title: BY4742-089_02mM-vs-untreated-rep1

city: Torino

first: Irene

last: Stefanini

address: via Accademia Albertina

country: Italy

institute: University of Turin

description: Fluorescent cDNA bound to the microarray was detected with a GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA, USA).

hyb_protocol: Reagents and Materials Nuclease Free Water SSC BUFFER 20X and 3X 10% SDS Ultrafree-MC 0.45µm centrifugal filter devices - Millipore #UFC30HVNB Thin-Wall PCR Tubes 0.5ml Slide Hybridization Chamber	- Telechem International Inc #AHC-1 Lifter (cover) Slips - Erie Scientific Company #22X50I-2-4711 Water bath at 65°C Microcentrifuge Thermocycler Scanner HYBRIDIZATION 1.	Add the following reagents to each 70 µl probe: 20x SSC		8.4µl 1M HEPES, pH 7.5	1.34µl 2.	For each combined probe, add 10 µl of nuclease free water to a 0.45 microfilter unit, and centrifuge it at 18,300 x g for 1 minute. 3.	Discard the effluent and collection tubes, and add each filter unit to fresh 1.5 ml collection tubes. 4.	Add a probe sample to each of these tubes, and centrifuge at 18,300 x g for 1 minute. 5.	To each effluent-probe add 1.26 µl  of 10% SDS. 6.	Transfer each probe sample to individually labeled PCR tubes, vortex, and centrifuge briefly to ensure sample is at the bottom of these tubes. 7.	Place tubes in thermocycler, denature 100C for 2 minutes. Use the hot bonnet. 8.	During this incubation, prepare the Slide Hybridization Chambers.  Remove dust from the chambers using a stream of pressurized inert gas. Place microarray slides upright in these chambers. Select an appropriate size Lifter Slip, clean using pressurized gas, and place onto the appropriate area of the microarray, making sure the "lifters" are face-down on the slide. 9.	Pipette 120 µl of 3X SSC into both of the chamber's hydration wells. 10.	After the above incubation, pipette the probe samples onto the appropriate arrays.  Place the pipette tip at the open interface of the Lifter Slip and the array, without touching either. Slowly pipette the sample, filling the entire area under the Lifter Slip. Pipette the entire sample, even if the sample starts to protrude from the sides of the slip.  This will ensure against drying.  If after pipetting, the probe sample does not fill the entire Lifter Slip area, carefully press down onto the slip with a pipette tip. 11.	Secure the covers on the hybridization chambers. Slightly tighten the screws with a screwdriver. 12.	Place the hybridization chambers into a 65C water bath, and incubate overnight in total darkness. POST-HYBRIDIZATION SLIDES WASHING Pre-procedure a. Prepare the following solutions, and place them into tanks. Wash Solution 1:	387 ml Milli-Q Water 12 ml 20X SSC 1 ml 10% SDS Wash Solution 2:	798ml Milli-Q Water 2 ml 20X SSC b. Prepare a slide rack with the appropriate number of balance slides, and place in centrifuge on rotor-platform. c. Set centrifuge settings at 1500rpm, 2 min, and 25C. Protocol 1.	Place a slide rack into the tank containing Wash Solution 1. 2.	Remove the hybridization chambers from the water bath while keeping them level. 3.	Remove each slide from the chambers using forceps. 4.	Invert each slide within Wash Solution 1, and agitate until Lifter Slips fall off. 5.	Repeat for each slide. 6.	Place slides in rack within Wash Solution 2. 7.	Plunge rack up and down 40 times within this solution. Wash with energy. 8.	Quickly transfer rack to rotor-platform, and spin dry. 9.	Scan slides as soon as possible.

scan_protocol: 1. Turn on scanner, start GenePix software 2. Slide scanner door open. Insert chip side down with label facing towards you into scanner. Clip the chip holder easily around the slide. 3. Set PMT’s to 600 in both 635 nm (Cy5) and 532 (Cy3) channels. These settings are controlled in the “hardware settings” window. 4. Perform low resolution “preview scan” to determine location of the spots and initial hybridization intensities. 5. Once you have determined scan location, draw a “scan area” marquis around the entire array. 6. Perform a quick visual inspection of hybridization and make initial adjustments to PMT’s. 7. For gene-expression experiments, you would like the ratio over the entire scan area to range from 0.8 to 1.2. You will want to raise or lower the red and green PMTs to achieve the right balance. This will be performed more stringently later. 8. Perform a high-resolution “data-scan”. As the image is scanning, go to the “histogram” tab located at the top of the screen. The histogram allows you to dynamically observe the relative intensities to both channels as you scan. 9. Observe the histograms and make adjustments to PMT’s. 10. Once the PMT levels have been set so that the intensity ratio is near 1.00 and there are no saturated features perform a “data scan” over the “scan area” and save the results. 11. To save your image, go to the “open/save” button and select “save images”. 12. We like to save as type=multi-image TIFF files and using a appropriate naming. 13. Open image with GenePixPro and load the appropriate GAL file (“load array list”) 14. Align features of the GAL file with your image. You might need some manual alignment step. 15. One the image and the GAL file are perfectly aligned, you can start image analysis. 16. Save results of your analysis with appropriate naming. The output file is a GPR file.

data_processing: The control microarray spot quality required following features: 50% as the minimum percentage of pixels for which the foreground intensity was greater than the background intensity + 2 standard deviations; 80 pixels as the minimum number of pixels; absence of saturated pixels. Median values for foreground and background for each channel were normalized using MIDAW web tool. For the selection of differentially expressed genes (DEGs) a fold change cut-off of 1.5, filtered by variance coefficient, was used.

source_name: yeast, strain BY4742, treated with 089 0.2 mM, 4 hours

label_protocol:
Reagents and Materials
Nuclease Free Water
Oligo(dT)12-18 Primer
Hexanucleotide Mix 10X
Superscript II Reverse Transcriptase Kit - Invitrogen # 18064-014
Aminoallyl dUTP (AA-dUTP) 100mM in nuclease free water
1N Sodium Hydroxide
EDTA 0.5M, pH 8.0
HEPES 1M,  pH 7.5
Sodium Bicarbonate 1M, pH 9.0
Cy3 Mono-Reactive Dye Pack
Cy5 Mono-Reactive Dye Pack
DMSO
PCR Purification Kit - Qiagen #28106
Microcon YM-30 centrifugal filter devices	- Millipore # 42410
Speed-vac
Microcentrifuge
Thermocycler
Pre-procedure
a.	Prepare Cy3 e Cy5 aliquots: Work away from direct light sources. Resuspend the dye powder in 20 µl of DMSO. Aliquot 2 µl of the suspension in 10 nuclease free tubes, appropriately labelled. Let the aliquots completely dry in a speed-vac. Generally it takes about 1 hour. Store the aliquots at 4°C and use within 2 months from preparation.
b.	Prepare Primer Solution: Combine equal volumes of Oligo(dT)12-18 Primer and Hexanucleotide Mix 10X
c.	Prepare 50X Aminoallyl-dUTP/dNTP Solution:
100mM dATP		10µl
100mM dCTP		10µl
100mM dGTP		10µl
100mM dTTP		6µl
100mM AA-dUPT		4µl
RETROTRANSCRIPTION
1.	For each reaction, calculate the volume of sample needed to process 35-40 µg of total RNA.  If this volume exceeds 14.5 µl, the RNA source sample will require concentrating.
2.	Add samples to PCR tubes, and bring their volumes to 14.5ul with nuclease free water.  Keep these tubes at on ice.
3.	Add 2 µl of the Primer Solution to each tube. Cap, vortex, and briefly centrifuge each.
4.	Place these reaction tubes into a thermocycler, and  incubate at 70C for 10 minutes. Put on ice for at least 5 minutes. Spin down.
5.	During this incubation, prepare the following Reaction Solution (x1 ):
5x Buffer				6 µl
50x Amino Allyl-dUTP/dNTP 		0.8 µl
0.1M DTT				3 µl
DEPC Water			2 µl
Total Volume			11.8µl
6.	Once the above incubation is complete add 11.8 µl  of the Reaction Solution to each tube.
7.	Add 2 µl  of Superscript II Reverse Transcriptase to each tube, and briefly vortex.
8.	Place these tubes into a thermocycler, and incubate at 42C for between two and three hours. After 1.5 hours add 1 µl of Superscript II Reverse Transcriptase to each tube.
9.	After the 2-3 hour incubation, remove the tubes from the thermocycler and add 10 µl of 1N NaOH and 10 µl of 0.5M EDTA to each.
10.	Vortex each tube and incubate for 15 minutes using the thermocycler  at 65C.
11.	After this incubation, add 25 µl of 1M HEPES to each tube.
CLEAN UP
12.	For each sample, weigh and label a Microcon YM-30 filter, and assemble with its collection tube.
13.	Add 450 µl of nuclease free water to each tube, and transfer samples to the appropriately labeled YM-30 filters unit.
14.	Centrifuge these units at 10,000 x g for 8 minutes.
15.	Remove the effluent from the collection tubes, and add 470 µl of nuclease water to the filter units.
16.	Again, centrifuge for 10,000 x g for 8 minutes.
17.	Remove the YM-30 filter units from their collection tubes and weigh in order to determine the retained liquid volume: 1mg = 1µl
18.	Continue centrifuging these units at 10,000 x g until the volume is between 10 µl and 18 µl.
Use the following chart to estimate duration.
> 100 µl		4 min
50-99 µl		2 min
25-49 µl	  	1 min
< 25 µl		Pulse to 10,000 x g, then stop
Avoid centrifuging to dryness, as it will be impossible to recover the sample.
19.	Invert the filter into a clean collection tube, and centrifuge for 1,900 x g for 5 minutes.
20.	Adjust the volume to 10 µl (avoid to have more volume!!).
COUPLING
21.	Add 1 µl of the Sodium Bicarbonate solution to each collected sample.
22.	Pipette each of these samples into an appropriate labeled Cy-dye tube. Vortex, and centrifuge to ensure that the liquid is at the bottom of the tube.
23.	Incubate this dye-probe coupling reaction for at least 1 hour at room temperature in total darkness.
PROBE PURIFICATION
24.	Add 50 µl of nuclease free water to each reaction tube and 20 µl of Sodium Acetate 3M pH 5.5.
25.	Add 500 µl of PB Buffer (from the PCR Purification Kit) to each tube.
26.	Add these solutions to appropriately labeled Qiaquick columns (from the PCR Purification Kit).
27.	Centrifuge at 18,300 x g for 1 minute.
28.	Decant the effluent from the collection tubes, and observe the columns' glass-fiber filters.  Successful probe synthesis will be indicated by obvious blue and pink tints to these filters.
29.	Add 700 µl of PE Buffer to each column, centrifuge at 18,300 x g for 1 minute. Decant effluent.
30.	Repeat step #29.
31.	Centrifuge the columns again, empty, to ensure dryness.
32.	Place the columns into fresh 1.5 ml collection tubes.
33.	Add 30 µl of EB Buffer to the columns' glass-fiber surface, incubate at room temperature for 5 minutes and centrifuge at 18,300 x g for 1 minute.
34.	Repeat step #33.
35.	Assemble one YM-30 filter unit for each dual-hybridization sample. Into each unit, combine the appropriate 60 µl of collected Cy3 and Cy5 labeled probes purified above.
36.	Centrifuge the filter units at 10,000 x g for 1’ 30”.
37.	Invert the filter into a fresh collection tube, and centrifuge at 1,900 x g for 5 minutes.
38.	Adjust the collected probe solution to 70 µl with nuclease free water.

growth_protocol: Yeast cells at the concentration of 10^9 cells/ml were treated in YPD (Yeast Extract 1%, Peptone 2%, Glucose 2%, pH 4.8) added with 089 0.2 mM and incubated in shaking at 28 °C for four hours

extract_protocol:
Reagents and Materials
AE Buffer (50mM Sodium Acetate pH 5.5, 1mM EDTA)
Acid Phenol:Chloroform (5:1 solution pH 4.5±0.2)
10% SDS
Chloroform
Ethanol 96%
Ethanol 70%
3M NaAcetate (pH 5.5)
1,5 ml microcentrifuge tubes
Water bath at 65°C.
Thermo-block at 65°C.
Microcentrifuge at 4°C.
Fume hood.
NanoDrop 1000 Spectrophotometer
Pre-procedure
a.	Pre-heat a water bath at 65°C and warm Phenol-Chloroform.
b.	Pre-heat a thermo-block at 65°C.
c.	Cool a centrifuge at 4°C.
d.	Aliquot 50µl of 10% SDS in a number of microcentrifuge tubes corresponding to the number of samples.
Protocol
1.	Harvest yeast cells by centrifuging at 4°C.
2.	Working on ice, resuspend the pellet in 450µl of AE buffer. Transfer each sample in an appropriately labelled microcentrifuge tube containing 50µl 10% SDS and briefly vortex.
3.	Add 500µl of pre-heated Acid Phenol:Chloroform and vortex for 10 seconds.
4.	Incubate at 65°C for exactly 10 minutes and vortex each sample every minute. During this incubation keep Acid Phenol:Chloroform in the heated water bath.
5.	Incubate at least 5 minutes on ice.
6.	Centrifuge at 12000-14000 rpm for 5 minutes at 4°C.
7.	Transfer the upper aqueous phase into a fresh appropriately labelled tube and add an equal volume (500µl) of pre-heated Acid Phenol:Choloroform for further purification.
8.	Vortex and centrifuge at 12000-14000 rpm for 5 minutes at 4°C.
9.	Transfer the upper aqueous phase into a fresh appropriately labelled tube and add an equal volume (500µl) of Chloroform.
10.	Vortex and centrifuge at 12000-14000 rpm for 5 minutes at 4°C.
11.	Transfer the upper aqueous phase into a fresh appropriately labelled tube and add 1/10 volume (50µl) of Sodium Acetate 3M pH 5.5 and 2 volume (1ml) of 96% Ethanol.
12.	Precipitate over-night at -20°C.
13.	The day after (Always work on ice with gloves)
14.	Centrifuge at 12000-14000 rpm 4°C for at least 20 minutes. A with pellet should appear at the bottom of the tube.

treatment_protocol: Yeast cells at the concentration of 10^9 cells/ml were treated in YPD (pH 4.8) added with 089 0.2 mM and incubated in shaking at 28 °C for four hours. Then they were washed with wather, precipitated and Nitrogen-freezed.

tag: strain

value: BY4742 [BY4742 MATα his3 leu2 lys2 ura3]

tag: agent

source_name: yeast, strain BY4742, 4 hours

growth_protocol: Yeast cells at the concentration of 10^9 cells/ml were grown in YPD (Yeast Extract 1%, Peptone 2%, Glucose 2%, pH 4.8) and incubated in shaking at 28 °C for four hours

treatment_protocol: Yeast cells at the concentration of 10^9 cells/ml were grown in YPD (pH 4.8) and incubated in shaking at 28 °C for four hours. Then they were washed with wather, precipitated and Nitrogen-freezed.

value: untreated


title: IHP rep2 vs ILP rep2 dye swap

status: Public on Dec 11 2009

type: RNA

city: Urbana

first: Stephen

middle: Patrick

last: Moose

state: IL

address: 1201 W Gregory

department: Crop Sciences

country: USA

institute: University of Illinois at Urbana-Champaign

hyb_protocol: Hybridizations were performed overnight in custom designed cassettes in 42 degree water bath, followed by 3 washes.

scan_protocol: Scanned on a Genepix 4000B scanner (Molecular Devices Corporation, Sunnyvale, CA). Used GenePix Pro 6.0 (Molecular Devices Corporation) for spotfinding.

data_processing: A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.

molecule: total RNA

organism: Zea mays

source_name: Total RNA from Illinois Low Protein labeled with Cyanine-5 (red)

label_protocol: The Amino Allyl MessageAmp™ II aRNA Amplification kit (Ambion, Austin, TX) with Cyanine-3 and -5 (GE Healthcare Bio-Sciences Corp., Piscataway, NJ) dyes were used to amplify and label samples.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen, Carlsbad, CA), digested by DNAse, then Rneasy purification kit (Qiagen, Valencia, CA).

tag: genotype

value: Illinois Low Protein line

tag: age

value: 8 Days after Pollination

tag: tissue

value: leaf

source_name: Total RNA from Illinois High Protein labeled with Cyanine-3 (green)

value: Illinois High Protein line


title: BY4742dsnq2-089_02mM-vs-untreated-rep1

organism: Saccharomyces cerevisiae

source_name: yeast, strain BY4742dsnq2, treated with 089 0.2 mM, 4 hours.

value: BY4742dsnq2 [by4742dsnq2 matα his3 leu2 lys2 ura3 snq2::kanMX]

source_name: yeast, strain BY4742dsnq2, 4 hours


title: IHP rep2 vs ILP rep2

source_name: Total RNA from Illinois High Protein labeled with Cyanine-5 (red)

source_name: Total RNA from Illinois Low Protein labeled with Cyanine-3 (green)


title: BY4742derg6-089_02mM-vs-untreated-rep1

source_name: yeast, strain BY4742derg6, treated with 089 0.2 mM, 4 hours

value: BY4742derg6 [by4742derg6 matα his3 leu2 lys2 ura3 erg6::kanMX4]

source_name: yeast, strain BY4742derg6, 4 hours


title: BY4742derg6-089_02mM-vs-untreated-rep2


title: Schmidt_DS-C2_Rep2_ATH1

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

description: After sowing on plates, seeds were stored in the dark at 4C for 3 days. Dry surface-sterilisation with chlorine gas generated by 100 ml household bleach and 3 ml concentrated HCl. Growth Room. Commercial soil: Scotts Levington Special Custom Mix Compost with Intercept 5GR 20C 70%.

hyb_protocol: Biotin Labelled cRNA using "Affymetrix GeneChip Hybridization, Wash and Stain Kit", according to guidelines set out by Affymetrix, Santa Clara, CA

scan_protocol: Scanned according to guidelines set out by Affymetrix, Santa Clara, CA.

data_processing: Raw data from the microarrays was normalized at probe-level using MAS5 algorithm. The detection calls (present, marginal, absent) for each probe set was obtained using the GCOS system

label: biotin

organism: Arabidopsis thaliana

label_protocol: Labelled using protocol described in manual "Affymetrix GeneChip Expression Analysis Technical Manual", One-Cycle target labelling

growth_protocol: Seeds of Arabidopsis thaliana ecotype Columbia (Col-0) and PVIP1 and PVIP2 RNAi transgenic lines (pvip1/pvip2; Dunoyer et al 2004, J Virol 78: 2301) were surface-sterilised in a desiccator by chlorine gas generated with a mixture of 100 ml commercial bleach and 3 ml concentrated hydrochloric acid for 4 h. Seeds were sown on MS agar (0.8%) that contained 20 mg/l phosphinothricin (Basta) for the pvip1/pvip2 line. After stratification in the dark at 4C for 3 days, the plates with the seeds were transferred to a growth room (20C, 16 h light). 14 days after germination, Col-0 plants and Basta-resistant pvip1/pvip2 plants were transferred to soil (Scotts Levington Special Custom Mix Compost with Intercept 5GR) and grown under short-day conditions (20C, 8 h light, 70% relative air humidity) for 3 weeks.

extract_protocol: Qiagen RNAeasy kit protocol

tag: ecotype

value: wildtype

tag: developmental stage

value: 35 days (1.13- Boyes Key)

value: whole rosettes


title: BY4742-089_02mM-vs-untreated-rep2


title: BY4742dsnq2-089_02mM-vs-untreated-rep2

label_protocol:
Reagents and Materials
Nuclease Free Water
Oligo(dT)12-18 Primer
Hexanucleotide Mix 10X
Superscript II Reverse Transcriptase Kit - Invitrogen # 18064-014
Aminoallyl dUTP (AA-dUTP) 100mM in nuclease free water
1N Sodium Hydroxide
EDTA 0.5M, pH 8.0
HEPES 1M,  pH 7.5
Sodium Bicarbonate 1M, pH 9.0
Cy3 Mono-Reactive Dye Pack
Cy5 Mono-Reactive Dye Pack
DMSO
PCR Purification Kit - Qiagen #28106
Microcon YM-30 centrifugal filter devices	- Millipore # 42410
Speed-vac
Microcentrifuge
Thermocycler
Pre-procedure
a.	Prepare Cy3 e Cy5 aliquots: Work away from direct light sources. Resuspend the dye powder in 20 µl of DMSO. Aliquot 2 µl of the suspension in 10 nuclease free tubes, appropriately labelled. Let the aliquots completely dry in a speed-vac. Generally it takes about 1 hour. Store the aliquots at 4°C and use within 2 months from preparation.
b.	Prepare Primer Solution: Combine equal volumes of Oligo(dT)12-18 Primer and Hexanucleotide Mix 10X
c.	Prepare 50X Aminoallyl-dUTP/dNTP Solution:
100mM dATP		10µl
100mM dCTP		10µl
100mM dGTP		10µl
100mM dTTP		6µl
100mM AA-dUPT		4µl
RETROTRANSCRIPTION
1.	For each reaction, calculate the volume of sample needed to process 35-40 µg of total RNA.  If this volume exceeds 14.5 µl, the RNA source sample will require concentrating.
2.	Add samples to PCR tubes, and bring their volumes to 14.5ul with nuclease free water.  Keep these tubes at on ice.
3.	Add 2 µl of the Primer Solution to each tube. Cap, vortex, and briefly centrifuge each.
4.	Place these reaction tubes into a thermocycler, and  incubate at 70°C for 10 minutes. Put on ice for at least 5 minutes. Spin down.
5.	During this incubation, prepare the following Reaction Solution (x1 ):
5x Buffer				6 µl
50x Amino Allyl-dUTP/dNTP 		0.8 µl
0.1M DTT				3 µl
DEPC Water			2 µl
Total Volume			11.8µl
6.	Once the above incubation is complete add 11.8 µl  of the Reaction Solution to each tube.
7.	Add 2 µl  of Superscript II Reverse Transcriptase to each tube, and briefly vortex.
8.	Place these tubes into a thermocycler, and incubate at 42C for between two and three hours. After 1.5 hours add 1 µl of Superscript II Reverse Transcriptase to each tube.
9.	After the 2-3 hour incubation, remove the tubes from the thermocycler and add 10 µl of 1N NaOH and 10 µl of 0.5M EDTA to each.
10.	Vortex each tube and incubate for 15 minutes using the thermocycler  at 65°C.
11.	After this incubation, add 25 µl of 1M HEPES to each tube.
CLEAN UP
12.	For each sample, weigh and label a Microcon YM-30 filter, and assemble with its collection tube.
13.	Add 450 µl of nuclease free water to each tube, and transfer samples to the appropriately labeled YM-30 filters unit.
14.	Centrifuge these units at 10,000 x g for 8 minutes.
15.	Remove the effluent from the collection tubes, and add 470 µl of nuclease water to the filter units.
16.	Again, centrifuge for 10,000 x g for 8 minutes.
17.	Remove the YM-30 filter units from their collection tubes and weigh in order to determine the retained liquid volume: 1mg = 1µl
18.	Continue centrifuging these units at 10,000 x g until the volume is between 10 µl and 18 µl.
Use the following chart to estimate duration.
> 100 µl		4 min
50-99 µl		2 min
25-49 µl	  	1 min
< 25 µl		Pulse to 10,000 x g, then stop
Avoid centrifuging to dryness, as it will be impossible to recover the sample.
19.	Invert the filter into a clean collection tube, and centrifuge for 1,900 x g for 5 minutes.
20.	Adjust the volume to 10 µl (avoid to have more volume!!).
COUPLING
21.	Add 1 µl of the Sodium Bicarbonate solution to each collected sample.
22.	Pipette each of these samples into an appropriate labeled Cy-dye tube. Vortex, and centrifuge to ensure that the liquid is at the bottom of the tube.
23.	Incubate this dye-probe coupling reaction for at least 1 hour at room temperature in total darkness.
PROBE PURIFICATION
24.	Add 50 µl of nuclease free water to each reaction tube and 20 µl of Sodium Acetate 3M pH 5.5.
25.	Add 500 µl of PB Buffer (from the PCR Purification Kit) to each tube.
26.	Add these solutions to appropriately labeled Qiaquick columns (from the PCR Purification Kit).
27.	Centrifuge at 18,300 x g for 1 minute.
28.	Decant the effluent from the collection tubes, and observe the columns' glass-fiber filters.  Successful probe synthesis will be indicated by obvious blue and pink tints to these filters.
29.	Add 700 µl of PE Buffer to each column, centrifuge at 18,300 x g for 1 minute. Decant effluent.
30.	Repeat step #29.
31.	Centrifuge the columns again, empty, to ensure dryness.
32.	Place the columns into fresh 1.5 ml collection tubes.
33.	Add 30 µl of EB Buffer to the columns' glass-fiber surface, incubate at room temperature for 5 minutes and centrifuge at 18,300 x g for 1 minute.
34.	Repeat step #33.
35.	Assemble one YM-30 filter unit for each dual-hybridization sample. Into each unit, combine the appropriate 60 µl of collected Cy3 and Cy5 labeled probes purified above.
36.	Centrifuge the filter units at 10,000 x g for 1’ 30”.
37.	Invert the filter into a fresh collection tube, and centrifuge at 1,900 x g for 5 minutes.
38.	Adjust the collected probe solution to 70 µl with nuclease free water.

source_name: yeast, strain BY4742dsnq2, 4 hours.


title: Schmidt_DS-C3_Re3p_ATH1

institute: Nottingham Arabidopsis Stock Centre (NASC)


title: IHP rep1 vs ILP rep1 dye swap


title: Schmidt_DS-M2_Rep2_ATH1

tag: genetic background

tag: genetic variation

value: RNAi - gene knock out

value: pvip1;pvip2 double-knockout


title: Schmidt_DS-M1_Rep1_ATH1


title: Peri-implantation D11 embryo -experimental 2

status: Public on Dec 10 2009

city: Beltsville

first: Le Ann

last: Blomberg

state: MD

address: 10300 Baltimore Ave

department: ANRI

institute: USDA-ARS

hyb_protocol: Labeled cRNA was fragmented in 1X fragmentation buffer (Agilent) with 2X blocking agent (Agilent) for 30 minutes at 60C.  An equal volume of fragmented cRNA and 2X GEx hybridization buffer HI-RPM were mixed and placed on arrays.  Hybridization was carried out for 17 hrs at 65C at 10 rpm in the Agilent SureHyb chamber. Arrays were disassembled in rm temperature GE wash buffer 1. Washed 1X in GE wash buffer 1 at rm temperature for 1 min. Washed 1X in GE wash buffer 2 at 37C for 1 min. Washed 1X in 100% acetonitrile 1 min. Stabilized in stablization buffer 30 sec.

scan_protocol: Scanned with the Agilent scanner. Cy3 red 100%; green 10% Cy5 green 100%; red 10% Scan 5 uM Extended dynamic range scan

data_processing:
Agilent scanner - Feature Extraction Software
Protocol GE2-v5 for two color.

organism: Sus scrofa

source_name: RNA from D11 7-8 mm ovoid embryo in early elongation - experimental 2

label_protocol: RNA labeled using Agilent low RNA input amplification kit.cRNA was quantified after labeling with the NanoDrop Microarray Measurement feature.

extract_protocol: Total RNA extracted with Qiagen MicroRNeasy Kit with on column digest with DNase I.  Integrity and quantification analyzed with BioAnalyzer 2100 RNA Nanochip.

value: embryos (collected from large white hybrid pigs)

label_protocol: RNA labeled using Agilent low RNA input amplification kit. cRNA was quantified after labeling with the NanoDrop Microarray Measurement feature.


title: Peri-implantation D11 embryo - experimental 3

source_name: RNA from D11 7-8 mm ovoid embryo in early elongation - experimental 3


title: Peri-implantation D11 embryo - experimental 1

source_name: RNA from D11 7-8 mm ovoid embryo in early elongation - experimental 1


title: Schmidt_DS-C1_Rep1_ATH1


title: Peri-implantation D11 embryo - control 2

source_name: RNA from D11 7-8 mm ovoid embryo in early elongation - control 2


title: Peri-implantation D11 embryo - control 1

source_name: RNA from D11 7-8 mm ovoid embryo in early elongation - control 1


title: Peri-implantation D11 embryo - control 3

source_name: RNA from D11 7-8 mm ovoid embryo in early elongation - control 3


title: Peri-implantation D11 embryo - experimental 4

source_name: RNA from D11 7-8 mm ovoid embryo in early elongation - experimental 4


title: Schmidt_DS-M3_Rep3_ATH1


title: Peri-implantation D11 embryo - control 4

source_name: RNA from D11 7-8 mm ovoid embryo in early elongation - control 4

treatment_protocol: Channel 1 and 2 samples the same the difference is dye label, i.e. cy5 or cy3


title: IHP low N rep4 vs IHP high N rep4

description: IHP low N rep4 vs IHP high N rep4

source_name: IHP low N rep4

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen, Carlsbad, CA) then Rneasy purification kit (Qiagen, Valencia, CA).

tag: treatment

value: low N (1 mM NO3-)

value: V8 growth stage

source_name: IHP high N rep4

value: high N (14mM NO3-)


title: STM60RO (isothermal)

type: genomic

city: New York

first: David

last: Gresham

state: NY

address: 100 Washington Sq East, 1009 Sliver Center

department: Biology

institute: New York University

description: custom tiling array design

hyb_protocol: Standard Agilent protocol at the specified temperature

scan_protocol: Agilent Feature Extractor using the XDR setting

data_processing:
Custom perl scripts
Data were normalized using an invariant probe set (Is Normalization Probe = 1) to compute a linear-loess normalization.  The data values are the log2 of the ratio between sample and reference.  This value was calculated on the basis of the log10 value computed by the Agilent Feature Extractor software.  For this particular ref vs. ref Sample, VALUE is defined as normalized log2 (Ch1/Ch2) ratio.

molecule: genomic DNA

source_name: reference

label_protocol: Klenow random primed labeling at 24C for 16 hours

growth_protocol: Over night growth in rich media with glucose as a carbon source

extract_protocol: Qiagen genomic tip

tag: hybridization temperature


title: DTM60RO4 (isothermal)

description: custom tiling array design

data_processing:
Custom perl scripts
Data were normalized using an invariant probe set (Is Normalization Probe = 1) to compute a linear-loess normalization.  The data values are the log2 of the ratio between sample and reference.  This value was calculated on the basis of the log10 value computed by the Agilent Feature Extractor software.

source_name: heterozygous non-reference


title: DTM65RO (isothermal)

description: custom tiling array design


title: 240 min - Replicate 1 (II)

status: Public on Jan 10 2010

city: Lincoln

first: James

middle: L

last: Van Etten

state: NE

address: 4240 Fair Street

department: Plant Pathology

institute: University of Nebraska-Lincoln

description: Technical replicate 1 of 4 (Biological replicate 2 of 3)

hyb_protocol: Arrays were hybridized (42ºC) for 16 hours in a Corning hybridization chamber (Corning, Lowell, MA).  Slides were washed twice (42ºC) in 2x SSC (1x SSC is 0.15 M sodium chloride/0.015 M sodium citrate), 0.5% SDS for 15 min followed by two washes in 0.5x SSC, 0.5% SDS for 15 min

scan_protocol: Slides were subjected to fluorescence detection with Axon 4000B scanner (Molecular Devices, Sunnyvale, CA)

data_processing: Midas v2.19 (TM4) software was used for : low intensity filter (<10,000), normalization of the intensities between the two channels using Lowess (Locfit), and SD regularization across blocks. In TMEV v4.1 (TM4), all time points from each set of experiments were loaded and columns (experiments) were normalized, ANOVA was used to detect genes that display statistically significant variation in expression in at least one of the experimental time points.

organism: Paramecium bursaria Chlorella virus 1

source_name: Chlorella NC64A infected with PBCV-1 (MOI=5)

label_protocol: 20 ug of total RNA was reverse-transcribed using oligo(dT) as primers and cDNAs were labeled with either Cy3 or Cy5-dUTP (GE Healthcare, Piscataway, NJ) using the SuperScript Indirect cDNA Labeling System (Invitrogen) following the supplier’s directions

growth_protocol: Log phase Chlorella NC64A cells were concentrated to 1 x 10*8 cells/ml with fresh MBBM media.

extract_protocol: Total RNA extracted using Absolutely RNA Miniprep Kit (Stratagene, La Jolla, CA) following manufacturer's instructions

treatment_protocol: Cells were infected with PBCV-1 with MOI = 5.

tag: infected cell

value: chlorella-like green alga, Chlorella NC64A

tag: time

value: 240 min

source_name: RNA control (II)

tag: control composition

value: a pool of transcripts obtained by mixing equal amounts of total RNA from each time point


title: DTM55RO (isothermal)

description: custom tiling array design


title: DTM60RO3 (isothermal)

description: custom tiling array design


title: HTM60RO4 (isothermal)

description: custom tiling array design

source_name: haploid non-reference


title: HTM60RO3 (isothermal)

description: custom tiling array design


title: DTM60RO2 (isothermal)

description: custom tiling array design


title: HTM65RO (isothermal)

description: custom tiling array design


title: Cell line mixture ref/ref, replicate 4

city: Rotterdam

first: Lambert

last: Dorssers

department: Josephine Nefkens Institute

country: Netherlands

institute: Erasmus MC- University Medical Center Rotterdam

description: Cell line mixture ref/ref, replicate 4

hyb_protocol: labeled aRNA was fragmented (Ambion RNA Fragmentation Reagents) and mixed with blocking solution containing Poly d(A), Cot-1 DNA and yeast t-RNA. Hybridization was overnight at 42C on a Tecan HS4800 hybridization station. Protocol: M016 (http://erasmusmc.nl/biomics). It included a 15 min pre-hybridization with a solution containing 4% (w/v) BSA.

scan_protocol: Perkin Elmer ScanArray Express HT instrument

data_processing: Imagene data (Imagene software version 6.0) was uploaded into the CMF database (NKI, The Netherlands) and normalized using lowess subarray method.

organism: Homo sapiens

source_name: Reference

label_protocol: 3 ug of RNA was converted into ds-CDNA using Superscript II (Invitrogen), amplified with the T7 Megascript (Ambion). 1 ug of amplified RNA was labeled using the ULS-Cy3/5 aRNA fluorescent labeling kit (Kreatech)

growth_protocol: The panel of tamoxifen-resistant cell lines was cultured in RPMI medium supplemented with 15% bovine calf serum, 10% CRIP supernatant and 1µM of 4-hydroxy-tamoxifen

extract_protocol: Total RNA was prepared form approximately 80% confluent 25 or 75 cm2 tissue culture flasks (Corning) by direct lysis with RNA-BeeTM (Bio-connect, Huissen, NL) according to the protocol of the supplier.

tag: Mixture of cell lines


title: Cell line mixture ref/ref, replicate 3

description: Cell line mixture ref/ref, replicate 3


title: Cell line mixture ref/ref, replicate 1

description: Cell line mixture ref/ref, replicate 1


title: D3055RP (30mers)

description: custom tiling array design


title: H2565RP (25mers)

description: custom tiling array design


title: H3065RP (30mers)

description: custom tiling array design


title: Cell line XIV-42, RNA 66A

description: Cell line XIV-42, RNA 66A


title: H3045RP (30mers)

description: custom tiling array design


title: H3055RP (30mers)

description: custom tiling array design


title: H3060RP (30mers)

description: custom tiling array design


title: Cell line XIV-42, RNA 66Bswap

description: Cell line XIV-42, RNA 66Bswap


title: H3050RP (30mers)

description: custom tiling array design


title: HTM60RO1 (isothermal)

description: custom tiling array design


title: Cell line XIV-42, RNA 66B

description: Cell line XIV-42, RNA 66B


title: HTM60RO2 (isothermal)

description: custom tiling array design


title: D3060RP (30mers)

description: custom tiling array design


title: D2560RP (25mers)

description: custom tiling array design


title: H2560RP (25mers)

description: custom tiling array design


title: HTM55RO (isothermal)

description: custom tiling array design


title: D3065RO (30mers)

description: custom tiling array design


title: D2565RO (25mers)

description: custom tiling array design


title: H2555RP (25mers)

description: custom tiling array design


title: DTM60RO1 (isothermal)

description: custom tiling array design


title: Cell line XIV-36, RNA 63A

description: Cell line XIV-36, RNA 63A


title: H2550RP (25mers)

description: custom tiling array design


title: Cell line XIV-36, RNA 63B

description: Cell line XIV-36, RNA 63B


title: D2555RP (25mers)

description: custom tiling array design


title: H2545RP (25mers)

description: custom tiling array design


title: Cell line mixture ref/ref, replicate 2

description: Cell line mixture ref/ref, replicate 2


title: Cell line XIV-36, RNA 63Bswap

description: Cell line XIV-36, RNA 63Bswap


title: Cell line XIV-17, RNA 56B

description: Cell line XIV-17, RNA 56B


title: Cell line X-8, RNA 20Aswap

description: Cell line X-8, RNA 20Aswap


title: Cell line XI-22, RNA 30B-rep2

description: Cell line XI-22, RNA 30B-rep2


title: Cell line XI-22, RNA 30A

description: Cell line XI-22, RNA 30A


title: Cell line X-8, RNA 20A

description: Cell line X-8, RNA 20A


title: Cell line X-8, RNA 20B

description: Cell line X-8, RNA 20B


title: Cell line X-10, RNA 14B

description: Cell line X-10, RNA 14B


title: Cell line VIII-18, RNA 05B

description: Cell line VIII-18, RNA 05B


title: Cell line X-7, RNA 19Bswap

description: Cell line X-7, RNA 19Bswap


title: Cell line X-10, RNA 14Bswap

description: Cell line X-10, RNA 14Bswap


title: Cell line X-7, RNA 19B

description: Cell line X-7, RNA 19B


title: Cell line XI-22, RNA 30B-rep1

description: Cell line XI-22, RNA 30B-rep1


title: Cell line X-7, RNA 19A

description: Cell line X-7, RNA 19A


title: Cell line XI-22, RNA 30Bswap

description: Cell line XI-22, RNA 30Bswap


title: Cell line X-10, RNA 14A

description: Cell line X-10, RNA 14A


title: Cell line VIII-11, RNA 01B

description: Cell line VIII-11, RNA 01B


title: Cell line IX-10, RNA 11Cswap

description: Cell line IX-10, RNA 11Cswap


title: Cell line IX-10, RNA 11D

description: Cell line IX-10, RNA 11D


title: Cell line VIII-11, RNA 01A

description: Cell line VIII-11, RNA 01A


title: Cell line XIV-16, RNA 55Aswap

description: Cell line XIV-16, RNA 55Aswap


title: Cell line VIII-18, RNA 05A

description: Cell line VIII-18, RNA 05A


title: Cell line VIII-11, RNA 01Aswap

description: Cell line VIII-11, RNA 01Aswap


title: Cell line VIII-18, RNA 05Bswap

description: Cell line VIII-18, RNA 05Bswap


title: Cell line XIV-16, RNA 55B

description: Cell line XIV-16, RNA 55B


title: Cell line XII-6, RNA 49Bswap

description: Cell line XII-6, RNA 49Bswap


title: Cell line XII-6, RNA 49B

description: Cell line XII-6, RNA 49B


title: Cell line IX-10, RNA 11C

description: Cell line IX-10, RNA 11C


title: Cell line XII-6, RNA 49A

description: Cell line XII-6, RNA 49A


title: Cell line IX-23, RNA 12B

description: Cell line IX-23, RNA 12B


title: Cell line IX-23, RNA 12A

description: Cell line IX-23, RNA 12A


title: Cell line XIV-39, RNA 65A

description: Cell line XIV-39, RNA 65A


title: Cell line VIII-22, RNA 08A

description: Cell line VIII-22, RNA 08A


title: Cell line XIV-39, RNA 65Aswap

description: Cell line XIV-39, RNA 65Aswap


title: Cell line VIII-22, RNA 08Bswap

description: Cell line VIII-22, RNA 08Bswap


title: Cell line VIII-20, RNA 06Dswap

description: Cell line VIII-20, RNA 06Dswap


title: Cell line XII-11, RNA 43Bswap

description: Cell line XII-11, RNA 43Bswap


title: Cell line XII-11, RNA 43B

description: Cell line XII-11, RNA 43B


title: Cell line VIII-20, RNA 06D

description: Cell line VIII-20, RNA 06D


title: Cell line VIII-22, RNA 08B

description: Cell line VIII-22, RNA 08B


title: Cell line XIV-39, RNA 65B

description: Cell line XIV-39, RNA 65B


title: Cell line XI-15, RNA 23B

description: Cell line XI-15, RNA 23B


title: Cell line XI-15, RNA 23C

description: Cell line XI-15, RNA 23C


title: Cell line VIII-20, RNA 06C

description: Cell line VIII-20, RNA 06C


title: Cell line XIV-34, RNA 62B

description: Cell line XIV-34, RNA 62B


title: Cell line X-6, RNA 18Bswap

description: Cell line X-6, RNA 18Bswap


title: Cell line XII-11, RNA 43A

description: Cell line XII-11, RNA 43A


title: Cell line XIV-34, RNA 62Bswap

description: Cell line XIV-34, RNA 62Bswap


title: Cell line XI-15, RNA 23Cswap

description: Cell line XI-15, RNA 23Cswap


title: Cell line X-6, RNA 18B

description: Cell line X-6, RNA 18B


title: Cell line X-4, RNA 16Bswap

description: Cell line X-4, RNA 16Bswap


title: Cell line X-6, RNA 18A

description: Cell line X-6, RNA 18A


title: Cell line XI-20, RNA 28B

description: Cell line XI-20, RNA 28B


title: Cell line X-4, RNA 16A

description: Cell line X-4, RNA 16A


title: Cell line XI-20, RNA 28Aswap

description: Cell line XI-20, RNA 28Aswap


title: Cell line X-4, RNA 16B

description: Cell line X-4, RNA 16B


title: Cell line XI-19, RNA 27Aswap

description: Cell line XI-19, RNA 27Aswap


title: Cell line XI-19, RNA 27A

description: Cell line XI-19, RNA 27A


title: Cell line XI-27, RNA 31B

description: Cell line XI-27, RNA 31B


title: Cell line XI-17, RNA 25Bswap / GRB7

description: Cell line XI-17, RNA 25Bswap / GRB7


title: Cell line XI-19, RNA 27B

description: Cell line XI-19, RNA 27B


title: Cell line XI-20, RNA 28A

description: Cell line XI-20, RNA 28A


title: Cell line XIV-10, RNA 53Bswap

description: Cell line XIV-10, RNA 53Bswap


title: Cell line XI-17, RNA 25B / GRB7

description: Cell line XI-17, RNA 25B / GRB7


title: Cell line XI-27, RNA 31Bswap

description: Cell line XI-27, RNA 31Bswap


title: Cell line XIV-9, RNA 74A

description: Cell line XIV-9, RNA 74A


title: Cell line XII-8, RNA 51B

description: Cell line XII-8, RNA 51B


title: Cell line XIV-26, RNA 59Aswap

description: Cell line XIV-26, RNA 59Aswap


title: Cell line XIV-9, RNA 74Aswap

description: Cell line XIV-9, RNA 74Aswap


title: Cell line XIV-9, RNA 74B

description: Cell line XIV-9, RNA 74B


title: Cell line XII-8, RNA 51Bswap

description: Cell line XII-8, RNA 51Bswap


title: Cell line XII-8, RNA 51A

description: Cell line XII-8, RNA 51A


title: Cell line XIV-26, RNA 59A

description: Cell line XIV-26, RNA 59A


title: Cell line XI-17, RNA 25A / GRB7

description: Cell line XI-17, RNA 25A / GRB7


title: Cell line XIV-26, RNA 59C

description: Cell line XIV-26, RNA 59C


title: Cell line XIV-43, RNA 79A / AKT1

description: Cell line XIV-43, RNA 79A / AKT1


title: Cell line XIV-43, RNA 67Bswap / AKT1

description: Cell line XIV-43, RNA 67Bswap / AKT1


title: Cell line XIV-10, RNA 53B

description: Cell line XIV-10, RNA 53B


title: Cell line XIV-17, RNA 56Bswap

description: Cell line XIV-17, RNA 56Bswap


title: Cell line XIV-43, RNA 67B / AKT1

description: Cell line XIV-43, RNA 67B / AKT1


title: Cell line XIV-43, RNA 79B / AKT1

description: Cell line XIV-43, RNA 79B / AKT1


title: Cell line XII-14, RNA 78A / AKT2

description: Cell line XII-14, RNA 78A / AKT2

tag: cVIS12 / AKT2


title: Cell line XII-10, RNA 42D / CVIS11

description: Cell line XII-10, RNA 42D / CVIS11


title: Cell line XII-14, RNA 46A / AKT2

description: Cell line XII-14, RNA 46A / AKT2


title: Cell line XII-14, RNA 78Bswap / AKT2

description: Cell line XII-14, RNA 78Bswap / AKT2


title: Cell line XII-14, RNA 46Bswap / AKT2

description: Cell line XII-14, RNA 46Bswap / AKT2


title: Cell line XIV-2, RNA 57B / AKT2

description: Cell line XIV-2, RNA 57B / AKT2


title: Cell line XII-10, RNA 42B / CVIS11

description: Cell line XII-10, RNA 42B / CVIS11


title: Cell line XIV-2, RNA 57Aswap / AKT2

description: Cell line XIV-2, RNA 57Aswap / AKT2


title: Cell line XIV-43, RNA 67A / AKT1

description: Cell line XIV-43, RNA 67A / AKT1


title: Cell line XII-14, RNA 46B / AKT2

description: Cell line XII-14, RNA 46B / AKT2


title: Cell line XI-30, RNA 32Cswap / CVIS11

description: Cell line XI-30, RNA 32Cswap / CVIS11


title: Cell line XIV-2, RNA 57A / AKT2

description: Cell line XIV-2, RNA 57A / AKT2


title: Cell line XII-10, RNA 42Dswap / CVIS11

description: Cell line XII-10, RNA 42Dswap / CVIS11


title: Cell line XIV-43, RNA 79Aswap / AKT1

description: Cell line XIV-43, RNA 79Aswap / AKT1


title: Cell line XIV-15, RNA 54F / cVIS10

description: Cell line XIV-15, RNA 54F / cVIS10


title: Cell line XII-14, RNA 78B / AKT2

description: Cell line XII-14, RNA 78B / AKT2


title: Cell line XI-30, RNA 32C / CVIS11

description: Cell line XI-30, RNA 32C / CVIS11


title: Cell line XII-4, RNA 48Bswap / cVIS10

description: Cell line XII-4, RNA 48Bswap / cVIS10


title: Cell line XI-30, RNA 32A / CVIS11

description: Cell line XI-30, RNA 32A / CVIS11


title: Cell line XIV-15, RNA 54Bswap / cVIS10

description: Cell line XIV-15, RNA 54Bswap / cVIS10


title: Cell line XIV-16, RNA 55A

description: Cell line XIV-16, RNA 55A


title: Cell line XIV-32, RNA 61A / CITED2

description: Cell line XIV-32, RNA 61A / CITED2

tag: cVIS9 / CITED2


title: Cell line XII-4, RNA 48A / cVIS10

description: Cell line XII-4, RNA 48A / cVIS10


title: Cell line XII-1, RNA 41Aswap / CITED2

description: Cell line XII-1, RNA 41Aswap / CITED2


title: Cell line XIV-32, RNA 61B / CITED2

description: Cell line XIV-32, RNA 61B / CITED2


title: Cell line XIV-32, RNA 61Bswap / CITED2

description: Cell line XIV-32, RNA 61Bswap / CITED2


title: Cell line X-5, RNA 77Aswap / CVIS7

description: Cell line X-5, RNA 77Aswap / CVIS7


title: Cell line XII-12, RNA 44B / EGFR

description: Cell line XII-12, RNA 44B / EGFR

tag: cVIS8 / EGFR


title: Cell line XII-12, RNA 44Bswap / EGFR

description: Cell line XII-12, RNA 44Bswap / EGFR


title: Cell line XII-1, RNA 41A / CITED2

description: Cell line XII-1, RNA 41A / CITED2


title: Cell line XI-22, RNA 30B-rep3

description: Cell line XI-22, RNA 30B-rep3


title: Cell line XII-7, RNA 50B / EGFR

description: Cell line XII-7, RNA 50B / EGFR


title: Cell line XII-7, RNA 50A / EGFR

description: Cell line XII-7, RNA 50A / EGFR


title: Cell line XII-7, RNA 50Bswap / EGFR

description: Cell line XII-7, RNA 50Bswap / EGFR


title: Cell line XII-1, RNA 41B / CITED2

description: Cell line XII-1, RNA 41B / CITED2


title: Cell line X-5, RNA 17Aswap / CVIS7

description: Cell line X-5, RNA 17Aswap / CVIS7


title: Cell line X-5, RNA 77C / CVIS7

description: Cell line X-5, RNA 77C / CVIS7


title: Cell line VIII-17, RNA 75B / cVIS6

description: Cell line VIII-17, RNA 75B / cVIS6


title: Cell line XII-12, RNA 44A / EGFR

description: Cell line XII-12, RNA 44A / EGFR


title: Cell line X-5, RNA 17A / CVIS7

description: Cell line X-5, RNA 17A / CVIS7


title: Cell line XII-2, RNA 47A / CVIS7

description: Cell line XII-2, RNA 47A / CVIS7


title: Cell line X-5, RNA 17B / CVIS7

description: Cell line X-5, RNA 17B / CVIS7


title: Cell line X-5, RNA 77A / CVIS7

description: Cell line X-5, RNA 77A / CVIS7


title: Cell line VIII-17, RNA 75Aswap / cVIS6

description: Cell line VIII-17, RNA 75Aswap / cVIS6


title: Cell line VIII-17, RNA 04Aswap / cVIS6

description: Cell line VIII-17, RNA 04Aswap / cVIS6


title: Cell line VIII-17, RNA 04B / cVIS6

description: Cell line VIII-17, RNA 04B / cVIS6


title: Cell line VIII-17, RNA 75A / cVIS6

description: Cell line VIII-17, RNA 75A / cVIS6


title: Cell line XII-2, RNA 47Bswap / CVIS7

description: Cell line XII-2, RNA 47Bswap / CVIS7


title: Cell line VIII-17, RNA 04A / cVIS6

description: Cell line VIII-17, RNA 04A / cVIS6


title: Cell line XII-4, RNA 48B / cVIS10

description: Cell line XII-4, RNA 48B / cVIS10


title: Cell line IX-6, RNA 13Dswap / CVIS5

description: Cell line IX-6, RNA 13Dswap / CVIS5


title: Cell line IX-6, RNA 13D / CVIS5

description: Cell line IX-6, RNA 13D / CVIS5


title: Cell line VIII-12, RNA 02A / CVIS5

description: Cell line VIII-12, RNA 02A / CVIS5


title: Cell line VIII-12, RNA 02Bswap / CVIS5

description: Cell line VIII-12, RNA 02Bswap / CVIS5


title: Cell line VIII-12, RNA 02B / CVIS5

description: Cell line VIII-12, RNA 02B / CVIS5


title: Cell line XIV-57, RNA 72A-rep2 / NCOR2

description: Cell line XIV-57, RNA 72A-rep2 / NCOR2

tag: cVIS4 / NCOR2


title: Cell line XIV-57, RNA 72A-rep1 / NCOR2

description: Cell line XIV-57, RNA 72A-rep1 / NCOR2


title: Cell line XIV-57, RNA 72Aswap / NCOR2

description: Cell line XIV-57, RNA 72Aswap / NCOR2


title: Cell line XIV-57, RNA 72A-rep3 / NCOR2

description: Cell line XIV-57, RNA 72A-rep3 / NCOR2


title: Cell line IX-6, RNA 13B / CVIS5

description: Cell line IX-6, RNA 13B / CVIS5


title: Cell line XIV-51, RNA 70A-rep3 / NCOR2

description: Cell line XIV-51, RNA 70A-rep3 / NCOR2


title: Cell line XIV-51, RNA 70A-rep2 / NCOR2

description: Cell line XIV-51, RNA 70A-rep2 / NCOR2


title: Cell line XIV-57, RNA 72B / NCOR2

description: Cell line XIV-57, RNA 72B / NCOR2


title: Cell line XIV-51, RNA 70Bswap / NCOR2

description: Cell line XIV-51, RNA 70Bswap / NCOR2


title: Cell line XIV-51, RNA 70A-rep1 / NCOR2

description: Cell line XIV-51, RNA 70A-rep1 / NCOR2


title: Cell line XIV-31, RNA 60B / NCOR2

description: Cell line XIV-31, RNA 60B / NCOR2


title: Cell line XIV-31, RNA 60A / NCOR2

description: Cell line XIV-31, RNA 60A / NCOR2


title: Cell line XIV-22, RNA 58B / NCOR2

description: Cell line XIV-22, RNA 58B / NCOR2


title: Cell line XIV-51, RNA 70B / NCOR2

description: Cell line XIV-51, RNA 70B / NCOR2


title: Cell line XI-35, RNA 36Bswap / NCOR2

description: Cell line XI-35, RNA 36Bswap / NCOR2


title: Cell line XIV-22, RNA 58A / NCOR2

description: Cell line XIV-22, RNA 58A / NCOR2


title: Cell line XI-35, RNA 36A / NCOR2

description: Cell line XI-35, RNA 36A / NCOR2


title: Cell line XIV-22, RNA 58Aswap / NCOR2

description: Cell line XIV-22, RNA 58Aswap / NCOR2


title: Cell line XIV-55, RNA 71B / BCAR3

description: Cell line XIV-55, RNA 71B / BCAR3

tag: cVIS3 / BCAR3


title: Cell line XIV-6, RNA 73B / BCAR3

description: Cell line XIV-6, RNA 73B / BCAR3


title: Cell line XIV-55, RNA 71A-rep2 / BCAR3

description: Cell line XIV-55, RNA 71A-rep2 / BCAR3


title: Cell line XIV-55, RNA 71A-rep3 / BCAR3

description: Cell line XIV-55, RNA 71A-rep3 / BCAR3


title: Cell line XIV-55, RNA 71Bswap / BCAR3

description: Cell line XIV-55, RNA 71Bswap / BCAR3


title: Cell line XIV-6, RNA 73Bswap / BCAR3

description: Cell line XIV-6, RNA 73Bswap / BCAR3


title: Cell line XI-39, RNA 39B / BCAR3

description: Cell line XI-39, RNA 39B / BCAR3


title: Cell line XI-35, RNA 36B / NCOR2

description: Cell line XI-35, RNA 36B / NCOR2


title: Cell line XIV-55, RNA 71A-rep1 / BCAR3

description: Cell line XIV-55, RNA 71A-rep1 / BCAR3


title: Cell line XII-9, RNA 52Bswap / BCAR3

description: Cell line XII-9, RNA 52Bswap / BCAR3


title: Baubec_2-9_mutant-line409_Rep3_ATH1

description:
Seeds were dried after harvesting and cold-treated for minimum 7 days at 4C 6 minutes shaking in 5% hypochloric acid, 0.05% Tween-80 solution. Subsequent washes with ddH2O (3x) and over night drying.  Cold treated seeds were surface-sterilized in 5% hypochloric acid and 0,05% Tween-80 for 6 minutes, washed and air-dried overnight. 25 seeds were sawn in a regular matrix on petri dishes containing semisolid germination medium with 0.8% agar and grown for 17 days in growth chambers at 16h light/8h dark cycles and 21C.  8 25/plate 21 C average, 21 C day, 21 C night ~100% % average, ~100% % day, ~100% % night.
Own medium: MS macro, 50ml
B5 micro, 1ml
ammonium iron citrate, 50mg
sucrose, 10g
MES, 350mg
8% Agar, 450ml

tag: line

value: whole plant

value: T-DNA knock out mutation


title: Cell line XII-9, RNA 52A / BCAR3

description: Cell line XII-9, RNA 52A / BCAR3


title: Baubec_2-6_mutant-line348_Rep3_ATH1

tag: tissue


title: Baubec_2-5_mutant-line348_Rep1_ATH1


title: Cell line XI-39, RNA 39Bswap / BCAR3

description: Cell line XI-39, RNA 39Bswap / BCAR3


title: Cell line XIV-6, RNA 73A / BCAR3

description: Cell line XIV-6, RNA 73A / BCAR3


title: Cell line XIV-15, RNA 54B / cVIS10

description: Cell line XIV-15, RNA 54B / cVIS10


title: Cell line XI-38, RNA 38Aswap / BCAR3

description: Cell line XI-38, RNA 38Aswap / BCAR3


title: Cell line XII-9, RNA 52B / BCAR3

description: Cell line XII-9, RNA 52B / BCAR3


title: Cell line XI-38, RNA 38C / BCAR3

description: Cell line XI-38, RNA 38C / BCAR3


title: Baubec_2-8_mutant-line409_Rep2_ATH1


title: Cell line XI-38, RNA 38A / BCAR3

description: Cell line XI-38, RNA 38A / BCAR3


title: Baubec_2-7_mutant-line409_Rep1_ATH1


title: Baubec_2-3_WT-control_Rep3_ATH1

value: knock out mutation


title: Cell line XI-36, RNA 37Bswap / BCAR3

description: Cell line XI-36, RNA 37Bswap / BCAR3


title: Cell line XI-32, RNA 34A / BCAR3

description: Cell line XI-32, RNA 34A / BCAR3


title: Johnson_2-7_32OE-1_Rep1_ATH1

description:
3 days 4 deg C. 70% EtOH, 0.05% Tween-20. Wash 100% EtOH.
Air dry. Plants were plated onto 0.5xMS media, 1% agar, 0.6% sucrose medium and stratified at 4 deg C for 3 days. Seedlings were transferred to soil after 7 days and grown under standard short day conditions.  Levingtons F2 + Sand + Perlite + Intercept  70% EtOH, 0.05% Tween-20  6 plants / 8 x 12 cm pot twice weekly 21 C average, 21 C day, 21 C night 76 % average, 85 % day, 60 % night Murashige & Skoog basal salt mixture. Modifications: 0.6% sugar and 1% agar.

source_name: ADEK1 calpain, overexpressing

value: leaf

value: T-DNA knock out mutation in At1g55350

tag: transgene

value: ADEK1 calpain


title: Johnson_2-8_32OE-2_Rep2_ATH1

tag: developmental stage


title: Cell line XI-32, RNA 34Bswap / BCAR3

description: Cell line XI-32, RNA 34Bswap / BCAR3


title: Cell line XI-32, RNA 34B / BCAR3

description: Cell line XI-32, RNA 34B / BCAR3


title: Baubec_2-2_WT-control_Rep2_ATH1


title: Baubec_2-1_WT-control_Rep1_ATH1


title: Johnson_2-9_32OE-3_Rep3_ATH1

tag: genetic background


title: Cell line XI-31, RNA 33Bswap / BCAR3

description: Cell line XI-31, RNA 33Bswap / BCAR3


title: Cell line XI-18, RNA 26Bswap / BCAR3

description: Cell line XI-18, RNA 26Bswap / BCAR3


title: Cell line XI-31, RNA 33A / BCAR3

description: Cell line XI-31, RNA 33A / BCAR3


title: Johnson_2-3_Col3_Rep3_ATH1

source_name: Col-0 (Columbia)

tag: strain

tag: stock code

tag: genotype

value: wild-type


title: Cell line XI-18, RNA 26B / BCAR3

description: Cell line XI-18, RNA 26B / BCAR3


title: Cell line XI-36, RNA 37B / BCAR3

description: Cell line XI-36, RNA 37B / BCAR3


title: Johnson_2-2_Col2_Rep2_ATH1


title: Cell line XI-36, RNA 37A / BCAR3

description: Cell line XI-36, RNA 37A / BCAR3


title: Johnson_2-4_32null-1_Rep1_ATH1

source_name: ADEK1 calpain null

tag: genetic variation

value: ADEK1 calpian null


title: Cell line XI-18, RNA 26A / BCAR3

description: Cell line XI-18, RNA 26A / BCAR3


title: Johnson_2-5_32null-2_Rep2_ATH1


title: Johnson_2-1_Col1_Rep1_ATH1


title: Cell line VIII-16, RNA 03Bswap / TRERF1

description: Cell line VIII-16, RNA 03Bswap / TRERF1

tag: cVIS2 / TRERF1


title: Cell line VIII-5, RNA 10A / TRERF1

description: Cell line VIII-5, RNA 10A / TRERF1


title: Cell line VIII-24, RNA 09A / TRERF1

description: Cell line VIII-24, RNA 09A / TRERF1


title: Cell line VIII-16, RNA 03A / TRERF1

description: Cell line VIII-16, RNA 03A / TRERF1


title: Cell line VIII-24, RNA 09Bswap / TRERF1

description: Cell line VIII-24, RNA 09Bswap / TRERF1


title: Cell line VIII-5, RNA 10Bswap / TRERF1

description: Cell line VIII-5, RNA 10Bswap / TRERF1


title: Cell line VIII-5, RNA 10B / TRERF1

description: Cell line VIII-5, RNA 10B / TRERF1


title: Cell line XI-41, RNA 40Aswap / BCAR1

description: Cell line XI-41, RNA 40Aswap / BCAR1

tag: cVIS1 / BCAR1


title: Cell line XII-13, RNA 45B / BCAR1

description: Cell line XII-13, RNA 45B / BCAR1

tag: Mixture of cell lines


title: Cell line VIII-16, RNA 03B / TRERF1

description: Cell line VIII-16, RNA 03B / TRERF1


title: Cell line XI-41, RNA 40A / BCAR1

description: Cell line XI-41, RNA 40A / BCAR1


title: RTS_fibroblast_AG18375

city: Philadelphia

first: Jay

last: Johnson

state: PA

address: 422 Curie Blvd

department: Pathology and Laboratory Medicine

institute: University of Pennsylvania

hyb_protocol: Labeled probe was hybridized to Affymetrix U133A 2.0 GeneChips, washed and stained according to the following fluidics protocol. Wash A1 Recovery Mixes	0 Wash A1 Temperature (C)	30 Number of Wash A1 Cycles	10 Mixes per Wash A1 Cycle	2 Wash B Recovery Mixes	0 Wash B Temperature (C)	50 Number of Wash B Cycles	6 Mixes per Wash B Cycle	15 Stain Temperature (C)	35 First Stain Time (seconds)	300 Wash A2 Recovery Mixes	0 Wash A2 Temperature (C)	30 Number of Wash A2 Cycles	10 Mixes per Wash A2 Cycle	4 Second Stain Time (seconds)	300 Third Stain Time (seconds)	300 Wash A3 Recovery Mixes	0 Wash A3 Temperature (C)	35 Number of Wash A3 Cycles	15 Mixes per Wash A3 Cycle	4 Holding Temperature (C)	25

scan_protocol: Affymetrix U133A 2.0 GeneChips were scanned using an Axon GenePix array scanner.

data_processing: Values in the VALUE column of the data table represent Log2 signal intensities normalized using R (package GCRMA).

label: Biotin

source_name: RTS human fibroblast

label_protocol: Total RNA was amplified by in vitro transcription using the Ovation RNA Amplification System V2 (NuGen). The resultant cDNA was fragmented and labeled using the FL-Ovation cDNA Biotin Module V2 (NuGen), and then purified using QIAquick columns (Qiagen), as specified by the Ovation System manual.

growth_protocol: Cells were cultured in MEM supplemented with Earle’s salts, 20% fetal bovine serum, 1x penicillin/streptomycin, and 1x fungizone in 3% O2 at 37oC and harvested for RNA extraction during active growth and at ~ 80% confluence.

extract_protocol: Total RNA was isolated by extraction with TRIzol (Invitrogen) and purified using the RNeasy system (Qiagen).

tag: type

value: RTS

tag: age

tag: gender

value: Male

tag: race

value: Caucasian

tag: population doubling level

tag: fibroblast cell strain


title: Cell line XI-41, RNA 40B / BCAR1

description: Cell line XI-41, RNA 40B / BCAR1


title: Cell line XII-13, RNA 45Bswap / BCAR1

description: Cell line XII-13, RNA 45Bswap / BCAR1


title: RTS_fibroblast_AG18371

value: Hispanic


title: Cell line XII-13, RNA 45A / BCAR1

description: Cell line XII-13, RNA 45A / BCAR1


title: Cell line XI-21, RNA 29C / BCAR1

description: Cell line XI-21, RNA 29C / BCAR1


title: Cell line XI-31, RNA 33B / BCAR3

description: Cell line XI-31, RNA 33B / BCAR3

tag: cVIS3 / BCAR3


title: Cell line XIV-31, RNA 60Aswap / NCOR2

description: Cell line XIV-31, RNA 60Aswap / NCOR2

tag: cVIS4 / NCOR2


title: Cell line VIII-24, RNA 09B / TRERF1

description: Cell line VIII-24, RNA 09B / TRERF1


title: Cell line XI-21, RNA 29Bswap / BCAR1

description: Cell line XI-21, RNA 29Bswap / BCAR1


title: RTS_fibroblast_AG05013


title: Bloom_fibroblast_GM16891

source_name: Bloom human fibroblast

value: Bloom


title: Cell line XI-21, RNA 29B / BCAR1

description: Cell line XI-21, RNA 29B / BCAR1


title: Cell line XI-39, RNA 39C / BCAR3

description: Cell line XI-39, RNA 39C / BCAR3


title: Cell line XI-14, RNA 22Bswap / BCAR1

description: Cell line XI-14, RNA 22Bswap / BCAR1


title: Cell line XI-14, RNA 22A / BCAR1

description: Cell line XI-14, RNA 22A / BCAR1


title: Werner_fibroblast_AG12797

source_name: Werner human fibroblast

value: Werner


title: Bloom_fibroblast_GM02932


title: Werner_fibroblast_AG12795


title: Cell line XI-13, RNA 21A / BCAR1

description: Cell line XI-13, RNA 21A / BCAR1


title: Cell line XI-13, RNA 21B / BCAR1

description: Cell line XI-13, RNA 21B / BCAR1


title: Cell line VIII-21, RNA 07B / BCAR1

description: Cell line VIII-21, RNA 07B / BCAR1


title: Bloom_fibroblast_GM03402


title: Normal_fibroblast_AG09975

source_name: Normal human fibroblast

value: Normal


title: whole uterus, ICI treated for 6 hr, rep2

city: Houston

first: Dong-Kee

last: Lee

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description:
Gene expression data from uterus treated oil or ICI 182,780
Mutant ICI-2

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized on Affymetrix mouse genome 430 2.0 arrays

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.

organism: Mus musculus

source_name: Mouse uterus treated with ICI for 6 hrs, total RNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA .

growth_protocol: Mice were maintained in the designated animal care facility at Baylor College of Medicine according to the institutional guidelines for the care and use of laboratory animals.

extract_protocol: RNeasy kit (Qiagen) was used for extraction of total RNA.

treatment_protocol: ovariectomized mice were treated with 3 daily injections of 100 ng of estrodial (E2) per mouse. After 2 days of rest, mice were then treated with daily injections of 1 mg of progesterone (P4) and 6.7 ng of E2 per mouse for 2 days, subcutaneously (s.c.). Oil or ICI 182,780 was treated at 34 hr of eP treatment for 6 hrs.

tag: tissue

value: whole uterus

tag: agent

value: ICI


title: Normal_fibroblast_AG06310


title: Cell line VIII-21, RNA 07Bswap / BCAR1

description: Cell line VIII-21, RNA 07Bswap / BCAR1


title: Cell line IX-23, RNA 12Aswap

description: Cell line IX-23, RNA 12Aswap


title: whole uterus, ICI treated for 6 hr, rep1

description:
Gene expression data from uterus treated oil or ICI 182,780
Mutant ICI-1


title: Normal_fibroblast_AG04054


title: whole uterus, oil control for 6 hr, rep1

description:
Gene expression data from uterus treated oil or ICI 182,780
Mutant Oil-1

source_name: Mouse uterus treated with oil for 6 hrs, total RNA

value: oil


title: whole uterus, oil control for 6 hr, rep2

description:
Gene expression data from uterus treated oil or ICI 182,780
Mutant Oil-2


title: embryo at E13 WD+IM, biological rep1

city: La Jolla

first: Yohan

last: Choi

state: CA

address: 9500 Gilman Drive, 0693

institute: UCSD

description: Gene expression data from E13  Wolffian ducts with attached mesodermal cells

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

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

data_processing: The data were analyzed with GCOS using Affymetrix's default analysis settings and global scaling as the normalization method.

organism: Rattus norvegicus

source_name: Rat embryo E13 isolated Wolffian duct with attached mesodermal cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2-5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: none (dissected directly)

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

treatment_protocol: UBs were isolated from the embryonic kidney following a light trypsinization, WDs were isolated without treatment

tag: strain

value: Sprague-Dawley


title: embryo at E13 WD+IM, biological rep2

value: Wolffian duct with attached mesodermal cells


title: embryo at E13 WD+IM, biological rep3


title: Werner_fibroblast_AG05229

value: Asian


title: Cell line XI-13, RNA 21Bswapwap / BCAR1

description: Cell line XI-13, RNA 21Bswapwap / BCAR1


title: Cell line XI-14, RNA 22B / BCAR1

description: Cell line XI-14, RNA 22B / BCAR1


title: Cell line VIII-21, RNA 07A / BCAR1

description: Cell line VIII-21, RNA 07A / BCAR1


title: Cell line XII-2, RNA 47B / CVIS7

description: Cell line XII-2, RNA 47B / CVIS7


title: embryo at E13 WD, biological rep3

description: Gene expression data from E13 isolated Wolffian ducts

source_name: Rat embryo E13 isolated Wolffian duct

value: Wolffian duct


title: embryo at E13 WD, biological rep2


title: G9a_Drd1_M1

first: Anne

last: Schaefer

address: 1230 York Avenue

institute: The Rockefeller University

hyb_protocol: Ten micrograms of labeled cRNA were hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 arrays (http://www.affymetrix.com/products/arrays/specific/mouse430_2.affx) for 16 hours at 45ºC.  The GeneChips were washed and stained according to the manufacturer’s recommendations (Affymetrix, Santa Clara, CA) using the GeneChips Fluidics Station 450 (Affymetrix, Santa Clara, CA). This procedure included staining the chips with phycoerythrin-streptavidin, signal amplification by a second staining with biotinylated anti-streptavidin, and a third staining with phycoerythrin-streptavidin.

scan_protocol: Mouse Genome 430 2.0 arrays were scanned using the GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA) and globally scaled to 150 using the Affymetrix GeneChip Operating Software (GCOS v1.4).

data_processing: GeneChip CEL files were imported into Genespring GX 7.3.1 (Agilent Technologies, Santa Clara, CA), processed with the GC-RMA algorithm, and expression values on each chip were normalized to that chip’s 50th percentile. Statistical analysis was carried out to determine which genes are differentially expressed in the GLP and G9a mutant cortex, striatum, hippocampus and hypothalamus as compared to their respective controls. Genes were filtered for a raw expression level of > 25 and a fold change of > 1.5, followed by a Welch t-test with a p value cutoff of 0.05 and Benjamin Hochberg false discovery rate (FDR) multiple test correction. To determine which genes are differentially upregulated in the G9a deficient Drd1 or Drd2 expressing neurons, statistical analysis comparing the Drd1-Cre; Drd1-bacTRAP; G9afl/fl or Drd2-Cre; Drd2-bacTRAP; G9afl/fl to their respective controls was carried out. Genes were filtered for a raw expression level of > 25 and a fold change of > 1.5, followed by a Welch t-test with a p value cutoff of 0.05.

source_name: Drd1-MSNs of Drd1-Cre; Drd1-bacTRAP; G9afl/fl mice 1

label_protocol: Purified mRNA or total RNA was converted to double-stranded cDNA using the SuperScript GeneChip Expression 3’-Amplification Reagents Two-Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, CA) and the GeneChip T7-Oligo(dT) Primer (Affymetrix, Santa Clara, CA). cDNA was used for the in vitro synthesis of cRNA using the MEGAscriptT7 Kit (Ambion, Austin, TX).  cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA). 600ng or less of clean cRNA was used in the second-cycle cDNA synthesis reaction using the SuperScript GeneChip Expression 3’-Amplification Reagents Two- Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, CA) and random primers (Affymetrix, Santa Clara, CA). The cDNA was purified using the GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA). Purified cDNA was used for the in vitro synthesis of biotin- labeled cRNA using the GeneChip IVT Labeling Kit (Affymetrix, Santa Clara, CA).  cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA) and fragmented into 35-200 base pair fragments using a magnesium acetate buffer (Affymetrix, Santa Clara, CA).

growth_protocol: All mice were raised under 12hr dark/12hr light conditions, housed ~5 mice per cage, with food and water ad libitum. All animal use protocols were approved by the Rockefeller University Institutional Animal Care and Use Committee.

extract_protocol: Total RNA from cortex, hippocampus, hypothalamus and striatum of twelve week-old Camk2a-Cre; GLPfl/fl, Camk2a-Cre; G9afl/fl, and Camk2a-Cre; GLPfl/fl; G9afl/fl mice and age and sex matched littermate controls (n=4/genotype) was extracted using the Trizol/Chloroform technique as recommended by the manufacturer (Invitrogen Corporation, Carlsbad, CA). After extraction, RNA was precipitated overnight at -80°C in isopropanol with sodium acetate and Glycoblue (Ambion, Austin, TX), washed twice with 70% ethanol, re-suspended in water, and further purified using an Rneasy Micro Kit (Qiagen, Valencia, CA) with in-column DNase digestion. Purified samples were analyzed using a Nanodrop 1000 spectrophotometer (Thermo Scientific, Wilmington, DE) and a Bioanalyzer (Agilent Technologies, Santa Clara, CA) in order to assess mRNA quantity and quality, as reflected by rRNA levels and integrity. Polyribosome associated mRNAs from age and sex matched Drd2-Cre; Drd2-bacTRAP; G9afl/fl and Drd2-bacTRAP; G9afl/fl, or Drd1-Cre; Drd1-bacTRAP; G9afl/fl and Drd1-bacTRAP; G9afl/fl mice (n=3x5 mice/genotype) were obtained as previously described using a mix of two monoclonal anti-GFP antibodies (19C8, 19F7) for the immunoprecipitation reaction (Doyle et al., 2008; Heiman et al., 2008).

tag: tissue type

value: mutant


title: embryo at E13 UB, biological rep3

description: Gene expression data from E13 isolated ureteric buds

source_name: Rat embryo E13 isolated ureteric bud

value: ureteric bud


title: Baubec_2-4_mutant-line348_Rep1_ATH1

tag: line

tag: developmental stage

value: whole plant

value: T-DNA knock out mutation


title: embryo at E13 UB, biological rep1


title: embryo at E13 WD, biological rep1


title: Johnson_2-6_32null-3_Rep3_ATH1

value: leaf

tag: genetic background

tag: genetic variation

value: T-DNA knock out mutation in At1g55350

tag: transgene

value: ADEK1 calpian null


title: G9a_Drd2_M3

source_name: Drd2-MSNs of Drd2-Cre; Drd2-bacTRAP; G9afl/fl mice 3

tag: genotype


title: Waters_1-10_24hr-induced_Rep2_ATH1

description: MS agar plates containing sterilised seed were placed in the dark at 4C for three days. Seed sterilisation was performed in 15 ml Falcon tubes. Seeds were washed in 70% ethanol for 5 minutes with shaking. The tubes were centrifuged and the ethanol replaced with freshly-prepared 50% sodium hypochlorite solution (BDH; available chlorine %), and the tubes were shaken for 10 minutes. The seeds were pelleted by centrifugation, the bleach solution replaced with sterile pure water, and the tubes shaken vigorously. The seeds were pelleted again and the rinsing was repeated twice more. To spread the seed evenly on MS agar plates, the sterilised seeds were resuspended in sterile 0.1% agar and transferred by pipette on to 10 cm square plates. The plates were shaken gently to disperse the seed/agar suspension. Growth Room Agar 0.7% Agar was added to a concentration of 0.7% (w/v) agar and the medium was autoclaved at 121 deg. C for 20 mins. The medium was allowed to cool to 50 deg. C. and hygromycin B was added to 20 ug/ml immediately before pouring into 10 cm square plates. ~200 seeds/plate 20oC 50% Murashige & Skoog basal salt mixture 1x Gamborg's vitamins and 1.5% (w/v) sucrose added and pH adjusted to 5.9. 20 ug/ml hygromycin B added after sterilisation

source_name: Atglk1;Atglk2, dexamethasone, 24hr

growth_protocol: Seed was surface-sterilised and spread on MS plates supplemented with 1.5% (w/v) sucrose, 0.7% (w/v) agar, 1x Gamborg's vitamins and 20 ug/ml hygromycin B. The plates were sealed, stratified for three days and transferred to an artificial growth room held at a constant 20C, with a 16h/8h light/dark cycle. Light was provided by fluorescent tubes, generating 85 umol/m2/s PAR. After ten days, seedlings were transferred from the plates into liquid MS media in a sterile Petri dish, in order to separate the seedlings. Using forceps, individual plants of a similar growth stage (first pair of leaves > 1 mm or Stage 1.02 as defined by Boyes et al., 2001) were selected and placed into 100 ml liquid MS medium in a 250 ml conical flask. Approximately 100 seedlings were transferred, and the flask was sealed with a foam bung. The flask was returned to the growth room and shaken at 76 rpm to provide aeration and adequate mixing. After 48 hours, the seedlings were harvested by filtering through one layer of cheesecloth, and quickly dabbing dry between two pieces of 3MM chromoatography paper. The seedlings were then flash-frozen in liquid nitrogen.

value: whole seedlings

value: transposon gene knock out

tag: treatment

value: dexamethasone

tag: time


title: G9a_Drd2_C3

source_name: Drd2-MSNs of Drd2-bacTRAP; G9afl/fl mice 3

value: control


title: G9a_Drd1_C1

source_name: Drd1-MSNs of Drd1-bacTRAP; G9afl/fl mice 1


title: G9a_Drd1_C2

source_name: Drd1-MSNs of Drd1-bacTRAP; G9afl/fl mice 2


title: embryo at E13 UB, biological rep2


title: G9a_Drd2_C1

source_name: Drd2-MSNs of Drd2-bacTRAP; G9afl/fl mice 1


title: Waters_1-6_24hr-control_Rep2_ATH1

source_name: Atglk1;Atglk2, control, 24hr

value: DMSO control


title: G9a_cortex_M2

source_name: cortex of Camk2a-Cre; G9afl/fl mice 2

value: cortex


title: G9a_Drd2_C2

source_name: Drd2-MSNs of Drd2-bacTRAP; G9afl/fl mice 2


title: G9a_cortex_C2

source_name: cortex of G9afl/fl mice 2


title: G9a_cortex_M1

source_name: cortex of Camk2a-Cre; G9afl/fl mice 1


title: G9a_Drd2_M1

source_name: Drd2-MSNs of Drd2-Cre; Drd2-bacTRAP; G9afl/fl mice 1


title: G9a_Drd1_M3

source_name: Drd1-MSNs of Drd1-Cre; Drd1-bacTRAP; G9afl/fl mice 3


title: Waters_1-9_24hr-induced_Rep1_ATH1


title: Waters_1-7_4hr-induced_Rep1_ATH1

source_name: Atglk1;Atglk2, dexamethasone, 4hr


title: Waters_1-8_4hr-induced_Rep2_ATH1


title: G9a_Drd2_M2

source_name: Drd2-MSNs of Drd2-Cre; Drd2-bacTRAP; G9afl/fl mice 2


title: G9a_striatum_C4

source_name: striatum of G9afl/fl mice 4

value: striatum


title: G9a_Drd1_C3

source_name: Drd1-MSNs of Drd1-bacTRAP; G9afl/fl mice 3


title: G9a_striatum_M4

source_name: striatum of Camk2a-Cre; G9afl/fl mice 4


title: Waters_1-4_4hr-control_Rep2_ATH1

source_name: Atglk1;Atglk2, control, 4hr


title: Waters_1-2_0hr-control_Rep2_ATH1

source_name: Atglk1;Atglk2, control, 0hr


title: G9a_hypoth_C3

source_name: hypothalamus of G9afl/fl mice 3

value: hypothalamus


title: G9a_striatum_M1

source_name: striatum of Camk2a-Cre; G9afl/fl mice 1


title: Waters_1-3_4hr-Control_Rep1_ATH1


title: G9a_striatum_M2

source_name: striatum of Camk2a-Cre; G9afl/fl mice 2


title: G9a_hypoth_C1

source_name: hypothalamus of G9afl/fl mice 1


title: G9a_hypoth_C2

source_name: hypothalamus of G9afl/fl mice 2


title: G9a_cortex_C1

source_name: cortex of G9afl/fl mice 1


title: G9a_striatum_M3

source_name: striatum of Camk2a-Cre; G9afl/fl mice 3


title: G9a_striatum_C1

source_name: striatum of G9afl/fl mice 1


title: Waters_1-5_24hr-Control_Rep1_ATH1

source_name: Atglk1;Atglk2, control, 24hr


title: G9a_hippo_C2

source_name: hippocampus of G9afl/fl mice 2

value: hippocampus


title: G9a_hypoth_M3

source_name: hypothalamus of Camk2a-Cre; G9afl/fl mice 3


title: Waters_1-1_0hr-Control_Rep1_ATH1


title: G9a_striatum_C2

source_name: striatum of G9afl/fl mice 2


title: G9a_hippo_C1

source_name: hippocampus of G9afl/fl mice 1


title: G9a_striatum_C3

source_name: striatum of G9afl/fl mice 3


title: G9a_hypoth_C4

source_name: hypothalamus of G9afl/fl mice 5


title: G9a_hypoth_M1

source_name: hypothalamus of Camk2a-Cre; G9afl/fl mice 1


title: G9a_hypoth_M4

source_name: hypothalamus of Camk2a-Cre; G9afl/fl mice 4


title: G9a_hypoth_M2

source_name: hypothalamus of Camk2a-Cre; G9afl/fl mice 2


title: G9a_hippo_M4

source_name: hippocampus of Camk2a-Cre; G9afl/fl mice 4


title: G9a_hippo_M3

source_name: hippocampus of Camk2a-Cre; G9afl/fl mice 3


title: G9a_hippo_C3

source_name: hippocampus of G9afl/fl mice 3


title: G9a_hippo_M2

source_name: hippocampus of Camk2a-Cre; G9afl/fl mice 2


title: GLP_cortex_C2

source_name: cortex of GLPfl/fl control mice 2


title: G9a_hippo_M1

source_name: hippocampus of Camk2a-Cre; G9afl/fl mice 1


title: GLP_cortex_C3

source_name: cortex of GLPfl/fl control mice 3


title: GLP_cortex_C1

source_name: cortex of GLPfl/fl control mice 1


title: GLP_striatum_M3

source_name: striatum of Camk2a-Cre; GLPfl/fl mice 3


title: GLP_cortex_M2

source_name: cortex of Camk2a-Cre; GLPfl/fl mice 2


title: GLP_striatum_C4

source_name: striatum of GLPfl/fl control mice 4


title: GLP_cortex_C4

source_name: cortex of GLPfl/fl control mice 4


title: GLP_cortex_M4

source_name: cortex of Camk2a-Cre; GLPfl/fl mice 4


title: GLP_hypoth_C3

source_name: hypothalamus of GLPfl/fl control mice 3


title: GLP_striatum_C3

source_name: striatum of GLPfl/fl control mice 3


title: Staphylococcus aureus Lug1430 (RsaX15 Mutant) / RN6390 (wild type) - Replicate #2

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

country: Switzerland

institute: Genomic Research Laboratory

hyb_protocol: Cy5-labeled total RNA (500 ng) and Cy3-labeled total RNA mixture was diluted in 50:l Agilent hybridization buffer, and hybridized at 60°C for 17 h in a dedicated hybridization oven.

data_processing: Fluorescence intensities were extracted using the Feature extraction software (Agilent, version 9.3). Local background subtracted signals were corrected for unequal dye incorporation or unequal load of the labeled product. The algorithm consisted of a rank consistency filter and a curve fit using the default LOWESS (locally weighted linear regression) method. Data consisting of two independent biological experiments were expressed as Log2 ratios and analyzed using GeneSpring (Agilent). Statistical significance of differentially expressed genes was identified by variance analysis (ANOVA, p<0.05) (46,49),  including the Benjamini and Hochberg false discovery rate correction (5%).

organism: Staphylococcus aureus

label_protocol: Batches of 8 µg total S. aureus RNA were labeled by Cy-3dCTP using the SuperScript II (Invitrogen, Basel, Switzerland) following manufacturer's instructions. Labeled products were then purified onto Qiaquick columns (Qiagen)

extract_protocol: Total RNAs were purified from late-exponential (7 h at 37°C) phase cultures grown in BHI. After additional DNase treatment, the absence of remaining DNA traces was evaluated by quantitative PCR.

value: RsaX15 (Mutant)

source_name: Staphylococcus aureus RN6390 (wild type) - Replicate #2

label_protocol: Samples were labeled with Cy-5 dCTP using the Klenow fragment of DNA polymerase I (BioPrime, Invitrogen, Carlsbad, CA)

extract_protocol: Purified total RNA was extracted with DNeasy (Qiagen)

value: RN6390 (wild type)


title: GLP_striatum_M4

source_name: striatum of Camk2a-Cre; GLPfl/fl mice 4

value: mutant


title: GLP_hypoth_C1

source_name: hypothalamus of GLPfl/fl control mice 1


title: GLP_hippo_C4

source_name: hippocampus of GLPfl/fl control mice 4


title: GLP_hypoth_M3

source_name: hypothalamus of Camk2a-Cre; GLPfl/fl mice 3


title: GLP_hypoth_M4

source_name: hypothalamus of Camk2a-Cre; GLPfl/fl mice 4


title: GLP_striatum_M1

source_name: striatum of Camk2a-Cre; GLPfl/fl mice 1


title: GLP_hypoth_C4

source_name: hypothalamus of GLPfl/fl control mice 4


title: GLP_hypoth_M1

source_name: hypothalamus of Camk2a-Cre; GLPfl/fl mice 1


title: GLP_striatum_C1

source_name: striatum of GLPfl/fl control mice 1


title: Staphylococcus aureus Lug1430 (RsaX15 Mutant) / RN6390 (wild type) - Replicate #1

source_name: Staphylococcus aureus RN6390 (wild type) - Replicate #1


title: GLP_cortex_M1

source_name: cortex of Camk2a-Cre; GLPfl/fl mice 1


title: GLP_striatum_M2

source_name: striatum of Camk2a-Cre; GLPfl/fl mice 2


title: GLP_hypoth_C2

source_name: hypothalamus of GLPfl/fl control mice 2


title: GLP_hypoth_M2

source_name: hypothalamus of Camk2a-Cre; GLPfl/fl mice 2


title: GLP_striatum_C2

source_name: striatum of GLPfl/fl control mice 2


title: GLP_cortex_M3

source_name: cortex of Camk2a-Cre; GLPfl/fl mice 3


title: GLP_hippo_C3

source_name: hippocampus of GLPfl/fl control mice 3


title: RNA_PolII_ChIP_Control_ArrayF

status: Public on Dec 09 2009

city: Lebanon

first: Mathieu

last: Lupien

state: NH

address: One Medical Center Drive

department: Genetics

institute: Norris Cotton Cancer Center/Dartmouth Medical School

hyb_protocol: according to (Carroll et al 2005)

scan_protocol: according to (Carroll et al 2005)

data_processing: CEL files analyzed with MAT algorithm

source_name: RNA Pol II ChIP

label_protocol: according to (Carroll et al 2005)

growth_protocol: phenol-red free DMEM supplemented with 10% charcoal dextran treated serum.

extract_protocol: according to (Carroll et al 2005)

treatment_protocol: control (ethanol) or estrogen (E2: 1x10-8M) for 45 minutes

tag: cell type

value: MCF7 breast cancer cells

tag: antibody

value: RNA Pol II


title: H3R17me2_ChIP_Estrogen_ArrayF

source_name: H3R17me2 ChIP

value: Estrogen


title: INPUT_ArrayB

data_processing: Cel files analyzed with MAT

source_name: MCF7 breast cancer cells

tag: reference

value: input


title: H3R17me2_ChIP_Control_ArrayB


title: GLP_hippo_C1

source_name: hippocampus of GLPfl/fl control mice 1


title: INPUT_ArrayF


title: H3R17me2_ChIP_Control_ArrayF


title: GLP_hippo_M4

source_name: hippocampus of Camk2a-Cre; GLPfl/fl mice 4


title: GLP_hippo_M3

source_name: hippocampus of Camk2a-Cre; GLPfl/fl mice 3


title: GLP_hippo_C2

source_name: hippocampus of GLPfl/fl control mice 2


title: H3R17me2_ChIP_Estrogen_ArrayB


title: Biofilms treated by 10b  vs control biofilms 2

city: Shanghai

first: Liang

last: Rong-mei

address: Guohe road 325

country: China

institute: smmu

description: compare gene expression profiles of   SC5314 biofilms treated by 10b with control SC5314 biofilms.

hyb_protocol: standard CapitalBio Methods

scan_protocol: Luxscan 10K (CapitalBio)

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed. For each test and control sample, two hybridizations were performed by using a reversal fluorescent strategy,the geometric mean  of lowess normalized log2 ratio (test/control) of two dye-swap slides was calculated.

organism: Candida albicans

source_name: Biofilms treated by 10b

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP, Amersham Pharmacia Biotech, Piscataway, NJ) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction. the amplified RNA (aRNA) was purified with NucleoSpin Extract II (MN). We took a cDNA labeling approach with Klenow enzyme after reverse transcription.

growth_protocol: Candida albicans SC5314 cells were propagated in yeast-peptone-dextrose (YPD) medium (1% w/v yeast extract, 2% w/v peptone, 2% w/v dextrose). Blastospores were harvested and washed twice in 0.15 M phosphate-buffered saline (PBS; pH 7.2). The cells were then suspended in RPMI-1640 medium supplemented with L-glutamine and buffered to PH 7.0 with morpholinepropanes-ulfonic acid (MOPS), counted in a haemocytometer and adjusted to the desired cell density (1.0×106 cfu.ml-1).

extract_protocol: Total RNA was isolated by the hot phenol method.

treatment_protocol: Cells were added to 25 mL portions of RPMI-1640 medium in 75 cm2 tissue culture ﬂasks with vented caps. The ﬂasks were incubated statically for 1 h to allow initial adherence of the cells, then the medium was decanted and replaced with 25 mL portions of fresh RPMI-1640 medium containing 10 μM 10b.The ﬂasks were then incubated statically for 48 h at 37 °C. A 10b-free control was also included.

source_name: Control biofilms


title: Biofilms treated by 10b  vs control biofilms 1


title: GLP_hippo_M2

source_name: hippocampus of Camk2a-Cre; GLPfl/fl mice 2


title: RNA_PolII_ChIP_Control_ArrayB


title: Non-small cell lung cancer cell line, PC-9 DR6

city: Boston

first: Pasi

last: Janne

state: MA

address: 44 Binney Street Dana 820

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Hybridized to 250K_Sty

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: CEL files and TXT files (generated by Affymetrix GTYPE using the DM algorithm) were processed by dChip and model-based expression performed using the PM/MM model. Normalization was performed using the invariant set probe selection method and the running median smoothing method. The data matrix contains the normalized expression values produced by that algorithm.

label_protocol: As per manufacturer (Affymetrix).

growth_protocol: Cell lines were grown to approximately 70% confluency in RPMI media supplemented with 10% FBS, 100 units/ml Penicillin, and 100 ug/ml Streptomycin.

extract_protocol: Genomic DNA was extracted from cell lines using the Qiagen DNeasy Blood and Tissue Kit according to manufacturer's instructions. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

treatment_protocol: None.

tag: cell line

value: PC-9 DR6

value: non-small cell lung cancer

tag: notable drug resistance

value: gefitinib + PF00299804


title: Non-small cell lung cancer cell line, PC-9 DR1

description: Hybridized to 250K_Sty

value: PC-9 DR1


title: H3R17me2_ChIP_Control_ArrayC


title: D2060RP (20mers)

description: custom tiling array design

source_name: heterozygous non-reference

tag: hybridization temperature

source_name: reference


title: INPUT_ArrayC


title: RNA_PolII_ChIP_Control_ArrayC

tag: agent


title: ppGpp0 strain, pvector, biological rep3, long term

city: Bethesda

first: Katarzyna

last: Potrykus

address: 6 Center Drive, 6B rm 316

department: NICHD

institute: NIH

description: Gene expression data from cells at OD~ 0.5

hyb_protocol: Following fragmentation, cDNA were hybridized for 16 hr at 45C on E. coli 2.0 arrays (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the Mini_prok2v1_450 protocol.

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

organism: Escherichia coli

source_name: E.coli ppGpp0 cells with vector control

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Prokaryotic Traget Preparation in Affymetrix GeneChip® Expression Analysis Technical Manual).

growth_protocol: E.coli cells were grown in LB at 37C, with vigorous shaking

extract_protocol: 5 OD units were removed from the culture and immediately added to an equal volume of ice-cold RNAlater reagent (Ambion). Thus treated samples were stored for 20min on ice. Total RNA was extracted with Trizol reagent (Invitrogen) following manufacturer's instructions.

treatment_protocol: At OD~0.5, IPTG was added to 1mM and growth was continued for 15min. The strains employed here did not contain lacIq on the chromosome, and thus GraL was beeing constitutivley overexpressed +/- IPTG. IPTG was added to mirror the experiments where GraL was overproduced for short periods of time.

tag: strain


title: ppGpp0 strain, pvector, biological rep2, long term


title: Non-small cell lung cancer cell line, PC-9 DR2

description: Hybridized to 250K_Sty

value: PC-9 DR2


title: H2060RP (20mers)

description: custom tiling array design

source_name: haploid non-reference


title: Non-small cell lung cancer cell line, PC-9 GR5

description: Hybridized to 250K_Sty

value: PC-9 GR5

value: gefitinib


title: genomic DNA isolated from C57BL/6 32-month old mice intestine, 2 of 2

first: Jiexin

last: Zhang

address: 1515 Holcombe Blvd

department: Bioinformatics & Computational Biology

institute: UT MD Anderson Cancer Center

description: 32m old intestine chr 9 to 19, X and Y

hyb_protocol: Followed Agilent protocol

scan_protocol: Scanned on an Agilent Technologies Scanner G2505B US23502362 Images were quantified using Agilent Feature Extraction Software (version 9.1.3.1).

data_processing: Agilent Feature Extraction Software (9.1.3.1) was used for background subtraction and normalization.

source_name: genomic DNA isolated from C57BL/6 32m old mice intestine

label_protocol: Followed Agilent protocol

growth_protocol: C57BL/6 mice (Jackson Laboratories, Bar Harbor, ME) were used.

extract_protocol: Genomic DNA was extracted using a standard phenol–chloroform method

tag: tissue

value: intestine

tag: age


title: Non-small cell lung cancer cell line, PC-9 DR4

description: Hybridized to 250K_Sty

value: PC-9 DR4


title: Non-small cell lung cancer cell line, PC-9 GR3

description: Hybridized to 250K_Sty

value: PC-9 GR3


title: Non-small cell lung cancer cell line, PC-9 DR5

description: Hybridized to 250K_Sty

value: PC-9 DR5


title: Macrophage Poly (I:C) reverse

city: Barcelona

first: Joan

middle: C

last: Balasch

address: UAB Bellaterra faculty of Biosciences

department: Dpt. Cell Biology, Physiology and Immunology

country: Spain

institute: Universitat Autonoma Barcelona

description: To assess differential expression of genes, the normalized log intensity ratios were analyzed with Student’s t-test (p<0.01). The Bayesian modification to the false discovery rate (FDR) was used to correct for multiple comparison tests, estimating the q-value for the set of differentially expressed genes

hyb_protocol: We used a dye swap experimental design and each sample was hybridized to two microarrays. For the first slide, immunodiet and control diet cDNA were labeled with Cy5 and Cy3 respectively, and for the second array dye assignment was reversed. All samples were analyses using the dye swap protocol. The slides were pre-treated with 1% BSA, fraction V, 5 x SSC, 0.1% SDS (30 min at 50ºC) and washed with 2 x SSC (3 min) and 0.2 x SSC (3 min) and hybridized overnight in cocktail containing 1.3 x Denhardt’s, 3 x SSC 0.3% SDS, 2.1 μg/μl polyadenylate and 1 μg/μl yeast tRNA.

scan_protocol: Scanning was performed with Axon scanner 4000B and images were processed with GenePix Pro 6.0.The measurements in spots were filtered by criteria I/B ≥ 3 and (I-B)/(SI+SB) ≥ 0.6, where I and B are the mean signal and background intensities and SI, SB are the standard deviations.

data_processing: Images were processed with GenePix Pro 6.0.The measurements in spots were filtered by criteria I/B = 3 and (I-B)/(SI+SB) = 0.6, where I and B are the mean signal and background intensities and SI, SB are the standard deviations.

organism: Oncorhynchus mykiss

source_name: MO control

label_protocol: cDNA Cy5 Labelling with Cy5-dCTP (Amersham Pharmacia) was completed using SuperScript III reverse transcriptase (Invitrogen) and oligo(dT) primer, and cDNA was purified with Microcon YM30 (Millipore).

extract_protocol: TriReagent manufacturer's protocol. RNA was extracted with the Trizol reagent (Life Technologies) or Tri Reagent (Molecular Research Center, Cincinnati, OH, USA) according to the manufacturer’s instructions.The RNA was stored at -80 ºC in ethanol 70% until use.

tag: RNA from control MO

source_name: MO Poly (I:C)

label_protocol: cDNA Cy3 Labelling with Cy3-dCTP (Amersham Pharmacia) was completed using SuperScript III reverse transcriptase (Invitrogen) and oligo(dT) primer, and cDNA was purified with Microcon YM30 (Millipore).

tag: RNA from MO stimulated with Poly (I:C)


title: genomic DNA isolated from C57BL/6 3-month old mice intestine, 2 of 2

description: 3m old intestine chr 9 to 19, X and Y

source_name: genomic DNA isolated from C57BL/6 3m old mice intestine


title: H2045TT (20mers)

description: custom tiling array design


title: Non-small cell lung cancer cell line, PC-9 GR6

description: Hybridized to 250K_Sty

value: PC-9 GR6


title: INPUT_ArrayD


title: Non-small cell lung cancer cell line, PC-9 GR2

description: Hybridized to 250K_Sty

value: PC-9 GR2


title: ppGpp0 strain, pvector, biological rep1, long term


title: D2055RP (20mers)

description: custom tiling array design


title: Non-small cell lung cancer cell line, PC-9 GR4

description: Hybridized to 250K_Sty

value: PC-9 GR4


title: G9a_Drd1_M2

source_name: Drd1-MSNs of Drd1-Cre; Drd1-bacTRAP; G9afl/fl mice 2

tag: tissue type

value: mutant


title: H3R17me2_ChIP_Control_ArrayD

source_name: H3R17me2 ChIP

value: MCF7 breast cancer cells


title: H3R17me2_ChIP_Estrogen_ArrayD

value: Estrogen


title: INPUT_ArrayE

source_name: MCF7 breast cancer cells

value: input


title: H3R17me2_ChIP_Control_ArrayE


title: ppGpp0 strain, pGraL, biological rep3, long term

source_name: E.coli ppGpp0 cells overexpressing GraL


title: INPUT_ArrayA


title: H3R17me2_ChIP_Estrogen_ArrayE


title: Non-small cell lung cancer cell line, PC-9 GR1

description: Hybridized to 250K_Sty

value: PC-9 GR1

value: non-small cell lung cancer


title: ppGpp0 strain, pGraL, biological rep2, long term


title: Macrophage LPS reverse

source_name: MO LPS

tag: RNA from MO stimulated with LPS


title: Non-small cell lung cancer cell line, PC-9 DR3

description: Hybridized to 250K_Sty

value: PC-9 DR3

value: gefitinib + PF00299804


title: RNA_PolII_ChIP_Control_ArrayE

source_name: RNA Pol II ChIP

value: RNA Pol II


title: RNA_PolII_ChIP_Control_ArrayD


title: wt strain, pvector, biological rep2, long term

source_name: E.coli wt cells with vector control


title: wt strain, pvector, biological rep3, long term


title: Non-small cell lung cancer cell line, PC-9

description: Hybridized to 250K_Sty

tag: sample type

value: reference


title: INPUT_ArrayG


title: Macrophage LPS direct


title: RNA_PolII_ChIP_Control_ArrayA


title: Macrophage Poly (I:C) direct


title: H3R17me2_ChIP_Control_ArrayA


title: H3R17me2_ChIP_Control_ArrayG


title: H3R17me2_ChIP_Estrogen_ArrayG


title: H2050RP (20mers)

description: custom tiling array design


title: wt strain, pvector, biological rep, long term


title: H3R17me2_ChIP_Estrogen_ArrayA


title: wt strain, pGraL, biological rep3, long term

source_name: E.coli wt cells overexpressing GraL


title: ppGpp0 strain, pGraL, biological rep1, long term


title: RNA_PolII_ChIP_Control_ArrayG


title: H2055RP (20mers)

description: custom tiling array design


title: wt strain, pGraL, biological rep2, long term


title: wt strain, pGraL, biological rep1, long term


title: ppGpp0 strain, pvector, biological rep1, short term

treatment_protocol: At OD~0.5, GraL overexpression was induced with 1mM IPTG and growth was continued for 15min. The strains emplyed contain lacIq on the chromosome allowing for tight regulation of GraL expression from the plasmid construct.


title: retinoblastoma Hela HPV pos_Array 350

city: Mexico City

first: Martha

middle: Veronica

last: Ponce-Castañeda

address: Av. Cuauhtemoc 330

department: Hospital de Pediatría, CMN SXXI

country: Mexico

institute: Instituto Mexicano del Seguro Social IMSS

description: Total RNA from each tissue culture was extracted using TRIzol reagent. Total RNA from exponentially growing Saccharomyces cerevisiae was extracted using an organic extraction protocol. 10 microg of total RNA were used for cDNA synthesis incorporating dUTP-Cy3 for yeast and dUTP-Cy5 for retinoblastoma.  RNA was reverse-transcribed into cDNA with  CyScribe First strand cDNA labeling kit (Amersham) following manufacturer’s instructions. After cleanup, fluorophore incorporation was analyzed  by spectrophotometric absorbance at 555nm for Cy3 and 655nm for Cy5. The 10K human oligos microarray was hybridized with equal amounts of labeled cDNA from yeast and retinoblastoma using  hybridization solution UniHyb (TeleChem International Inc. Sunnyvale,CA)  for 14 hr at 42°C. After hybridization acquisition and quantification of microarrays images  was performed using ScanArray 4000 scanner and its accompanying software from Packard BioChips. All images were captured using 65% PMT gain, 70 to 75% laser power and 10 microm resolution at 50% scan rate. For each spot the Cy3 and Cy5 density mean value and corresponding background mean value were calculated with ArrayPro Analyzer from Media Cibernetics

hyb_protocol: Equal quantities of labeled cDNA were hybridized using hybridization solution UniHyb (TeleChem International INC), to the ten thousand human oligos arrays for 14 h at 42°C

scan_protocol: Acquisition and quantification of array images was performed in ScanArray 4000 with its accompanying software ScanArray 4000 from Packard BioChips. All images were captured using 65% PMT gain, 70 to 75% laser power and 10µm resolution at 50% scan rate. For each spot the Cy3 and Cy5 density mean value and the Cy3 and Cy5 background mean value were calculated with software ArrayPro Analyzer from Media Cibernetics

data_processing: Raw data was normalized by Local Lowess with MIDAS V2.19 (The Institute for Genomics Reseach, Wei Linag and John Quackenbush, 2004). We used block mode and a smoothing parameter of 0.33.  Replicates on the same array were averaged and the log2 ratio was calculated of Sc5/Sc3. For expressions of zero the log ratio is null.

source_name: Saccharomyces cerevisiae

label_protocol: 10 µg of total RNA were used for cDNA synthesis incorporating dUTP-Cy3 employing the CyScribe Firs-Strand cDNA labeling kit (Amersham). Incorporation of fluorophore was analyzed by using the absorbance at 555 nm

growth_protocol: YPD medium

extract_protocol: Total RNA was extracted with a Phenol/Chloroform/Isoamyl-alcohol protocol

source_name: Hela cell line

label_protocol: 10 µg of total RNA were used for cDNA synthesis incorporating dUTP-Cy5 employing the CyScribe Firs-Strand cDNA labeling kit (Amersham). Incorporation of fluorophore was analyzed by using the absorbance at 655 nm for Cy5

growth_protocol: Minimal essential medium (MEM) suplemented with 10% fetal bovine serum

extract_protocol: Tumors cells were harvested by centrifugation, drained and total RNA was extracted using TRIzol reagent according to manufacturer’s instructions. (Invitrogen, Carlsbad, CA)

value: Retinoblastoma tumor. Status:Hpv positive, malignant tumor harboring Hpv type 18.


title: retinoblastoma Y79 HPV neg_Array 216

description: Total RNA from each tissue culture was extracted using TRIzol reagent. Total RNA from exponentially growing Saccharomyces cerevisiae was extracted using an organic extraction protocol. 10 microg of total RNA were used for cDNA synthesis incorporating dUTP-Cy3 for yeast and dUTP-Cy5 for retinoblastoma.  RNA was reverse-transcribed into cDNA with  CyScribe First strand cDNA labeling kit (Amersham) following manufacturer’s instructions. After cleanup, fluorophore incorporation was analyzed  by spectrophotometric absorbance at 555nm for Cy3 and 655nm for Cy5. The 10K human oligos microarray was hybridized with equal amounts of labeled cDNA from yeast and retinoblastoma using  hybridization solution UniHyb (TeleChem International Inc. Sunnyvale,CA)  for 14 hr at 42°C. After hybridization acquisition and quantification of microarrays images  was performed using ScanArray 4000 scanner and its accompanying software from Packard BioChips. All images were captured using 65% PMT gain, 70 to 75% laser power and 10 m resolution at 50% scan rate. For each spot the Cy3 and Cy5 density mean value and corresponding background mean value were calculated with ArrayPro Analyzer from Media Cibernetics

source_name: Y79 retinobalstoma cell line

growth_protocol: RPMI 1640 medium suplemented with 20% fetal bovine serum

value: Retinoblastoma tumor. Status:Hpv negative, from a  patient with strong maternal family history of retinoblastoma established in 1971.


title: ppGpp0 strain, pGraL, biological rep3, short term

source_name: E.coli ppGpp0 cells overexpressing GraL for 15 minutes


title: ppGpp0 strain, pGraL, biological rep1, short term


title: ppGpp0 strain, pvector, biological rep2, short term

source_name: E.coli ppGpp0 cells with vector control


title: ppGpp0 strain, pGraL, biological rep2, short term


title: ppGpp0 strain, pvector, biological rep3, short term


title: H3R17me2_ChIP_Estrogen_ArrayC


title: wt strain, pvector, biological rep3, short term