title: M. galloprovincialis_32-degree heat shock_replicate 1

description: Biological replicate 1 of 6. M. galloprovincialis heat shock, 32 degrees-C, 32-degree time-point in heat ramp.


title: M. trossulus_13-degrees control, 24-degree-time-point_replicate 2

status: Public on Oct 11 2010

type: RNA

city: Pacific Grove

first: Brent

middle: L

last: Lockwood

state: CA

address: 120 Oceanview Blvd.

department: Biology

country: USA

institute: Hopkins Marine Station of Stanford University

description: Biological replicate 2 of 6. M. trossulus control, 13 degrees-C, 24-degree time-point in heat ramp.

hyb_protocol: Competitive hybridization (experimental - AlexaFluor 647 versus reference - AlexaFluor 555). We followed the recommended protocols from Agilent Technologies, Inc for all hybridization and washing steps.

scan_protocol: Microarrays were scanned with an AXON GenePix 4000B scanner (Axon Instruments, Molecular Devices, Sunnyvale, CA, USA).

data_processing:
Fluorescent signal intensities for each spot on the microarray were extracted and Lowess normalized within each microarray using Feature Extraction software (version 9.5.3.1; Agilent Technologies, Inc.). Only spots that Feature Extraction Software measured to have good hybridization among all samples were included in further analysis. We then computed the log2-ratios of the experimental channel divided by the reference channel and normalized these expression values to the median log2-ratio of the control samples of the same species from the same temperature-point on the heat ramp (i.e. 13°C, 24°C, 28°C and 32°C). Log2-ratios of the samples from the 13°C temperature-point were normalized to the median log2-ratio within that group, separately for each species.
Used data only from those probes that performed well for both species in our comparison.

label: Alexa Fluor 647

molecule: total RNA

organism: Mytilus trossulus

source_name: 13-degrees control, 24-degree-time-point, M. trossulus

label_protocol: Total RNA was reverse-transcribed and amplified with the AminoAllyl MessageAmp II kit (Ambion; Foster City, CA, USA). To reduce problems in transcript binding due to sequence differences between species, we employed a reference design that used separate pools of reference RNA for each species. Reference amplified RNA (aRNA) was created for each species by pooling RNA before and after amplification. The reference pool was made up of RNA from six different samples: one control sample from the beginning of the experiment, one treatment sample from each temperature-point, and one control sample from each temperature-point. aRNAs from reference and experimental samples were separately labeled with Alexa Fluor fluorescent dyes (Invitrogen, Carlsbad, CA, USA), 555 for reference and 647 for control or treatment.

growth_protocol: We collected mussels from floating boat docks: Mytilus trossulus (Gould 1850) from Newport Harbor, Newport, OR, USA (44°38’25” N, 124°03’10” W) and Mytilus galloprovincialis (Lamarck 1819) from Santa Barbara Harbor, Santa Barbara, CA, USA (34°24’15” N, 119°41’30” W). All specimens thus were acclimatized to conditions of continuous immersion. Care was taken to collect animals of similar size (5 – 7 cm) to avoid potential artifacts from size-related influences on gene expression. Specimens were returned to the laboratory at California Polytechnic State University San Luis Obispo and placed in a re-circulating seawater tank in which they were common-garden acclimated at 13°C for 4 weeks, in order to limit the effects of past thermal history. We chose both collection sites to be well outside of the hybrid zone (McDonald, 1988; Braby and Somero, 2006a) to ensure no hybrid individuals were included in our study. We confirmed the species identification by genotyping each mussel using published methods (Heath et al., 1995; Rawson et al., 1996). The 13°C acclimation temperature mimicked an ecologically realistic thermal environment for both species.

extract_protocol: Total RNA was extracted from gill tissues with a TissueLyser homogenizer (Qiagen; Valencia, CA, USA) and RNeasy kit (Qiagen).

treatment_protocol: Treatment animals were transferred from the common-garden aquarium to a tank in which they were exposed to a heat-ramp of +6°C h-1, from 13°C to 32°C, to simulate thermal heating on a hot day during falling tide. Control animals were simultaneously transferred to a separate tank that remained at 13°C. At designated temperature-points on the heat-ramp (24°C, 28°C and 32°C), six treatment mussels from each species were transferred to a separate tank and maintained at each respective temperature for an additional hour. Treatment and control mussels corresponding to each temperature-point were then sacrificed and their gill tissues dissected and frozen on liquid nitrogen. Tissues were stored at -70°C prior to RNA extraction.

tag: stress

value: CONTROL, transferred to 13-degrees from 24-degree-time-point

label: Alexa Fluor 555

source_name: M. trossulus pooled: Time-point zero, 24-control, 24-heat-shock, 28-control, 28-heat-shock, 32-control, 32-heat-shock

tag: reference

value: pooled samples

tag: tissue

value: gill


title: M. galloprovincialis_13-degrees control, 32-degree-time-point_replicate 1

description: Biological replicate 1 of 6. M. galloprovincialis control, 13 degrees-C, 32-degree time-point in heat ramp.

organism: Mytilus galloprovincialis

source_name: 13-degrees control, 32-degree-time-point, M. galloprovincialis

value: CONTROL, transferred to 13-degrees from 32-degree-time-point

source_name: M. galloprovincialis pooled: Time-point zero, 24-control, 24-heat-shock, 28-control, 28-heat-shock, 32-control, 32-heat-shock


title: M. galloprovincialis_13-degrees control, 32-degree-time-point_replicate 2

description: Biological replicate 2 of 6. M. galloprovincialis control, 13 degrees-C, 32-degree time-point in heat ramp.


title: M. galloprovincialis_28-degree heat shock_replicate 3

description: Biological replicate 3 of 6. M. galloprovincialis heat shock, 28 degrees-C, 28-degree time-point in heat ramp.

source_name: 28-degree heat shock, M. galloprovincialis

value: 28-degree heat shock


title: M. galloprovincialis_13-degrees control, 32-degree-time-point_replicate 4

description: Biological replicate 4 of 6. M. galloprovincialis control, 13 degrees-C, 32-degree time-point in heat ramp.


title: M. galloprovincialis_28-degree heat shock_replicate 6

description: Biological replicate 6 of 6. M. galloprovincialis heat shock, 28 degrees-C, 28-degree time-point in heat ramp.


title: M. galloprovincialis_28-degree heat shock_replicate 4

description: Biological replicate 4 of 6. M. galloprovincialis heat shock, 28 degrees-C, 28-degree time-point in heat ramp.


title: M. galloprovincialis_28-degree heat shock_replicate 5

description: Biological replicate 5 of 6. M. galloprovincialis heat shock, 28 degrees-C, 28-degree time-point in heat ramp.


title: M. galloprovincialis_13-degrees control, 28-degree-time-point_replicate 4

description: Biological replicate 4 of 6. M. galloprovincialis control, 13 degrees-C, 28-degree time-point in heat ramp.

source_name: 13-degrees control, 28-degree-time-point, M. galloprovincialis

value: CONTROL, transferred to 13-degrees from 28-degree-time-point


title: M. galloprovincialis_13-degrees control, 28-degree-time-point_replicate 3

description: Biological replicate 3 of 6. M. galloprovincialis control, 13 degrees-C, 28-degree time-point in heat ramp.


title: M. galloprovincialis_13-degrees control, 28-degree-time-point_replicate 5

description: Biological replicate 5 of 6. M. galloprovincialis control, 13 degrees-C, 28-degree time-point in heat ramp.


title: M. galloprovincialis_13-degrees control, 28-degree-time-point_replicate 2

description: Biological replicate 2 of 6. M. galloprovincialis control, 13 degrees-C, 28-degree time-point in heat ramp.


title: M. galloprovincialis_13-degrees control, 28-degree-time-point_replicate 1

description: Biological replicate 1 of 6. M. galloprovincialis control, 13 degrees-C, 28-degree time-point in heat ramp.


title: M. galloprovincialis_28-degree heat shock_replicate 1

description: Biological replicate 1 of 6. M. galloprovincialis heat shock, 28 degrees-C, 28-degree time-point in heat ramp.


title: M. galloprovincialis_28-degree heat shock_replicate 2

description: Biological replicate 2 of 6. M. galloprovincialis heat shock, 28 degrees-C, 28-degree time-point in heat ramp.


title: M. galloprovincialis_24-degree heat shock_replicate 2

description: Biological replicate 2 of 6. M. galloprovincialis heat shock, 24 degrees-C, 24-degree time-point in heat ramp.

source_name: 24-degree heat shock, M. galloprovincialis

value: 24-degree heat shock


title: M. galloprovincialis_24-degree heat shock_replicate 5

description: Biological replicate 5 of 6. M. galloprovincialis heat shock, 24 degrees-C, 24-degree time-point in heat ramp.


title: M. galloprovincialis_24-degree heat shock_replicate 3

description: Biological replicate 3 of 6. M. galloprovincialis heat shock, 24 degrees-C, 24-degree time-point in heat ramp.


title: M. galloprovincialis_24-degree heat shock_replicate 1

description: Biological replicate 1 of 6. M. galloprovincialis heat shock, 24 degrees-C, 24-degree time-point in heat ramp.


title: M. galloprovincialis_13-degrees control, 24-degree-time-point_replicate 3

description: Biological replicate 3 of 6. M. galloprovincialis control, 13 degrees-C, 24-degree time-point in heat ramp.

source_name: 13-degrees control, 24-degree-time-point, M. galloprovincialis


title: M. galloprovincialis_13-degrees control, 28-degree-time-point_replicate 6

description: Biological replicate 6 of 6. M. galloprovincialis control, 13 degrees-C, 28-degree time-point in heat ramp.


title: M. galloprovincialis_13-degrees control, 24-degree-time-point_replicate 6

description: Biological replicate 6 of 6. M. galloprovincialis control, 13 degrees-C, 24-degree time-point in heat ramp.


title: M. galloprovincialis_24-degree heat shock_replicate 6

description: Biological replicate 6 of 6. M. galloprovincialis heat shock, 24 degrees-C, 24-degree time-point in heat ramp.


title: M. galloprovincialis_24-degree heat shock_replicate 4

description: Biological replicate 4 of 6. M. galloprovincialis heat shock, 24 degrees-C, 24-degree time-point in heat ramp.


title: control_2nd_rep3

city: Helsinki

first: Heli

last: Pessa

address: Haartmaninkatu 8

department: Faculty of Medicine; Research Programme in Translational Immunology

country: Finland

institute: University of Helsinki

description:
GFP2_s2a1_488
raw data file: slide002_A1_635GFP3_532GFP1_0488.gpr

hyb_protocol: 0.75 μg of each three samples per array were hybridized with Gene Expression Hybridization Kit (Agilent) according to the protocol for Two-Color Microarray-Based Gene Expression Analysis.

scan_protocol: The arrays were scanned with Genepix 4200A scanner and Genepix Pro 6.1.0.2 software.

data_processing:
The gpr files were imported into R 2.9.0 (cran.r-project.org) and analyzed with the BioConductor (www.bioconductor.org) package Limma. The median foreground probe intensities without background correction from each channel were log2 transformed and normalized by the quantile method. Exon-exon junction probes were excluded from the analysis due to unreliability.
Exon-level data reported in the Data table below.

label: Alexa Fluor 488

organism: Drosophila melanogaster

source_name: whole larvae, control, 2nd instar

label_protocol: 1 μg of each RNA sample was amplified with Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion/Applied Biosystems) according to manufacturer's instructions. In vitro transcription reaction was incubated for 8 hours. The resulting aminoallyl-modified RNA was labelled with Cy3 or Cy5 dyes (Invitrogen) or ARES Labeling Kit with Alexa Fluor 488 (Invitrogen).

growth_protocol: Flies were grown on standard food at 25 °C.

extract_protocol: Total RNA was extracted from larvae with Trizol reagent (Invitrogen).

treatment_protocol: 1st stage larvae were collected from apple juice agar plates, 2nd and 3rd stage larvae from fly food vials.

value: whole larva

tag: larval stage

tag: genotype/variation

value: U6atac/CyO-GFP (control)


title: control_1st_rep3

description:
GFP1_s1a2_488
raw data file: slide001_A2_635-U6a2_532-DNA_0488.gpr

source_name: whole larvae, control, 1st instar


title: control_3rd_rep2

description:
GFP3_s3a2_488
raw data file: slide003_A2_635GFP1_532GFP2_0488.gpr

source_name: whole larvae, control, 3rd instar


title: control_1st_rep2

description:
GFP1_s2a1_532
raw data file: slide002_A1_635GFP3_532GFP1_0488.gpr


title: mutant_3rd_rep3

description:
U6a3_s3a1_488
raw data file: slide003_A1_635U6a1_532U6a2_0488.gpr

source_name: whole larvae, mutant, 3rd instar

value: U6atac/U6atac (mutant)


title: mutant_1st_rep3

description:
U6a1_s1a1_488
raw data file: slide001_A1_635GFP2_532-U6a3_0489.gpr

source_name: whole larvae, mutant, 1st instar


title: M. galloprovincialis_13-degrees control, 24-degree-time-point_replicate 4

description: Biological replicate 4 of 6. M. galloprovincialis control, 13 degrees-C, 24-degree time-point in heat ramp.


title: M. galloprovincialis_13-degrees control, 24-degree-time-point_replicate 2

description: Biological replicate 2 of 6. M. galloprovincialis control, 13 degrees-C, 24-degree time-point in heat ramp.


title: M. galloprovincialis_13-degrees control, 24-degree-time-point_replicate 5

description: Biological replicate 5 of 6. M. galloprovincialis control, 13 degrees-C, 24-degree time-point in heat ramp.


title: mutant_2nd_rep3

description:
U6a2_s2a2_488
raw data file: slide002_A2_635U6a3_532U6a1_0488.gpr

source_name: whole larvae, mutant, 2nd instar


title: K_STA18

status: Public on Oct 12 2010

city: Stanford

first: Li

last: Li

address: 300 pastuer dr.,

department: Pediatric

institute: Stanford University

hyb_protocol: 1. Mix the following for each target, scaling up volumes if necessary for hybridization to multiple probe arrays. 2. Equilibrate probe array to room temperature immediately before use. 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block. 4. Meanwhile, wet the array with an appropriate volume of Pre- Hybridization Mix (see Table 3.2) by filling it through one of the septa. 5. Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation. 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes. 7. Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture. 8. Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube (see Table 3.2). 9. Place probe array into the hybridization oven, set to 45°C. 10. To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm. 11. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Chapter 4 to prepare reagents for the washing and staining steps required immediately after completion of hybridization.

scan_protocol: 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run. 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list. 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required. 4. Once the experiment has been selected, click the Start button. A dialog box prompts you to load an array into the scanner. 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam. • Pixel value = 3 μm • Wavelength = 570 nm If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed. 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. If you are using the GeneChip Scanner 3000, do not attempt to close the door by hand. The door closes automatically through the User Interface when start scan is selected or the scanner goes into stand-by mode. 7. Click OK in the Start Scanner dialog box. The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.

data_processing: Dchip MBEI processing, quantile-quantile normalization

label: Biotin

organism: Homo sapiens

source_name: STA18 kidney allograft biopsy, stable

label_protocol: GeneChip One-cycle target labeling and control reagents

extract_protocol: For each kidney allograft biopsy, a separate biopsy core was placed in RNAlater (Ambion, Inc) and stored at -20ºC until RNA extraction. The cDNA fragments obtained after amplification were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, California, USA).

tag: stable


title: control_2nd_rep2

description:
GFP2_s3a2_532
raw data file: slide003_A2_635GFP1_532GFP2_0488.gpr


title: mutant_1st_rep2

description:
U6a1_s2a2_532
raw data file: slide002_A2_635U6a3_532U6a1_0488.gpr


title: mutant_2nd_rep2

description:
U6a2_s3a1_532
raw data file: slide003_A1_635U6a1_532U6a2_0488.gpr


title: mutant_3rd_rep2

description:
U6a3_s1a1_532
raw data file: slide001_A1_635GFP2_532-U6a3_0489.gpr


title: M. trossulus_Time-point zero control_replicate 6

description: Biological replicate 6 of 6. M. trossulus control, 13 degrees-C, beginning of heat ramp.

source_name: Time-point zero control M. trossulus

value: CONTROL, time-point zero


title: M. trossulus_Time-point zero control_replicate 4

description: Biological replicate 4 of 6. M. trossulus control, 13 degrees-C, beginning of heat ramp.


title: control_1st_rep1

description:
GFP1_s3a2_635
raw data file: slide003_A2_635GFP1_532GFP2_0488.gpr


title: M. trossulus_Time-point zero control_replicate 5

description: Biological replicate 5 of 6. M. trossulus control, 13 degrees-C, beginning of heat ramp.


title: M. trossulus_Time-point zero control_replicate 2

description: Biological replicate 2 of 6. M. trossulus control, 13 degrees-C, beginning of heat ramp.


title: M. trossulus_Time-point zero control_replicate 3

description: Biological replicate 3 of 6. M. trossulus control, 13 degrees-C, beginning of heat ramp.


title: M. galloprovincialis_Time-point zero control_replicate 6

description: Biological replicate 6 of 6. M. galloprovincialis control, 13 degrees-C, beginning of heat ramp.

source_name: Time-point zero control M. galloprovincialis


title: M. trossulus_Time-point zero control_replicate 1

description: Biological replicate 1 of 6. M. trossulus control, 13 degrees-C, beginning of heat ramp.


title: M. galloprovincialis_13-degrees control, 24-degree-time-point_replicate 1

description: Biological replicate 1 of 6. M. galloprovincialis control, 13 degrees-C, 24-degree time-point in heat ramp.


title: mutant_3rd_rep1

description:
U6a3_s2a2_635
raw data file: slide002_A2_635U6a3_532U6a1_0488.gpr


title: control_2nd_rep1

description:
GFP2_s1a1_635
raw data file: slide001_A1_635GFP2_532-U6a3_0489.gpr


title: M. galloprovincialis_Time-point zero control_replicate 5

description: Biological replicate 5 of 6. M. galloprovincialis control, 13 degrees-C, beginning of heat ramp.


title: mutant_2nd_rep1

description:
U6a2_s1a2_635
raw data file: slide001_A2_635-U6a2_532-DNA_0488.gpr


title: M. galloprovincialis_Time-point zero control_replicate 4

description: Biological replicate 4 of 6. M. galloprovincialis control, 13 degrees-C, beginning of heat ramp.


title: M. galloprovincialis_Time-point zero control_replicate 3

description: Biological replicate 3 of 6. M. galloprovincialis control, 13 degrees-C, beginning of heat ramp.


title: rat nucleus pulposus cell, co-culture, rep1

city: Tokyo

first: Takashi

last: Miyamoto

address: 1-5-45 Yushima, Bunkyo-ku

department: Department of Orthopedic Surgery

country: Japan

institute: Tokyo Medical and Dental University

description: Gene expression data from rat nucleus pulposus cells co-cultured with human synovial mesenchymal stem cells.

hyb_protocol: Following fragmentation, cRNA were hybridized to GeneChip® Rat Genome 230 2.0 probe arrays (Affymetrix) and/or GeneChip® Human U-133 plus 2.0 probe arrays according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

organism: Rattus norvegicus

source_name: co-culture of rat nucleus pulposus cells and human synovial mesenchymal stem cells

label_protocol: Biotinylated cRNA were prepared using a GeneChip IVT Labeling kit (Affymetrix) from 3 ug total RNA .

growth_protocol: Synovium from knee joints was digested in a 3 mg/ml collagenase type V (Sigma). Bone marrow was filtered through a cell strainer with 70-μm pore size. Nucleus pulposus was digested with 0.01% trypsin-EDTA.

extract_protocol: Total RNA was extracted with the RNeasy Total RNA Mini Kit (Qiagen).

treatment_protocol: Cells isolated from synovium, bone marrow and nucleus pulposus were cultured in alpha-MEM (Invitrogen). For co-culture, human synovial mesenchymal stem cells and rat nucleus pulposus cells were cultured together at same density for a week.

tag: strain

value: Wistar

tag: cell type

value: nucleus pulposus cell

tag: culture protocol


title: rat nucleus pulposus cell, co-culture, rep2

value: co-culture of rat nucleus pulposus cells and human synovial mesenchymal stem cells


title: rat nucleus pulposus cell, mono-culture, rep2

description: Gene expression data from rat nucleus pulposus cells.

source_name: mono-culture of rat nucleus pulposus cells

value: mono-culture


title: control_3rd_rep1

description:
GFP3_s2a1_635
raw data file: slide002_A1_635GFP3_532GFP1_0488.gpr


title: mutant_1st_rep1

description:
U6a1_s3a1_635
raw data file: slide003_A1_635U6a1_532U6a2_0488.gpr


title: rat nucleus pulposus cell, mono-culture, rep1


title: M. galloprovincialis_Time-point zero control_replicate 1

description: Biological replicate 1 of 6. M. galloprovincialis control, 13 degrees-C, beginning of heat ramp.


title: rat synovial mesenchymal stem cell, mono-culture, rep1

description: Gene expression data from rat synovial mesenchymal stem cells.

source_name: mono-culture of rat synovial mesenchymal stem cells

value: synovial mesenchymal stem cell


title: 13749452 - Col0;A vs mkk1-/-;mkk2+/-;A

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Functional redundancy of the two MAPKKs MKK1 and MKK2.

hyb_protocol: mkk1-/-;mkk2+/-;A Cy5 / Col0;A Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

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

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

organism: Arabidopsis thaliana

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

growth_protocol: seedling - Media   1/2MS, no sucrose hygrometry  sealed petridishes Temperature  2°C Light   8h

treatment_protocol: no treatment

tag: sample type

value: arabidopsis thaliana (col-0)  mutant (mkk1-/-;mkk2+/-) - age  14day dev.stage (Boyes et al. Plant Cell 2001) boyes  1.03

tag: genetic background

tag: genotype

tag: age

tag: developmental stage

value: boyes 1.03

value: seedling

extract_protocol: Col0;A:30ug. (Qiagen_RNeasy.pdf)

value: arabidopsis thaliana (col-0)  - age  14day dev.stage (Boyes et al. Plant Cell 2001) boyes  1.03

value: wild type


title: 13749450 - mkk1-/-;mkk2-/-;B vs Col0;B

hyb_protocol: Col0;B Cy5 / mkk1-/-;mkk2-/-;B Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Col0;B:30ug. (Qiagen_RNeasy.pdf)


title: M. galloprovincialis_Time-point zero control_replicate 2

description: Biological replicate 2 of 6. M. galloprovincialis control, 13 degrees-C, beginning of heat ramp.

source_name: M. galloprovincialis pooled: Time-point zero, 24-control, 24-heat-shock, 28-control, 28-heat-shock, 32-control, 32-heat-shock

value: pooled samples

value: gill


title: human synovial mensenchymal stem cell, co-culture, rep1

description: Gene expression data from human synovial mesenchymal stem cells co-cultured with rat nucleus pulposus cells.


title: 13749495 - mkk1-/-;mkk2-/-;A vs Col0;A

hyb_protocol: Col0;A Cy5 / mkk1-/-;mkk2-/-;A Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: rat bone marrow mesenchymal stem cell, mono-culture, rep1

description: Gene expression data from rat bone marrow mesenchymal stem cells.

source_name: mono-culture of rat bone marrow mesenchymal stem cells

value: bone marrow mesenchymal stem cell


title: 13749453 - mkk1-/-;mkk2+/-;A vs Col0;A

hyb_protocol: Col0;A Cy5 / mkk1-/-;mkk2+/-;A Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13749454 - Col0;B vs mkk1-/-;mkk2+/-;B

hyb_protocol: mkk1-/-;mkk2+/-;B Cy5 / Col0;B Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: human synovial mensenchymal stem cell, mono-culture, rep1

description: Gene expression data from human synovial mesenchymal stem cells.

source_name: mono-culture of human synovial mesenchymal stem cells


title: Oryza sativa roots 4-6cm without vs. with Silicium

status: Public on Oct 10 2010

city: Hannover

first: Frank

last: Stahl

address: Callinstr. 3

department: Institut für Technische Chemie

country: Germany

institute: Universität Hannover

description:
This study was performed to study the effect of silicon (Si) nutrition on suberization and lignification in roots of rice. Besides physiological and histochemical examinations of the roots, transcription of candidate genes related to synthesis of suberin and lignin was investigated using microarray analysis.
B0_Biotin_B9_Fluorescin

hyb_protocol: The Fl and B labeled cDNA of both samples were hybridized simultaneously in one experiment to the same array. After hybridization, the unbound and unspecifically fixed cDNA was removed from the array by stringent washing. Specifically bound Fl and B labeled cDNAs were sequentially detected with a series of conjugate reporter molecules according to the tyramide signal amplification process, ultimately with Tyramide-Cy3 and Tyramide-Cy5

scan_protocol: The scanning process of the hybridized chips with the Axon 4000B scanner (Axon Instruments, Foster City, CA, USA) included a six fold scan of each chip at different settings, both changing the photomultiplier tube and the laser power settings

data_processing: The following primary analysis served as a quantification method and was performed with the software tool Gene Pix Pro 6.0™. Next, the secondary analysis was conducted using the data from the primary analysis. Therefore, data from different scans were first normalized by using the median of all background intensities, which were therefore checked for outliers. Three replicates for each gene were tested for outliers.Assuming, that the majority of genes on a whole genome microarray are not differently expressed, a locally weighted linear regression (Lowess) has been employed as a normalization method in order to account for such intensity-dependent effects. The mean of the data for differently labelled targets for each gene on respectively two microarrays is taken. It seems reasonable to make a convenient assumption that the distribution of the pre-processed data is normal and hence subsequently, a standard two-state pooled-variance t-test (5% probability of error) is applicable in order to detect differentially expressed genes.The values are normalized log2 Cy5/Cy3

organism: Oryza sativa

source_name: Oryza sativa roots 4-6cm

label_protocol: During reverse transcription 8 µg of purified total RNA was copied into biotin (B) labeled cDNA.

growth_protocol: The plants were grown in a growth chamber (photoperiod: 14 h light, 10 h dark; temperature 25°C day / 20°C night; relative humidity 75 %; light intensity 220 µmol m2 s-1).

extract_protocol: Adventitious roots were harvested at 4-6 cm distance from the root tip and frozen immediately in liquid nitrogen. For RNA isolation, roots were ground under liquid nitrogen and total RNA was isolated using TRIsure® Reagent (Bioline, Luckenwalde, Germany) following the instructions of the manufacturer

treatment_protocol: 14 days old rice seedlings (Oryza sativa, cv. Selenio) were cultivated for 28 days in non-aerated nutrient solution (mM: 1.43 NH4NO3, 0.32 NaH2PO4 x H2O, 0.51 K2SO4, 1 CaCl2 x 2 H2O, 1.6 MgSO4 x 7 H2O; µM: 1.82 MnSO4, 0.03 (NH4)6Mo7O24, 9 H3BO3, 0.3 ZnSO4 x 7 H2O and 0.15 CuSO4). The pH-value was adjusted to 6.0 by addition of 10 % (v/v) H2SO4 and 0.75 M KOH.Plants were supplied with Si in form of K2SiO3 at concentrations 0 ppm Si (control).

tag: cultivar

value: Selenio

tag: organ

value: roots 4-6cm

tag: treatment

value: without Silicium

label_protocol: During reverse transcription 8 µg of purified total RNA was copied into fluorescein (Fl) labeled cDNA.

extract_protocol: Adventitious roots were harvested  4-6 cm distance from the root tip and frozen immediately in liquid nitrogen. For RNA isolation, roots were ground under liquid nitrogen and total RNA was isolated using TRIsure® Reagent (Bioline, Luckenwalde, Germany) following the instructions of the manufacturer

treatment_protocol: 14 days old rice seedlings (Oryza sativa, cv. Selenio) were cultivated for 28 days in non-aerated nutrient solution (mM: 1.43 NH4NO3, 0.32 NaH2PO4 x H2O, 0.51 K2SO4, 1 CaCl2 x 2 H2O, 1.6 MgSO4 x 7 H2O; µM: 1.82 MnSO4, 0.03 (NH4)6Mo7O24, 9 H3BO3, 0.3 ZnSO4 x 7 H2O and 0.15 CuSO4). The pH-value was adjusted to 6.0 by addition of 10 % (v/v) H2SO4 and 0.75 M KOH.Plants were supplied with Si in form of K2SiO3 at concentrations 50 ppm Si (1.78 mM).

value: with Silicium


title: Oryza sativa roots 4-6cm with vs. without Silicium

description:
This study was performed to study the effect of silicon (Si) nutrition on suberization and lignification in roots of rice. Besides physiological and histochemical examinations of the roots, transcription of candidate genes related to synthesis of suberin and lignin was investigated using microarray analysis.
B0_Fluorescin_B9_Biotin

scan_protocol: The scanning process of the hybridized chips with the Axon 4000B scanner (Axon Instruments, Foster City, CA, USA) included a six fold scan of each chip at different settings, both changing the photomultiplier tube and the laser power settings.

data_processing: The following primary analysis served as a quantification method and was performed with the software tool Gene Pix Pro 6.0™. Next, the secondary analysis was conducted using the data from the primary analysis. Therefore, data from different scans were first normalized by using the median of all background intensities, which were therefore checked for outliers. Three replicates for each gene were tested for outliers. Assuming, that the majority of genes on a whole genome microarray are not differently expressed, a locally weighted linear regression (Lowess) has been employed as a normalization method in order to account for such intensity-dependent effects. The mean of the data for differently labelled targets for each gene on respectively two microarrays is taken. It seems reasonable to make a convenient assumption that the distribution of the pre-processed data is normal and hence subsequently, a standard two-state pooled-variance t-test (5% probability of error) is applicable in order to detect differentially expressed genes. The values are normalized log2 Cy5/Cy3


title: Oryza sativa roots 0-2cm without vs. with Silicium

description:
This study was performed to study the effect of silicon (Si) nutrition on suberization and lignification in roots of rice. Besides physiological and histochemical examinations of the roots, transcription of candidate genes related to synthesis of suberin and lignin was investigated using microarray analysis.
A0_Fluorescin_A9_Biotin

source_name: Oryza sativa roots 0-2cm

extract_protocol: Adventitious roots were harvested at 0-2 cm and 4-6 cm distance from the root tip and frozen immediately in liquid nitrogen. For RNA isolation, roots were ground under liquid nitrogen and total RNA was isolated using TRIsure® Reagent (Bioline, Luckenwalde, Germany) following the instructions of the manufacturer

value: roots 0-2cm


title: 13749451 - Col0;B vs mkk1-/-;mkk2-/-;B

hyb_protocol: mkk1-/-;mkk2-/-;B Cy5 / Col0;B Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13749494 - Col0;A vs mkk1-/-;mkk2-/-;A

hyb_protocol: mkk1-/-;mkk2-/-;A Cy5 / Col0;A Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Oryza sativa roots 0-2cm with vs. without Silicium

description:
This study was performed to study the effect of silicon (Si) nutrition on suberization and lignification in roots of rice. Besides physiological and histochemical examinations of the roots, transcription of candidate genes related to synthesis of suberin and lignin was investigated using microarray analysis.
A0_Biotin_A9_Fluorescin

extract_protocol: Adventitious roots were harvested at 0-2 cm distance from the root tip and frozen immediately in liquid nitrogen. For RNA isolation, roots were ground under liquid nitrogen and total RNA was isolated using TRIsure® Reagent (Bioline, Luckenwalde, Germany) following the instructions of the manufacturer


title: 13749455 - mkk1-/-;mkk2+/-;B vs Col0;B

hyb_protocol: Col0;B Cy5 / mkk1-/-;mkk2+/-;B Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: human synovial mensenchymal stem cell, co-culture, rep2


title: human synovial mensenchymal stem cell, mono-culture, rep2


title: KU-812 Imatinib-treated

city: Los Angeles

first: Markus

last: Müschen

address: 4650 Sunset Blvd

department: Childrens Hospital Los Angeles

institute: University of Southern California

description:
KU-812 leukemia cells were incubated with 10 µM STI571 (Imatinib) for 16 hours.
For more information about the cell line, please check: www.dsmz.de
Q249_A_HG_U133_Plus_2_01_1__UU812_STI_.CEL

hyb_protocol: Standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual)

data_processing: RMA signal intensities obtained using BRB-arraytool software which calculates the RMA-values with the affy package from Bioconductor.

source_name: CML cell line: KU-812

extract_protocol: Extraction Method: Qiagen RNeasy Kit

tag: cell line

value: Myeloid leukemia cells

tag: agent

value: Imatinib


title: BN_HCC_Replicate 7

status: Public on Oct 09 2010

city: Sassari

first: Rosa

middle: M.

last: Pascale

address: Via P. Manzella 4

department: Dept. of Biomedical Sciences

country: Italy

institute: University of Sassari

description:
Biological replicate 7 of 8. BN HCC, treated
7 HCC BN vs Normal BN.txt

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Packard BioScience ScanArray Express scanner. Images were quantified using ScanArray Express Software.

data_processing: ScanArray Express Software was used for background subtraction and LOWESS normalization.

source_name: Normal liver BN

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

extract_protocol: Total RNA extracted using Tripure following manufacturer's instructions

value: Brown Norway

tag: tissue

value: Normal liver

source_name: HCC BN

value: Fisher 344

value: hepatocarcinoma

tag: tumor stage


title: JURL-MK1 non-treated

description:
JURL-MK1 leukemia cells were cultured in absence of STI571 (Imatinib).
For more information about the cell line, please check: www.dsmz.de
Q250_A_HG_U133_Plus_2_01_1__3WL_.CEL

scan_protocol: Standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual)

source_name: CML cell line: JURL-MK1

value: untreated


title: JURL-MK1 Imatinib-treated

description:
JURL-MK1 leukemia cells were incubated with 10 µM STI571 (Imatinib) for 16 hours.
For more information about the cell line, please check: www.dsmz.de
Q251_A_HG_U133_Plus_2_01_1__3WL_STI_.CEL

label_protocol: Standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual)


title: BN_HCC_Replicate 4

description:
Biological replicate 4 of 8. BN HCC, treated
4 HCC BN vs Normal BN.txt


title: BN_HCC_Replicate 5

description:
Biological replicate 5 of 8. BN HCC, treated
5 HCC BN vs Normal BN.txt


title: KU-812 non-treated

description:
KU-812 leukemia cells were cultured in absence of STI571 (Imatinib).
For more information about the cell line, please check: www.dsmz.de
Q248_A_HG_U133_Plus_2_01_1__UU812_.CEL


title: BN_HCC_Replicate 1

description:
Biological replicate 1 of 8. BN HCC, treated
1 HCC BN vs Normal BN.txt


title: KCL-22 non-treated

description:
KCL-22 leukemia cells were cultured in absence of STI571 (Imatinib).
For more information about the cell line, please check: www.dsmz.de
Q246_A_HG_U133_Plus_2_01_1__UCL22_.CEL

source_name: CML cell line: KCL-22


title: BN_HCC_Replicate 2

description:
Biological replicate 2 of 8. BN HCC, treated
2 HCC BN vs Normal BN.txt


title: BN_HCC_Replicate 6

description:
Biological replicate 6 of 8. BN HCC, treated
6 HCC BN vs Normal BN.txt


title: F344_HCC_Replicate 5

description:
Biological replicate 5 of 8. F344 HCC, treated
5 HCC F344 vs Normal F344.txt

source_name: Normal liver F344

source_name: HCC F344


title: BN_HCC_Replicate 3

description:
Biological replicate 3 of 8. BN HCC, treated
3 HCC BN vs Normal BN.txt


title: KCL-22 Imatinib-treated

description:
KCL-22 leukemia cells were incubated with 10 µM STI571 (Imatinib) for 16 hours.
For more information about the cell line, please check: www.dsmz.de
Q247_A_HG_U133_Plus_2_01_1__UCL22_STI_.CEL


title: F344_HCC_Replicate 3

description:
Biological replicate 3 of 8. F344 HCC, treated
3 HCC F344 vs Normal F344.txt


title: F344_HCC_Replicate 6

description:
Biological replicate 6 of 8. F344 HCC, treated
6 HCC F344 vs Normal F344.txt


title: F344_HCC_Replicate 1

description:
Biological replicate 1 of 8. F344 HCC, treated
1 HCC F344 vs Normal F344.txt


title: BN_DN_Replicate 6

description:
Biological replicate 6 of 8. BN Dysplastic nodules, treated
6 DN BN vs Normal BN.txt

source_name: Dysplastic nodules BN

value: dysplastic nodules


title: F344_HCC_Replicate 4

description:
Biological replicate 4 of 8. F344 HCC, treated
4 HCC F344 vs Normal F344.txt


title: BN_DN_Replicate 4

description:
Biological replicate 4 of 8. BN Dysplastic nodules, treated
4 DN BN vs Normal BN.txt


title: BN_DN_Replicate 8

description:
Biological replicate 8 of 8. BN Dysplastic nodules, treated
8 DN BN vs Normal BN.txt


title: BN_DN_Replicate 7

description:
Biological replicate 7 of 8. BN Dysplastic nodules, treated
7 DN BN vs Normal BN.txt


title: BN_DN_Replicate 5

description:
Biological replicate 5 of 8. BN Dysplastic nodules, treated
5 DN BN vs Normal BN.txt


title: F344_HCC_Replicate 7

description:
Biological replicate 7 of 8. F344 HCC, treated
7 HCC F344 vs Normal F344.txt


title: BN_DN_Replicate 1

description:
Biological replicate 1 of 8. BN Dysplastic nodules, treated
1 DN BN vs Normal BN.txt


title: BN_DN_Replicate 2

description:
Biological replicate 2 of 8. BN Dysplastic nodules, treated
2 DN BN vs Normal BN.txt


title: F344_HCC_Replicate 2

description:
Biological replicate 2 of 8. F344 HCC, treated
2 HCC F344 vs Normal F344.txt


title: F344_DN_Replicate 8

description:
Biological replicate 8 of 8. F344 Dysplastic nodules, treated
8 DN F344 vs Normal F344.txt

source_name: Dysplastic nodules F344


title: BN_DN_Replicate 3

description:
Biological replicate 3 of 8. BN Dysplastic nodules, treated
3 DN BN vs Normal BN.txt


title: codY mutant_rep2

city: Boston

first: Abraham

last: Sonenshein

state: MA

address: 136 Harrison Avenue

department: Molecular Biology & Microbiology

institute: Tufts University

description: Analysis compared transcript levels in codY+ and codY mutant strains.

scan_protocol: The microarray slides were scanned using a ScanArray 4000 (Packard Instrument Co.) and fluorescence intensities were quantified using ImaGene (BioDiscovery) software version 8.0.1.

data_processing: Raw expression data from three arrays, representing three biological replicates, were lowess normalized and averaged using GeneSpring (Agilent Technologies) software version 7.3.

organism: Clostridioides difficile

source_name: bacterial culture

label_protocol: Ten μg of starting RNA was used for the cDNA synthesis reactions.The Genisphere 3DNA Array 900 MPX microarray kit was used for cDNA synthesis, labeling, and hybridization as recommended by the manufacturer with specific protocol modifications described by O’Connor et al. (Mol Microbiol. 2006 61(5):1335-1351).

growth_protocol: Overnight cultures of C. difficile grown in TYG were diluted to an OD600 of 0.05 in TY medium and incubated anaerobically at 37°C. Samples were removed for RNA isolation at an OD600 of 0.4 (exponential phase), diluted with an equal volume of ice-cold acetone-ethanol (1:1) and stored at -80°C.

extract_protocol: The cell suspensions were thawed and centrifuged at 4°C; the pellets were air-dried, washed twice with 500 μl of TE (pH 7.6), and resuspended in 1 ml of Buffer RLT from the Qiagen RNeasy kit. Silica glass beads (0.1 mm) were added and cells were disrupted using a Mini-BeadBeater (BioSpecs Products). Silica beads were removed by centrifugation and total RNA was isolated from the supernatant fluid using the Qiagen RNeasy kit.

treatment_protocol: Exponential phase samples were harvested without any treatment.

tag: genotype/variation

value: codY mutant

source_name: bacterial cells

value: codY+


title: codY mutant_rep1

hyb_protocol: The Genisphere 3DNA Array 900 MPX microarray kit was used for cDNA synthesis, labeling, and hybridization as recommended by the manufacturer with specific protocol modifications described by O’Connor et al. (Mol Microbiol. 2006 61(5):1335-1351).


title: F344_DN_Replicate 6

description:
Biological replicate 6 of 8. F344 Dysplastic nodules, treated
6 DN F344 vs Normal F344.txt


title: F344_DN_Replicate 5

description:
Biological replicate 5 of 8. F344 Dysplastic nodules, treated
5 DN F344 vs Normal F344.txt


title: F344_DN_Replicate 4

description:
Biological replicate 4 of 8. F344 Dysplastic nodules, treated
4 DN F344 vs Normal F344.txt


title: codY mutant_rep3


title: SW480 treated with U0126

city: Berlin

first: Karsten

last: Jürchott

address: Luisenstraße

department: Rahel Hirsch Center

institute: BIH at Charité

description: Gene expression data from SW480 cells treated with U0126 for 48 hours

hyb_protocol: Hybridization and post-hybridization procedures were performed according to protocols provided by Affymetrix.

scan_protocol: Arrays were scanned twice at 3µm resolution using a confocal argon laser scanner (Hewlett-Packard, Santa Clara, CA), controlled by Microarray Suite 5.0 software (Affymetrix). Photoemission was detected by a photomultiplier tube through a 570-nm long-pass filter.

data_processing: Computer-generated array images were overlayed with a virtual grid, controlled by Microarray Suite 5.0 software. About 40 pixels within each feature were averaged after discarding outliers and pixels close to feature boundaries.

source_name: SW480 cell line

label_protocol: Labelling of RNA targets were performed according to protocols provided by Affymetrix.

growth_protocol: SW480, HT29 and HCT116 cells were cultured in complete L-15 medium at 37 °C and 5% CO2 in a humified incubator.

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

treatment_protocol: After 24 hours, the cells were treated once with the indicated inhibitors for 48 hours.

value: colorectal cancer

value: aneuploide

value: passage not known


title: F344_DN_Replicate 1

description:
Biological replicate 1 of 8. F344 Dysplastic nodules, treated
1 DN F344 vs Normal F344.txt


title: F344_DN_Replicate 2

description:
Biological replicate 2 of 8. F344 Dysplastic nodules, treated
2 DN F344 vs Normal F344.txt


title: F344_DN_Replicate 3

description:
Biological replicate 3 of 8. F344 Dysplastic nodules, treated
3 DN F344 vs Normal F344.txt


title: F344 liver_Control _Replicate 4

description:
Biological replicate 4 of 4. Control, untreated
4 Normal F344 vs Normal BN.txt


title: SW480 treated with Sulindac Sulfide

description: Gene expression data from SW480 cells treated with Sulindac Sulfide for 48 hours


title: F344 liver_Control _Replicate 1

description:
Biological replicate 1 of 4. Control, untreated
1 Normal F344 vs Normal BN.txt


title: SW480 treated with PD98059

description: Gene expression data from SW480 cells treated with PD98059 for 48 hours


title: F344 liver_Control _Replicate 2

description:
Biological replicate 2 of 4. Control, untreated
2 Normal F344 vs Normal BN.txt


title: F344 liver_Control _Replicate 3

description:
Biological replicate 3 of 4. Control, untreated
3 Normal F344 vs Normal BN.txt


title: F344_DN_Replicate 7

description:
Biological replicate 7 of 8. F344 Dysplastic nodules, treated
7 DN F344 vs Normal F344.txt


title: SW480 treated with AG1478

description: Gene expression data from SW480 cells treated with AG1478 for 48 hours


title: SW480 treated with DMSO

description: Gene expression data from SW480 cells treated with DMSO for 48 hours (control)


title: SW480 treated with Sulindac Sulfone

description: Gene expression data from SW480 cells treated with Sulindac Sulfone for 48 hours


title: YBX1_promoter_part_2

type: genomic

description: Chip-chip HCT116 cells YBX1

hyb_protocol: Hybridisation was done by Nimblegen.

scan_protocol: Arrays were scaned by Nimblegen.

data_processing: The raw intensities of each channel were normalized and log-transformed using Bioconductor VSN package . Fold changes for each probe were calculated by subtraction of Cy3 (input) from Cy5 intensity (ChIP sample). Normalized probe levels were smoothed along chromosomal coordinates using a sliding window method. For each probe position the smoothed probe level was computed as the median over the probe levels in an 800-bp window centered at that position.

molecule: genomic DNA

source_name: Input DNA from HCT116 cells

label_protocol: DNA fragments were labled by Nimblegen.

growth_protocol: HCT116 cells were grown in L15 for 72 hours.

extract_protocol: 1x10E7 cells were fixed with 1% formaldehyde in culture medium for 10 min on ice followed by quenching with 0.125 M glycine for 5 min. The cells were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (0.25% Triton, 0.5% NP40, 10% Glycerol, 1 mM EDTA, 140 mM NaCl, 50 mM Hepes pH7.5) for at least 10 min on ice. After centrifugation, the supernatant was discarded and the pellets were washed once with buffer (200mM NaCl, 1mM EDTA, 0.5mM EGTA, 10mM Tris/HCL pH8.0). The pellets were resuspended in 600µl buffer (10mM Tris/HCl pH8.0, 1mM EDTA, 0.5mM EGTA, protease inhibitors) sheared to an average size of 600 bp by 5 cycles of 20 pulses (duty cycle 30/70, power 4) using a Branson Sonifier. The lysate was then centrifuged to remove cell debris, and the chromatin was quantified in a UV spectrophotometer. The chromatin (400 µg) was diluted in dilution buffer (1% Triton X-100, 0.1% Sodium Deoxycholate, 1.2 mM EDTA 16.7 mM Tris pH8.10, protease inhibitors) and centrifuged to remove aggregated material. The chromatin supernatant was then incubated overnight with 10 µg of antibody coupled to Dynabeads at 4C. The immune complexes were collected by centrifugation and washed 8 times with buffer (50mM Hepes pH8.0, 1mM EDTA, 1% NP40, 0.7% Sodium Deoxycholate,  0.5M LiCl, protease inhibitors), and 1x TE (20 mM Tris pH8.0, 2 mM EDTA). The protein-DNA complexes were eluted from the beads in 50 µl elution buffer (1% SDS, 10mM Tris/HCl pH8.0, 1mM EDTA) at 65C for 10 minutes. Supernatants were diluted with 120 µl elution buffer and incubated at 65C over night. ProteinaseK was added to 230 µg/ml and incubated at 37C for two hours. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input (1/100 of the material used for ChIP) by phenol extraction and ethanol precipitation. The fragments were treated with RNAse A and purified using Qiaquick PCR purification kit. DNA fragments were amplified according (Iyer et al., 2001).

value: mut KRAS, mut beta-catenin, wt P53, wt APC

value: colorectal cancer cell

tag: chip antibody

value: no, Input DNA

source_name: YBX1 precipitated DNA from HCT116 cells

value: polyclonal, peptide specific anti YBX1 (c-terminus)


title: BN liver_Control_Replicate 2

description:
Biological replicate 2 of 4. Control, untreated
2 Normal BN vs Normal F344.txt

tag: strain


title: Strain_α710_Adhesion replicate2

city: Wuerzburg

first: Biju Joseph

last: Ampattu

address: Josef-Schneider Str 2

department: Department of Microbiology

institute: University of Wuerzburg

description: replicate 2 of 2

hyb_protocol: The labelled DNA were mixed together in hybridization buffer (3 x SSC and 0.1% SDS) and hybridized onto prehybridized microarray slides using a Tecan Hybridization station.

scan_protocol: The slides were scanned using a Genepix Pro scanner with settings to avoid more than 10% of the spots being saturated.

data_processing: Raw data generated after flagging for obvious cases of stray background and spots with a signal to noise ratio of less than 3 were further analyses using the R package limma. Loess normalization was used for within slide and Rquantile normalization was used for between slide normalization.

organism: Neisseria meningitidis

source_name: RNA from strain α710 adherent to FaDu cells

label_protocol: 5 µg of test RNA and 5 µg of common reference RNA were labelled with Cy3 dCTP and Cy5 dCTP using reverse transcriptase (Invitrogen)and random nonamers and the labelled DNA was precipitated and purified.

growth_protocol: The strains were grown in RPMI 1640 medium to a mid log phase and harvested for RNA isolation. For isolation of adherent meningococci, strains were preincubated in RPMI after overnight growth on blood agar and confluent layers of FaDu cells were infected at an MOI of between 100-200 for 3 hrs and harvested.

extract_protocol: Total RNA extracted using RNeasy kit from Qiagen following manufacturer's instructions

tag: protocol

value: α710 adherent to FaDu cells

source_name: Common Reference

value: Pool of all individual RNA´s


title: BN liver_Control_Replicate 3

description:
Biological replicate 3 of 4. Control, untreated
3 Normal BN vs Normal F344.txt

value: Brown Norway


title: YBX1_promoter_part_1

description: Chip-chip HCT116 cells YBX1

tag: cell type


title: BN liver_Control_Replicate 4

description:
Biological replicate 4 of 4. Control, untreated
4 Normal BN vs Normal F344.txt

value: Normal liver


title: Strain_α710_Adhesion replicate1

description: replicate 1 of 2

tag: sample type


title: Strain_MC58_Adhesion replicate2

description: replicate 2 of 2

source_name: RNA from strain MC58 adherent to FaDu cells

value: MC58 adherent to FaDu cells


title: Strain_MC58_Adhesion replicate1

description: replicate 1 of 2


title: HT29 treated with U0126

description: Gene expression data from HT29 cells treated with U0126 for 48 hours

source_name: HT29 cell line


title: BN liver_Control_Replicate 1

description:
Biological replicate 1 of 4. Control, untreated
1 Normal BN vs Normal F344.txt

value: Fisher 344

source_name: Normal liver BN


title: HT29 treated with PD98059

description: Gene expression data from HT29 cells treated with PD98059 for 48 hours


title: Strain_α710_RPMI replicate2

description: replicate 2 of 2

source_name: RNA from strain α710 grown in RPMI

value: α710 grown in RPMI


title: HT29 treated with Sulindac Sulfone

description: Gene expression data from HT29 cells treated with Sulindac Sulfone for 48 hours


title: HT29 treated with Sulindac Sulfide

description: Gene expression data from HT29 cells treated withSulindac Sulfide for 48 hours


title: Strain_MC58_RPMI replicate2

description: replicate 2 of 2

source_name: RNA from strain MC58 grown in RPMI

value: MC58 grown in RPMI


title: Strain_α710_RPMI replicate1

description: replicate 1 of 2


title: HT29 treated with AG1478

description: Gene expression data from HT29 cells treated with AG1478 for 48 hours


title: HCT116 treated with Sulindac Sulfone

description: Gene expression data from HCT116 cells treated withSulindac Sulfone for 48 hours

source_name: HCT116 cell line

value: pseudo diploide


title: HCT116 treated with PD98059

description: Gene expression data from HCT116 cells treated with PD98059 for 48 hours


title: Fish/Fungal Fed Liver P450 Reductase knock out  livers replicate 2

city: Lincoln

first: Concetta

middle: Christine

last: DiRusso

state: NE

department: Nutrtion and Health Science

institute: University of Nebraska

description: Gene expression data from livers of liver-specific cytochrome P450 reductase knockout mice

hyb_protocol: Hybridization of cDNA, washing, and scanning of the Affymetrix GeneChip Mouse Genome 430 2.0 [GPL1261]  (containing 45,101 probe sets representing over 34,000 mouse genes) was performed according to standard Affymetrix protocol (performed by The Applied Genomics Technologist Core at the New York State Department of Health, Wadsworth Center).

scan_protocol: standard Affymetrix protocol

data_processing: RMA normalization

organism: Mus musculus

source_name: Livers from 12 week old male mice fed the synthetic diet from week 4 to week 12

label_protocol: Five micrograms of total RNA were used for synthesis of biotinylated antisense RNA (aRNA) with MESSAGEAMPTM aRNA kit from Ambion. The labeled aRNA was then fragmented and stored at   20 °C until hybridization.

growth_protocol: Generation of the founder line with hepatic ablation of POR is described in Wu, et al. ((2003) Genesis 36, 177-181).  Male test animals used in this study had the genotype Alb-Cre+/-/POR-lox+/+ and were called LivPORKOs. For each series of experiments, mice were placed on one of three synthetic diets upon weaning. Siblings of the same genotype were randomized between dietary groups. Upon weaning (four weeks after birth) male mice of each genotype were placed on one of the test diets for eight weeks.

extract_protocol: Total RNA was prepared from individual liver samples using TRIzol (Invitrogen) and was further purified using Qiagen RNeasy mini columns.  To reduce variability between arrays, three RNA samples from individual mice of the same genotype/diet group were pooled using equivalent RNA amounts for each animal.  Three microarrays on three pools were done per genotype/diet.  The quality of RNA was analyzed using an Agilent 2100 Bioanalyzer.

treatment_protocol: 9 mice of each genotype were fed one of the 3 syntheic diet differing only in the fat source: lard, canola or fish/fungal

value: Male Alb-Cre+/-/POR-lox+/+ 12 wk old fed synthetic diet containing 7% fish and fungal oils

value: liver

value: Alb-Cre+/-/POR-lox+/+

tag: diet

value: Fish/Fungal

value: 12 wk


title: Fish/Fungal Fed Control Livers replicate 1

description: Gene expression data from liver of control mice

value: Male  Alb-Cre-/-/POR-lox+/+ 12 wk old fed synthetic diet containing 7% fish and fungal oils

tag: genotype

value: Alb-Cre-/-/POR-lox+/+


title: HCT116 treated with U0126

description: Gene expression data from HCT116 cells treated with U0126 for 48 hours

value: colorectal cancer

tag: age

value: passage not known


title: Fish/Fungal Fed Liver P450 Reductase knock out  livers replicate 1


title: Fish/Fungal Fed Control Livers replicate 2


title: Strain_MC58_RPMI replicate1

description: replicate 1 of 2

value: Pool of all individual RNA´s


title: HT29 treated with DMSO

description: Gene expression data from HT29 cells treated with DMSO for 48 hours (control)

value: aneuploide


title: Canola Fed Liver P450 Reductase knock out livers replicate 1

value: Male Alb-Cre+/-/POR-lox+/+ 12 wk old fed synthetic diet containing 7% canola oil

value: Canola


title: Canola Fed Liver P450 Reductase knock out livers replicate 2


title: Fish/Fungal Fed Control Livers replicate 3


title: Canola Fed Liver P450 Reductase knock out livers replicate 3


title: Canola Fed Control Livers replicate 3

value: Male  Alb-Cre-/-/POR-lox+/+ 12 wk old fed synthetic diet containing 7% canola oil


title: Fish/Fungal Fed Liver P450 Reductase knock out  livers replicate 3


title: Canola Fed Control Livers replicate 1


title: HCT116 treated with AG1478

description: Gene expression data from HCT116 cells treated with AG1478 for 48 hours


title: Lard Fed Liver P450 Reductase knock out livers replicate 1

value: Male  Alb-Cre+/-/POR-lox+/+ 12 wk old fed synthetic diet containing 7% lard

value: Lard


title: Lard Fed Liver P450 Reductase knock out livers replicate 3

value: Male Alb-Cre+/-/POR-lox+/+  12 wk old fed synthetic diet containing 7% lard


title: HCT116 treated with DMSO

description: Gene expression data from HCT116 cells treated with DMSO for 48 hours (control)

value: pseudo diploide


title: HCT116 treated with Sulindac Sulfide

description: Gene expression data from HCT116 cells treated with Sulindac Sulfide for 48 hours


title: Lard Fed Control Livers replicate 3

value: Male  Alb-Cre-/-/POR-lox+/+ 12 wk old fed synthetic diet containing 7% lard

value: liver


title: Lard Fed Control Livers replicate 1

value: Male Alb-Cre-/-/POR-lox+/+ 12 wk old fed synthetic diet containing 7% lard


title: ZR75

status: Public on Oct 08 2010

city: Durham

first: Igor

last: Shats

state: NC

address: 101 Science Drive

institute: Duke University

description: Gene expression data from breast cancer cell lines

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A plus 2.0 arrays. Affymetrix GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with RMA (Robust Multichip Average) using Bioconductor

source_name: Cultured cell line

label_protocol: Biotinylated cRNA were prepared using Ambion MessageAmp Premier labeling kit.

growth_protocol: Subconfuent breast cancer cell lines

extract_protocol: RNeasy mini kit (Qiagen)

treatment_protocol: No treatment

value: breast cancer cell


title: Lard Fed Liver P450 Reductase knock out livers replicate 2

value: Alb-Cre+/-/POR-lox+/+

value: 12 wk


title: BT549


title: MDA-MB-361


title: BT474


title: T47D


title: Hs578t


title: HCC1806


title: MCF7


title: Lard Fed Control Livers replicate 2

value: Alb-Cre-/-/POR-lox+/+


title: HCC1428


title: Canola Fed Control Livers replicate 2


title: MDA-MB-231


title: BT20


title: SKBR3


title: BT483


title: MDA-MB-157


title: SF culture in control medium rep 3

first: Thomas

last: Häupl

address: Charitéplatz 1

department: Rheumatology

institute: Charité

description: gene expression data of human synovial fibroblast cells

hyb_protocol: 50µg/ml of labeled cRNA was hybridized at 45°C for 16h using the Affymetrix GeneChip hybridization oven. Washing and staining was performed on the Affymetrix Fluidics 450 using the EukGE-WS2v4 protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Data were processed with GCOS 1.4 (TGT = 150) and subsequently imported and further analyzed in the online database (www.bioretis.de).

source_name: synovial fibroblast cells in control medium from a healthy knee joint of donor 3

label_protocol: 2µg of total RNA was amplified and labeled using the GeneChip® one-cycle target labeling and control reagents (Affymetrix)

growth_protocol: Olfactory mucosae were immediately placed on ice in DMEM/ HAM’S F12 (Invitrogen, Carlsbad, CA) supplemented with fetal bovine serum (FBS, 10%), penicillin (1%), and streptomycin (1%) and then incubated for 45 min at 37°C in a 2.4 U/mL Dispase II solution (Boehringer). Laminae propriae were carefully separated from the epithelium under a dissection microscope with a microspatula. Sheets of olfactory epithelium were discarded while laminae propriae were cut into pieces using microscissors. Each piece was then placed under a sterile glass coverslip in a well of 4-well plates (Nunc) and fed with 500 μL of serum-containing DMEM/HAM’S F12. Two to three weeks after the initial plating (when confluency was reached), the coverslip was removed, inserted upside down in a well of a 6-well plate, and cells were fed with the same serum-containing medium. When confluent, adherent cells, on both the glass slide and the plastic culture dish, were passaged and replated at a density of 1,000 cells/cm2. For comparison experiments, human olfactory lamina propria stem cells were grown in the culture medium used for bone marrow stem cells. Bone marrow nuclear cells were plated at a density of 5 × 104 cells/cm2 in α-minimum essential medium (α-MEM), supplemented with 10% FBS, 1 ng/mL fibroblast growth factor 2 (FGF2), 100 U/mL penicillin, and 100 μg/mL streptomycin. When cultures reached near confluence, cells were detached with 0.05% trypsin and 0.53 mM ethylene diamine tetracetic acid (EDTA) and subsequently replated at a density of 1,000 cells/cm2. Total RNA was isolated with the RNeasy kit (Qiagen SA., Courtaboeuf, France). For comparison, samples were prepared with similar culture conditions, level of confluency (80%–90%), and equal passaging (P3).

extract_protocol: RNA was collected using the RNeasy mini kit (Qiagen)

treatment_protocol: CD235a+, CD45+ and CD11b+ hematopoietic fractions were isolated from BM samples using MACS (Miltenyi).

value: SF of a female donor cultured in Dulbecco’s Minimum Essential Medium (DMEM) containing 10 % FCS, 100 U/ml penicillin and 100 μg/ml streptomycin


title: SF culture in control medium rep 2

source_name: synovial fibroblast cells in control medium from a healthy knee joint of donor 2

value: SF of a male donor cultured in Dulbecco’s Minimum Essential Medium (DMEM) containing 10 % FCS, 100 U/ml penicillin and 100 μg/ml streptomycin


title: BM-MSC culture rep 8

description: gene expression data of human bone marrow derived mesenchymal stem cells

source_name: bone marrow MSC in culture from normal donor 8

value: BM-MSC of a male donor cultured in alpha-MEM + 10% FCS + 1 ng/mL FGF2  for 1 passage


title: BM-MSC culture rep 9

source_name: bone marrow MSC in culture from normal donor 9

value: BM-MSC of a female donor cultured in alpha-MEM + 10% FCS + 1 ng/mL FGF2  for 1 passage


title: SF culture in control medium rep 1

source_name: synovial fibroblast cells in control medium from a healthy knee joint of donor 1


title: BM-MSC culture rep 7

source_name: bone marrow MSC in culture from normal donor 7


title: SF culture in control medium rep 4

source_name: synovial fibroblast cells in control medium from a healthy knee joint of donor 4


title: Lncap1_MeDNA_IP1

city: Zuerich

first: Mark

last: Robinson

address: Winterthurerstrasse 190

department: Institute of Molecular Life Sciences

country: Switzerland

institute: University of Zuerich

hyb_protocol: As per standard Affymetrix protocol for the Human Promoter 1.0R tiling arrays

data_processing:
All analysis was performed with UCSC hg18 version of the human genome. The data was processed using the MAT (Johnson WE et al PNAS 2006) implementation available in the R/aroma.affymetrix package, as well as the R/Repitools package (Statham AL et al Bioinformatics 2010). Untargeted differentially methylated regions (DMRs) between LNCaP and PrEC cells were determined using the regionStats() procedure in the Repitools package. DMRs at transcription start sites were determined using the blocksStats() procedure in the Repitools package.
The Series supplemental archive 'GSE24546_MeDIP-chip_results.tar' contains the differential methylation calls from the different methods (regionStats_d_ELUTION_5.txt, regionStats_d_MEDIP.txt, regionStats_d_SF.txt) as well as the complete RMA normalized inputs (inputsRMA.txt).

source_name: LNCaP

label_protocol: Samples (7.5μg of DNA) were enzymatically fragmented and labeled using the WT Labeling Kit (Affymetrix) to add biotinylated compound to the ends of the fragments

growth_protocol: 37 deg C with 5% CO2

extract_protocol: The MeDIP assay was performed on 4 µg of sonicated genomic DNA (300-500 bp) in 1x IP buffer (10 mM sodium phosphate pH 7.0, 140 mM NaCl and 0.05% Triton X-100). Ten µg anti-5-methylcytosine mouse monoclonal antibody (Calbiochem clone 162 33 D3 Cat No. NA81) was incubated overnight in 500 µl 1x IP buffer and the DNA/antibody complexes were collected with 80 µl Protein A/G PLUS agarose beads (Santa Cruz sc-2003). The beads were washed 3 times with 1x IP buffer at 4C and twice with 1 ml TE buffer at room temperature. The immune complexes were eluted with freshly prepared 1% SDS, 0.1 M NaHCO3, and the DNA was purified by phenol/chloroform extraction, ethanol precipitation and resuspended in 30 µl H2O.  Immunoprecipitated and Input DNA was amplified with 14 cycles of whole genome amplification (WGA2 kit, Sigma) according to manufacturers instructions.  MBDCap: The MethylMiner™ Methylated DNA Enrichment Kit (Invitrogen) was used to isolate methylated DNA. 1 µg of genomic DNA was sonicated to 100-500 bps. 3.5 µg (7 µl) of MBD-Biotin Protein were coupled to 10 µl of Dynabeads M-280 Streptavidin according to the manufacturer’s instructions. The MBD-magnetic beads conjugates were washed 3 times and resuspended in 1 volume of 1 x Bind/Wash buffer. The capture reaction was performed by adding 1 µg sonicated DNA to the MBD-magnetic beads on a rotating mixer for 1 hour at room temperature. All capture reactions were done in duplicate. The beads were washed three times with 1 x Bind/Wash buffer. The methylated DNA was eluted in one of two ways: (1) as a single fraction with a High Salt Elution Buffer (2000mM NaCl), denoted MBD-SF, or (2) as distinct subpopulations based on the degree of methylation using an increasing NaCl concentration of the elution buffer, from 200mM to 2000mM in a stepwise gradient (Elution 1- 200mM, Elution 2 – 350mM, Elution 3 – 450mM, Elution 4 -600mM, Elution 5 -1000mM and Elution 6 – 2000mM). Each fraction was concentrated by ethanol precipitation using 1 µl glycogen (20 µg/µl), 1/10th volume of 3M sodium acetate, pH 5.2 and two sample volumes of 100% ethanol and resuspended in 60 µl H20.

treatment_protocol: MeDIP

value: cell line

tag: cell source

value: LNCaP

tag: treatment group

value: MeDIP


title: Lncap1_MeDNA_IP2

scan_protocol: As per standard Affymetrix protocol for the Human Promoter 1.0R tiling arrays


title: Berry skin stage 38 Nor38A

city: Mountain Grove

first: Susanne

last: Howard

state: MO

address: 9740 Red Spring Rd

department: William H. Darr School of Agriculture

institute: Missouri State University

description: Berry skins at stage 38

hyb_protocol: One hundred and thirty μL of hybridization solution containing 50 ng/µl of fragmented aRNA was hybridized to the Affymetrix GRAPEGEN GeneChip (Affymetrix, Santa Clara, CA) at 45 ºC for 20 hrs.  After hybridization, the chips were washed and stained with R-phycoerythrin-streptavidin in an Affymetrix fluidics station 450 using fluidics protocol Midi_euk2v3-450.

scan_protocol: The image data were acquired by Affymetrix GeneChip scanner 3000 and Affymetrix GCOS software.

data_processing: The probeset data was processed with the Microarray 5 software using the MAS 5.0 algorithym

organism: Vitis sp. cv. 'Norton'

source_name: Berry skin stage 38

label_protocol: A total of 0.5 μg of total RNA was used to make the biotin-labeled antisense RNA (aRNA) target using the MessageAmpTM Premier RNA amplification kit (Ambion, Austin, TX) following the manufacturer’s protocol.

growth_protocol: Vines are grown in a vineyard at the Missouri State Fruit Experiment Station, Mountain Grove 65711, Missouri, USA. The vinyard is managed by the locally defined best viticultural practices.

extract_protocol: Total RNA was extracted using a CTAB-spermidine buffer according to the the procedure described by Reid et al.Total RNA was treated with 1 unit of DNase I (Ambion, Austin, Texas, USA) for 30 minutes at 37 °C and purified using RNeasy MinElute Cleanup kit (Qiagen, Valencia, CA, USA). RNA quantity and quality were assessed by Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). For cDNA synthesis, two μg of total RNA was reverse transcribed with oligo-dT in a 20 μl reaction mixture using the MultiScribe reverse transcriptase (Applied Biosystems, Branchburg, NJ, USA) according to the manufacturer's instructions.

treatment_protocol: no treatments applied

tag: developmental stage (coombe)

value: berry skin

tag: cultivar

value: Norton


title: Berry skin stage 38 Nor38B

description: Berry skins at stage 38


title: BM-MSC culture rep 4

source_name: bone marrow MSC in culture from normal donor 4


title: BM-MSC culture rep 6

source_name: bone marrow MSC in culture from normal donor 6


title: BM-MSC culture rep 5

source_name: bone marrow MSC in culture from normal donor 5


title: Berry skin stage 37 Nor37A

description: Berry skins at stage 37

source_name: Berry skin stage 37


title: Berry skin stage 38 Nor38C

description: Berry skins at stage 38


title: Olfactory mucosa derived stem cell culture rep 3

description: gene expression data of human olfactory lamina propria stem cells

source_name: olfactory mucosa derived stem cell in culture from normal donor rep 3

value: human olfactory lamina propria stem cells of a male donor cultured in alpha-MEM + 10% FCS + 1 ng/mL FGF2  for 1 passage


title: Olfactory mucosa derived stem cell culture rep 2

source_name: olfactory mucosa derived stem cell in culture from normal donor rep 2

value: human olfactory lamina propria stem cells of a female donor cultured in alpha-MEM + 10% FCS + 1 ng/mL FGF2  for 1 passage


title: Berry skin stage 37 Nor37B

description: Berry skins at stage 37


title: Lncap1_MeDNA_Input1


title: Berry skin stage 36 Nor36A

description: Berry skins at stage 36

source_name: Berry skin stage 36


title: Berry skin stage 36 Nor36B

description: Berry skins at stage 36


title: Berry skin stage 35 Nor35A

description: Berry skins at stage 35

source_name: Berry skin stage 35


title: Berry skin stage 35 Nor35C

description: Berry skins at stage 35


title: Prec1_MeDNA_IP1

source_name: PrEC

value: PrEC


title: Prec1_MeDNA_IP2


title: Berry skin stage 35 Nor35B

description: Berry skins at stage 35


title: Prec1_MeDNA_Input1


title: Berry skin stage 36 Nor36C

description: Berry skins at stage 36


title: Lncap2_MeDNA_IP2


title: Lncap2_MeDNA_Input1


title: Berry skin stage 34 Nor34B

description: Berry skins at stage 34

source_name: Berry skin stage 34


title: Berry skin stage33 Nor33C

description: Berry skins at stage 33

source_name: Berry skin stage33


title: Berry skin stage 34 Nor34C

description: Berry skins at stage 34


title: Berry skin stage 34 Nor34A

description: Berry skins at stage 34


title: Prec2_MeDNA_IP1


title: Berry skin stage33 Nor33B

description: Berry skins at stage 33


title: Prec2_MeDNA_Input1


title: Berry skin stage33 Nor33A

description: Berry skins at stage 33


title: Prec2_MeDNA_IP2


title: Diosgenin

city: Shizuoka

first: Noriyuki

last: Miyoshi

institute: University of Shizuoka

description: Gene expression data from liver of mice administered with diosgenin

hyb_protocol: Aliquots (20 µg) of biotin-labeled cRNA were hybridized to Mouse Genome 430 2.0 Array (Affimetrix).

scan_protocol: After washing steps, the microarray plates were analyzed with a GeneChip Scanner 3000 (Affimetrix).

data_processing: Data analysis was performed using the GeneChip Operating System (GCOS; Affimetrix).

source_name: ICR mouse administered with diosgenin

label_protocol: Aliquots (5 µg) of total RNA pooled from 3 mice were converted to cRNA and labeled with biotin using a one-cycle labeling kit (Affymetrix, Tokyo, Japan).

growth_protocol: Eight-weeks old ICR mice were housed in plastic cages (3 mice/cages) and had free access to drinking water and a basal diet (CRF-1) ad libitum, under controlled conditions of humidity (50±10%), light (12/12 hr light/dark cycle) and temperature (23±2°C). Animals were quarantined for 7 days before starting the supplemented diet.

extract_protocol: Total RNA was extracted from the liver using Rneasy mini kit (QIAGEN).

treatment_protocol: Nine-week old ICR mice were fed with a basal diet (CRF-1) or that containing 500 ppm diosgenin for 4 weeks ad libitum (n = 3 in each group). The mice were sacrificed and organs collected for gene expression analyses were stored in RNAlater solution (Ambion, Austin, TX).

value: 13-week old

tag: treatment

value: Diosgenin

value: ICR

value: liver


title: Olfactory mucosa derived stem cell culture rep 1

source_name: olfactory mucosa derived stem cell in culture from normal donor rep 1


title: ROCHEinput_WGAamp

source_name: ROCHE

value: ROCHE


title: ROCHEinput_unamplified


title: Lncap2_MeDNA_IP1


title: elution_6_LNCaP

treatment_protocol: MBDCap-SF

value: MBDCap-SF


title: elution_6_PrEC


title: Berry skin stage 37 Nor37C

description: Berry skins at stage 37


title: elution_5_PrEC


city: Lausanne

first: Eric

middle: R

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

institute: EPFL

description: Differential expression of genes in liver of mice with a nonfunctional helicase domain of the Wrn protein treated with resveratrol compared to untreated wild type mice. #3 [dye-swap]

hyb_protocol: Hybridization and washing was performed using the in situ Hybridization Plus kit (Agilent) and following the manufacturer's instructions.

scan_protocol: Arrays were scanned on an Axon GenePix® 4000B. Data were extracted from images using GenePix® version 6.0 with local background estimation.

data_processing: Data were processed using limma in BioConductor (www.bioconductor.org). The data were background subtracted using normexp and also normalized using the loess method. Correction for multiple hypothesis testing was performed using Benjamini-Hochberg. The emperical bayes method within limma was used for significant events detection.

source_name: liver from wild type animal #2

label_protocol: Protocol from Agilent

growth_protocol: Mice were maintained on a reversed 12:12-h light-dark cycle with controlled temperature (21 ± 1°C) and humidity. Food and water were provided ad libitum.

extract_protocol: Sambrook et al., 1989. Molecular cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press.

value: wild type

tag: gender

value: Male

value: 9 months

value: liver tissue

source_name: liver from resveratrol Wrn mutant #3

value: Wrn mutant


description: Differential expression of genes in liver of mice with a nonfunctional helicase domain of the Wrn protein treated with resveratrol compared to untreated wild type mice. #2

source_name: liver from wild type animal #4

tag: tissue

source_name: liver from resveratrol Wrn mutant #2


title: LNCaP_input

source_name: LNCaP

value: cell line

value: LNCaP


title: elution_5_LNCaP


title: PrEC_input


title: SssI_El6-1

source_name: SssI

treatment_protocol: M.SssI treated MBDCap-SF

value: SssI

value: M.SssI treated MBDCap-SF


title: SssI_El6-2


title: SssI_El5

treatment_protocol: M.SssI treated MBDCap-Elu5

value: M.SssI treated MBDCap-Elu5


description: Differential expression of genes in liver of mice with a nonfunctional helicase domain of the Wrn protein treated with resveratrol compared to untreated wild type mice. #4 [dye-swap]

source_name: liver from resveratrol Wrn mutant #4


description: Differential expression of genes in liver of mice with a nonfunctional helicase domain of the Wrn protein treated with resveratrol compared to untreated wild type mice. #1

source_name: liver from resveratrol Wrn mutant #1


title: SssI_MeDIP_IP1

treatment_protocol: M.SssI treated MeDIP

value: M.SssI treated MeDIP


title: IL-16 knock-out BMDM_Tw_3_6h

city: Marseille

first: Benoit

last: Desnues

address: 27 boulevard Jean Moulin

department: URMITE UMR CNRS 6236

institute: Faculté de Médecine de la Timone

description: Gene expression after 6 hours infection with T. whipplei of IL-16 knock-out BMDM

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 014868_D_20060807mouse) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: IL-16 knock-out BMDM, 6h, T. whipplei

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 300 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations.  The protocol includes an on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: BMDM were stimulated with T. whipplei (MOI 50) or left untreated in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum. The cultures were incubated for 6 at 37 ºC in a humidified incubator with 5% CO2.

value: IL-16 knock-out Bone-marrow derived macrophages


title: IL-16 knock-out BMDM_Tw_1_6h


title: SssI_MeDIP_IP2


title: Control

description: Gene expression data from liver of mice

source_name: ICR mouse

value: 13-week old

value: Control


title: ROCHEinput_WGA_betaine


title: ROCHEinput_WGA_DMSO


title: ROCHEinput_WGA_ethyleneglycol


title: IL-16 knock-out BMDM_LPS_3_6h

description: Gene expression after 6 hours infection with LPS of IL-16 knock-out BMDM

source_name: IL-16 knock-out BMDM, 6h, LPS

treatment_protocol: BMDM were stimulated E. coli LPS (100 ng/ml) or left untreated in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum. The cultures were incubated for 6 at 37 ºC in a humidified incubator with 5% CO2.


title: IL-16 knock-out BMDM_LPS_2_6h


title: ROCHEinput_WGA_12propanediol


title: ROCHEinput_WTA


title: IL-16 knock-out BMDM_Tw_2_6h


title: BMDM_LPS_3_6h

description: Gene expression after 6 hours infection with LPS of BMDM

source_name: BMDM, 6h, LPS

treatment_protocol: BMDM were stimulated with E. coli LPS (100 ng/ml) or left untreated in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum. The cultures were incubated for 6 at 37 ºC in a humidified incubator with 5% CO2.

value: Bone-marrow derived macrophages


title: IL-16 knock-out BMDM_control_3_6h

description: Gene expression after 6 hours incubation of uninfected IL-16 knock-out BMDM

source_name: IL-16 knock-out BMDM, 6h, control


title: IL-16 knock-out BMDM_control_2_6h


title: BMDM_LPS_1_6h


title: Cord Blood Mesenchymal Stomal Cells 2

city: Ann Arbor

first: Marc

middle: B

last: Hershenson

state: MI

address: 1150 W Medical Center Dr

department: Pediatrics

institute: University of Michigan Medical School

description: Biological Replicate 2

hyb_protocol: Per standard Illumina hybridization protocol, cRNA was hybridized to HumanRef-8 v3 Expression BeadChips for 16 hours at 58 degrees

scan_protocol: Per standard Illumina hybridization protocol, BeadChips were scanned using an Illumina BeadArray Reader to generate .idat files which were analyzed with the GenomeStudio Data Analysis Software with Gene Expression Module (Illumina, Inc.).

data_processing: The data were normalised using average normalisation with the Illumina GenomeStudio Gene Expression Analysis Module v1.7.0.  Software framework: Illumina GenomeStudioV2010.2.

source_name: Cord Blood

label_protocol: Total RNA was used to generate biotinylated amplified cRNA with the Illumina TotalPrep RNA Amplification Kit (Applied Biosystems)

extract_protocol: QIAGEN RNeasy Mini Kit

value: Mesenchymal Stomal Cells

value: Cord Blood

tag: chip#


title: Cord Blood Mesenchymal Stomal Cells 1

description: Biological Replicate 1


title: Lung Fibroblast 1

description: Biological Replicate 1

source_name: Lung

value: Fibroblast Cells

value: Lung


title: BMDM_LPS_2_6h


title: Lung Fibroblast 2

description: Biological Replicate 2


title: ROCHEinput_WGA

value: ROCHE


title: IL-16 knock-out BMDM_LPS_1_6h


title: Lung Mesenchymal Stomal Cells 4

description: Biological Replicate 4


title: necrotic synthetic wheat-seedling shoot meristem with low temperature-rep2

status: Public on Oct 07 2010

city: Kobe

first: Shigeo

last: Takumi

state: Hyogo

address: Rokkodai 1-1, Nada

department: Graduate School of Agricultural Science

institute: Kobe University

description: Gene expression in shoot apical meristem under low temperature

hyb_protocol: Hybridization of the Cy3-labeled cRNA to the microarrays and washing were performed using a Gene Expression Hybridization kit and Gene Expression Wash Pack (Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: Signal intensities were detected by Feature Extraction software (Agilent Technologies). Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Triticum aestivum

source_name: synthetic hexaploid wheat

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted, using an RNeasy Plant Mini kit (Qiagen). RNA quality was checked using an Agilent 2100 BioAnalyzer.

treatment_protocol: Plants were grown at 23°C for 3 weeks, and then incubated at 4°C for 6 weeks.

value: shoots containig shoot apical meristem

tag: phenotype

value: cold-induced hybrid necrosis


title: Lung Mesenchymal Stomal Cells 3

description: Biological Replicate 3


title: wild type synthetic wheat-seedling shoot meristem with low temperature-rep1

value: wild-type


title: IL-16 knock-out BMDM_control_1_6h


title: Lung Fibroblast 3

description: Biological Replicate 3


title: Lung Mesenchymal Stomal Cells 2

description: Biological Replicate 2


title: necrotic synthetic wheat-seedling leaf with low temperature-rep2

description: Gene expression in 3-week-old seedling leaves under low temperature

treatment_protocol: Plants were grown at 23°C for 3 weeks, and then incubated at 4°C for 12 weeks.

value: leaf


title: necrotic synthetic wheat-seedling leaf with low temperature-rep1


title: wild type synthetic wheat-seedling leaf with low temperature-rep2


title: necrotic synthetic wheat-seedling leaf-rep2

description: Gene expression in 3-week-old seedling leaves

treatment_protocol: Plants were grown at 23°C for 3 weeks


title: necrotic synthetic wheat-seedling leaf-rep1


title: genotype: Robust - time: 3 days - rep1

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

description: Robust grains after 3 days of germination replication 1

hyb_protocol: Affy- Eukaryotic Target Hybridization

scan_protocol: Affy- Array Scanning

data_processing: The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org). The target value is 500 for all cases. The code was developed using R2.4.1, Bioconductor 1.9, and simpleaffy 2.8.0. The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html. The normalization scripts are available from the PLEXdb team by request.

organism: Hordeum vulgare

source_name: seed (genotype: Robust - time: 3 days)

label_protocol: Affymetrix one-cycle target labeling

extract_protocol: Trizol RNA extraction followed by RNeasy purification

tag: germplasm name

value: hv cv. robust

tag: organism part

tag: development stage

tag: growth media

value: not specified

value: 3 days


title: genotype: Robust - time: 0 days - rep3

description: Robust grains after steeping replication 3

source_name: seed (genotype: Robust - time: 0 days)

value: 0 days


title: genotype: Stander - time: 0 days - rep3

description: Stander grains after steeping replication 3

source_name: seed (genotype: Stander - time: 0 days)

value: hv cv. stander


title: genotype: Morex - time: 3 days - rep3

description: Morex grains after 3 days of germination replication 3

source_name: seed (genotype: Morex - time: 3 days)

value: hv cv. morex


title: genotype: Robust - time: 3 days - rep3

description: Robust grains after 3 days of germination replication 3


title: genotype: Morex - time: 0 days - rep1

description: Morex grains after steeping replication 1

source_name: seed (genotype: Morex - time: 0 days)


title: genotype: Morex - time: 3 days - rep2

description: Morex grains after 3 days of germination replication 2


title: genotype: Manker - time: 3 days - rep2

description: Manker grains after 3 days of germination replication 2

source_name: seed (genotype: Manker - time: 3 days)

value: hv cv. manker


title: genotype: Robust - time: 0 days - rep2

description: Robust grains after steeping replication 2


title: genotype: Stander - time: 3 days - rep1

description: Stander grains after 3 days of germination replication 1

source_name: seed (genotype: Stander - time: 3 days)


title: genotype: Robust - time: 0 days - rep1

description: Robust grains after steeping replication 1


title: genotype: Morex - time: 0 days - rep2

description: Morex grains after steeping replication 2


title: genotype: Stander - time: 3 days - rep2

description: Stander grains after 3 days of germination replication 2


title: genotype: Morex - time: 0 days - rep3

description: Morex grains after steeping replication 3