Five ml of 3 days-old suspension cells was incubated with lipids for 3 h under the conditions of culture. Lipids were emulsified by sonication for 1 mi, four times, at 4degre Celsius, in one ml of culture medium then added to 4 ml suspension cells. Cells were filtrated under vacuum, frozen in liquid nitrogen and RNA extracted.


title: Construct Q23 Line 5 1 days (Q23_1_5_1)


title: Construct Q23 Line 5 5 days (Q23_5_5_1)


title: Construct Q23 Line 5 5 days (Q23_5_5_2)


title: 13420176 - Control_set2 vs DGPP_set2

hyb_protocol: DGPP 18:1 300(u)M set2 Cy5 / Control set2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Construct Q74 Line 4 0 days (Q74_0_4_1)


title: Construct Q74 Line 4 1 days (Q74_1_4_1)


title: Construct Q23 Line 1 5 days (Q23_5_1_1)


title: 13419751 - Control_set1 vs DGPP_set1

hyb_protocol: DGPP 18:1 300(u)M set1 Cy5 / Control set1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: DGPP 18:1 300uM, set1

source_name: Control, set1

extract_protocol: Control set1:10.8ug.


title: Construct Q23 Line 1 0 days (Q23_0_1_1)


title: 13419791 - ABA_set3 vs Control_DMSO_set2

hyb_protocol: Control DMSO set2 Cy5 / ABA 10-5M set3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Control DMSO, set2

extract_protocol: Control DMSO set2:5.85ug.

treatment_protocol: Name:DMSO - compound based treatment - compound addition,dmso:time 3hour . 5ml of 3 days-old suspension cells were incubated with ABA or DGPP 18:1 for 3hours under the conditions of culture. DGPP was emulsified by sonication for 1min 4 times at 4degre Celsius in 1ml of culture medium then added to 4ml of suspension cells, for 3h. Cells were filtrated under vacuum, frozen in liquid nitrogen.

source_name: ABA 10-5M, set3

treatment_protocol: Name:ABA 10-5M - compound based treatment - compound addition,aba:quantity 0.01mM time 3hour . Five ml of 3 days-old suspension cells was incubated with ABA for 3 h under the conditions of culture. Lipids were emulsified by sonication for 1 mi, four times, at 4degre Celsius, in one ml of culture medium then added to 4 ml suspension cells. Cells were filtrated under vacuum, frozen in liquid nitrogen and RNA extracted.


title: 13419762 - Control_DMSO_set1 vs ABA_set1

hyb_protocol: ABA 10-5M set1 Cy5 / Control DMSO set1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: ABA 10-5M, set1

source_name: Control DMSO, set1

extract_protocol: Control DMSO set1:10.8ug.


title: 13420178 - Control_DMSO_set2 vs ABA_set3

hyb_protocol: ABA 10-5M set3 Cy5 / Control DMSO set2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13419752 - DGPP_set1 vs Control_set1

hyb_protocol: Control set1 Cy5 / DGPP 18:1 300(u)M set1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 76N3

status: Public on Sep 26 2008

city: Chicago

first: Simon

last: Lin

state: IL

department: Bioinformatics Core

institute: Northwestern University

description: Gene expression data from normal human mammary epithelial cells

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA

source_name: Normal human mammary epithelial cells

label_protocol: standard Affymetrix protocol

growth_protocol: Reduction mammoplasty-derived human mammary epithelial cell strains, 76N and RhoA immortalized 76N cells  were grown in the DFCI-1 medium

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.For each cell line,  RNA was isolated in three independent experiments.

treatment_protocol: No treatment. Logarithmically growing cells were collected for RNA extraction.

tag: Reduction mammoplasty


title: 76N RhoA G14V1

description: gene expression data from constitutively active form of RhoA ( G14V) immortalized human mammary epithelial cells

source_name: Constitutively active form of RhoA ( G14V) immortalized human mammary epithelial cells


title: ash2I1_larvae_(Replicate4)

city: Barcelona

first: Sergi

last: Beltran

address: Baldiri Reixac 10

department: Serveis Cientificotècnics

country: Spain

institute: Universitat de Barcelona

description: Total RNA from w1118;+;+ larvae was pooled and used as a common reference in four microarrays against w1118;+;ash2I1 total RNA coming from two different extractions to take biological differences into account. Amplified RNA (aRNA) was obtained with the Amino-Allyl Messageamp II aRNA Amplification Kit (Ambion, Inc) from w1118;+;+ and w1118;+;ash2I1 prior to hybridization.

hyb_protocol: Samples were diluted in 2X Hybridization Buffer #5185-5973(Agilent Technologies) and hybridization was carried out at 60ºC for 18 hours with a G2534A SureHyb Chamber in a G2545A Hybridization Oven (Agilent Technologies).

scan_protocol: GenePix Results (GPR) data files were obtained for each microarray with an Axon 4000B scanner and GenePix Pro 6 (Axon Instruments, Inc).

data_processing: GPR files were analyzed with Limma package from BioConductor (Gentleman et al., 2004; Genome Biol 5, R80; Smyth, 2004; Statistical Applications in Genetics and Molecular Biology 3, Article 3) using the same criteria. Data was background corrected with the "normexp" method and normalized with OLIN (Futschik and Crompton, 2005; Bioinformatics 21, 1724-1726). Spots not fulfilling the quality thresholds (based on spot size, foreground versus background signals, saturation, coincidence between differently calculated ratio measures and R2 of regression ratio) were eliminated from further analysis.

organism: Drosophila melanogaster

source_name: w1118;+;ash2I1 isogenized larvae (Biological Replicate 2)

label_protocol: 1.5ug total RNA were amplified and indirectly labelled with Amino-Allyl Messageamp II aRNA Amplification Kit (Ambion, Inc). Fragmentation was done with RNA Fragmentation Reagents #8740(Ambion, Inc).

growth_protocol: Flies were kept on standard media with 0.025% bromophenol blue at 25ºC.

extract_protocol: Larvae were squashed in PBS and total RNA extraction was performed with RNeasy Protect Mini Kit (QIAGEN Inc.). Quality was assessed using the Eukaryote Total RNA Nano Assay on a 2100 Bioanalyzer (Agilent Technologies).

tag: Strain

value: w1118;+;ash2I1 isogenized from wt strain.

tag: Stage

value: third instar larvae (bromophenol blue staged)

tag: Tissue

value: whole larvae

source_name: w1118;+;+ isogenic wt larvae (pool)

value: w1118;+;+ isogenic wt strain (Ryder, E., 2004; Genetics 167, 797-813).


title: ash2I1_larvae_(Replicate3)


title: trxE3/trxB11_larvae_(Replicate4)

description: Total RNA from w1118;+;+ larvae was pooled and used as a common reference in four microarrays against w1118;+;trxE3/trxB11 total RNA coming from two different extractions to take biological differences into account. Two amplifications from w1118;+;+ and one from each w1118;+;trxE3/trxB11 replicate were performed with the Amino-Allyl Messageamp II aRNA Amplification Kit (Ambion, Inc) to obtain amplified RNA (aRNA). The arrays from each replicate pair were hybridized with the same amplified RNA from sample and common reference but with dyes (Cy3 and Cy5 from Amersham, Inc) swapped to take dye-bias into account.

source_name: w1118;+;trxE3/trxB11 isogenized larvae (Biological Replicate 2)

growth_protocol: Flies were kept on standard media with 0.025% bromophenol blue at 21ºC.

value: w1118;+;trxE3/trxB11 isogenized from wt strain.


title: 13420175 - ABA_set1 vs Control_DMSO_set1

hyb_protocol: Control DMSO set1 Cy5 / ABA 10-5M set1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 76N RhoA WT1

description: Gene expression data from wild type RhoA immortalized human mammary epithelial cells

source_name: Wild type RhoA immortalized human mammary epithelial cells


title: 13372754 - DRN+DEX vs Col-0+DEX

description: Identification of the target genes of the ESR1/DRN TF using dexamethasone induction

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

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

growth_protocol: whole plant - MS/2, sacharose 7g/L, agar 10g/L 25°C Light 16h/8h

extract_protocol: Pool of extract, Col-0+DEX_1:0.5ug, Col-0+DEX_2:0.5ug.

treatment_protocol: Name:DEX - compound based treatment - protein activator,dexamethasone:quantity 0.01mM time 2min . 2min and 1h of incubation, 2min and 2h of incubation

tag: Arabidopsis thaliana (columbia)  - age:15daydev.stage (Boyes et al. Plant Cell 2001):boyes = 1.04

source_name: DRN+DEX

extract_protocol: Pool of extract, DRN+DEX_1:0.5ug, DRN+DEX_2:0.5ug.

tag: Arabidopsis thaliana (columbia)  mutant (DRN) - age:15daydev.stage (Boyes et al. Plant Cell 2001):boyes = 1.04


title: ash2I1_larvae_(Replicate1)

source_name: w1118;+;ash2I1 isogenized larvae (Biological Replicate 1)


title: 13372756 - DRN+DEX+Cyclo vs DRN+Cyclo

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

source_name: DRN+Cyclo

extract_protocol: Pool of extract, DRN+Cyclo_1:0.5ug, DRN+Cyclo_2:0.5ug.

treatment_protocol: Name:Cyclo - compound based treatment - traduction inhibitor,cycloheximide:quantity 0.01mM time 2min . 2min and 1h of incubation, 2min and 2h of incubation

source_name: DRN+DEX+Cyclo

extract_protocol: Pool of extract, DRN+DEX+Cyclo_1:0.5ug, DRN+DEX+Cyclo_2:0.5ug.

treatment_protocol: Name:Cyclo+DEX - compound based treatment - traduction inhibitor+protein activator,cyclo+dex:quantity 0.01mM time 2min . Cyclo 10(u)M +DEX 10(u)M 2min and 1h of incubation, 2min and 2h of incubation


title: 13489208 - DRN+DEX+Cyclo 2 vs DRN+Cyclo 2

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

source_name: DRN+Cyclo 2

source_name: DRN+DEX+Cyclo 2