title: PS214

status: Public on Nov 21 2009

city: Atlanta

first: Benjamin

middle: G

last: Barwick

state: GA

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

institute: Emory University

description: Medulloblastoma

hyb_protocol: Preheat the oven (with rocking platform) to 58°C. Mix with Hyb Reagents 1. Prepare cRNA samples (dried down, if necessary to achieve required concentration). 2. To 1.5 μg RNA, add RNase-free water up to 10 μL and mix. 3. Leave at RT for 10 minutes to resuspend cRNA. 4. Place the GEX-HYB and GEX-HCB tubes in the 58°C oven for 10 minutes to dissolve any salts that may have precipitated in storage. Inspect the solution; if any salts remain undissolved, incubate at 58°C for another 10 minutes. After allowing to cool to room temperature, mix thoroughly before using. 5. Add 20 μL GEX-HYB to each cRNA sample. Set Up Hybridization 1. Place Illumina Hyb Chamber Gaskets into BeadChip Hyb Chamber. 2. Dispense 200 μL GEX-HCB into each of the two humidifying buffer reservoirs in each Hyb Chamber. 3. Only add buffer to chambers that will be used. 4. Seal Hyb Chamber with lid and keep on bench at room temperature (~22°C) until ready to load BeadChips into Hyb Chamber. 5. Remove all BeadChips from their packages. 6. Holding BeadChip by coverseal tab with tweezers using powder-free gloved hands, slide BeadChip into Hyb Chamber Insert such that the barcode lines up with barcode symbol on the Insert. 7. Preheat the assay sample at 65°C for 5 minutes. 8. Briefly vortex, then briefly centrifuge to collect the liquid in the bottom of the tube. Allow sample to cool to room temperature before using. Pipet sample immediately after cooling to room temp. 9. Load Hyb Chamber Inserts containing BeadChips into the Hyb Chamber with barcode on BeadChip aligned to barcode symbol on the Hyb Chamber. 10. Dispense 30 μL assay sample onto the large sample port of each array. 11. Seal lid onto the Hyb Chamber carefully to avoid dislodging the Hyb Chamber Insert(s). 12. Incubate for 16-20 hours at 58°C with rocker speed at 5. ] Caution: Proceed to “Prepare for High-Temp Wash & Overnight Incubation” on page 2 before stopping for the day. 13. Prepare for High-Temp Wash & Overnight Incubation 14. Prepare 1X High-Temp Wash buffer (add 50 mL 10X stock to 450 mL RNAse-free water). 15. Place waterbath insert into heat block, and add 500 mL prepared 1X High-Temp Wash buffer. 16. Set heat block temp to 55°C and pre-warm High-Temp Wash buffer to that temperature. 17. Close heat block lid and leave overnight. Prepare Reagents 1. The next day, make Wash E1BC solution (add 3 mL E1BC buffer to 1 L RNase-free water). 2. Pre-warm Block E1 buffer (4 mL/chip) to room temperature. 3. Prepare Block E1 buffer (2 mL/chip) with streptavidin-Cy3 (2 μL of 1 mg/mL stock per chip). Use a single conical tube for all BeadChips. Store in dark until detection step. Room-Temp Incubation 1. Remove Hyb Chamber from oven and disassemble. Caution: When removing the coverseal, some splattering may occur. To avoid contact with the buffer, which contains formamide, remove the seals in a shielded area such as a fume hood with the sash lowered. 2. Remove coverseal from the BeadChip. Using tweezers or powder-free gloved hands, place the BeadChip into the slide rack submerged in the staining dish containing 250 mL Wash E1BC solution. 3. Repeat disassembly and placement in E1BC solution for all BeadChips. 4. Using the slide rack handle, transfer the rack into the Hybex Waterbath insert containing High-Temp Wash buffer. High-Temp Wash 1. Incubate static for 10 minutes with the Hybex lid closed. 2. During the 10-minute High-Temp Wash buffer incubation, add fresh 250 mL Wash E1BC solution to a clean staining dish. 3. After the 10-minute High-Temp Wash buffer incubation is complete, immediately transfer the slide rack into the staining dish containing E1BC. 4. Briefly agitate using rack, then shake on orbital shaker for 5 minutes at the highest speed possible without allowing solution to splash out of dish. Ethanol Wash 1. Transfer rack to a clean staining dish containing 250 mL 100% Ethanol (use fresh from Ethanol source bottle). 2. Briefly agitate using rack handle, then shake on orbital shaker for 10 minutes. 2nd Room-Temp Wash 1. Transfer rack to a clean staining dish containing fresh 250 mL Wash E1BC solution. 2. Briefly agitate using rack handle, then shake on orbital shaker for 2 minutes. Block 1. Pipette 4 mL Block E1 buffer into the Wash Tray(s). 2. Transfer the BeadChip, face up into BeadChip Wash Tray(s) on rocker. 3. Rock at medium speed for 10 minutes. Detect 1. Pipette 2 mL Block E1 buffer + streptavidin-Cy3 into fresh Wash Tray(s). 2. Transfer the BeadChip, face up into Wash Tray(s) on rocker. 3. Place cover on tray and rock at medium speed for 10 minutes. 3rd Room-Temp Wash 1. Add 250 mL of Wash E1BC solution to a clean staining dish. 2. Transfer the BeadChip to the slide rack submerged in the staining dish. 3. Briefly agitate using rack, and then shake at RT on orbital shaker for 5 minutes. Dry 1. Prepare centrifuge with plateholders, paper towels and balance rack. Set speed to 275 rcf. 2. Transfer rack of BeadChips from staining dish to centrifuge and spin at RT for 4 minutes. 3. Store dry chips in slide box until scanned.

scan_protocol: Beadchips were scanned at the same time on an Illumina 500GX Beadstation using Illumina BeadScan v. 3 software

data_processing: Data was interpreted in GenomeStudio v. 1.0.2 and quantile normalized

source_name: cerebellar tumor: medulloblastoma

label_protocol:
Reverse Transcription to Synthesize First Strand cDNA:
1. Bring RNA samples to 11 µl with RNase-free water (50-500 ng)
2. Add 9 µl of RT Master Mix (mix well and centrifuge briefly): T7 oligo(dT) primer (1 µl), 10X first strand buffer (2 µl), dNTP mix (4 µl), RNase inhibitor (1 µl), ArrayScript (1 µl),
3. Incubate at 42°C for 2 hrs (use a thermal cycler with the lid off or heated to the same temperature)
4. Place tubes on ice and immediately proceed to the next step
Second Strand cDNA Synthesis:
1. Add 80 µl of Second Strand Master Mix to each sample (vortex and spin down): Nuclease-free water (63 µl), 10X Second Strand Buffer (10 µl), dNTP mix (4 µl), DNA polymerase (2 µl), RNase H (1 µl)
2. Place at 16°C for 2 hrs (make sure the block is pre-cooled and the lid is off or at the same temperature)
3. Pre-heat nuclease-free water to 50-55°C for the next step
4. Place tubes on ice and proceed to the next step (the reactions can be frozen at -20°C overnight, but it is better to purify them first)
cDNA Purification:
1. Pre-heat nuclease-free water to 50-55°C for at least 10 min
2. Check the cDNA Binding Buffer for precipitation – place at 37°C for up to 10 min and vortex vigorously; cool to RT before use
3. Add 250 µl of cDNA Binding Buffer to each sample, mix by pipetting up and down and quickly spin; proceed quickly to the next step
4. Check that the filter is firmly seated in its tube
5. Pipet the cDNA sample with the cDNA Binding Buffer onto the center of the cDNA Filter Cartridge
6. Centrifuge at 10,000 rpm for 1 min
7. Discard flow-through and replace the cDNA Filter cartridge in the wash tube
8. Make sure 100% EtOH has been added to the Wash Buffer
9. Apply 500 µl of Wash Buffer to each sample
10. Centrifuge at 10,000 rpm for 1 min; discard flow-through
11. Centrifuge at 10,000 rpm for 1 min
12. Transfer the cDNA Filter Cartridge to a cRNA Elution Tube
13. Apply 10 µl of pre-heated nuclease-free water to the cDNA Filter Cartridge
14. Incubate at RT for 2 min
15. Centrifuge at 10,000 rpm for 1.5 min
16. Apply 9 µl of pre-heated nuclease-free water to the cDNA Filter Cartridge
17. Incubate at RT for 2 min
18. Centrifuge at 10,000 rpm for 2 min
19. The eluate is now in about 17.5 µl and it can be stored at -20°C if needed (better to proceed to the next step immediately)
In vitro Transcription to Synthesize cRNA:
1. Prepare the IVT Master Mix at room temperature: T7 10x Reaction Buffer (2.5 µl), T7 Enzyme Mix (2.5 µl), Biotin-NTP Mix (2.5 µl)
2. Transfer 17.5 µl of sample to a new 0.2 ml tube
3. Add 7.5 µl of the IVT Master Mix to each sample
4. Place tubes at 37°C for 14 hrs in a thermal cycler (add a 4°C hold at the end)
Day 2:
5. Add 75 µl of nuclease-free water to each sample
6. Proceed to the RNA purification step
cRNA Purification:
1. Pre-heat nuclease-free water to 50-55°C
2. Add 350 µl of cRNA binding buffer to each sample; proceed immediately to next step
3. Add 250 µl of 100% EtOH to each cRNA sample; mix by pipetting up and down; proceed immediately to the next step
4. Pipet the mixture from above onto the cRNA Filter Cartridge (one per sample)
5. Centrifuge at 10,000 rpm for 1 min; discard flow-through
6. Add 650 µl of Wash Buffer to each filter
7. Centrifuge at 10,000 rpm for 1 min; discard flow-through
8. Centrifuge at 10,000 rpm for 1 min to dry
9. Transfer the Filter cartridge to a new collection tube
10. Add 100 µl of pre-heated nuclease-free water to the center of the filter
11. Incubate at RT for 2 min
12. Centrifuge at 10,000 rpm for 1.5 min

extract_protocol:
Qiagen RNeasy Kit
1. Disrupt and homogenize the sample immediately using Buffer RLT (β-ME added) and a Polytron for 40 sec. Starting material Volume of Buffer RLT Up to 20 mg 350 μL 20 to 30 mg or tissue is difficult to lyse 600 μL
2. Centrifuge lysate for 3 min at maximum speed in a microcentrifuge, and transfer the supernatant into a new Eppendorf tube.
3. Add 1 volume (350 or 600 μL) of 70% ethanol to the cleared lysate, and mix well by pipetting.
4. Apply 700 μL of the sample to an RNeasy mini spin column sitting in a 2-mL collection tube.
5. Centrifuge for 15 sec at maximum speed. Discard flow-through, and reuse the collection tube.
6. Apply aliquots successively onto the RNeasy column and centrifuge as above. Discard flow-through and reuse the collection tube.
7. Pipet 700 μL Buffer RW1 onto the RNeasy column, incubate RNeasy column for 5 min, and centrifuge for 15 sec at maximum speed. Discard flow-through and the collection tube.
8. Transfer RNeasy column to a new 2-mL collection tube.
9. Pipet 500 μL Buffer RPE onto RNeasy column, and centrifuge for 15 sec at maximum speed to wash. Discard flow-through and reuse the collection tube.
10. Pipet 500 μL Buffer RPE onto RNeasy column, and centrifuge for 2 min at maximum speed to dry the RNeasy membrane. Discard flow-through and the collection tube. Note: Residual ethanol may interfere with subsequent reaction. Remove the RNeasy column so that the column does not contact the flow-through as this will result in carryover of ethanol.
11. (Optional): Place the RNeasy spin column in a new 2-mL collection tube, and discard the old collection tube with filtrate. Centrifuge at full speed for 1 min.
12. Transfer RNeasy column into a new 1.5-mL Eppendorf tube (remove the lid) and pipet 30 μL of DEPC water directly onto the RNeasy membrane. Centrifuge for 1 min at maximum speed to elute.
13. Pipet 30 μL of DEPC water successively directly onto the RNeasy membrane. Centrifuge for 5 min at maximum speed to elute.
14. Transfer elute to a new Eppendorf tube.

tag: genotype/variation

value: pten +/-, smoa +

tag: survival

value: 10 weeks


title: Mammary lactating standardG M216S

status: Public on Nov 23 2009

type: RNA

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

country: USA

institute: Van Andel Institute

description: Gene expression data from three tissue types within rats in lactation/pregnancy and micro/standard/hyper gravity.

hyb_protocol: 2.2ug of biotin labeled, fragmented cDNA hybridized to Rat 230 2.0 Affy GeneChips.

scan_protocol: Affymetrix Genearray scanner 3000, with 7G upgrade

data_processing: Data analyzed with RMA and MAANOVA.

label: R-Phycoerythrin Streptavidin (SAPE), from Molecular Probes, 1 mg/ml  ( we use 6 ul per reaction )

molecule: total RNA

organism: Rattus norvegicus

source_name: Rattus norvegicus

label_protocol: 25ng total RNA for cDNA synthesis, amplification and biotin labeling with NuGEN Ovation Biotin System.

extract_protocol: Total RNA was isolated with TRIzol (Invitrogen) for mammary and liver; RNeasy Lipid (QIAGEN) for adipose.

tag: subtype


title: Adipose lactating standardG A216S


title: Liver lactating standardG L216S


title: Mammary pregnant standardG M52S


title: Adipose lactating hyperG A210H


title: MLL-AF4 infant ALL, 603

type: genomic

city: Rotterdam

first: Dominique

last: Stumpel

address: Dr. Molewaterplein 50-room Ee15-14

department: Pediatric Oncology/ Hematology

country: Netherlands

institute: Erasmus MC _ Sophia Children's Hospital

description:
pro-B

Please refer to Differential Methylation Hybridization (DMH) protocol by Dr. Tim H. Huang and coworkers. (PMID 18987809: Yan PS, Potter D, Deatherage DE, Huang TH, Lin S., Differential methylation hybridization: profiling DNA methylation with a high-density CpG island microarray.Methods Mol Biol. 2009;507:89-106.)

hyb_protocol: Oligoarray control targets and hybridization buffer (the Oligo aCGH/ChIP-on-Chip Hybridization Kit) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially according to the Agilent protocol.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing:
Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).
Agilent Feature Extraction Software (v 8.5.1.1) was used for data extraction. The R and Bioconductor statistical environment (version 2.7) were used for quality control and LOESS normalization (limma package). No background correction was performed.

molecule: genomic DNA

organism: Homo sapiens

source_name: bone marrow, t(4;11)

label_protocol: Using the BioPrime Array-CGH Genomic Labeling kit (Invitrogen, Carlsbad, USA), amino-allyl dUTPs were incorporated into 500ng of the methylated amplicons (generated by DMH) , allowing the amplicons to be labeled with the fluorescent dyes Cy5 (patient samples) and Cy3 (common reference samples).

growth_protocol: All cell lines were maintained as suspension cultures in RPMI 1640 with L-Alanyl-L-Glutamine (Invitrogen) supplemented with 10% FCS (Integro), 100 IU/ml  penicillin, 100 μg/ml streptomycin, and 0.125 μg/ml fungizone (Invitrogen) at 37°C in humidified air containing 5% CO2.

extract_protocol: Total DNA extracted using Trizol following manufacturer's instructions.

treatment_protocol: Only applicable for the cell lines: treated with 100nM of zebularine for 10 days.

tag: tissue

value: bone marrow

tag: gender

value: female

tag: genotype

source_name: peripheral blood, healthy

value: peripheral blood

tag: sample description

value: mix from 5 healthy males and 5 healthy females

tag: sample type

value: reference


title: PS213

description: Medulloblastoma

label: Biotin

organism: Mus musculus

value: 9.1 weeks


title: MLL-AF4 infant ALL, 598

source_name: peripheral blood, t(4;11)

value: male


title: MLL-AF4 infant ALL, 607


title: PS184

description: Medulloblastoma

value: 12.4 weeks


title: mSMC-TNF-2h-0

city: Munich

first: Andreas

middle: Johann Richard

last: Habenicht

state: Bavaria

address: Pettenkoferstraße 9a

department: Medicine

country: Germany

institute: Ludwig Maximilians Universität München

description: Staining with Fluidic Station 450 Protocol: EukGe-WS2v4

hyb_protocol: 60rpm, 18h, 45°C in Affymetrix Hybridization Buffer

scan_protocol: Affymetrix Scanner 3000, single scan

data_processing: GCOS 1.4, scaled to 500

label: Biotin/SAPE with Anti Streptavidin signal amplification

source_name: Aortic Smooth Muscle Cells

label_protocol: ENZO T7 High Yield Transcript Labelling Kit, 16h IVT

growth_protocol: Maintained in DMEM/F12, 10% FCS, feed every 48h

extract_protocol: Qiagen RNEasy Lipid Tissue Mini Kit, Standard protocol

treatment_protocol: Cells were feed 24h prior to stimulation, stimuli were added in PBS, Cells were stimulated with 1ng/ml TNFalpha

tag: strain

value: C57BL/6J, Gender:male, Age:10-12 weeks, Tissue:aorta


title: PS182

description: Medulloblastoma


title: PS161

description: Medulloblastoma

value: 19 weeks


title: 777: matched fibroid vs myemetrium

city: La Jolla

first: Yong

last: Jiang

state: CA

address: 3855 Health Science Dr.

institute: UCSD-Moores Cancer Center

description:
myometrium-cy5, fibroid-cy3: YS_A.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): YS_B.gpr

hyb_protocol: cy5 and cy3 labeled cRNA probe hybridized with in-house TK chip at 42oC in hybridization buffer (3xSSC, 0.1%SDS, 20% Formaldehyde) for 14h to 17h.

scan_protocol: after hybridization, the slides were scanned with Axon 4000B scanner.

data_processing: the raw image was transformed into raw fluorescence reading units by Genepix software, the raw data was normalized with quantile normalization(R package DNAMR), and fitted with linear mixture-model (R package NLM).

source_name: myometrium

label_protocol: convert total RNA to cRNA with Low RNA Input Linear Amplification Kit, cy5- or cy3-CTP(from PE) was incorporated into cRNA probe

extract_protocol: Hysterectomy specimen were snap frozen in liquid nitrogen, extracted total RNA with Qiagen fibrous tissue RNA kit

value: myometrium

source_name: uterine fibroid

value: uterine fibroid


title: 608: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: VM_A.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): VM_B.gpr


title: PS63

description: Medulloblastoma

value: pten +/+, smoa +

value: 24.1 weeks


title: 506: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: SB_A_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): SB_B_n.gpr


title: 602: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: SW_rA.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): SW_rB.gpr


title: Mammary lactating hyperG M210H


title: 504: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: RT_A.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): RT_B.gpr


title: PS136

description: Medulloblastoma

value: 9 weeks


title: PS25

description: Medulloblastoma

value: 17 weeks


title: 606: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: TA_A.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): TA_B.gpr


title: 503: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: RDrA.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): RDrB.gpr


title: 609: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: VRnA.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): VRnB.gpr


title: 502: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: PW_A.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): PW_B.gpr


title: PS137

description: Medulloblastoma

value: pten +/-, smoa +

value: 18.5 weeks


title: 48-h stretched human periodontal ligament cells part2

city: Suita

first: Chiharu

last: Fujihara

state: Osaka

address: 1-8, Yamadaoka

department: Periodontology

country: Japan

institute: Osaka University Graduate School of Dentistry

description: Human periodontal ligament cells were transferred onto the chambers. The chambers were applied to a stretch apparatus, Scholertec NS-350 (STREX), and the cells were repeatedly stretched and relaxed at 0.5 Hz (30 cycles/min) with 110% elongation for 48 hours. The cells seeded on the chambers without stretching served as controls, non-stretched human periodontal ligament cells.

hyb_protocol: Hybridized for 16 h at 42 °C. Hybridization buffer was provided by Hitachi Software Engineering Co., Ltd.. Hybridized DNA chips were washed according to the manufacturer's protocols..

scan_protocol: Scan Array Lite (PerkinElmer Life Science) was used for scanning. The resulting image was analyzed using Scan Array Express ver. 2.0.

data_processing: The Cy3/Cy5 ratio values were log-transformed and Normalization using LOWELL was performed for data obtained from the raw data.

label_protocol: Amino Allyl aRNA was synthesized by Amino Allyl MessageAmp aRNA Amplification Kit (Ambion).CyeDye coupling and fragmentation were performed using the protocol of  Hitachi Software Engineering Co., Ltd.

extract_protocol: Total RNA was extracted from the stretched human periodontal ligament cells using RNA Bee (TEL-TEST).

tag: cell

value: primary periodontal ligament cells

source_name: 48-h non-stretched human periodontal ligament cells


title: PS30

description: Medulloblastoma

value: 23 weeks


title: 500: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: PL_A.gpr
myometrium-cy5, fibroid-cy3: PL_C.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): PL_B.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): PL_D.gpr


title: PS23

description: Medulloblastoma

value: 43.6 weeks


title: 350: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: 041505A2_n.gpr
myometrium-cy5, fibroid-cy3: 041405C_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 041405B_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 041405D_n.gpr


title: MLL-AF4 infant ALL, 597

description:
pre-B

Please refer to Differential Methylation Hybridization (DMH) protocol by Dr. Tim H. Huang and coworkers. (PMID 18987809: Yan PS, Potter D, Deatherage DE, Huang TH, Lin S., Differential methylation hybridization: profiling DNA methylation with a high-density CpG island microarray.Methods Mol Biol. 2009;507:89-106.)

value: bone marrow

value: female

value: peripheral blood

value: mix from 5 healthy males and 5 healthy females

value: reference


title: 345: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: 5725G_n.gpr
myometrium-cy5, fibroid-cy3: 5725I_n.gpr
myometrium-cy5, fibroid-cy3: 5725K_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 5725H_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 5725J_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 5725L_n.gpr


title: 48-h stretched human periodontal ligament cells

data_processing: The Cy5/Cy3 ratio values were log-transformed and Normalization using LOWELL was performed for data obtained from the raw data.

source_name: 48-h non-stretched human periodontal ligament cell


title: PS34

description: Medulloblastoma

value: 13.4 weeks


title: 349: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: 040805A_n.gpr
myometrium-cy5, fibroid-cy3: 040805C_n.gpr
myometrium-cy5, fibroid-cy3: 918G_n.gpr
myometrium-cy5, fibroid-cy3: 918NA_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 040805B_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 040805D_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 918H_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 918NB_n.gpr

value: myometrium


title: 347: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: 1130a_n.gpr
myometrium-cy5, fibroid-cy3: 1130c_n.gpr
myometrium-cy5, fibroid-cy3: no6_I_n.gpr
myometrium-cy5, fibroid-cy3: 6nA_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 1130b_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 1130d_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): no6_J_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 6nB_n.gpr

value: uterine fibroid


title: MLL-AF4 infant ALL, 601

description:
pro-B

Please refer to Differential Methylation Hybridization (DMH) protocol by Dr. Tim H. Huang and coworkers. (PMID 18987809: Yan PS, Potter D, Deatherage DE, Huang TH, Lin S., Differential methylation hybridization: profiling DNA methylation with a high-density CpG island microarray.Methods Mol Biol. 2009;507:89-106.)

value: male


title: 342: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: 0202a_n.gpr
myometrium-cy5, fibroid-cy3: 0202c_n.gpr
myometrium-cy5, fibroid-cy3: 2E_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 0202b_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 0202d_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 2F_n.gpr


title: 344: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: 070505A_n.gpr
myometrium-cy5, fibroid-cy3: 1121A_n.gpr
myometrium-cy5, fibroid-cy3: 0311A_n.gpr
myometrium-cy5, fibroid-cy3: 0311C_n.gpr
myometrium-cy5, fibroid-cy3: 070605a_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 070505B_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 1121B_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 0311B_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 0311D_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 070605b_n.gpr


title: 341: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: 1123A_n.gpr
myometrium-cy5, fibroid-cy3: 1128A_n.gpr
myometrium-cy5, fibroid-cy3: 1129A_n.gpr
myometrium-cy5, fibroid-cy3: 1129C_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 1123B_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 1128B_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 1129B_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 1129D_n.gpr


title: 338: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: 040505B_n.gpr
myometrium-cy5, fibroid-cy3: 171AA_n.gpr
myometrium-cy5, fibroid-cy3: 171NA_n.gpr
myometrium-cy5, fibroid-cy3: 171nA_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 040505c_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 171BB_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 171NB_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 171B_n.gpr


title: 337: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: 0118a_n.gpr
myometrium-cy5, fibroid-cy3: 0118c_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 0118b_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 0118d_n.gpr


title: 334: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: 1012A.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 1012B.gpr


title: 335: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: 070505C_n.gpr
myometrium-cy5, fibroid-cy3: 0112a_n.gpr
myometrium-cy5, fibroid-cy3: 0112c_n.gpr
myometrium-cy5, fibroid-cy3: 070605A_n.gpr
myometrium-cy5, fibroid-cy3: 0917A_n.gpr
myometrium-cy5, fibroid-cy3: 0918c_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 070505D_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 0112b_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 0112d_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 070605B_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 0917B_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 0918d_n.gpr


title: 320: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: 1008_A.gpr
myometrium-cy5, fibroid-cy3: 1008_C_n.gpr
myometrium-cy5, fibroid-cy3: 1008_E_n.gpr
myometrium-cy5, fibroid-cy3: 1008nA_n.gpr
myometrium-cy5, fibroid-cy3: 1008A.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 1008_B.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 1008_D_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 1008_F_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 1008nB_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 1008B.gpr


title: 322: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: 1009A_n.gpr
myometrium-cy5, fibroid-cy3: 1009_C.gpr
myometrium-cy5, fibroid-cy3: 1009_A.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 1009B_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 1009_D.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 1009_B.gpr


title: 312: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: 1006EE_n.gpr
myometrium-cy5, fibroid-cy3: 1006G_n.gpr
myometrium-cy5, fibroid-cy3: 100605A_n.gpr
myometrium-cy5, fibroid-cy3: 100605C_n.gpr
myometrium-cy5, fibroid-cy3: 1006NA_n.gpr
myometrium-cy5, fibroid-cy3: 1006nnA_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 1006FF_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 1006H_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 100605B_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 100605D_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 1006NB_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 1006nnB_n.gpr


title: 314: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: 1007C.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 1007D.gpr


title: 229: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: 090805A_n.gpr
myometrium-cy5, fibroid-cy3: 091905A_n.gpr
myometrium-cy5, fibroid-cy3: 091905C_n.gpr
myometrium-cy5, fibroid-cy3: 1004nA_n.gpr
myometrium-cy5, fibroid-cy3: 1004M_n.gpr
myometrium-cy5, fibroid-cy3: 1004O_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 090805B_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 091905B_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 091905D_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 1004nB_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 1004N_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 1004P_n.gpr


title: 311: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: 091105A_n.gpr
myometrium-cy5, fibroid-cy3: 091805A_n.gpr
myometrium-cy5, fibroid-cy3: 1005M_n.gpr
myometrium-cy5, fibroid-cy3: 1005O_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 091105B_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 091805B_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 1005N_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 1005P_n.gpr


title: 226: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: 082905a.gpr
myometrium-cy5, fibroid-cy3: 090705A.gpr
myometrium-cy5, fibroid-cy3: 1003M.gpr
myometrium-cy5, fibroid-cy3: 1003O.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 082905b.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 090705B.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 1003N.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 1003P.gpr


title: 333: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: 1011_E.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 1011_F.gpr


title: 223: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: 092505A_n.gpr
myometrium-cy5, fibroid-cy3: 092705A.gpr
myometrium-cy5, fibroid-cy3: 1001M_n.gpr
myometrium-cy5, fibroid-cy3: 1001O_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 092505B_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 092705B.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 1001N_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 1001P_n.gpr


title: 201: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: nA_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): nB_n.gpr


title: 204: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: KB_A.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): KB_B.gpr


title: 206: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: LH_rA.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): LH_rB.gpr


title: 211: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: NM_A.gpr
myometrium-cy5, fibroid-cy3: NM_C.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): NM_B.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): NM_D.gpr


title: 139: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: FW_rA.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): FW_rB.gpr


title: 202: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: JW_A_n.gpr
myometrium-cy5, fibroid-cy3: JW_C.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): JW_B_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): JW_D.gpr


title: Normal_Skeletal_Muscle_4

city: Durham

first: Jeffrey

last: Mito

state: NC

institute: Duke University Medical Center

description: Gene expression data from to normal muscle isolated from mice without tumors.

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hours at 45C on Mouse genome 430A 2.0 arrays and underwent automated washing and staining on the fluidics station.

scan_protocol: Genechips were scanned using the GeneChip Scanner 3000 7g.

data_processing: Data was normalized using the RMA algorithm.

label: biotin

source_name: Normal Muscle

label_protocol: Labeled RNA was prepared from 2 µg total RNA using one-cycle target labeling kit (Affymetrix).

growth_protocol: Tumors were induced via injection of Adeno-Cre ~3 months prior to surgical removal of the tumor.

extract_protocol: Trizol extraction of total RNA was followed by clean up using the RNeasy kit (Qiagen) per manufacturer's protocol.

treatment_protocol: Tumors were isolated from surrounding normal tissue.

value: Normal Skeletal Muscle

value: LSL-KrasG12D; Trp53Fl/Fl


title: 222: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: 0117a_n.gpr
myometrium-cy5, fibroid-cy3: 0117c_n.gpr
myometrium-cy5, fibroid-cy3: 062405a_n.gpr
myometrium-cy5, fibroid-cy3: no1_m.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 0117b_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 0117d_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 062405b_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): no1_n.gpr


title: Normal_Skeletal_Muscle_3


title: Sarcoma_16

description: Gene expression data from soft tissue sarcomas compared to normal muscle isolated from mice without tumors.

source_name: Soft Tissue Sarcoma

value: Soft Tissue Sarcoma


title: 168: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: IB_A.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): IB_B.gpr


title: Normal_Skeletal_Muscle_1


title: 127: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: EB_A.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): EB_B.gpr


title: Normal_Skeletal_Muscle_2


title: KK1_4_normalized,dye-swap

city: Planegg-Martinsried

first: Sonja

last: Grath

address: Grosshaderner Str. 2

department: Department Biology II

institute: LMU

description: PCR-amplicon microarrays with 148 genes + gDNA controls were produced and hybridized

hyb_protocol: Labelled male and female cDNA was competitively hybridized to the arrays for 20 hours at 42°C.

scan_protocol: Arrays were scanned using a Genetix aQuire 2-laser microarray scanner and the Genetix Qscan software.

data_processing:
Quality control
1. Only spots with mean intensity 20% above the mean local background intensity in at least one of the channels were used
This is a bit more lenient than requiring 1 SD above background (typically the SD is 20-30% of the mean)
2. For any one array, it was required that at least half of the replicate spots per gene (in this case 4) had good signal as defined by #1 above.
If so, the median Cy3/Cy5 ratio (after normalization) of all good replicate spots was used.
Normalization
1. The signal for each spot was calculated by subtracting the MEDIAN local background from the MEAN spot intensity.
If the above result was negative for one channel, that channel was given a value of 0.5 (MINIMUM approach of limma).
2. For each replicate array (162 spots, 1 per gene), the Cy3/Cy5 ratio was calculated for each of the gDNA control spots
3. The mean of the above Cy3/Cy5 ratios was taken and used as a "corrector".
This corrector was multiplied by the raw Cy5 value of each spot to get a corrected Cy5 value that was used to calculate the ratio.
Note: this is a local normalization, with a different corrector for each replicate array. There are 8 replicate arrays per hybridization.

label: Alexa Fluor 647 (Cy5)

organism: Drosophila ananassae

source_name: KK1, biological replicate 4, female

label_protocol: cDNA was labelled with fluorescent dyes (Alexa Fluor 555 and 647) using the amino-allyl labelling system (Invitrogen)

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen) and the manufacturer's protocol and RNA was reverse transcribed to cDNA using 25 microgramm of total RNA and an anchored oligo(dT) primer.

tag: age

value: 4-5 days

label: Alexa Fluor 555 (Cy3)

source_name: KK1, biological replicate 4, male


title: KK2_2_normalized,dye-swap

source_name: KK2, biological replicate 2, female

source_name: KK2, biological replicate 2, male


title: 125: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: DN_A.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): DN_B.gpr


title: KK2_1_normalized,dye-swap

source_name: KK2, biological replicate 1, male

source_name: KK2, biological replicate 1, female


title: Sarcoma_15


title: Sarcoma_17


title: Sarcoma_12


title: 123: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: BG_A.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): BG_B.gpr


title: Sarcoma_13


title: Sarcoma_14


title: KK1_3_normalized,dye-swap

source_name: KK1, biological replicate 3, male

source_name: KK1, biological replicate 3, female


title: KK1_1_normalized,dye-swap

source_name: KK1, biological replicate 1, male

source_name: KK1, biological replicate 1, female


title: KK1_2_normalized,dye-swap

source_name: KK1, biological replicate 2, male

source_name: KK1, biological replicate 2, female


title: KK2_2_normalized


title: Sarcoma_9


title: KK1_4_normalized


title: Sarcoma_8


title: Sarcoma_10


title: KK2_1_normalized


title: Sarcoma_5


title: Sarcoma_4


title: Sarcoma_7


title: Sarcoma_6


title: KK1_3_normalized


title: KK1_2_normalized


title: KK1_1_normalized


title: AID-slienced clone of J558 cells, pair 2

status: Public on Nov 20 2009

city: Columbus

first: Yi

last: Xiao

state: OH

address: 1640 Neil Ave

department: Pathology

institute: Ohio State University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on mouse Genechip 430-2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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.

source_name: AID-silenced clone pair 2 (J558 cells)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The plasmacytoma J558 (BALB/c, H-2Ld) cell line was cultured in RPMI 1640 medium containing 5% FCS and 100 μg/ml of penicillin and streptomycin.

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

treatment_protocol: AID targeting sequence was inserted into pSilencerTM1.0 vector and co-transfected with a selection vector containing the Neo gene into J558 tumor cells. As control, an empty targeting vector and Neo vector were co-transfected J558 cells. The transfected J558 cells were then selected by G418, and Neo-resistant J558 clones were obtained.

value: BALB/c, H-2Ld

value: plasmacytoma cell line


title: Sarcoma_2


title: clone of control vector transfected J558 cells, pair 2

source_name: silence control vector transfected clone pair 2 (J558 cells)


title: clone of control vector transfected J558 cells, pair 1

source_name: silence control vector transfected clone pair 1 (J558 cells)


title: Sarcoma_1


title: AID-slienced clone of J558 cells, pair 1

source_name: AID-silenced clone pair 1 (J558 cells)


title: Sarcoma_3

source_name: Soft Tissue Sarcoma


title: 13469669

city: Ames

first: Patrick

middle: S.

last: Schnable

state: IA

address: 2035B Roy J Carver Co-Lab

institute: Iowa State University

description: Maize seedlings were grown under controlled conditions and were harvested at the 14 day old stage. Total RNA was isolated from four replications of RIL@, B73xRIL, and Mo17xRIL for 30 RILs (with 6 individual seedlings pooled for each genotype in each replication) using Trizol reagent. Approximately 500 micrograms of total RNA were used for mRNA isolation with the OligoTex mRNA midi kit (Qiagen, Valencia, CA ) as per manufacturer's protocol with slight modification. Two micrograms of mRNA were labeled according to Nakozono et al. (2003) with slight modifications. Each sample was labeled with Cy dye and hybridized to the GPL3333 platform (4 replications) and GPL3538 platform (2 replications).

hyb_protocol: Fluorescent targets were hybridized as described in the "cDNA microarray protocol" file at http://schnablelab.plantgenomics.iastate.edu/resources/protocols/

scan_protocol: Each microarray chip was scanned a minimum of four times with constant PMT and increasing laser power settings.  Slides were scanned with a Pro Scan Array HT (Perkin Elmer, Wellesley, MA).

data_processing: All scans from each slide were quantified using ImaGene (BioDiscovery, El Segundo, CA). For each slide and dye combination, median scan intensities were extrapolated using data from the multiple scans collected using a variation of a previously published linear regression method (DUDLEY et al. 2002).  Non-informative spots were removed prior to analysis.  In total, 14,401 (GPL3333) and 14,260 (GPL3538) informative spots were analyzed. Within-slide correlation coefficient between the Cy3 and Cy5 background-corrected raw signal intensities was used to quantify the quality of each slide in the eQTL experiment.  A correlation coefficient cutoff of 0.90 flagged 4% (N=15) of the SAM1.1 slides for removal prior to analysis.  In many cases, these slides had visually apparent technical artifacts.  Using the same cutoff for SAM3.0 slides, less than 1% (N=1) of the slides were below this cutoff, and none were removed. For the remaining slides, lowess normalization was applied to the natural log (ie, log base e) of the background-corrected raw signal intensities to remove signal-intensity-dependent dye effects on each slide (CUI et al. 2003; DUDOIT et al. 2002).  Normalization was conducted separately for each slide to avoid introducing dependencies among expression values.  After normalization, data for each slide/dye combination were median-centered so expression measures would be comparable across slides.  Post-normalized data was summarized by taking the average of all technical and biological replicates within a genotype.

organism: Zea mays

source_name: Seedling stage above ground tissue

extract_protocol: total RNA extraction with Trizol, mRNA isolation with Oligotex Kit (Qiagen, Valencia, CA) as per manufacturer's instructions

value: Above ground seedling

tag: developmental stage

value: 14 days old

tag: sample name

value: Rep 3 BxRILM0045

label_protocol: Fluorescent cDNA targets were synthesized and hybridized as described at http://schnablelab.plantgenomics.iastate.edu/resources/protocols/. Labeled targets containing a minimum of 3000 picomoles of cDNA, 50 picomoles of Cy dye, and more than one dye molecule per 50 (100) bases of Cy3 (Cy5) were used for hybridizations.

value: Rep 3 MxRILM0045


title: 13466984

label_protocol: Fluorescent cDNA targets were synthesized and hybridized as described at http://schnablelab.plantgenomics.iastate.edu/resources/protocols/

value: Rep 2 RILM0067

value: Rep 2 BxRILM0067


title: 13469661

value: Rep 4 MxRILM0045

value: Rep 4 BxRILM0045


title: 13466960

value: Rep 4 MxRILM0328

value: Rep 4 BxRILM0328


title: 13469667

value: Rep 2 BxRILM0272

value: Rep 2 RILM0272


title: 13466988

value: Rep 2 BxRILM0007

value: Rep 2 RILM0007


title: 13466875

value: Rep 1 MxRILM0364

value: Rep 1 RILM0364


title: 13469660

value: Rep 4 RILM0045


title: 13469659

value: Above ground seedling


title: 339: matched fibroid vs myemetrium

description:
myometrium-cy5, fibroid-cy3: 0113A_n.gpr
myometrium-cy5, fibroid-cy3: 0113C_n.gpr
myometrium-cy5, fibroid-cy3: 0111A_n.gpr
myometrium-cy5, fibroid-cy3: 18E_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 0113B_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 0113D_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 0111B_n.gpr
myometrium-cy3, fibroid-cy5 (reverse-labeled): 18F_n.gpr

source_name: myometrium

value: myometrium

source_name: uterine fibroid

value: uterine fibroid


title: 13466963

value: 14 days old

value: Rep 1 RILM0328

value: Rep 1 BxRILM0328


title: 13466876

value: Rep 1 BxRILM0364


title: 13466962

value: Rep 2 BxRILM0328

value: Rep 2 RILM0328


title: 13466874


title: 13466964

value: Rep 1 MxRILM0328


title: 13469666

value: Rep 3 RILM0045

value: Rep 3 BxRILM0045


title: 13469662

value: Rep 4 RILM0317

value: Rep 4 MxRILM0317


title: 13466802

value: Rep 4 BxRILM0296

value: Rep 4 RILM0296


title: 13466805

value: Rep 4 RILM0328

value: Rep 4 MxRILM0328


title: 13466873

value: Above ground seedling

value: Rep 4 MxRILM0364

value: Rep 4 BxRILM0364


title: 13466721

value: 14 days old

value: Rep 3 BxRILM0364

value: Rep 3 MxRILM0364


title: 13466724

value: Rep 4 RILM0079

value: Rep 4 BxRILM0079


title: 13466723

value: Rep 3 RILM0364


title: 13466700

value: Rep 4 BxRILM0076

value: Rep 4 MxRILM0076


title: 13466699

value: Rep 1 RILM0076

value: Rep 1 MxRILM0076


title: 13466725


title: 13466697

value: Rep 1 BxRILM0076


title: 13465154

value: Rep 1 MxRILM0328

value: Rep 1 RILM0328


title: 13465153

value: Rep 2 RILM0328

value: Rep 2 MxRILM0328


title: 13466803

value: Above ground seedling

value: Rep 4 BxRILM0328

value: Rep 4 RILM0328


title: 13466720

value: 14 days old

value: Rep 4 RILM0364

value: Rep 4 MxRILM0364


title: 13465151

value: Rep 4 MxRILM0296

value: Rep 4 BxRILM0296


title: 13465155

value: Rep 2 MxRILM0007

value: Rep 2 BxRILM0007


title: 13463643

value: Rep 1 BxRILM0296

value: Rep 1 MxRILM0296


title: 13463641

value: Rep 2 MxRILM0364

value: Rep 2 BxRILM0364


title: 13466696

value: Rep 2 RILM0076

value: Rep 2 BxRILM0076


title: 13465150

value: Rep 2 MxRILM0328

value: Rep 2 BxRILM0328


title: 13466698

value: Above ground seedling

value: Rep 1 MxRILM0076

value: Rep 1 BxRILM0076


title: 13463644

value: 14 days old

value: Rep 2 MxRILM0296

value: Rep 2 BxRILM0296


title: 13463612

value: Rep 4 MxRILM0007

value: Rep 4 RILM0007


title: 13465152

value: Rep 4 RILM0296

value: Rep 4 MxRILM0296


title: 13463611

value: Rep 4 BxRILM0007


title: 13463610


title: 13463596

value: Rep 3 RILM0076

value: Rep 3 MxRILM0076


title: 13463580

value: Rep 4 MxRILM0063

value: Rep 4 RILM0063


title: 13463582

value: Rep 1 MxRILM0067

value: Rep 1 BxRILM0067


title: 13463593

value: Above ground seedling

value: Rep 3 BxRILM0076


title: 13463423

value: Rep 2 RILM0007

value: Rep 2 MxRILM0007


title: 13463434

value: 14 days old

value: Rep 2 BxRILM0364

value: Rep 2 RILM0364


title: 13463583

value: Rep 2 RILM0057

value: Rep 2 BxRILM0057


title: 13463584

value: Rep 1 BxRILM0063

value: Rep 1 MxRILM0063


title: 13463424

value: Rep 4 BxRILM0317

value: Rep 4 RILM0317


title: 13463414

value: Rep 1 MxRILM0045

value: Rep 1 BxRILM0045


title: 13463609

value: Rep 1 MxRILM0007

value: Rep 1 RILM0007


title: 13463416

value: Above ground seedling

value: Rep 2 RILM0063

value: Rep 2 MxRILM0063


title: 13463581

value: Rep 2 MxRILM0052

value: Rep 2 BxRILM0052


title: 13463595

value: 14 days old

value: Rep 4 RILM0076

value: Rep 4 BxRILM0076


title: 13463412

value: Rep 1 RILM0045


title: 13463411

value: Rep 4 BxRILM0058

value: Rep 4 RILM0058


title: 13463594

value: Rep 4 MxRILM0076


title: 13463431

value: Rep 2 MxRILM0272

value: Rep 2 BxRILM0272


title: 13463433

value: Rep 2 RILM0272


title: 13463422

value: Rep 3 MxRILM0328

value: Rep 3 RILM0328


title: 13463425

value: Above ground seedling

value: Rep 1 BxRILM0007

value: Rep 1 MxRILM0007


title: 13463293

value: Rep 3 BxRILM0079

value: Rep 3 RILM0079


title: 13463413

value: 14 days old

value: Rep 1 BxRILM0045


title: 13463430

value: Rep 2 RILM0364

value: Rep 2 MxRILM0364


title: 13463292

value: Rep 3 MxRILM0079


title: 13463291


title: 13463072

value: Rep 3 RILM0007

value: Rep 3 MxRILM0007


title: 13463290

value: Rep 4 BxRILM0079

value: Rep 4 MxRILM0079


title: 13463074

value: Rep 2 BxRILM0067

value: Rep 2 MxRILM0067


title: 13463076

value: Rep 3 BxRILM0007


title: 13463002

value: Above ground seedling

value: Rep 4 RILM0079


title: 13463001

value: Rep 1 MxRILM0272

value: Rep 1 RILM0272


title: 13463073

value: Rep 3 RILM0027

value: Rep 3 MxRILM0027


title: 13463592

value: 14 days old

value: Rep 3 BxRILM0076

value: Rep 3 RILM0076


title: 13462999

value: Rep 4 BxRILM0364

value: Rep 4 RILM0364


title: 13463000

value: Rep 1 BxRILM0272


title: 13462986

value: Rep 2 MxRILM0076

value: Rep 2 RILM0076


title: 13462980

value: Rep 4 BxRILM0272

value: Rep 4 MxRILM0272


title: 13462981

value: Rep 4 RILM0272


title: 13462983

value: Above ground seedling


title: 13462925

value: Rep 2 BxRILM0296

value: Rep 2 RILM0296


title: 13462979

value: Rep 2 BxRILM0076


title: 13462924

value: Rep 3 RILM0296

value: Rep 3 BxRILM0296


title: 13462881

value: 14 days old

value: Rep 3 MxRILM0272

value: Rep 3 BxRILM0272


title: 13462878

value: Rep 2 MxRILM0058

value: Rep 2 RILM0058


title: 13462923

value: Rep 3 MxRILM0296


title: 13462922

value: Rep 2 MxRILM0296


title: 13462876

value: Rep 3 RILM0272


title: 13462864

value: Rep 3 MxRILM0007

value: Rep 3 BxRILM0007


title: 13462862

value: Rep 3 RILM0017

value: Rep 3 MxRILM0017


title: 13462877

value: Above ground seedling


title: 13462863

value: Rep 3 BxRILM0017


title: 13462861


title: 13462926


title: 13450852

value: Rep 3 BxRILM0328

value: Rep 3 MxRILM0328


title: 13450878

value: Rep 3 RILM0264

value: Rep 3 MxRILM0264


title: 13450846

value: 14 days old

value: Rep 2 BxRILM0045

value: Rep 2 MxRILM0045


title: 13450877

value: Rep 4 BxRILM0264

value: Rep 4 MxRILM0264


title: 13450876

value: Rep 3 BxRILM0264


title: 13450851

value: Rep 2 MxRILM0264

value: Rep 2 BxRILM0264


title: 13450874


title: 13450847

value: Rep 3 RILM0321

value: Rep 3 BxRILM0321


title: 13450842

value: Rep 2 RILM0045


title: 13450841

value: Above ground seedling


title: 13450872

value: Rep 4 RILM0264


title: 13450848

value: Rep 1 RILM0264

value: Rep 1 BxRILM0264


title: 13450834

value: Rep 1 MxRILM0321

value: Rep 1 BxRILM0321


title: 13450832

value: 14 days old

value: Rep 2 MxRILM0321

value: Rep 2 RILM0321


title: 13450824

value: Rep 3 BxRILM0317

value: Rep 3 MxRILM0317


title: 13450845

value: Rep 4 BxRILM0264


title: 13450831

value: Rep 4 RILM0321

value: Rep 4 MxRILM0321


title: 13450835

value: Rep 2 BxRILM0321


title: 13450810

value: Rep 1 MxRILM0264


title: 13450806

value: Rep 2 RILM0264

value: Rep 2 MxRILM0264


title: 13450830

value: Above ground seedling

value: Rep 3 RILM0317


title: 13450788

value: Rep 3 MxRILM0321

value: Rep 3 RILM0321


title: 13450805

value: Rep 2 BxRILM0264


title: 13450786

value: 14 days old

value: Rep 4 BxRILM0321


title: 13450787


title: 13450773

value: Rep 1 BxRILM0321

value: Rep 1 RILM0321


title: 13428917

value: Rep 4 MxRILM0046

value: Rep 4 RILM0046


title: 13428922

value: Rep 3 RILM0046

value: Rep 3 MxRILM0046


title: 13428924

value: Rep 3 BxRILM0046


title: 13450785

value: Rep 3 BxRILM0321


title: 13428918

value: Rep 4 BxRILM0046


title: 13450764

value: Rep 4 MxRILM0317

value: Rep 4 BxRILM0317


title: 13428915

value: Above ground seedling

value: Rep 1 MxRILM0046

value: Rep 1 RILM0046


title: 13428911

value: Rep 1 MxRILM0079

value: Rep 1 BxRILM0079


title: 13428879

value: 14 days old

value: Rep 2 RILM0046

value: Rep 2 MxRILM0046


title: 13428878


title: 13428908

value: Rep 1 RILM0079


title: 13428912

value: Rep 1 MxRILM0345

value: Rep 1 RILM0345


title: 13428880

value: Rep 2 BxRILM0046


title: 13428881


title: 13428877

value: Rep 1 BxRILM0046


title: 13428907

value: Rep 4 RILM0058

value: Rep 4 MxRILM0058


title: 13428904

value: Rep 4 RILM0345

value: Rep 4 BxRILM0345


title: 13428829

value: Above ground seedling

value: Rep 1 BxRILM0345


title: 13450756

value: Rep 1 RILM0321

value: Rep 1 MxRILM0321


title: 13428828

value: Rep 4 MxRILM0345


title: 13428827

value: 14 days old

value: Rep 2 MxRILM0345

value: Rep 2 BxRILM0345


title: 13428824

value: Rep 2 RILM0345


title: 13462880

value: Rep 1 RILM0058

value: Rep 1 MxRILM0058


title: 13428812

value: Rep 3 MxRILM0058

value: Rep 3 RILM0058


title: 13450811

value: Rep 1 BxRILM0264

value: Rep 1 MxRILM0264


title: 13428826


title: 13428811

value: Rep 3 BxRILM0058


title: 13428794

value: Rep 1 MxRILM0010

value: Rep 1 BxRILM0010


title: 13428797

value: Above ground seedling

value: Rep 2 BxRILM0010

value: Rep 2 MxRILM0010


title: 13428809

value: Rep 4 MxRILM0058

value: Rep 4 BxRILM0058


title: 13428787

value: 14 days old

value: Rep 1 BxRILM0058


title: 13428795

value: Rep 1 RILM0010


title: 13428799

value: Rep 2 RILM0010


title: 13428763

value: Rep 2 BxRILM0052

value: Rep 2 RILM0052


title: 13428759

value: Rep 1 MxRILM0052

value: Rep 1 RILM0052


title: 13428761

value: Rep 1 BxRILM0052


title: 13428810

value: Rep 3 RILM0058

value: Rep 3 BxRILM0058


title: 13428786

value: Rep 1 MxRILM0058


title: 13428762

value: Above ground seedling

value: Rep 2 MxRILM0052


title: 13428634

value: Rep 4 BxRILM0010

value: Rep 4 RILM0010


title: 13428654

value: Rep 3 BxRILM0345

value: Rep 3 RILM0345


title: 13428760

value: 14 days old

value: Rep 3 BxRILM0063

value: Rep 3 RILM0063


title: 13428657

value: Rep 3 MxRILM0345


title: 13428635

value: Rep 3 BxRILM0010

value: Rep 3 MxRILM0010


title: 13428653

value: Rep 1 RILM0345

value: Rep 1 BxRILM0345


title: 13428783

value: Rep 2 RILM0058

value: Rep 2 BxRILM0058


title: 13428796

value: Rep 2 MxRILM0010

value: Rep 2 RILM0010


title: 13428658

value: Above ground seedling


title: 13428906

value: Rep 2 MxRILM0058


title: 13424011

value: Rep 2 MxRILM0057

value: Rep 2 RILM0057


title: 13424015

value: Rep 1 MxRILM0057

value: Rep 1 BxRILM0057


title: 13424040

value: 14 days old

value: Rep 3 MxRILM0051

value: Rep 3 RILM0051


title: 13428624

value: Rep 1 RILM0051

value: Rep 1 BxRILM0051


title: 13424041

value: Rep 1 BxRILM0022

value: Rep 1 MxRILM0022


title: 13428620

value: Rep 2 MxRILM0317

value: Rep 2 BxRILM0317


title: 13428578

value: Rep 3 BxRILM0067

value: Rep 3 MxRILM0067


title: 13424014

value: Above ground seedling

value: Rep 1 RILM0057


title: 13424013


title: 13424003

value: Rep 4 MxRILM0067

value: Rep 4 BxRILM0067


title: 13428577

value: Rep 3 RILM0067


title: 13428597

value: Rep 3 MxRILM0052

value: Rep 3 BxRILM0052


title: 13428599

value: 14 days old

value: Rep 4 MxRILM0052

value: Rep 4 RILM0052


title: 13424039

value: Rep 1 RILM0017

value: Rep 1 BxRILM0017


title: 13428623

value: Rep 4 BxRILM0051

value: Rep 4 RILM0051


title: 13428598

value: Rep 3 RILM0052


title: 13428596


title: 13424042

value: Rep 3 BxRILM0051

value: Rep 3 MxRILM0051


title: 13428621

value: Above ground seedling

value: Rep 4 MxRILM0051


title: 13424043

value: Rep 3 RILM0051


title: 13428921

value: Rep 4 RILM0046

value: Rep 4 BxRILM0046


title: 13428631

value: Rep 4 RILM0010

value: Rep 4 MxRILM0010


title: 13423995

value: 14 days old

value: Rep 2 MxRILM0079

value: Rep 2 RILM0079


title: 13428579

value: Rep 2 BxRILM0057

value: Rep 2 MxRILM0057


title: 13423998

value: Rep 1 MxRILM0063

value: Rep 1 RILM0063


title: 13424002

value: Rep 4 RILM0067

value: Rep 4 MxRILM0067


title: 13424001

value: Rep 4 BxRILM0067


title: 13423996

value: Above ground seedling

value: Rep 4 BxRILM0052

value: Rep 4 MxRILM0052


title: 13423974

value: Rep 2 BxRILM0039

value: Rep 2 MxRILM0039


title: 13423969

value: Rep 2 MxRILM0051

value: Rep 2 BxRILM0051


title: 13423991

value: 14 days old

value: Rep 2 BxRILM0079


title: 13423972

value: Rep 3 BxRILM0039

value: Rep 3 RILM0039


title: 13423994

value: Rep 4 RILM0052


title: 13423965

value: Rep 1 MxRILM0027

value: Rep 1 RILM0027


title: 13423962

value: Rep 4 BxRILM0039

value: Rep 4 MxRILM0039


title: 13423973

value: Rep 3 MxRILM0039


title: 13423964

value: Above ground seedling

value: Rep 1 RILM0010

value: Rep 1 MxRILM0010


title: 13476449

value: Rep 3 RILM0051

value: Rep 3 BxRILM0051


title: 13476411

value: Rep 3 MxRILM0052

value: Rep 3 RILM0052


title: 13476450

value: 14 days old

value: Rep 3 MxRILM0051


title: 13476448


title: 13423970


title: 13423966

value: Rep 1 BxRILM0027


title: 13423963

value: Rep 4 RILM0039


title: 13423967


title: 13423901

value: Rep 1 RILM0039

value: Rep 1 MxRILM0039


title: 13423956

value: Rep 2 RILM0039

value: Rep 2 BxRILM0039


title: 13476408

value: Rep 1 RILM0067

value: Rep 1 BxRILM0067


title: 13423961

value: Above ground seedling

value: Rep 4 BxRILM0039


title: 13423960

value: Rep 2 MxRILM0039


title: 13476410

value: Rep 1 MxRILM0067


title: 13476406

value: Rep 2 BxRILM0067

value: Rep 2 RILM0067


title: 13423897

value: Rep 3 RILM0010

value: Rep 3 BxRILM0010


title: 13476394

value: 14 days old

value: Rep 4 RILM0051

value: Rep 4 MxRILM0051


title: 13476409


title: 13476392

value: Rep 4 BxRILM0051


title: 13476395

value: Rep 1 MxRILM0321

value: Rep 1 RILM0321


title: 13423893

value: Rep 1 MxRILM0039

value: Rep 1 BxRILM0039


title: 13476393

value: Rep 1 BxRILM0321


title: 13423824

value: Above ground seedling

value: Rep 1 BxRILM0051

value: Rep 1 MxRILM0051


title: 13423825

value: Rep 1 RILM0051


title: 13476390


title: 13423826

value: Rep 2 RILM0051

value: Rep 2 MxRILM0051


title: 13423892

value: Rep 3 MxRILM0010

value: Rep 3 RILM0010


title: 13476385

value: 14 days old

value: Rep 2 MxRILM0023

value: Rep 2 BxRILM0023


title: 13423823

value: Rep 4 MxRILM0051

value: Rep 4 BxRILM0051


title: 13423895

value: Rep 1 RILM0039


title: 13476384

value: Rep 2 RILM0023


title: 13476381

value: Rep 2 BxRILM0040

value: Rep 2 RILM0040


title: 13476382

value: Above ground seedling


title: 13423821

value: Rep 2 BxRILM0051


title: 13423749

value: Rep 1 RILM0067

value: Rep 1 MxRILM0067


title: 13423695

value: Rep 2 MxRILM0063

value: Rep 2 BxRILM0063


title: 13476354

value: Rep 3 RILM0052

value: Rep 3 BxRILM0052


title: 13423692

value: 14 days old

value: Rep 3 MxRILM0063

value: Rep 3 BxRILM0063


title: 13476353

value: Rep 3 MxRILM0052


title: 13423751

value: Rep 1 BxRILM0067


title: 13476355

value: Rep 4 RILM0052

value: Rep 4 MxRILM0052


title: 13423752

value: Rep 3 RILM0063


title: 13423611

value: Rep 2 BxRILM0040

value: Rep 2 RILM0040


title: 13476356

value: Above ground seedling

value: Rep 4 BxRILM0052


title: 13476383

value: Rep 2 MxRILM0040


title: 13476357


title: 13423609

value: Rep 4 RILM0022

value: Rep 4 MxRILM0022


title: 13476352

value: Rep 1 MxRILM0063

value: Rep 1 RILM0063


title: 13476350

value: 14 days old

value: Rep 1 BxRILM0063


title: 13262254

value: Rep 1 BxRILM0030

value: Rep 1 RILM0030


title: 13476348

value: Rep 2 BxRILM0063

value: Rep 2 RILM0063


title: 13476278

value: Rep 2 RILM0067

value: Rep 2 MxRILM0067


title: 13423580

value: Rep 1 RILM0052

value: Rep 1 BxRILM0052


title: 13476349

value: Above ground seedling

value: Rep 2 MxRILM0063


title: 13476275

value: Rep 2 BxRILM0321

value: Rep 2 RILM0321


title: 13262252

value: Rep 1 RILM0022

value: Rep 1 BxRILM0022


title: 13262251

value: Rep 1 MxRILM0022


title: 13476277

value: 14 days old

value: Rep 2 BxRILM0067


title: 13262253

value: Rep 1 MxRILM0030

value: Rep 1 BxRILM0030


title: 13261933

value: Rep 3 BxRILM0034

value: Rep 3 MxRILM0034


title: 13261935

value: Rep 3 RILM0030

value: Rep 3 BxRILM0030


title: 13261934

value: Rep 3 RILM0034


title: 13476273

value: Rep 2 MxRILM0321


title: 13261932

value: Above ground seedling


title: 13259714

value: Rep 2 MxRILM0029

value: Rep 2 RILM0029


title: 13470909

value: Rep 2 BxRILM0364

value: Rep 2 RILM0364


title: 13470916

value: Rep 2 RILM0328

value: Rep 2 MxRILM0328


title: 13470912

value: 14 days old

value: Rep 2 MxRILM0364


title: 13259713

value: Rep 1 RILM0029

value: Rep 1 MxRILM0029


title: 13254153

value: Rep 3 RILM0048

value: Rep 3 MxRILM0048


title: 13476212

value: Rep 4 BxRILM0051

value: Rep 4 RILM0051


title: 13470913


title: 13476351

value: Rep 1 RILM0063

value: Rep 1 BxRILM0063


title: 13259712

value: Above ground seedling

value: Rep 2 BxRILM0029


title: 13254154

value: Rep 3 BxRILM0048


title: 13259711

value: Rep 2 RILM0029


title: 13470882

value: Rep 3 BxRILM0057

value: Rep 3 MxRILM0057


title: 13476274

value: Rep 2 MxRILM0321

value: Rep 2 BxRILM0321


title: 13470915

value: 14 days old

value: Rep 2 BxRILM0076

value: Rep 2 RILM0076


title: 13254155

value: Rep 4 RILM0017

value: Rep 4 BxRILM0017


title: 13470879

value: Rep 1 RILM0040

value: Rep 1 BxRILM0040


title: 13470881

value: Rep 1 MxRILM0040


title: 13254146

value: Rep 2 RILM0017

value: Rep 2 MxRILM0017


title: 13254020

value: Above ground seedling


title: 13254151

value: Rep 4 MxRILM0017


title: 13254018

value: Rep 1 RILM0030

value: Rep 1 MxRILM0030


title: 13470875

value: Rep 1 RILM0328

value: Rep 1 BxRILM0328


title: 13423691

value: Rep 2 BxRILM0063

value: Rep 2 RILM0063


title: 13470874

value: 14 days old

value: Rep 1 MxRILM0328


title: 13254019

value: Rep 3 BxRILM0023

value: Rep 3 MxRILM0023


title: 13470876


title: 13254016

value: Rep 3 RILM0023


title: 13470873

value: Rep 2 BxRILM0328

value: Rep 2 RILM0328


title: 13254017


title: 13470860

value: Rep 2 MxRILM0076

value: Rep 2 BxRILM0076


title: 13470861

value: Above ground seedling

value: Rep 1 BxRILM0076

value: Rep 1 MxRILM0076


title: 13470862

value: Rep 1 RILM0076


title: 13253950

value: Rep 1 MxRILM0017

value: Rep 1 RILM0017


title: 13253973

value: Rep 2 RILM0317

value: Rep 2 MxRILM0317


title: 13470872

value: 14 days old

value: Rep 2 MxRILM0328


title: 13253949

value: Rep 2 BxRILM0017

value: Rep 2 RILM0017


title: 13470863


title: 13253951

value: Rep 1 BxRILM0017


title: 13253955

value: Rep 4 BxRILM0040

value: Rep 4 RILM0040


title: 13470878

value: Rep 1 MxRILM0040

value: Rep 1 RILM0040


title: 13470857

value: Above ground seedling

value: Rep 2 RILM0076

value: Rep 2 MxRILM0076


title: 13253682

value: Rep 3 BxRILM0022

value: Rep 3 MxRILM0022


title: 13253680

value: Rep 3 RILM0022


title: 13470646

value: Rep 3 RILM0057

value: Rep 3 BxRILM0057


title: 13470645

value: 14 days old

value: Rep 4 MxRILM0057

value: Rep 4 BxRILM0057


title: 13470643

value: Rep 4 RILM0057


title: 13253679


title: 13470512

value: Rep 4 BxRILM0039

value: Rep 4 RILM0039


title: 13470510

value: Rep 3 BxRILM0034

value: Rep 3 MxRILM0034


title: 13253678

value: Rep 2 MxRILM0022

value: Rep 2 BxRILM0022


title: 13470509

value: Above ground seedling

value: Rep 3 RILM0034


title: 13470493

value: Rep 2 MxRILM0040

value: Rep 2 BxRILM0040


title: 13253642

value: Rep 4 RILM0048

value: Rep 4 BxRILM0048


title: 13470490

value: Rep 1 MxRILM0023

value: Rep 1 RILM0023


title: 13253644

value: 14 days old

value: Rep 2 RILM0022


title: 13470491

value: Rep 1 BxRILM0023


title: 13253677


title: 13470492

value: Rep 2 RILM0063

value: Rep 2 MxRILM0063


title: 13470467

value: Rep 3 RILM0079

value: Rep 3 BxRILM0079


title: 13470469

value: Rep 4 MxRILM0079

value: Rep 4 BxRILM0079


title: 13253641

value: Above ground seedling

value: Rep 4 MxRILM0048


title: 13470465

value: Rep 2 RILM0007

value: Rep 2 MxRILM0007


title: 13253638

value: Rep 3 BxRILM0048

value: Rep 3 RILM0048


title: 13253629

value: Rep 2 MxRILM0048

value: Rep 2 RILM0048


title: 13470468

value: 14 days old

value: Rep 4 RILM0079


title: 13470466

value: Rep 3 MxRILM0079


title: 13253636

value: Rep 4 BxRILM0048


title: 13470877

value: Rep 3 MxRILM0057

value: Rep 3 RILM0057


title: 13470507

value: Rep 3 MxRILM0034

value: Rep 3 RILM0034


title: 13470456

value: Rep 4 BxRILM0034

value: Rep 4 RILM0034


title: 13470458

value: Above ground seedling

value: Rep 3 MxRILM0022

value: Rep 3 RILM0022


title: 13470454

value: Rep 4 MxRILM0034


title: 13253628

value: Rep 2 BxRILM0048


title: 13470489

value: Rep 1 RILM0023

value: Rep 1 BxRILM0023


title: 13467346

value: 14 days old

value: Rep 3 BxRILM0017

value: Rep 3 MxRILM0017


title: 13467342

value: Rep 3 MxRILM0264

value: Rep 3 RILM0264


title: 13470457


title: 13470453

value: Rep 1 RILM0010

value: Rep 1 BxRILM0010


title: 13253625

value: Rep 2 MxRILM0048


title: 13467347

value: Rep 3 RILM0017


title: 13467341

value: Rep 3 BxRILM0264


title: 13467115

value: Above ground seedling

value: Rep 2 BxRILM0272

value: Rep 2 RILM0272


title: 13253624

value: Rep 1 MxRILM0034

value: Rep 1 RILM0034


title: 13467063

value: Rep 3 MxRILM0058

value: Rep 3 RILM0058


title: 13467116

value: 14 days old

value: Rep 4 BxRILM0029

value: Rep 4 RILM0029


title: 13253623

value: Rep 1 BxRILM0034


title: 13467066

value: Rep 3 BxRILM0058


title: 13253574

value: Rep 4 BxRILM0022

value: Rep 4 RILM0022


title: 13467003

value: Rep 4 MxRILM0029


title: 13467061

value: Rep 4 MxRILM0058

value: Rep 4 BxRILM0058


title: 13467062

value: Above ground seedling

value: Rep 4 RILM0058


title: 13467065


title: 13253510


title: 13466973


title: 13466974

value: Rep 2 MxRILM0010

value: Rep 2 BxRILM0010


title: 13253566

value: Rep 2 MxRILM0034

value: Rep 2 BxRILM0034


title: 13466976

value: Rep 3 RILM0022

value: Rep 3 BxRILM0022


title: 13466970

value: 14 days old

value: Rep 4 MxRILM0022


title: 13253509

value: Rep 2 MxRILM0030

value: Rep 2 RILM0030


title: 13470641

value: Rep 4 BxRILM0057

value: Rep 4 RILM0057


title: 13466956

value: Rep 2 MxRILM0007

value: Rep 2 BxRILM0007


title: 13466959

value: Rep 2 RILM0007


title: 13466958

value: Above ground seedling

value: Rep 1 MxRILM0007

value: Rep 1 RILM0007


title: 13253505

value: Rep 1 BxRILM0029

value: Rep 1 RILM0029


title: 13466955

value: Rep 1 BxRILM0007


title: 13466954


title: 13466953

value: Rep 4 BxRILM0048

value: Rep 4 RILM0048


title: 13466975

value: 14 days old

value: Rep 3 BxRILM0022

value: Rep 3 MxRILM0022


title: 13470513

value: Rep 4 RILM0039

value: Rep 4 MxRILM0039


title: 13250096

value: Rep 4 RILM0063

value: Rep 4 BxRILM0063


title: 13250097

value: Rep 3 MxRILM0045

value: Rep 3 RILM0045


title: 13253507

value: Above ground seedling

value: Rep 2 BxRILM0030

value: Rep 2 MxRILM0030


title: 13250093

value: Rep 4 MxRILM0023

value: Rep 4 BxRILM0023


title: 13466949

value: Rep 3 RILM0264

value: Rep 3 BxRILM0264


title: 13466936

value: Rep 1 RILM0364

value: Rep 1 BxRILM0364


title: 13466951

value: 14 days old

value: Rep 4 BxRILM0264

value: Rep 4 RILM0264


title: 13466937

value: Rep 1 MxRILM0364


title: 13466915

value: Rep 3 BxRILM0039

value: Rep 3 MxRILM0039


title: 13250098

value: Rep 1 MxRILM0296

value: Rep 1 RILM0296


title: 13466935

value: Above ground seedling


title: 13253506

value: Rep 2 RILM0030

value: Rep 2 BxRILM0030


title: 13250095

value: Rep 4 RILM0023

value: Rep 4 MxRILM0023


title: 13466950

value: Rep 4 MxRILM0264


title: 13466916

value: Rep 3 RILM0039


title: 13250092

value: Rep 4 BxRILM0023


title: 13253571

value: Rep 4 MxRILM0022

value: Rep 4 BxRILM0022


title: 13466914

value: 14 days old


title: 13250091

value: Rep 4 RILM0040

value: Rep 4 MxRILM0040


title: 13466885

value: Rep 4 BxRILM0058

value: Rep 4 RILM0058


title: 13466913

value: Rep 4 MxRILM0039

value: Rep 4 BxRILM0039


title: 13250090

value: Above ground seedling

value: Rep 4 BxRILM0040


title: 13250032

value: Rep 1 RILM0023

value: Rep 1 MxRILM0023


title: 13465870

value: Rep 1 BxRILM0345

value: Rep 1 MxRILM0345


title: 13250030

value: Rep 2 RILM0040

value: Rep 2 MxRILM0040


title: 13465891

value: Rep 1 MxRILM0045

value: Rep 1 RILM0045


title: 13466884

value: 14 days old

value: Rep 4 RILM0296

value: Rep 4 MxRILM0296


title: 13466882

value: Rep 4 BxRILM0296


title: 13465867

value: Rep 4 RILM0017

value: Rep 4 MxRILM0017


title: 13250031

value: Rep 1 MxRILM0040

value: Rep 1 RILM0040


title: 13250012

value: Above ground seedling

value: Rep 3 MxRILM0040

value: Rep 3 RILM0040


title: 13465861

value: Rep 4 MxRILM0317

value: Rep 4 BxRILM0317


title: 13465860

value: Rep 4 RILM0317


title: 13465868

value: Rep 1 BxRILM0045


title: 13465869

value: Rep 2 RILM0045

value: Rep 2 MxRILM0045


title: 13250010

value: 14 days old

value: Rep 2 MxRILM0040

value: Rep 2 BxRILM0040


title: 13465863

value: Rep 1 RILM0345

value: Rep 1 BxRILM0345


title: 13465862


title: 13465858

value: Rep 3 MxRILM0317

value: Rep 3 RILM0317


title: 13465859

value: Rep 3 BxRILM0317


title: 13465823

value: Above ground seedling


title: 13465819

value: Rep 3 BxRILM0079

value: Rep 3 MxRILM0079


title: 13250008

value: Rep 3 BxRILM0040

value: Rep 3 MxRILM0040


title: 13466883

value: Rep 4 BxRILM0296

value: Rep 4 RILM0296


title: 13465806

value: Rep 4 MxRILM0017

value: Rep 4 BxRILM0017


title: 13465820

value: 14 days old

value: Rep 4 BxRILM0079

value: Rep 4 RILM0079


title: 13465818

value: Rep 3 RILM0027

value: Rep 3 BxRILM0027


title: 13249889

value: Rep 4 BxRILM0030

value: Rep 4 RILM0030


title: 13249890

value: Rep 4 MxRILM0030


title: 13465805

value: Above ground seedling

value: Rep 2 MxRILM0045

value: Rep 2 BxRILM0045


title: 13465804

value: Rep 3 RILM0017

value: Rep 3 BxRILM0017


title: 13463655

value: Rep 2 MxRILM0345

value: Rep 2 BxRILM0345


title: 13249880

value: Rep 3 BxRILM0030

value: Rep 3 MxRILM0030


title: 13249888

value: 14 days old


title: 13463653

value: Rep 1 MxRILM0345

value: Rep 1 RILM0345


title: 13463390

value: Rep 2 RILM0345


title: 13463391


title: 13463394

value: Rep 4 BxRILM0017

value: Rep 4 RILM0017


title: 13249870

value: Rep 4 RILM0034

value: Rep 4 MxRILM0034


title: 13463349

value: Above ground seedling

value: Rep 1 MxRILM0010

value: Rep 1 RILM0010


title: 13463344

value: Rep 1 BxRILM0010


title: 13249879

value: Rep 3 RILM0030


title: 13465801

value: Rep 2 BxRILM0045

value: Rep 2 RILM0045


title: 13463345

value: Rep 2 RILM0010

value: Rep 2 MxRILM0010


title: 13249868

value: 14 days old

value: Rep 2 RILM0034

value: Rep 2 MxRILM0034


title: 13463343

value: Rep 4 MxRILM0022

value: Rep 4 BxRILM0022


title: 13249869

value: Rep 4 BxRILM0034


title: 13463342

value: Rep 2 BxRILM0010


title: 13466952

value: Rep 4 MxRILM0264

value: Rep 4 BxRILM0264


title: 13249867

value: Above ground seedling

value: Rep 4 RILM0034


title: 13249866

value: Rep 2 BxRILM0034


title: 13463313

value: Rep 3 RILM0048

value: Rep 3 BxRILM0048


title: 13463314

value: Rep 3 MxRILM0048


title: 13463312


title: 13249864

value: Rep 4 MxRILM0029

value: Rep 4 RILM0029


title: 13463272

value: 14 days old

value: Rep 4 BxRILM0030

value: Rep 4 RILM0030


title: 13249859

value: Rep 3 BxRILM0029

value: Rep 3 RILM0029


title: 13249865

value: Rep 4 BxRILM0029


title: 13249838

value: Rep 4 MxRILM0027

value: Rep 4 RILM0027


title: 13463310

value: Rep 4 RILM0048

value: Rep 4 MxRILM0048


title: 13463303

value: Above ground seedling

value: Rep 2 RILM0272

value: Rep 2 MxRILM0272


title: 13463271

value: Rep 4 MxRILM0030


title: 13249863


title: 13463307

value: Rep 1 RILM0272

value: Rep 1 BxRILM0272


title: 13463305

value: Rep 1 MxRILM0272


title: 13463269

value: 14 days old

value: Rep 4 BxRILM0027


title: 13250011

value: Rep 3 RILM0040

value: Rep 3 BxRILM0040


title: 13249858

value: Rep 3 MxRILM0029

value: Rep 3 BxRILM0029


title: 13463268

value: Rep 4 MxRILM0027


title: 13463306


title: 13249837

value: Rep 3 MxRILM0027

value: Rep 3 BxRILM0027


title: 13463262

value: Rep 3 RILM0029


title: 13463270

value: Above ground seedling

value: Rep 4 RILM0030


title: 13465803

value: Rep 1 BxRILM0045

value: Rep 1 MxRILM0045


title: 13463263

value: Rep 2 MxRILM0272

value: Rep 2 BxRILM0272


title: 13463259


title: 13463261


title: 13463258

value: Rep 4 MxRILM0029

value: Rep 4 BxRILM0029


title: 13463246

value: 14 days old

value: Rep 4 BxRILM0027


title: 13249833

value: Rep 1 MxRILM0029

value: Rep 1 BxRILM0029


title: 13249824

value: Rep 2 BxRILM0027

value: Rep 2 RILM0027


title: 13463245

value: Rep 3 BxRILM0030

value: Rep 3 MxRILM0030


title: 13463243

value: Rep 3 RILM0030


title: 13462953

value: Above ground seedling

value: Rep 3 MxRILM0296

value: Rep 3 RILM0296


title: 13463087

value: Rep 3 BxRILM0296


title: 13462952


title: 13462951

value: Rep 4 MxRILM0046

value: Rep 4 BxRILM0046


title: 13249827

value: Rep 2 MxRILM0027


title: 13463244


title: 13249823

value: Rep 3 RILM0029

value: Rep 3 MxRILM0029


title: Bc14579 pH4.8 t60_t0

status: Public on Nov 25 2009

city: Wageningen

first: Maarten

last: Mols

address: Bomenweg 2

department: ATV

institute: Wageningen University

description: No extra description.

hyb_protocol: The target was denatured by boiling for 1 min and immediate cooling on ice prior to hybridization. A total of 200ng of both samples was mixed and applied with the Agilent hybridization buffer to the microarray, according to Agilent manual. Hybridization was performed at 60 °C. The slide was washed according to the Agilent microarray wash protocol.

scan_protocol: Microarrays were scanned with the Agilent DNA Microarray Scanner, Model G2565BA, according to the Agilent protocol at 50% laser intensity, and 10 micron scan resolution.

data_processing: Lowess-normalization, performed in Feature Extract, Agilent. Subsequently normalized data was processed with the Vampire webbased microarray suite.

organism: Bacillus cereus

label_protocol: Complementary DNA was synthesized and labeled using 15 μg of total RNA, and the CyScribe Post-Labeling kit (Amersham Biosciences Europe GmbH) according to the supplier's instructions.

extract_protocol: RNA was extracted as described by van Schaik et al., 2007

tag: Bc ATCC 14579 OD600 0.5 exposed to pH4.8 for 60 min

tag: Bc ATCC 14579 OD600 0.5 exposed to pH4.8 for 0 min


title: 13462950

value: 14 days old

value: Rep 4 RILM0046


title: wild type, Pst_48h, biological rep3

city: Saskatoon

first: Yangdou

last: Wei

state: SK

address: 112 Sceince Place

department: Biology

country: Canada

institute: University of Saskatchewan

description:
Gene expression data from 3-week-old wild type leaves.
bot0818

hyb_protocol: Prehyb, hybridisation and wash were performed by Bio-Array Resource (BAR) center, University of Toronto (http://www.csb.utoronto.ca/resources/facilities/affymetrix-genechip).

scan_protocol: The scannings were performed by Bio-Array Resource (BAR) center, University of Toronto (http://www.csb.utoronto.ca/resources/facilities/affymetrix-genechip).

organism: Arabidopsis thaliana

source_name: wild type, Pst-infiltrated leaves, 48h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6-10 ug total RNA. For the detailed protocol, please check the website http://www.csb.utoronto.ca/resources/facilities/affymetrix-genechip.

growth_protocol: The seedlings were grown in a growth chamber with a short day (8h light) illumination at 20C.

extract_protocol: Phenol/chloroform extraction and LiCl purification of total RNA were performed.

treatment_protocol: The leaves of wild type and mutant plants were or were not infiltrated with a Pst suspension at the concentration of 10-5 cfu ml-1.

tag: ecotype

value: wild type

value: leaf

value: three weeks

tag: treatment

value: Pseudomonas syringae pv. tomato DC3000 (Pst) infection

tag: treatment time


title: 13249805

value: Rep 4 MxRILM0010

value: Rep 4 BxRILM0010


title: 13462931

value: Above ground seedling

value: Rep 3 RILM0046

value: Rep 3 BxRILM0046


title: 13249803

value: Rep 1 RILM0040

value: Rep 1 BxRILM0040


title: 13462949

value: Rep 4 BxRILM0046


title: 13462932

value: Rep 3 MxRILM0046


title: 13463311

value: Rep 4 MxRILM0048

value: Rep 4 BxRILM0048


title: 13249786

value: 14 days old

value: Rep 1 MxRILM0048

value: Rep 1 BxRILM0048


title: 13249807

value: Rep 4 RILM0027

value: Rep 4 BxRILM0027


title: 13462930


title: 13462929

value: Rep 3 MxRILM0027

value: Rep 3 RILM0027


title: 13249785

value: Rep 1 RILM0048


title: 13249784

value: Above ground seedling


title: RASMC_BB_rep1

city: Charlottesville

first: Brian

middle: R

last: Wamhoff

state: VA

address: 409 Lane Road Bldg MR4 Rm6022

department: Cardiology

institute: University of Virginia

hyb_protocol: cRNA was hybridized accoring to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

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

data_processing: Raw .CEL files were normalized using invariant set normalization and the PM-MM model of expression was used to contruct gene expression measures and standard errors for each probe set (dCHIP).

source_name: Rat aortic smooth muscle cells, PDGF-BB-treated, 3 hrs

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: RASMCs were plated at 1E4 cells/cm2 in 10% FBS for 24 hrs. RASMCs were then serum-starved for 72 hrs in serum-free, insulin-free media.

extract_protocol: RNeasy Mini Kit spin columns were used for RNA extraction (Qiagen).

treatment_protocol: RASMCs were first washed with PBS and stimulated with either PDGF-BB (30ng/mL) or vehicle (0.2% BSA in 10mM acetic acid) in serum-free, insulin-free media. RASMCs were treated for 3 hours.

value: vascular smooth muscle


title: 13249783

value: Rep 4 BxRILM0017

value: Rep 4 MxRILM0017


title: 13249743

value: Rep 1 BxRILM0023

value: Rep 1 RILM0023


title: 13462927

value: Rep 3 BxRILM0027


title: siRNA, collagen plate, rep3

city: Washington

first: Junfeng

last: Sun

state: DC

address: Suite 180, 4000 Reservior Rd NW

institute: Georgetown Univ

description: siRNA, Collagen plate

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Raw images were processed using Microarray Suite 5.0 software. For the processing of the microarray data, we used SemiRMA (Bebu et al., 2007).

label_protocol: per Affymetrix Genechip Expression Analysis Technical Manual

treatment_protocol: Syk siRNA knockdown or control

tag: sirna

value: Syk siRNA knockdown

tag: plate

value: collagen coated

tag: cell line


title: RASMC_BB_rep2

tag: tissue


title: 13249741

tag: genotype

value: 14 days old

value: Rep 2 BxRILM0023

value: Rep 2 MxRILM0023


title: 13249595

value: Rep 2 MxRILM0017

value: Rep 2 BxRILM0017


title: 13249742

value: Rep 2 RILM0023


title: siRNA, plastic plate, rep2

description: siRNA, plastic plate

value: plastic


title: RASMC_VEH_rep1

source_name: Rat aortic smooth muscle cells, VEH-treated, 3 hrs


title: 13211142

value: Rep 2 BxRILM0317

value: Rep 2 RILM0317


title: siRNA, collagen plate, rep2

description: siRNA, Collagen plate


title: RASMC_VEH_rep2

value: vascular smooth muscle


title: siRNA, plastic plate, rep3

description: siRNA, plastic plate


title: 13249738

value: Above ground seedling


title: 13249740

value: Rep 1 MxRILM0023


title: 13211145

value: Rep 1 RILM0317

value: Rep 1 BxRILM0317


title: 13249831

value: Rep 2 MxRILM0027

value: Rep 2 BxRILM0027


title: siRNA, plastic plate, rep1

description: siRNA, plastic plate

value: Syk siRNA knockdown


title: siRNA, collagen plate, rep1

description: siRNA, Collagen plate

value: collagen coated


title: 13211141

value: 14 days old

value: Rep 3 BxRILM0057

value: Rep 3 RILM0057


title: Empty vector, collagen plate, rep3

description: Empty vector, Collagen plate

value: control


title: 13571777

description: Maize seedlings were grown under controlled conditions and were harvested at the 14 day old stage. Total RNA was isolated (with 6 individual seedlings pooled for each genotype in each replication) using Trizol reagent. Approximately 500 micrograms of total RNA were used for mRNA isolation with the OligoTex mRNA midi kit (Qiagen, Valencia, CA) as per manufacturer's protocol with slight modification. Two micrograms of mRNA were labeled according to Nakozono et al. (2003) with slight modifications. Each sample was labeled with Cy dye and hybridized to the GPL4521 platform.

scan_protocol: Each microarray chip was scanned a minimum of six times with constant PMT and increasing laser power settings.  Slides were scanned with a Pro Scan Array HT (Perkin Elmer, Wellesley, MA)

data_processing: All scans from each slide were quantified using ImaGene (BioDiscovery, El Segundo, CA). For each slide and dye combination, median scan intensities were extrapolated using data from the multiple scans collected using a variation of a previously published linear regression method (DUDLEY et al. 2002). Non-informative spots were removed prior to analysis.  In total, 14,118 informative spots were analyzed. For each selected scan, lowess normalization was applied to the natural log (ie, log base e) of the background-corrected raw signal intensities to remove signal-intensity-dependent dye effects on each slide (CUI et al. 2003; DUDOIT et al. 2002).  Normalization was conducted separately for each slide to avoid introducing dependencies among expression values.  After normalization, data for each slide/dye combination were median-centered so expression measures would be comparable across slides.  Post-normalized data was summarized by taking the average of all technical and biological replicates within a genotype.

value: Rep F B73xMo17

value: Rep F Mo17xB73


title: Empty vector, plastic plate, rep3

description: Empty vector, plastic plate

value: plastic


title: Empty vector, collagen plate, rep2

description: Empty vector, Collagen plate


title: 13211118

value: Rep 4 BxRILM0057

value: Rep 4 MxRILM0057


title: 13211120

value: Above ground seedling

value: Rep 4 RILM0057


title: 13571772

value: Rep D Mo17xB73

value: Rep D B73xMo17


title: Empty vector, plastic plate, rep2

description: Empty vector, plastic plate


title: 13211136

value: Rep 3 MxRILM0057


title: Empty vector, plastic plate, rep1

description: Empty vector, plastic plate


title: 13571775

value: Rep E B73xMo17

value: Rep E Mo17xB73


title: 13211117


title: 13211135

value: Rep 1 BxRILM0317

value: Rep 1 MxRILM0317


title: 13571774

value: 14 days old

value: Rep C Mo17xB73

value: Rep C B73xMo17


title: 13211114

value: Rep 1 RILM0317


title: T1QBC_AH597_Cy3_AMES_Cy5_43095

city: Rockville

first: Chun-Hua

last: Wan

state: MD

address: 9407 Medical Center Dr

department: PFGRC

institute: J Craig Venter Institute

hyb_protocol: Aminosaline coated slides were prehybridized in 5x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate) (Invitrogen), 0.1% sodium dodecyl sulfate, and 1% bovine serum albumin at 42 degree Celcius for 45 min.  The slides then were washed at room temperature with distilled water, dipped in isopropanol, and spun dry.  Equal concentrations of DNA probe from the appropriate Cy3 and Cy5 labeled probes were combined, dried and then resuspended in a solution of 50% formamide, 5x SSC, and 0.1% sodium dodecyl sulfate.  Resuspended probes were denatured at 95 degree Celcius prior to hybridization.  The probe mixture then was added to the microarray slide and allowed to hybridize overnight at 42 degree Celcius.   Hybridized slides were washed sequentially in solutions of 1x SSC-0.2% SDS, 0.1x SSC-0.2% SDS, and 0.1x SSC at room temperature

scan_protocol: Scanned on Axon GenePix 4000 scanner.  PMT values were optimized during scanning to balance channel intensities.

data_processing:
Procedures to calculate the value of log2 ratio:
1. Use software suite TM4 (www.tm4.org) to analyze spotted arrays.
2. Use Spotfinder with background correction to compute the spot intensities of the hybridized arrays.
3. Perform the following filtering steps:
All PFGRC arrays used in this study have 3 types of spots.
      (1). Species spot: oligos designed for the species under investigation.
      (2). Reserved spot or control spot: oligos designed from Arabidopsis genes as controls.
      (3). Empty spots: no oligos or any DNA.
Step 1: Identify the replicates.
      Sort the .mev file from Spotfinder by oligo_id.
Step 2: Identify the outliers within each set of replicates for each channel.
      Outliers are identified using the Sprents method (The Handbook of Parametric and Nonparametric Statistical Procedures, Third Edition by David J. Sheskin, PP 400-402).
      |Xi - M|/MAD > Max
      Xi = Each intensity value from the set of replicates.
      M = Median intensity value from the set of replicates.
      MAD = Median absolute deviation.
      Max = the critical value that the result of the inequality must exceed in order to conclude that the Xi value is an outlier. The value of 5 was used for Max.
Step 3: Replace the outliers.
      Replace the outliers by the value closest to them from the tail that they occur. For example, if the outlier identified is the highest value in channel A, that value will be replaced by the next highest value of its replicate set in channel A.
Step 4: Subtract the 95th percentile of the reserved spots.
      Calculate the 95th percentile of all the reserved spots and subtract that value from all the species spots and reserved spots.
Step 5: Replace zero (0) by one (1).
      After subtracting the 95th percentile of the reserved spots, if one of the channel intensities is less than zero (0), replace that value by one (1); If both channels become less than zero (0), set both channels to zero (0).
Step 6. Output the filtered .mev file.
4. Use Midas X for CGH normalization:
    1). Plot the histogram of the Log2 ratio data (Reference/Query) from the filtered .mev file, and identify the central peak containing oligos predicted to be shared by both the reference and query strains.
    2). Fit a Gaussian curve to the central peak by 'tweaking' the log ratio mean and by shrinking or stretching the standard deviation of the curve to find the smallest least sum of squares difference.
    3). Perform Log Mode Centering normalization on the channel that contains the query sample only (Either Cy3 or Cy5).
    4). Output the normalized *.mev file.
5. Calculate the value of log2 ratio (Reference/Query) from the normalized .mev file:
    1). If both channels (QUERY_MEDIAN_INTENSITY and REF_MEDIAN_INTENSITY) are zero, assign the value "null".
    2). If one channel is zero and the other is not zero, substitute the zero with one (1) and then, assign the log2 ratio of QUERY_MEDIAN_INTENSITY/REF_MEDIAN_INTENSITY to VALUE
    3). If neither channel is zero, assign the log2 ratio of QUERY_MEDIAN_INTENSITY/REF_MEDIAN_INTENSITY to VALUE.

organism: Bacillus anthracis

source_name: Ames

label_protocol: 4ug of genomic DNA was labeled at 37 degree Celcius overnight using DNA polymerase I Klenow fragment (New England Biolabs), a 25X 2:1 amino allyl dUTP (Ambion) dNTP mix, and random hexamers (Invitrogen).  Labeled DNA was purified with Qiaquick PCR purification kit (QIAGEN).The purified labelled DNA was then dye coupled with the appropriate cye dye (CY3/CY5).

growth_protocol: Cells grown in Lysogeny broth (LB) at 37 degrees Celcius overnight.

extract_protocol: Epicentre MasterPure DNA Extraction Kit

value: Ames


title: 13211034

value: Rep 1 BxRILM0079

value: Rep 1 RILM0079


title: SH-SY5Ycells_DMSO_treated_4hours_rep3

status: Public on Nov 19 2009

city: Trieste

first: Paola

last: Roncaglia

state: TS

address: via Bonomea 265

department: Neurobiology

country: Italy

institute: SISSA/ISAS (International School for Advanced Studies)

hyb_protocol: Labelled cRNA was hybridized on Affymetrix GeneChip Human U133A 2.0 Arrays containing over 14,500 transcripts. Hybridized GeneChips were stained and washed using the GeneChip Fluidic Station 450.

scan_protocol: GeneChips were scanned with the GeneChip Scanner 3000 7G. Cell intensity values and probe detection calls were computed from the raw array data using the Affymetrix GeneChip Operating Software (GCOS).

data_processing: Further data processing was performed in the R computing environment (http://www.r-project.org/, version R 2.5.0 for Windows) using packages from the BioConductor software project (http://www.bioconductor.org/). Variance-stabilizing normalization was applied, using the justvsn function from the vsn library. Normalized data were then filtered based on the Affymetrix detection call, so that only probes that had a Present call in at least one of the arrays were retained. Data were then imported in the MultiExperiment Viewer (MeV) software (version 4.0.01 for Windows XP), and statistical analysis was performed with the SAM (Significance Analysis of Microarrays) module.

source_name: Human neuroblastoma SH-SY5Y cells, treated with dimethyl sulfoxide (DMSO) 0.6%, for 4 hours

label_protocol: 10 μg of each total RNA sample was labelled according to the standard one-cycle amplification and labelling protocol developed by Affymetrix (Santa Clara, CA).

growth_protocol: SH-SY5Y human neuroblastoma cells (ATCC CRL-2266) were cultured in a humidified incubator at 37°C and 5 % CO2 in F12-EMEM (1:1) containing 15 % foetal bovine serum (FBS), 2 mM L-glutamine, 25 µg/mL gentamicin, 100 U/ml penicillin, and 100 µg/mL streptomycin at 37°C with 5 % CO2. Cells were seeded at 6 x 10e6 cells in 75 cm2 flasks and grown for 24 h (cells reached 70-80% confluence).

extract_protocol: Total RNA was isolated using the TRIzol reagent (Invitrogen) following the manufacturer’s instructions. It was then purified using the RNeasy mini kit (Qiagen). The quality of total RNA was assessed using a bioanalyzer (Agilent 2100; Agilent Technologies) and RNA was quantified by using a ND-1000 Nanodrop spectrophotometer.

treatment_protocol: The growth medium was replaced with experimental medium, which was either 140 nM Bf medium (Bf 140 nM samples) or 0.6 % DMSO medium (DMSO 0.6 % samples), and cells were allowed to grow. After 4 h, cells were collected and processed for microarray analysis. Separate flasks of cells were used for each of the treatments and assays. Experiments were performed using at least three independent biological replicates.

tag: atcc

tag: cell type

value: neuroblastoma

value: DMSO

value: 4 hours


title: SH-SY5Ycells_bilirubin_treated_140nM_4hours_rep3

source_name: Human neuroblastoma SH-SY5Y cells, treated with free bilirubin (Bf) 140nM, for 4 hours

value: free bilirubin


title: SH-SY5Ycells_DMSO_treated_4hours_rep1


title: SH-SY5Ycells_bilirubin_treated_140nM_4hours_rep2


title: 13568753

value: Above ground seedling

value: Rep B Mo17xB73

value: Rep B B73xMo17


title: Empty vector, collagen plate, rep1

description: Empty vector, Collagen plate

value: control

value: collagen coated


title: SH-SY5Ycells_bilirubin_treated_140nM_1hour_rep3

source_name: Human neuroblastoma SH-SY5Y cells, treated with free bilirubin (Bf) 140nM, for 1 hour

treatment_protocol: The growth medium was replaced with experimental medium, which was either 140 nM Bf medium (Bf 140 nM samples) or 0.6 % DMSO medium (DMSO 0.6 % samples), and cells were allowed to grow. After 1 h, cells were collected and processed for microarray analysis. Separate flasks of cells were used for each of the treatments and assays. Experiments were performed using at least three independent biological replicates.

value: 1 hour


title: SH-SY5Ycells_DMSO_treated_1hour_rep2

source_name: Human neuroblastoma SH-SY5Y cells, treated with dimethyl sulfoxide (DMSO) 0.6%, for 1 hour


title: SH-SY5Ycells_bilirubin_treated_140nM_1hour_rep2


title: SH-SY5Ycells_DMSO_treated_1hour_rep1


title: 13571778

value: 14 days old

value: Rep A B73xMo17

value: Rep A Mo17xB73


title: SH-SY5Ycells_DMSO_treated_1hour_rep3


title: SH-SY5Ycells_bilirubin_treated_140nM_1hour_rep1


title: SH-SY5Ycells_bilirubin_treated_140nM_24hours_rep3

data_processing: Further data processing was performed in the R computing environment (http://www.r-project.org/, version R 2.5.0 for Windows) using packages from the BioConductor software project (http://www.bioconductor.org/). Variance-stabilizing normalization was applied, using the justvsn function from the vsn library. Normalized data were then filtered based on the Affymetrix detection call, so that only probes that had a Present call in at least one of the arrays were retained. Data were then imported in the MultiExperiment Viewer (MeV) software (version 4.0.01 for Windows XP), and statistical analysis was performed with the SAM (Significance Analysis of Microarrays) module. A False Discovery Rate (FDR) of about 10% (i.e. 9.317%) was applied to detect significantly differentially expressed genes.

source_name: Human neuroblatoma SH-SY5Y cells, treated with free bilirubin (Bf) 140nM, for 24 hours

growth_protocol: SH-SY5Y human neuroblastoma cells (ATCC CRL-2266) were cultured in a humidified incubator at 37°C and 5 % CO2 in F12-EMEM (1:1) containing 15 % foetal bovine serum (FBS), 2 mM L-glutamine, 25 µg/mL gentamicin, 100 U/ml penicillin, and 100 µg/mL streptomycin at 37°C with 5 % CO2. Cells were seeded at 6 x 106 cells in 75 cm2 flasks and grown for 24 h (cells reached 70-80% confluence).

treatment_protocol: The medium was then replaced with experimental medium, which was either 140 nM Bf medium (Bf 140 nM samples), or 0,6 % DMSO medium (DMSO 0.6 % samples) and cells were allowed to grow. After 24 h cells were collected and processed for microarray analysis. Separate flasks of cells were used for each of the treatments and assays. Experiments were performed at least in three independent biological replicates.

value: Human neuroblatoma SH-SY5Y cells

tag: agent

value: free bilirubin (Bf) 140nM, for 24 hours


title: SH-SY5Ycells_bilirubin_treated_140nM_24hours_rep2


title: SH-SY5Ycells_DMSO_treated_24hours_rep1

source_name: Human neuroblatoma SH-SY5Y cells, treated with dimethyl sulfoxide (DMSO) 0.6%, for 24 hours


title: SH-SY5Ycells_DMSO_treated_24hours_rep3

value: dimethyl sulfoxide (DMSO) 0.6%, for 24 hours


title: 185999

description: no additional information

hyb_protocol: See NimbleGen Array User's Guide: CGH Analysis (cgh_userguide_v5p1.pdf)

data_processing: We used a subset of 840,289 probes that were known to have identical sequence in B73 and Mo17 (based on B73 BAC sequences and Mo17 WGS data) as a control set to obtain a best-fitting cubic spline function (Workman et al., 2002), assuming that most of these probes should have the same hybridization intensities after normalization. The spline function was then globally applied for all probes to normalize the two channels.  After within-chip normalization, linear model analyses using LIMMA (Smyth 2004; Smyth 2005) were conducted for the data from all microarrays. The linear model for each probe included effects for dyes and genotypes (B73, Mo17, RIL M0022, and RIL M0023), and p-values were calculated to test for a signal difference between Mo17 and B73 genotypes as part of each linear model analysis.

extract_protocol: Total genomic DNA of the samples were isolated using NimbleGen's standard protocols (see supplemental file: cgh_userguide_v5p1.pdf)

value: two-week-old etiolated seedlings

tag: developmental state


title: 270482

description: no additional information

scan_protocol: See NimbleGen Array User's Guide: CGH Analysis (cgh_userguide_v5p1.pdf)


title: IQ 25 µM  sample 1

city: Maastricht

first: Kevin

last: Hochstenbach

address: Universiteitssingel 50

department: Health Risk Analysis and Toxicology

institute: Maastricht University

hyb_protocol: Hybridization according to Agilent instructions.

scan_protocol: Slides were scanned on a GenePix® 4000B Microarray Scanner (Molecular Devices, Sunnyvale, USA). Cy3 and Cy5 were excited at wavelengths of 532 and 635 nm, respectively. Laser power was set to 100%. The photo multiplier tube gain was set to a saturation tolerance of 0.02% to minimize background and saturated spots. Photomultiplier gain was set to 587 (Cy3) and 705 (Cy5) for replicates 1 and 2, and 628 (Cy3) and 560 (Cy5) for replicates 3 and 4, based on automatic establishment of ideal scan settings. The images obtained (resolution 5 micron, 16 bit tiff image) were processed with Imagene 8.0.1 software (Biodiscovery, El Segundo, USA) to measure mean signal intensities for spots and local backgrounds followed by a quality control in Microsoft Excel.

data_processing: Data preparations were performed in GeneSight software (BioDiscovery) and included in chronological order: background subtraction, omission of bad spots (controls and irregularly shaped spots), LOWESS normalization, log (base=2) transformations, calculation of difference of test compound versus respective vehicle control.

source_name: control for 60_IQ_10%

label_protocol: The Two-Color Microarray-Based Gene Expression Analysis kit from Agilent Technologies (Amstelveen, The Netherlands) was used to generate Cyanine (Cy) labelled cRNA according to the manufacturer’s protocol.

growth_protocol: Isolated PBMC were resuspended in tissue culture medium RPMI 1640 supplemented with L-glutamine, 10% heat inactivated foetal calf serum (FCS) (Gibco, Paisley, UK) and 100 U/ml penicillin G and 0.1 mg/ml streptomycin (PAA Laboratories GmbH, Pasching, Austria) to a final concentration of 2,4*106  cells/ml.

extract_protocol: RNA was isolated from TRIzol® suspended cells according to the manufacturer’s protocol with minor modifications, followed by a clean up, using an RNeasy Mini Kit (Qiagen, Venlo, The Netherlands) with DNase treatment.

treatment_protocol: For analysis of whole genome gene expression by microarray PBMC from five independent donors per compound were exposed for 20 hours to three concentrations, i.e. the 100% and two serial ten-fold dilutions (10% and 1%), and a DMSO or PBS vehicle control. All exposures were performed in the presence of freshly prepared S9-mix.

value: PBMC

value: IQ

tag: dose

tag: concentration

tag: immunotoxicity

value: non-immunotoxic


title: 271902

description: no additional information

label_protocol: See NimbleGen Array User's Guide: CGH Analysis (cgh_userguide_v5p1.pdf)

tag: developmental stage


title: SH-SY5Ycells_DMSO_treated_4hours_rep2

value: neuroblastoma

value: DMSO

value: 4 hours


title: SH-SY5Ycells_DMSO_treated_24hours_rep2


title: SH-SY5Ycells_bilirubin_treated_140nM_24hours_rep1


title: 271904

description: no additional information


title: IQ 25 µM  sample 4

source_name: control for 90_IQ_10%


title: IQ 25 µM  sample 2

source_name: control for 61_IQ_10%


title: PhIP 2.5 µM sample 4

source_name: control for 32_PhIP_1%

value: PhIP


title: BaP 10 µM sample 3

source_name: control for 41_BaP_10%

value: control

value: BaP

value: immunotoxic


title: BaP 100 µM sample 2

source_name: control for 40_BaP_100%


title: IQ 25 µM  sample 5

source_name: control for 91_IQ_10%


title: SH-SY5Ycells_bilirubin_treated_140nM_4hours_rep1

value: free bilirubin


title: 270491-1

description: no additional information


title: 238943

description: no additional information


title: BaP 100 µM sample 5

source_name: control for 43_BaP_100%


title: BaP 100 µM sample 1

source_name: control for 39_BaP_100%