title: Ileum E18.5_LGR5 null mice_Biological replica 4_2

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

country: Belgium

institute: ULB

description: Sample were hybridized to MEEBO arrays containing 38784 mouse 70mer oligonucleotide probes (Stanford Functional Genomics Facility, California, USA).

hyb_protocol: Slides were incubated at 42°C for 60 min in the following preheated (42°C) solution: 5xSSC, SDS 0.1%, HEPES 24mM, BSA 0.1mg/ml. Slides were rinsed for 30s in deionized water followed by a centrifugation at 800 rpm for 10 min. Cyanine-labeled cRNA samples were mixed with 30 µg of mouse cot-1, incubated for 2 min at 100°C, centrifuged for 10 min at 13,000 rpm, and then kept at 65°C. After hybridization of the samples on the microarray slides overnight at 65°C, slides were washed twice for 2 min at 60°C with 2xSSC, 0.03% SDS, once 2 min at 60°C with 2xSSC, and finally briefly washed in 0.2xSSC at room temperature. They were dried by centrifugation at 800 rpm for 13 min and stored in the dark at room temperature.

scan_protocol: Slides were scanned using a Molecular Devices 4000B laser scanner and expression levels were quantified using GenePix Pro 6.1 image analysis software (Axon Instruments, CA, USA). Image acquisitions were performed with automatic photomultiplier gains (PMT) adjustement. Artifact-associated spots were eliminated by both visual and software guided flags.

data_processing:
A non-linear Lowess (locally weighted scatter plot) normalization method applied to each individual block (print-tip option) was carried out.
VALUE is the normalized Log (base 2) ratio of the median of Channel 1 to Channel 2

source_name: Ileum E18.5 LGR5-/-

label_protocol: Double-stranded cDNA was synthesized from 1 µg of total RNA, followed by production of antisense RNA containing the modified nucleotide 5-(3-aminoallyl)-UTP using the Amino Allyl MessageAmpTM II aRNA Amplification kit (Ambion, Texas, USA). Labelling with Cy5 or Cy3 (GE Healthcare Bio-Sciences, New Jersey, USA) was performed for 30min in 50% DMSO at room temperature in a dark environment.

extract_protocol: Ileum total RNA was extracted using the Mirvana kit (Ambion, Texas, USA).

treatment_protocol: Animals were housed in a temperature (21±1°C) and humidity (55±10%)-controlled room with a 12 h light: 12 h dark cycle. Food and water were available ad libitum. Animal procedures were conducted in accordance with the guidelines of the European Communities Directive 86/609/EEC regulating animal research and were approved by the Local Ethical Committee.

tag: LGR5/GPR49-LacZ (LGR5-/-) mutant mice were generated in the C57BL/6 background by replacement of exon 18 from the LGR5 gene with a trans-gene containing the LacZ-MC1 neo (neomycin resistance) cassette.  Then, studies were performed on embryos generated by crossing heterozygous male and female LGR5+/− mice. RNA was extracted from four independent littermate E18.5. Biological replica 4, technical replica 2 (dye-swap)

source_name: Ileum E18.5 LGR5 +/+

tag: Reference RNA  was extracted from the ileum of an embryo LGR5 +/+ of the same littermate E18.5 as the LGR5 null mice.


title: Ileum E18.5_LGR5 null mice_Biological replica 4_1

status: Public on Oct 01 2009

type: RNA

molecule: total RNA

organism: Mus musculus

tag: LGR5/GPR49-LacZ (LGR5-/-) mutant mice were generated in the C57BL/6 background by replacement of exon 18 from the LGR5 gene with a trans-gene containing the LacZ-MC1 neo (neomycin resistance) cassette.  Then, studies were performed on embryos generated by crossing heterozygous male and female LGR5+/− mice. RNA was extracted from four independent littermate E18.5. Biological replica 4, technical replica 1 (dye-swap)


title: Ileum E18.5_LGR5 null mice_Biological replica 3_2

tag: LGR5/GPR49-LacZ (LGR5-/-) mutant mice were generated in the C57BL/6 background by replacement of exon 18 from the LGR5 gene with a trans-gene containing the LacZ-MC1 neo (neomycin resistance) cassette.  Then, studies were performed on embryos generated by crossing heterozygous male and female LGR5+/− mice. RNA was extracted from four independent littermate E18.5. Biological replica 3, technical replica 2 (dye-swap)


title: Ileum E18.5_LGR5 null mice_Biological replica 3_1

tag: LGR5/GPR49-LacZ (LGR5-/-) mutant mice were generated in the C57BL/6 background by replacement of exon 18 from the LGR5 gene with a trans-gene containing the LacZ-MC1 neo (neomycin resistance) cassette.  Then, studies were performed on embryos generated by crossing heterozygous male and female LGR5+/− mice. RNA was extracted from four independent littermate E18.5. Biological replica 3, technical replica 1 (dye-swap)


title: KAT_10B_R4: Katahdin - Cy3,water / Cy5,P. infestans - 10 hpi

city: Madison

first: Lara

middle: Colton

last: Kramer

state: WI

address: 1575 Linden Drive

department: Horticulture

country: USA

institute: University of Wisconsin - Madison

description: Biological replicate 4 of 4. S. tuberosum Cultivar: Katahdin. Samples taken 10 hpi

hyb_protocol: Slides placed in pre-heated pre-hyb buffer (5X SSC, 0.1% SDS, 1% BSA @ 42C) filter sterilized for 45 min. Wash slides once in Milli Q water and then isopropanol and centrifuge 500 rpm for 1 min. Put probe on slides diluted in hybridization solution (50% formamide, 5X SSC, 0.1% SDS) and incubate overnight at 42C in corning chambers placed in a hybridization oven. The next day wash slides: 2X SSC, 0.1% SDS at 42C for 5 min, 0.05X SSC, 0.1% SDS for 10 min at RT, 0.05X SSC for 1 min and repeat 4x with fresh solution and a final dip in dd water. Dry in centrifuge 500 rpm for 1 min.

scan_protocol: Slides were scanned using an Axon scanner at maximum laser power (Axon Instruments, UnionCity, CA) at both 532 and 635 nm. The PMT values for both wavelengths were adjusted to capture a similar number of normalized counts for each channel.

data_processing: The TIFF images were quantified using Genepix 5.0. Local background was subtracted from the signal value and the data was normalized using the vsn method in the limma package of bioconductor.

organism: Solanum tuberosum

source_name: Katahdin - 10 hpi - Inoculated with P. infestans

label_protocol: Total RNA was extracted using Qiagens Plant Rneasy kit, followed by the MessageAmp aRNA amplification kit from Ambion (Ambion, Austin, Texas). 2 ug of Amplified RNA (aRNA) was converted into aminoallyl cDNA using the SuperScript III enzyme and random primers (Invitrogen, Carlsbad, CA).  Aminoallyl cDNA from each experimental unit was then labeled with Cy3 or Cy5 esters (Amersham Biosciences, Piscataway, NJ).

growth_protocol: Plants were grown in a CRD for five weeks in a greenhouse set for 18 hours of daylight, day temp 17 and 19˚C and at night 13 and 15˚C.

extract_protocol: Tissue: Leaf tissue disks directly under the inoculation (water or P. infestans) site were harvested using hole punchers and frozen in an eppendorf tube until RNA extraction

treatment_protocol:
Samples collected 10 hours after inoculation
Inoculated with 91,841 sporangia/mL of P. infestans

tag: S. tuberosum Cultivar

value: Katahdin

tag: Age

value: 4 weeks of Growth

tag: Tissue

source_name: Katahdin - 10 hpi - Mock Inoculated with water

treatment_protocol:
Samples collected 10 hours after inoculation
Mock Inoculated with water


title: Ileum E18.5_LGR5 null mice_Biological replica 2_1

tag: LGR5/GPR49-LacZ (LGR5-/-) mutant mice were generated in the C57BL/6 background by replacement of exon 18 from the LGR5 gene with a trans-gene containing the LacZ-MC1 neo (neomycin resistance) cassette.  Then, studies were performed on embryos generated by crossing heterozygous male and female LGR5+/− mice. RNA was extracted from four independent littermate E18.5. Biological replica 2, technical replica 1 (dye-swap)


title: KAT_10B_R2: Katahdin - Cy3,water / Cy5,P. infestans - 10 hpi

description: Biological replicate 2 of 4. S. tuberosum Cultivar: Katahdin. Samples taken 10 hpi

treatment_protocol:
Samples collected 10 hours after inoculation
Inoculated with 92,036 sporangia/mL of P. infestans

value: Leaf tissue disks directly under the inoculation (water or P. infestans) site


title: Monocytes_100nM AM580 48h_donor2

city: DIJON

first: Cédric

last: REBE

address: 2 av marechal de Lattre de Tassigny

department: Hopital du Bocage

country: France

description: All the experiments from RNA extraction to data processing were performed by Miltenyi Biotec Microarray Service (Cologne).

hyb_protocol: The hybridization procedure was performed according to the the “One-Color Microarray-Based Gene Expression Analysis protocol (version 5.5, part number G4140-90040) using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 1.65 µg Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Human Genome Oligo Microarrays 4x44K using Agilent’s recommended hybridization chamber and oven. Following hybridization, the microarrays were washed once with 6x SSPE buffer containing 0.005% N-lauroylsarcosine for 1 min at room temperature followed by a second wash with preheated 0.06x SSPE buffer (37 °C) containing 0.005% N-lauroylsarcosine for 1 min. The last washing step was performed with acetonitrile for 30 sec.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies). The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware).

organism: Homo sapiens

source_name: Monocytes from donor2 treated for 48h with 100nM AM580

label_protocol: Sample labeling was performed as detailed in the “One-Color Microarray-Based Gene Expression Analysis protocol (version 5.5, part number G4140-90040). Briefly, 1 µg of each total RNA samples was used for the amplification and labeling step using the Agilent Low RNA Input Linear Amp Kit (Agilent Technologies) in the presence of cyanine 3-CTP (Perkin Elmer). Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).

growth_protocol: Cells were grown in RPMI 1640 medium with glutamax-I (Invitrogen, Paisley, UK) supplemented with 10% (vol/vol) fetal bovine serum (FBS; Invitrogen) in an atmosphere of 95% air and 5% CO2 at 37°C.

extract_protocol: Human total RNA was isolated with the use of Trizol (Sigma-Aldrich). RNA quality and integrity were determined using the Agilent RNA 6000 Nano Kit on the Agilent 2100 Bioanalyzer (Agilent Technologies). RNA was quantified by measuring A260nm on the ND-1000 Spectrophotometer (NanoDrop Technologies).

treatment_protocol: Human peripheral-blood monocytes were obtained from the Etablissement Français du Sang (Besançon, France). Briefly, mononuclear cells were isolated by Ficoll gradient centrifugation and monocyte negative selection was performed via magnetic activated cell sorting using the Monocyte Isolation Kit II (Miltenyi Biotec, Bergisch Gladbach, Germany) according to the manufacturer’s instructions.

tag: Monocytes were isolated from healthy donor2 with inform consent and treated in vitro with DMSO for 48h and 100nM AM580 during the last 24h


title: KAT_10B_R1: Katahdin - Cy3,water / Cy5,P. infestans - 10 hpi

description: Biological replicate 1 of 4. S. tuberosum Cultivar: Katahdin. Samples taken 10 hpi

treatment_protocol:
Samples collected 10 hours after inoculation
Inoculated with 107,036 sporangia/mL of P. infestans


title: Ileum E18.5_LGR5 null mice_Biological replica 1_1

tag: LGR5/GPR49-LacZ (LGR5-/-) mutant mice were generated in the C57BL/6 background by replacement of exon 18 from the LGR5 gene with a trans-gene containing the LacZ-MC1 neo (neomycin resistance) cassette.  Then, studies were performed on embryos generated by crossing heterozygous male and female LGR5+/− mice. RNA was extracted from four independent littermate E18.5. Biological replica 1, technical replica 1 (dye-swap)


title: Ileum E18.5_LGR5 null mice_Biological replica 2_2

tag: LGR5/GPR49-LacZ (LGR5-/-) mutant mice were generated in the C57BL/6 background by replacement of exon 18 from the LGR5 gene with a trans-gene containing the LacZ-MC1 neo (neomycin resistance) cassette.  Then, studies were performed on embryos generated by crossing heterozygous male and female LGR5+/− mice. RNA was extracted from four independent littermate E18.5. Biological replica 2, technical replica 2 (dye-swap)


title: Monocytes_DMSO 48h_donor1

description: All experiments from RNA extraction to data processing were performed by Miltenyi Biotec Microarray Service (Cologne).

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies). The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files.

data_processing: For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware).

source_name: Monocytes from donor1 treated for 48h with DMSO

tag: Monocytes were isolated from healthy donor1 with inform consent and treated in vitro with DMSO for 48h


title: Monocytes_DMSO 48h_donor2

description: All the experiments from RNA extraction to data processing were performed by Miltenyi Biotec Microarray Service (Cologne)

source_name: Monocytes from donor2 treated for 48h with DMSO

tag: Monocytes were isolated from healthy donor2 with inform consent and treated in vitro with DMSO for 48h


title: Monocytes_10µM T0901317 48h_donor2

source_name: Monocytes from donor2 treated for 48h with 10µM T0901317

tag: Monocytes were isolated from healthy donor2 with inform consent and treated in vitro with 10µM T0901317 for 48h


title: Ileum E18.5_LGR5 null mice_Biological replica 1_2

tag: LGR5/GPR49-LacZ (LGR5-/-) mutant mice were generated in the C57BL/6 background by replacement of exon 18 from the LGR5 gene with a trans-gene containing the LacZ-MC1 neo (neomycin resistance) cassette.  Then, studies were performed on embryos generated by crossing heterozygous male and female LGR5+/− mice. RNA was extracted from four independent littermate E18.5. Biological replica 1, technical replica 2 (dye-swap)

tag: Reference RNA  was extracted from the ileum of an embryo LGR5 +/+ of the same littermate E18.5 as the LGR5 null mice


title: KAT_10B_R3: Katahdin - Cy3,water / Cy5,P. infestans - 10 hpi

description: Biological replicate 3 of 4. S. tuberosum Cultivar: Katahdin. Samples taken 10 hpi

treatment_protocol:
Samples collected 10 hours after inoculation
Inoculated with 103,888 sporangia/mL of P. infestans


title: KAT_10A_R1: Katahdin - Cy3,P. infestans / Cy5,water - 10 hpi


title: KAT_10A_R4: Katahdin - Cy3,P. infestans / Cy5,water - 10 hpi


title: KAT_5B_R1: Katahdin - Cy3,water / Cy5,P. infestans - 5 hpi

description: Biological replicate 1 of 4. S. tuberosum Cultivar: Katahdin. Samples taken 5 hpi

source_name: Katahdin - 5 hpi - Inoculated with P. infestans

treatment_protocol:
Samples collected 5 hours after inoculation
Inoculated with 107,036 sporangia/mL of P. infestans

source_name: Katahdin - 5 hpi - Mock Inoculated with water

treatment_protocol:
Samples collected 5 hours after inoculation
Mock Inoculated with water


title: KAT_5A_R3: Katahdin - Cy3,P. infestans / Cy5,water - 5 hpi

description: Biological replicate 3 of 4. S. tuberosum Cultivar: Katahdin. Samples taken 5 hpi

treatment_protocol:
Samples collected 5 hours after inoculation
Inoculated with 103,888 sporangia/mL of P. infestans


title: Monocytes_10 µM T0901317 48h_donor1

source_name: Monocytes from donor1 treated for 48h with 10µM T0901317

tag: Monocytes were isolated from healthy donor1 with inform consent and treated in vitro with 10µM T0901317 for 48h


title: Monocytes_100 nM AM580 48h_donor1

source_name: Monocytes from donor1 treated for 48h with 100nM AM580

tag: Monocytes were isolated from healthy donor1 with inform consent and treated in vitro with DMSO for 48h and 100nM AM580 during the last 24h


title: KAT_5A_R4: Katahdin - Cy3,P. infestans / Cy5,water - 5 hpi

description: Biological replicate 4 of 4. S. tuberosum Cultivar: Katahdin. Samples taken 5 hpi

treatment_protocol:
Samples collected 5 hours after inoculation
Inoculated with 91,841 sporangia/mL of P. infestans


title: Monocytes_10µM T0901317 + 100nM AM580 48h_donor1

source_name: Monocytes from donor1 treated for 48h with 10µM T0901317 + 100nM AM580

tag: Monocytes were isolated from healthy donor1 with inform consent and treated in vitro with 10µM T0901317 for 48h and 100 nM AM580 during the last 24h


title: KAT_10A_R2: Katahdin - Cy3,P. infestans / Cy5,water - 10 hpi


title: KAT_10A_R3: Katahdin - Cy3,P. infestans / Cy5,water - 10 hpi


title: KAT_2B_R4: Katahdin - Cy3,water / Cy5,P. infestans - 2 hpi

description: Biological replicate 4 of 4. S. tuberosum Cultivar: Katahdin. Samples taken 2 hpi

source_name: Katahdin - 2 hpi - Inoculated with P. infestans

treatment_protocol:
Samples collected 2 hours after inoculation
Inoculated with 91,841 sporangia/mL of P. infestans

source_name: Katahdin - 2 hpi - Mock Inoculated with water

treatment_protocol:
Samples collected 2 hours after inoculation
Mock Inoculated with water


title: Monocytes_10µM T0901317 + 100nM AM580 48h_donor2

source_name: Monocytes from donor2 treated for 48h with 10µM T0901317 + 100nM AM580

tag: Monocytes were isolated from healthy donor2 with inform consent and treated in vitro with 10µM T0901317 for 48h and 100nM AM580 during the last 24h


title: KAT_5A_R2: Katahdin - Cy3,P. infestans / Cy5,water - 5 hpi

description: Biological replicate 2 of 4. S. tuberosum Cultivar: Katahdin. Samples taken 5 hpi

treatment_protocol:
Samples collected 5 hours after inoculation
Inoculated with 92,036 sporangia/mL of P. infestans


title: KAT_5B_R2: Katahdin - Cy3,water / Cy5,P. infestans - 5 hpi


title: KAT_2A_R3: Katahdin - Cy3,P. infestans / Cy5,water - 2 hpi

description: Biological replicate 3 of 4. S. tuberosum Cultivar: Katahdin. Samples taken 2 hpi

treatment_protocol:
Samples collected 2 hours after inoculation
Inoculated with 103,888 sporangia/mL of P. infestans


title: KAT_2A_R2: Katahdin - Cy3,P. infestans / Cy5,water - 2 hpi

description: Biological replicate 2 of 4. S. tuberosum Cultivar: Katahdin. Samples taken 2 hpi

treatment_protocol:
Samples collected 2 hours after inoculation
Inoculated with 92,036 sporangia/mL of P. infestans


title: KAT_2A_R4: Katahdin - Cy3,P. infestans / Cy5,water - 2 hpi


title: KAT_2B_R1: Katahdin - Cy3,water / Cy5,P. infestans - 2 hpi

description: Biological replicate 1 of 4. S. tuberosum Cultivar: Katahdin. Samples taken 2 hpi

treatment_protocol:
Samples collected 2 hours after inoculation
Inoculated with 107,036 sporangia/mL of P. infestans


title: KAT_2B_R2: Katahdin - Cy3,water / Cy5,P. infestans - 2 hpi


title: KAT_5A_R1: Katahdin - Cy3,P. infestans / Cy5,water - 5 hpi


title: KAT_5B_R3: Katahdin - Cy3,water / Cy5,P. infestans - 5 hpi


title: 64_10B_R2: RB transgenic Katahdin - Cy3,water / Cy5,P. infestans - 10 hpi

description: Biological replicate 2 of 4. S. tuberosum Cultivar: Katahdin with four insertions of the RB gene. Samples taken 10 hpi

source_name: RB transgenic Katahdin - 10 hpi - Inoculated with P. infestans

tag: Four insertions of the RB Late Blight resistance gene

source_name: RB transgenic Katahdin - 10 hpi - Mock Inoculated with water


title: KAT_2B_R3: Katahdin - Cy3,water / Cy5,P. infestans - 2 hpi

tag: S. tuberosum Cultivar


title: KAT_5B_R4: Katahdin - Cy3,water / Cy5,P. infestans - 5 hpi

tag: Age


title: KAT_2A_R1: Katahdin - Cy3,P. infestans / Cy5,water - 2 hpi

tag: Tissue


title: 64_10B_R4: RB transgenic Katahdin - Cy3,water / Cy5,P. infestans - 10 hpi

description: Biological replicate 4 of 4. S. tuberosum Cultivar: Katahdin with four insertions of the RB gene. Samples taken 10 hpi


title: 64_10A_R2: RB transgenic Katahdin - Cy3,P. infestans / Cy5,water - 10 hpi


title: 64_10B_R3: RB transgenic Katahdin - Cy3,water / Cy5,P. infestans - 10 hpi

description: Biological replicate 3 of 4. S. tuberosum Cultivar: Katahdin with four insertions of the RB gene. Samples taken 10 hpi


title: 64_10B_R1: RB transgenic Katahdin - Cy3,water / Cy5,P. infestans - 10 hpi

description: Biological replicate 1 of 4. S. tuberosum Cultivar: Katahdin with four insertions of the RB gene. Samples taken 10 hpi


title: 64_10A_R4: RB transgenic Katahdin - Cy3,P. infestans / Cy5,water - 10 hpi


title: 64_5A_R1: RB transgenic Katahdin - Cy3,P. infestans / Cy5,water - 5 hpi

description: Biological replicate 1 of 4. S. tuberosum Cultivar: Katahdin with four insertions of the RB gene. Samples taken 5 hpi

source_name: RB transgenic Katahdin - 5 hpi - Mock Inoculated with water

source_name: RB transgenic Katahdin - 5 hpi - Inoculated with P. infestans


title: 64_5B_R3: RB transgenic Katahdin - Cy3,water / Cy5,P. infestans - 5 hpi

description: Biological replicate 3 of 4. S. tuberosum Cultivar: Katahdin with four insertions of the RB gene. Samples taken 5 hpi


title: 64_5B_R2: RB transgenic Katahdin - Cy3,water / Cy5,P. infestans - 5 hpi

description: Biological replicate 2 of 4. S. tuberosum Cultivar: Katahdin with four insertions of the RB gene. Samples taken 5 hpi


title: 64_5A_R2: RB transgenic Katahdin - Cy3,P. infestans / Cy5,water - 5 hpi


title: 64_5B_R1: RB transgenic Katahdin - Cy3,water / Cy5,P. infestans - 5 hpi


title: 64_10A_R3: RB transgenic Katahdin - Cy3,P. infestans / Cy5,water - 10 hpi


title: 64_5A_R3: RB transgenic Katahdin - Cy3,P. infestans / Cy5,water - 5 hpi


title: 64_2A_R4: RB transgenic Katahdin - Cy3,P. infestans / Cy5,water - 2 hpi

description: Biological replicate 4 of 4. S. tuberosum Cultivar: Katahdin with four insertions of the RB gene. Samples taken 2 hpi

source_name: RB transgenic Katahdin - 2 hpi - Mock Inoculated with water

source_name: RB transgenic Katahdin - 2 hpi - Inoculated with P. infestans


title: 64_5A_R4: RB transgenic Katahdin - Cy3,P. infestans / Cy5,water - 5 hpi

description: Biological replicate 4 of 4. S. tuberosum Cultivar: Katahdin with four insertions of the RB gene. Samples taken 5 hpi


title: 64_10A_R1: RB transgenic Katahdin - Cy3,P. infestans / Cy5,water - 10 hpi


title: N1.1vsN4.1

city: Pathumthani

first: nitsara

last: karoonuthaisiri

state: Pathumthani

address: Paholyothin

department: Central

country: Thailand

institute: BIOTEC

description: no additional information

hyb_protocol: The probe was resuspended in hybridization solution (50% Formamide; 5x SSC; 0.1% SDS; 1 mg/ml Human Placental DNA; 10mM Tris, pH 7.5) and placed onto the post-processed slides.  The slides were hybridized at 420C for 16 hrs before they were washed according to Corning’s protocol.

scan_protocol: The slides were scanned with either ScanArray Express (PerkinElmer, Waltham, MA) or GenePix 4000B (Molecular Devices, Sunnyvale, CA).  Microarray spots on scanned images are located using GenePix Pro version 6.1.

data_processing: All “empty” and “bad” spots were removed from the analysis.  “Empty” spots were failed PCR products whereas “bad” spots were flagged by visual inspection of the spot images.  From the remaining spots, only the spots with intensities more than one standard deviation above the background intensity were further analyzed.  The processed data were normalized within each array by the scaled print-tip (Lowess) method, and across arrays, using the Aroma package (Bengtsson, available from: http://www.maths.lth.se/help/R/aroma/) run in R project environment (http://cran.r-project.org).  Data from replicated arrays were averaged before clustering.  Logarithmic base 2 values of intensities from both Cy3- and Cy5- samples (M values) were used as inputs for clustering.  Cluster program was used to perform hierarchical clustering and Treeview program was used to visualized the clustered results (Eisen et al., 1998)

organism: Penaeus monodon

source_name: ovary

label_protocol: The aa-dUTP cDNA was fluorescently labeled with Cy3- or Cy5- dyes (GE Healthcare, #RPN5661, Piscataway, NJ) in a presence of 0.1M sodium borate buffer pH 8.7 at room temperature for 1 hour in the dark.  The unincorporated dye was removed using a Microcon YM-50 filter and resuspended in 6 l TE.

extract_protocol: RNA samples of the four developmental stages, categorized by gonad somatic index (GSI) and histology, were extracted from ovaries dissected from P. monodon female broodstocks using TriReagent (Molecular Research Center, #TR118, Cincinnati, OH) as recommended by the manufacture.

tag: GSI = reproductive Stage  I, Normal broodstocks, female

tag: Reference.

tag: GSI = reproductive Stage  IV, Normal broodstocks, female


title: 64_2B_R1: RB transgenic Katahdin - Cy3,water / Cy5,P. infestans - 2 hpi

description: Biological replicate 1 of 4. S. tuberosum Cultivar: Katahdin with four insertions of the RB gene. Samples taken 2 hpi


title: N1.1vsN2.1

description: no additional information

tag: GSI = reproductive Stage II, Normal broodstocks, female


title: 64_5B_R4: RB transgenic Katahdin - Cy3,water / Cy5,P. infestans - 5 hpi


title: N1.1vsN3.1

description: no additional information

tag: GSI = reproductive Stage  III, Normal broodstocks, female


title: 64_2B_R2: RB transgenic Katahdin - Cy3,water / Cy5,P. infestans - 2 hpi

description: Biological replicate 2 of 4. S. tuberosum Cultivar: Katahdin with four insertions of the RB gene. Samples taken 2 hpi


title: PGP9 iPS clone #3-derived embryoid bodies

status: Public on Sep 30 2009

city: Boston

first: Je

middle: Hyuk

last: Lee

state: MA

address: 3 Blackfan Circle, CLSB 528

department: Wyss Institute

institute: Harvard Medical School

description: Data from HPGCC

hyb_protocol: See manufacturer's protocol (http://www.illumina.com/downloads/WholeGenomeExpressionTechnicalBulletin.pdf)

scan_protocol: See manufacturere's (Illumina,Inc) technical manual (BeadXpress Reader) (http://www.illumina.com/downloads/BeadXpressReaderDataSheet.pdf)

data_processing:
Quantile Normalization
BeadStudio (Illumina, Inc). For details, see http://www.illumina.com/downloads/GXBeadStudioNormalization_TechNote.pdf

label: Biotin

extract_protocol: Per Qiagen RNeasy Mini Protocol

tag: PGP9 (normal female) iPS clone #3 (derived by Daley Lab). 2 week old embryoid bodies.


title: 64_2B_R3: RB transgenic Katahdin - Cy3,water / Cy5,P. infestans - 2 hpi

description: Biological replicate 3 of 4. S. tuberosum Cultivar: Katahdin with four insertions of the RB gene. Samples taken 2 hpi


title: 64_2A_R3: RB transgenic Katahdin - Cy3,P. infestans / Cy5,water - 2 hpi


title: 64_2B_R4: RB transgenic Katahdin - Cy3,water / Cy5,P. infestans - 2 hpi


title: PGP9f (Illumina Ref-8 v3.0)

description: Data from HPGCC

source_name: Human primary keratinocytes, PGP9

label_protocol: See manufacturer's protocol (http://www.illumina.com/downloads/WholeGenomeExpressionTechnicalBulletin.pdf)

growth_protocol: 15% NCS DMEM/F12 + 10ng/ml EGF

tag: Derived from 3-mm skin biopsy on 4-Dec-2008.

tag: Healthy adult female

tag: Matched EBV-B-lymphocyte GM21833 (Coriell)


title: 64_2A_R1: RB transgenic Katahdin - Cy3,P. infestans / Cy5,water - 2 hpi


title: PGP9 iPS clone #3

description: Data from HPGCC

source_name: PGP9 iPS clone #3 (Illumina Ref8 v3)

growth_protocol: Normal human ES media (http://ink.primate.wisc.edu/~thomson/protocol.html#media)

tag: iPS derived from PGP9f (Daley Lab). Clone number 3.


title: PGP9TD

description: Data from UCSD Kun Zhang

source_name: Human primary fibroblasts, PGP9

growth_protocol: ES media

treatment_protocol: Adenoviral OCT4,SOX2,KLF4,MYC at 10 MOI for 7 days

tag: Human primary fibroblasts (female) infected with adenoviral pluripotency factors


title: 64_2A_R2: RB transgenic Katahdin - Cy3,P. infestans / Cy5,water - 2 hpi


title: PGP1lymph_techrepB

description: Data from HPGCC

source_name: PGP1 B-lymphocyte

tag: EBV transformed B-cells

value: GM20431 (19-Apr-2006 established by Coriell)

tag: Healthy

value: Yes.

tag: Male; 54 yrs old


title: PGP1lymph_techrepA

description: Data from HPCGG


title: PGP1TD

description: Data from UCSD Kun Zhang

source_name: Human primary fibroblasts, PGP1

tag: Male human primary fibroblasts infected with adenoviral pluripotency factors


title: PGP1k

description: Data from HPCGG

source_name: Human primary keratinocytes, PGP1

growth_protocol: Cultures are refed every two days and are used as needed for experiments.  Exponentially growing cultures 5-8 days old are used as the source of cells for the next passage.  It is important to subculture keratinocytes no more than 8 days after they have been plated, even if they have not reached the desired density.

tag: Human adult primary keratinocytes derived 19-May-2006 (Harvard). Matched EBV-B-cells

value: GM20431 (19-Apr-2006 established by Coriell) and PGP1f fibroblasts


title: PGP1f (Illumina Ref-8 v2.0)

description: Data from UCSD Kun Zhang.

tag: Human adult primary fibroblasts (passage #6) derived 19-May-2006 (Harvard). Matched EBV-B-cells


title: S_uberis_strain_FSL Z1-266

status: Public on Sep 13 2009

type: genomic

city: Ithaca

first: Michael

middle: J

last: Stanhope

state: NY

address: Schurman Hall

department: Population Medicine and Diagnostic Sciences

institute: Cornell University

description:
test strain supplementary file names: D2S2H1.gpr (array 3) D2S3H2.gpr (array 4)
reference strain supplementary file names: D2S1H1.gpr (array 3) D2S1H3.gpr (array 2) D2S2H1.gpr (array 2) D2S3H1.gpr (array 4)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4887

hyb_protocol: Standard hybridization conditions for the biotinylated target included preblocking for 30 min at 50°C with 6x SSPE (1x SSPE is 0.18 M NaCl, 10 mM NaH2PO4, and 1 mM EDTA [pH 7.7]) containing 0.05% Tween 20, 5x Denhardt's solution, and 100ng/ul salmon sperm DNA followed by hybridization of the biotinylated target in hybridization solution (6x SSPE, 20-50ng/ul labeled DNA and 0.05% SDS) overnight at 50°C. The arrays were then washed once for at least 15 min with SSPE wash 1 (6x SSPE, 0.05% Tween-20) and then for 1 min with each of the following solutions: SSPE wash 2 (3x SSPE, 0.05% Tween-20), SSPE wash 3 (0.5x SSPE, 0.05% Tween-20), and PBST wash (2x PBS, 0.1% Tween-20), followed by a final 2x PBS wash at room temperature. The hybridized array was then blocked with 5X PBS-Casein Blocking Buffer (Cat # P804901, BioFX Laboratories, Owings Mills, MD) for 15 min at room temperature and labeled for 30 min with Cy5-streptavidin (Cat # PA45001, GE Healthcare, Amersham Biosciences, Piscataway, NJ) using the 1 mg/ml stock solution diluted 1:1,000 in 5X PBS-Casein buffer. The arrays were scanned after they were washed twice with each of PBST and PBS solutions.

scan_protocol: Hybridized microarrays covered with the imaging solution and the coverslip were scanned with an Axon GenePix™ 4000B laser scanner (Axon Instruments, Union City, CA) using the following parameters:Wavelengths=635, ScanPower=100, FocusPosition=100, PixelSize=5 .

data_processing: After scanning, the image was saved as a .tiff file from which the data were extracted using GenePix software.  The raw hybridization signal values, displayed in the GenePix Pro analysis Results (GPR) file, were log2-transformed to be used in subsequent analysis. Signal intensities of replicate microarrays of the reference strain 0140J were averaged, and served as denominator to obtain log-ratio values of the intensities between each array of test strain and reference strain. The log-ratio values for each array were normalized by median subtraction so that the median log ratio of each array was equal to 0.  The normalized log2 (test/reference) values of replicate arrays for each test strain were averaged to determine the presence or absence of a gene in each strain.  The cutoff was empirically set at -2.

molecule: genomic DNA

organism: Streptococcus uberis

source_name: bovine milk, individual

label_protocol: Genomic DNA was digested by sonication to sizes of 200-600bp, as visualized by agarose gel electrophoresis, then purified by using the Qiagen Qiaquick PCR purification kit.  Purified fragments (1 to 2 ug) of test strain as well as reference strain 0140J were labeled with Biotin, using Mirus Label IT® µArray® Biotin Labeling Kit (Cat #MIR 8050, Mirus Corp., Madison, WI) according to the manufacturer’s instructions, followed by removal of unincorporated dyes using Qiaquick (Qiagen) columns and then hybridized to the microarray.

extract_protocol:
using BioRad Aquapure Kit

1. Grow overnight culture of Streptococcus uberis in Todd Hewitt Broth at 37C
2. Pipet 1ml of culture into 1.7ml microfuge tube
3. Pellet cells at 13,000-16,000g for 15 seconds. Discard supernatant
4. Add 300ul of Genomic DNA lysis Solution and pipet up and down to suspend
5. Add 1.5ul of 4,000u/ml lysozyme (up to 10,000u/ml)
6. Incubate at 80C for 5 minutes to lyse cells
7. Add 1.5ul RNase solution (4mg/ml) to lysate
8. Mix by invertin 25 times and incubate at 37C for 45 minutes
9. Allow to cool to room temperature
10. Add 100ul Protein Precipitation Solution
11. Vortex vigorously for 20 seconds
12. Precipitate on ice for 5 minutes
13. Pellet at 13,000-16,000g for 3 minutes
14. Transfer supernatant into clean 1.7ml tube containing 300ul 100% isoproponol
15. Mix sample by inverting 50 times
16. Centrifuge 13,000-16,000g for 1 minute to pellet DNA
17. Discard supernatant
18. Wash pellet with 300ul 70% ethanol by inverting tube several times
19. Centrifuge 13,000-16,000g 1 minute. Carefully pour off ethanol. Pellet may be loose.
20. Invert and drain tube, allow to air dry for 10-15 minutes
21. Add 50ul DNA hydration solution
22. Incubate at 65C for 5 minutes (up to an hour). Additional incubation at room temperature may be required.
23. Mix gently, pulse spin.

tag: Country:New Zealand

tag: reference strain 0140J, Country:UK


title: Bexp_Kstat_dyeswap2

status: Public on Sep 28 2009

city: Seoul

first: Sung Ho

last: Yoon

address: 120 Neungdong-ro, Gwangjin-gu

department: Department of Bioscience and Biotechnology

country: South Korea

institute: Konkuk University

description: The microarray contains two large blocks, onto each of which the probes were spotted in duplicate. The data is for one of the blocks (dye-swap experement).

hyb_protocol: Hybridization and washes were performed according to the instruction of the manufacturer (Digital Genomics).

scan_protocol: The hybridized slides were scanned with GenePix 4000B (Molecular Devices) and scanned images were analyzed by GenePix Pro 6.0.

data_processing: Following background subtraction, spot signal intensities were calculated as percentages of total signal intensities of Cy-3 or Cy-5 signals on each microarray, as a means of normalization. Spots with low intensities were excluded.

organism: Escherichia coli

source_name: MG1655, stationary phase, LB

label_protocol: Fluorescently-labeled cDNA was synthesized by reverse transcription of total RNA with aminoallyl-dUTP and random primers followed by the coupling of Cy3 or Cy5 dyes (Amersham Pharmacia).

extract_protocol: Total RNA was isolated from cells grown in LB medium using the Qiagen RNeasy column.

tag: MG1655, stationary phase, LB

source_name: REL606, exponential phase, LB

tag: REL606, exponential phase, LB


title: PGP9f (Illumina Ref-8 v2.0)

description: Data from UCSD Kun Zhang.


title: Bexp_Kstat_rep2

description: The microarray contains two large blocks, onto each of which the probes were spotted in duplicate. The data is for one of the blocks.


title: S_uberis_strain_QMP B5-157

description:
test strain supplementary file names: D2S1H2.gpr (array 3) D2S2H3.gpr (array 2)
reference strain supplementary file names: D2S1H1.gpr (array 3) D2S1H3.gpr (array 2) D2S2H1.gpr (array 2) D2S3H1.gpr (array 4)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4887


title: S_uberis_strain_QMP B5-143

description:
test strain supplementary file names: D2S1H4.gpr (array 1) D2S2H3.gpr (array 4)
reference strain supplementary file names: D2S1H1.gpr (array 3) D2S1H3.gpr (array 2) D2S2H1.gpr (array 2) D2S3H1.gpr (array 4)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4887


title: Bexp_Kstat_dyeswap1


title: S_uberis_strain_QMP B5-144

description:
test strain supplementary file names: D2S3H3.gpr (array 4) D2S1H4.gpr (array 2)
reference strain supplementary file names: D2S1H1.gpr (array 3) D2S1H3.gpr (array 2) D2S2H1.gpr (array 2) D2S3H1.gpr (array 4)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4887


title: PGP1f (Illumina Ref-8 v3.0)

description: Data from HPCGG


title: hues42 (Illumina Ref8 v.2.0)

description: Data from UCSD Kun Zhang

data_processing: BeadStudio (Illumina, Inc). For details, see http://www.illumina.com/downloads/GXBeadStudioNormalization_TechNote.pdf

source_name: Human ES cell, hues42

growth_protocol: Routine

tag: Human ES cell


title: S_uberis_strain_QMP B5-149

description:
test strain supplementary file names: D2S2H2.gpr (array 2) D2S3H1.gpr (array 1)
reference strain supplementary file names: D2S1H1.gpr (array 3) D2S1H3.gpr (array 2) D2S2H1.gpr (array 2) D2S3H1.gpr (array 4)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4887


title: Bexp_Kstat_rep1


title: Bexp_Bstat_rep1

source_name: REL606, stationary phase, LB

tag: REL606, stationary phase, LB


title: Bexp_Bstat_dyeswap2


title: Bexp_Kexp_dyeswap1

source_name: MG1655, exponential phase, LB

tag: MG1655, exponential phase, LB


title: Bexp_Kexp_dyeswap2


title: S_uberis_strain_QMP B5-154

description:
test strain supplementary file names: D2S3H3.gpr (array 2) D2S2H2.gpr (array 3)
reference strain supplementary file names: D2S1H1.gpr (array 3) D2S1H3.gpr (array 2) D2S2H1.gpr (array 2) D2S3H1.gpr (array 4)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4887


title: S_uberis_strain_QMP B5-153

description:
test strain supplementary file names: D2S1H4.gpr (array 4) D2S3H3.gpr (array 3)
reference strain supplementary file names: D2S1H1.gpr (array 3) D2S1H3.gpr (array 2) D2S2H1.gpr (array 2) D2S3H1.gpr (array 4)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4887


title: Bexp_Kexp_rep1


title: S_uberis_strain_FSL Z3-369

description:
test strain supplementary file names: D2S1H1.gpr (array 1) D2S2H4.gpr (array 3)
reference strain supplementary file names: D2S1H1.gpr (array 3) D2S1H3.gpr (array 2) D2S2H1.gpr (array 2) D2S3H1.gpr (array 4)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4887


title: Bexp_Bstat_rep2


title: Bexp_Kexp_rep2


title: Bexp_Bstat_dyeswap1


title: S_uberis_strain_QMP B5-173

description:
test strain supplementary file names: D2S3H3.gpr (array 1) D2S2H2.gpr (array 4)
reference strain supplementary file names: D2S1H1.gpr (array 3) D2S1H3.gpr (array 2) D2S2H1.gpr (array 2) D2S3H1.gpr (array 4)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4887


title: Murine model of gastrointestinal stromal tumors harboring a germline Kit K641E oncogenic mutant_Biological replica 1_2

status: Public on Sep 25 2009

description: Sample were hybridized to MEEBO arrays containing 38784 mouse 70mer oligonucleotide probes (Stanford Functional Genomics Facility, California, USA).

source_name: Antrum  harboring a germline Kit K641E oncogenic mutant

growth_protocol: No growth

extract_protocol: Antrum total RNA was extracted using the Mirvana kit (Ambion, Texas, USA)

treatment_protocol: Animals were housed in a temperature (21±1°C) and humidity (55±10%)-controlled room with a 12 h light: 12 h dark cycle. Food and water were available ad libitum. Animal procedures were conducted in accordance with the guidelines of the European Communities Directive 86/609/EEC regulating animal research and were approved by the Local Ethical Committee of the Faculty of medicine, Université Libre de Bruxelles, Brussels, Belgium.

tag: A mouse model of gastrointestinal stromal tumor (GIST) has been developed by a knock-in gene targeting strategy, which introduced a Kit gene K641E mutation, originally identified in sporadic human GISTs and in the germ line of familial GIST syndrome patients. All Kit K641E homozygotes die by age 3 weeks due to gastrointestinal obstruction by hyperplastic interstitial cells of Cajal or GISTs. Total RNA was extracted from antral tissue of three independent Kit K641E:Neo homozygote littermates at P14 stage. Biological replica 1, technical replica 2 (dye-swap)

source_name: Antrum Kit wt/wt

treatment_protocol: Animals were maintained and experiments performed as described above.

tag: Reference RNA  was extracted from the antrum of a Kit wt/wt of the same littermate P14 as the knock-in GIST Kit K641E mice.


title: S_uberis_strain_FSL Z3-396

description:
test strain supplementary file names: D2S2H2.gpr (array 1) D2S3H4.gpr (array 4)
reference strain supplementary file names: D2S1H1.gpr (array 3) D2S1H3.gpr (array 2) D2S2H1.gpr (array 2) D2S3H1.gpr (array 4)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4887


title: Murine model of gastrointestinal stromal tumors harboring a germline Kit K641E oncogenic mutant_Biological replica 1_1

tag: A mouse model of gastrointestinal stromal tumor (GIST) has been developed by a knock-in gene targeting strategy, which introduced a Kit gene K641E mutation, originally identified in sporadic human GISTs and in the germ line of familial GIST syndrome patients. All Kit K641E homozygotes die by age 3 weeks due to gastrointestinal obstruction by hyperplastic interstitial cells of Cajal or GISTs. Total RNA was extracted from antral tissue of three independent Kit K641E:Neo homozygote littermates at P14 stage. Biological replica 1, technical replica 1 (dye-swap)


title: S_uberis_strain_FSL Z1-390

description:
test strain supplementary file names: D2S2H4.gpr (array 4) D2S3H4.gpr (array 3)
reference strain supplementary file names: D2S1H1.gpr (array 3) D2S1H3.gpr (array 2) D2S2H1.gpr (array 2) D2S3H1.gpr (array 4)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4887


title: S_uberis_strain_FSL Z1-036

description:
test strain supplementary file names: D2S1H3.gpr (array 3) D2S3H2.gpr (array 1)
reference strain supplementary file names: D2S1H1.gpr (array 3) D2S1H3.gpr (array 2) D2S2H1.gpr (array 2) D2S3H1.gpr (array 4)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4887

tag: Country:The Netherlands


title: S_uberis_strain_FSL Z1-124

description:
test strain supplementary file names: D2S1H4.gpr (array 3) D2S3H2.gpr (array 3)
reference strain supplementary file names: D2S1H1.gpr (array 3) D2S1H3.gpr (array 2) D2S2H1.gpr (array 2) D2S3H1.gpr (array 4)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4887


title: S_uberis_strain_QMP B5-104

description:
test strain supplementary file names: D2S1H2.gpr (array 2) D2S3H1.gpr (array 3)
reference strain supplementary file names: D2S1H1.gpr (array 3) D2S1H3.gpr (array 2) D2S2H1.gpr (array 2) D2S3H1.gpr (array 4)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4887


title: S_uberis_strain_FSL S3-314

description:
test strain supplementary file names: D2S2H1.gpr (array 1) D2S3H4.gpr (array 1)
reference strain supplementary file names: D2S1H1.gpr (array 3) D2S1H3.gpr (array 2) D2S2H1.gpr (array 2) D2S3H1.gpr (array 4)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4887

source_name: bovine milk, bulk tank


title: S_uberis_strain_QMP B5-005

description:
test strain supplementary file names: D2S1H2.gpr (array 1) D2S3H1.gpr (array 2)
reference strain supplementary file names: D2S1H1.gpr (array 3) D2S1H3.gpr (array 2) D2S2H1.gpr (array 2) D2S3H1.gpr (array 4)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4887


title: S_uberis_strain_QMP B5-001

description:
test strain supplementary file names: D2S2H1.gpr (array 4) D2S2H3.gpr (array 1)
reference strain supplementary file names: D2S1H1.gpr (array 3) D2S1H3.gpr (array 2) D2S2H1.gpr (array 2) D2S3H1.gpr (array 4)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4887


title: S_uberis_strain_FSL Z3-343

description:
test strain supplementary file names: D2S1H1.gpr (array 4) D2S2H4.gpr (array 2)
reference strain supplementary file names: D2S1H1.gpr (array 3) D2S1H3.gpr (array 2) D2S2H1.gpr (array 2) D2S3H1.gpr (array 4)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4887


title: S_uberis_strain_FSL Z3-329

description:
test strain supplementary file names: D2S1H1.gpr (array 2) D2S2H4.gpr (array 1)
reference strain supplementary file names: D2S1H1.gpr (array 3) D2S1H3.gpr (array 2) D2S2H1.gpr (array 2) D2S3H1.gpr (array 4)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4887


title: negative control_SEZ

description:
test strain supplementary file name: S3H2.gpr (array 4)
reference strain supplementary file names: S3H2.gpr (array 3) S3H3.gpr (array 4) S3H4.gpr (array 2) S4H1.gpr (array 3) S5H1.gpr (array 4) S7H1.gpr (array 3) S7H4.gpr (array 3)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4231.

organism: Streptococcus equi subsp. zooepidemicus

source_name: negative control_SEZ

extract_protocol: refer to ATCC website

source_name: reference strain 0140J, Country:UK


title: negative control_SEE

description:
test strain supplementary file name: S3H2.gpr (array 2)
reference strain supplementary file names: S3H2.gpr (array 3) S3H3.gpr (array 4) S3H4.gpr (array 2) S4H1.gpr (array 3) S5H1.gpr (array 4) S7H1.gpr (array 3) S7H4.gpr (array 3)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4231.

organism: Streptococcus equi subsp. equi

source_name: negative control_SEE


title: S_uberis_strain_QMP B5-154

description:
test strain supplementary file names: S7H1.gpr (array 1) S7H3.gpr (array 3)
reference strain supplementary file names: S3H2.gpr (array 3) S3H3.gpr (array 4) S3H4.gpr (array 2) S4H1.gpr (array 3) S5H1.gpr (array 4) S7H1.gpr (array 3) S7H4.gpr (array 3)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4231


title: S_uberis_strain_QMP B5-166

description:
test strain supplementary file names: S4H2.gpr (array 4) S5H3.gpr (array 1)
reference strain supplementary file names: S3H2.gpr (array 3) S3H3.gpr (array 4) S3H4.gpr (array 2) S4H1.gpr (array 3) S5H1.gpr (array 4) S7H1.gpr (array 3) S7H4.gpr (array 3)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4231

source_name: buffalo milk, individual


title: S_uberis_strain_QMP B5-149

description:
test strain supplementary file names: S6H1.gpr (array 3) S7H3.gpr (array 1)
reference strain supplementary file names: S3H2.gpr (array 3) S3H3.gpr (array 4) S3H4.gpr (array 2) S4H1.gpr (array 3) S5H1.gpr (array 4) S7H1.gpr (array 3) S7H4.gpr (array 3)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4231


title: S_uberis_strain_FSL Z3-369

description:
test strain supplementary file names: S4H1.gpr (array 4) S5H4.gpr (array 1)
reference strain supplementary file names: S3H2.gpr (array 3) S3H3.gpr (array 4) S3H4.gpr (array 2) S4H1.gpr (array 3) S5H1.gpr (array 4) S7H1.gpr (array 3) S7H4.gpr (array 3)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4231


title: S_uberis_strain_FSL Z1-036

description:
test strain supplementary file names: S4H3.gpr (array 2) S5H2.gpr (array 3)
reference strain supplementary file names: S3H2.gpr (array 3) S3H3.gpr (array 4) S3H4.gpr (array 2) S4H1.gpr (array 3) S5H1.gpr (array 4) S7H1.gpr (array 3) S7H4.gpr (array 3)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4231


title: S_uberis_strain_QMP B5-157

description:
test strain supplementary file names: S4H2.gpr (array 3) S5H3.gpr (array 2)
reference strain supplementary file names: S3H2.gpr (array 3) S3H3.gpr (array 4) S3H4.gpr (array 2) S4H1.gpr (array 3) S5H1.gpr (array 4) S7H1.gpr (array 3) S7H4.gpr (array 3)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4231


title: S_uberis_strain_FSL Z3-396

description:
test strain supplementary file names: S4H4.gpr (array 4) S5H1.gpr (array 1)
reference strain supplementary file names: S3H2.gpr (array 3) S3H3.gpr (array 4) S3H4.gpr (array 2) S4H1.gpr (array 3) S5H1.gpr (array 4) S7H1.gpr (array 3) S7H4.gpr (array 3)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4231


title: S_uberis_strain_FSL Z1-266

description:
test strain supplementary file names: S3H2.gpr (array 1) S3H3.gpr (array 2)
reference strain supplementary file names: S3H2.gpr (array 3) S3H3.gpr (array 4) S3H4.gpr (array 2) S4H1.gpr (array 3) S5H1.gpr (array 4) S7H1.gpr (array 3) S7H4.gpr (array 3)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4231


title: S_uberis_strain_QMP B5-144

description:
test strain supplementary file names: S6H1.gpr (array 2) S6H3.gpr (array 3)
reference strain supplementary file names: S3H2.gpr (array 3) S3H3.gpr (array 4) S3H4.gpr (array 2) S4H1.gpr (array 3) S5H1.gpr (array 4) S7H1.gpr (array 3) S7H4.gpr (array 3)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4231


title: S_uberis_strain_QMP B5-153

description:
test strain supplementary file names: S6H3.gpr (array 1) S7H1.gpr (array 4)
reference strain supplementary file names: S3H2.gpr (array 3) S3H3.gpr (array 4) S3H4.gpr (array 2) S4H1.gpr (array 3) S5H1.gpr (array 4) S7H1.gpr (array 3) S7H4.gpr (array 3)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4231


title: S_uberis_strain_QMP B5-173

description:
test strain supplementary file names: S7H1.gpr (array 2) S7H3.gpr (array 4)
reference strain supplementary file names: S3H2.gpr (array 3) S3H3.gpr (array 4) S3H4.gpr (array 2) S4H1.gpr (array 3) S5H1.gpr (array 4) S7H1.gpr (array 3) S7H4.gpr (array 3)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4231


title: S_uberis_strain_QMP B5-143

description:
test strain supplementary file names: S6H1.gpr (array 1) S6H3.gpr (array 4)
reference strain supplementary file names: S3H2.gpr (array 3) S3H3.gpr (array 4) S3H4.gpr (array 2) S4H1.gpr (array 3) S5H1.gpr (array 4) S7H1.gpr (array 3) S7H4.gpr (array 3)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4231


title: S_uberis_strain_FSL Z1-048

description:
test strain supplementary file names: D2S1H3.gpr (array 4) D2S3H2.gpr (array 2)
reference strain supplementary file names: D2S1H1.gpr (array 3) D2S1H3.gpr (array 2) D2S2H1.gpr (array 2) D2S3H1.gpr (array 4)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4887


title: S_uberis_strain_FSL Z1-124

description:
test strain supplementary file names: S3H4.gpr (array 1) S6H1.gpr (array 4)
reference strain supplementary file names: S3H2.gpr (array 3) S3H3.gpr (array 4) S3H4.gpr (array 2) S4H1.gpr (array 3) S5H1.gpr (array 4) S7H1.gpr (array 3) S7H4.gpr (array 3)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4231


title: S_uberis_strain_FSL Z1-390

description:
test strain supplementary file names: S3H3.gpr (array 3) S3H4.gpr (array 4)
reference strain supplementary file names: S3H2.gpr (array 3) S3H3.gpr (array 4) S3H4.gpr (array 2) S4H1.gpr (array 3) S5H1.gpr (array 4) S7H1.gpr (array 3) S7H4.gpr (array 3)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4231


title: S_uberis_strain_QMP B5-104

description:
test strain supplementary file names: S4H4.gpr (array 1) S5H3.gpr (array 3)
reference strain supplementary file names: S3H2.gpr (array 3) S3H3.gpr (array 4) S3H4.gpr (array 2) S4H1.gpr (array 3) S5H1.gpr (array 4) S7H1.gpr (array 3) S7H4.gpr (array 3)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4231


title: S_uberis_strain_FSL Z1-048

description:
test strain supplementary file names: S4H4.gpr (array 2) S5H1.gpr (array 3)
reference strain supplementary file names: S3H2.gpr (array 3) S3H3.gpr (array 4) S3H4.gpr (array 2) S4H1.gpr (array 3) S5H1.gpr (array 4) S7H1.gpr (array 3) S7H4.gpr (array 3)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4231


title: S_uberis_strain_FSL Z3-343

description:
test strain supplementary file names: S4H1.gpr (array 2) S5H4.gpr (array 3)
reference strain supplementary file names: S3H2.gpr (array 3) S3H3.gpr (array 4) S3H4.gpr (array 2) S4H1.gpr (array 3) S5H1.gpr (array 4) S7H1.gpr (array 3) S7H4.gpr (array 3)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4231


title: S_uberis_strain_QMP B5-005

description:
test strain supplementary file names: S4H2.gpr (array 1) S5H3.gpr (array 4)
reference strain supplementary file names: S3H2.gpr (array 3) S3H3.gpr (array 4) S3H4.gpr (array 2) S4H1.gpr (array 3) S5H1.gpr (array 4) S7H1.gpr (array 3) S7H4.gpr (array 3)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4231


title: S_uberis_strain_FSL Z3-329

description:
test strain supplementary file names: S4H1.gpr (array 1) S5H4.gpr (array 4)
reference strain supplementary file names: S3H2.gpr (array 3) S3H3.gpr (array 4) S3H4.gpr (array 2) S4H1.gpr (array 3) S5H1.gpr (array 4) S7H1.gpr (array 3) S7H4.gpr (array 3)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4231


title: S_uberis_strain_FSL S3-314

description:
test strain supplementary file names: S4H3.gpr (array 1) S5H2.gpr (array 4)
reference strain supplementary file names: S3H2.gpr (array 3) S3H3.gpr (array 4) S3H4.gpr (array 2) S4H1.gpr (array 3) S5H1.gpr (array 4) S7H1.gpr (array 3) S7H4.gpr (array 3)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4231


title: S_uberis_strain_QMP B5-001

description:
test strain supplementary file names: S3H3.gpr (array 1) S3H4.gpr (array 3)
reference strain supplementary file names: S3H2.gpr (array 3) S3H3.gpr (array 4) S3H4.gpr (array 2) S4H1.gpr (array 3) S5H1.gpr (array 4) S7H1.gpr (array 3) S7H4.gpr (array 3)
Array numbers of referenced GPR files (array 1, array 2, array 3, array 4) can be found in the referenced platform's full_array.txt.gz file, CombiMatrixdesign #4231


title: Response to ZA 60min

status: Public on Sep 01 2009

city: Toulouse

first: Serguei

last: Sokol

address: 135 av de Rangueil

department: Lab. Biotech. and Bioprocess

institute: INSA

description:
Yeast cells were cultivated in YPD medium at 28°C to OD600 1.0. Then they were diluted to an initial OD600 0.05 and grown until OD600 0.2.
The culture was then quickly divided in several parts. One part was allowed to grow under the same conditions (control), while others were treated with the various concentrations of the appropriate drugs. After indicated times, yeast cells were collected by centrifugation, rapidly frozen in a liquid nitrogen and kept at -80°C until use.

hyb_protocol: Prehybridisation was performed with solution of 1% BSA, 2 ×SSC, 0.2% (v/v) SDS over 1hour at 42°C. After automatic washing according to manufacturer’s instructions, the slides were hybridised for 10 h in 200 µl of ChipHybeTM buffer (Ventana Medical System, Inc). After hybridisation, the slides were washed for 2 min in 2 ×SSC/0.2% (v/v) SDS, for 2 min in 0.2 ×SSC/0.2% (v/v) SDS and for 2 min in 0.2 ×SSC, immersed briefly in isopropanol and then dried under a stream of air.

scan_protocol: The hybridization signal was detected by scanning with GenePix 4000B laser Scanner (Axon Instruments)

data_processing:
the signal quantification was transformed to numerical values using the integrated GenePix software version 3.01.
The raw intensities were corrected from the local background measured around each spot. The mean expression value of a whole genome was considered as a reference for noralisation.  First step in averaging was to calculate the mean value over spot duplicates for a given gene on the same array and then an average on both arrays was calculated. Log-ratios of normalized intensities from duplicate samples were tested for statistical significance using Student’s test.

organism: Saccharomyces cerevisiae

source_name: yeast culture

label_protocol: Incorporation of Cyanine 3- or Cyanine 5-dCTP (Amersham Bioscience) was performed during reverse transcription of 20 µg of denaturated RNA using Label Star Reverse Transcriptase (Qiagen). Labeled cDNA was purified with MinElute spin columns (Qiagen).

extract_protocol: Frozen cells (10 units of OD600) were mechanically disrupted (MicroDismembrator Braun, Melsungen) and total RNA was isolated using RNeasy Mini kit (Qiagen) following the protocol of the manufacturer.

tag: Strain

tag: treatment

tag: incubation

value: zaragozic acid 10µg/mL


title: Response to Lo 60min

value: lovastatin 25µg/mL


title: Response to ZA 10min


title: Response to ZA 30min


title: Response to Lo 30min

tag: yeast culture


title: TKO EB (7-4-1)

city: Stanford

first: Julien

last: Sage

state: CA

address: 265 Campus Drive

department: Pediatrics and Genetics

institute: Stanford

hyb_protocol: The RNA was hybridized according to manufacturer’s protocol (Affymetrix).

scan_protocol: The sample was scanned according to manufacturer’s protocol (Affymetrix).

data_processing: The Invariant Set Normalization method was used to normalize the arrays using dChip software.

label_protocol: The RNA was labeled according to manufacturer’s protocol (Affymetrix).

extract_protocol: Total RNA was extracted with Trizol (Invitrogen)

tag: This sample is Rb family triple knock-out (TKO) mouse differentiated embryoid bodies (EB).


title: TKO EB (Dutch)

source_name: TKO EB (Dutch)


title: TKO EB (Ta1-12)

source_name: TKO EB (Ta1-12)


title: TKO ESC (Ta1-12)

source_name: TKO ESC (Ta1-12)

tag: This sample is Rb family triple knock-out (TKO) mouse embryonic stem cells (ESC).


title: TKO ESC (7-4-1)


title: TKO ESC (Dutch)

source_name: TKO ESC (Dutch)


title: Response to Lo 10min

data_processing:
the signal quantification was transformed to numerical values using the integrated GenePix software version 3.01.
The raw intensities were corrected from the local background measured around each spot. The mean expression value of a whole genome was considered as a reference for normalisation.  First step in averaging was to calculate the mean value over spot duplicates for a given gene on the same array and then an average on both arrays was calculated. Log10-ratios of normalized intensities from duplicate samples were tested for statistical significance using Student’s test.


title: 0320-b5

city: beijing

first: guangyuan

last: song

address: 167 BeiLiShi Rd, Beijing

department: Center of Coronary Heart Disease

country: China

institute: Cardiovascular Institute & Fu-Wai Hospital

description: According to previous studies, we used the sample pooling strategies for microarray analysis in order to reduce the whole cost of the study. 3 samples were randomly chosen from each time point, and then total RNA was isolated from the frozen tissue fragments using  TRIzol (Invitrogen). After the ethanol precipitation step in the TRIzol extraction procedure, we performed a cleanup using the QIAGEN RNeasy Mini Kit. The RNA fractions from the three rats in each group at the time point were balanced pooled for GeneChip analysis.

data_processing:
Algorithm: Expression Console PLIER, available at manufacturer's web site
www.affymetrix.com

label: biotin

organism: Rattus norvegicus

source_name: myocardium, the remote zone tissues of left ventricular free wall, STZ

growth_protocol: When the rats is 8 weeks old, STZ 65mg/kg, single intraperitoneal injection, then they were raised without blood sugar control for 10 weeks before the ligation of left anterior descending coronary artery, and then they were again raised without blood sugar control for 8 weeks after the ligation before sacrifice.

treatment_protocol: When the rats is 8 weeks old, STZ 65mg/kg, single intraperitoneal injection, then they were raised without blood sugar control for 10 weeks before the ligation of left anterior descending coronary artery.

value: Sprague-Dawley rats

tag: Gender

value: male

tag: Age

value: 26 weeks

tag: Tissue

value: myocardium, the remote zone tissues of left ventricular free wall post AMI


title: 0320-08

description: According to previous studies, we used the sample pooling strategies for microarray analysis in order to reduce the whole cost of the study. 3 samples were randomly chosen from each time point, and then total RNA was isolated from the frozen tissue fragments using TRIzol (Invitrogen). After the ethanol precipitation step in the TRIzol extraction procedure, we performed a cleanup using the QIAGEN RNeasy Mini Kit.The RNA fractions from the three rats in each group at the time point were balanced pooled for GeneChip analysis.

data_processing:
Algorithm: Expression Console PLIER, available at manufacturers's web site
www.affymetrix.com

growth_protocol: When the rats is 8 weeks old, STZ 65mg/kg, single intraperitoneal injection, then they were raised without blood sugar control for 10 weeks before the ligation of left anterior descending coronary artery, and then they were again raised without blood sugar control for 24h after the ligation before sacrifice.

extract_protocol:
available at manufacturer's web site
www.affymetrix.com

value: 18 weeks


title: 0320-b16

hyb_protocol: available at manufacturers's web site www.affymetrix.com

source_name: myocardium, the remote zone tissues of left ventricular free wall, sodium citrate buffer

growth_protocol: When the rats is 8 weeks old, the same dose of sodium citrate buffer, single intraperitoneal injection, then they were raised without blood sugar control for 10 weeks before the ligation of left anterior descending coronary artery, and then they were again raised without blood sugar control for 8 weeks after the ligation before sacrifice.

treatment_protocol: When the rats is 8 weeks old, the same dose of sodium citrate buffer, single intraperitoneal injection, then they were raised without blood sugar control for 10 weeks before the ligation of left anterior descending coronary artery.

value: 22 weeks


title: 0320-DMA

data_processing:
Algorithm: Expression Console PLIER available at manufacturer's web site
www.affymetrix.com

growth_protocol: When the rats is 8 weeks old, STZ 65mg/kg, single intraperitoneal injection, then they were raised without blood sugar control for 10 weeks before the sham operation, and then they were sacrificed for microarray analysis.

treatment_protocol: When the rats is 8 weeks old, STZ 65mg/kg, single intraperitoneal injection, then they were raised without blood sugar control for 10 weeks before the sham operation.


title: WT ESC (R1)

source_name: WT ESC (R1)

tag: This sample is wildtype (WT) mouse embryonic stem cells (ESC).


title: 0320-29

scan_protocol: available at manufacturers's web site www.affymetrix.com

growth_protocol: When the rats is 8 weeks old, STZ 65mg/kg, single intraperitoneal injection, then they were raised without blood sugar control for 10 weeks before the ligation of left anterior descending coronary artery, and then they were again raised without blood sugar control for 1 weeks after the ligation before sacrifice.

value: 19 weeks


title: 0320-CA

label_protocol:
available at manufacturers's web site
www.affymetrix.com

growth_protocol: When the rats is 8 weeks old, the same dose of sodium citrate buffer, single intraperitoneal injection, then they were raised without blood sugar control for 10 weeks before the sham operation, and then they were sacrificed for microarray analysis.

treatment_protocol: When the rats is 8 weeks old, the same dose of sodium citrate buffer, single intraperitoneal injection, then they were raised without blood sugar control for 10 weeks before the sham operation.


title: 0320-16

description: According to previous studies, we used the sample pooling strategies for microarray analysis in order to reduce the whole cost of the study. 3 samples were randomly chosen from each time point, and then total RNA was isolated from the frozen tissue fragments using  TRIzol (Invitrogen). After the ethanol precipitation step in the TRIzol extraction procedure, we performed a cleanup using the QIAGEN RNeasy Mini Kit.The RNA fractions from the three rats in each group at the time point were balanced pooled for GeneChip analysis.

growth_protocol: When the rats is 8 weeks old, the same dose of sodium citrate buffer, single intraperitoneal injection, then they were raised without blood sugar control for 10 weeks before the ligation of left anterior descending coronary artery, and then they were again raised without blood sugar control for 24h after the ligation before sacrifice.

extract_protocol:
available at manufacturers's web site
www.affymetrix.com


title: WT EB (R1)

source_name: WT EB (R1)

tag: This sample is wildtype (WT) mouse differentiated embryoid bodies (EB).


title: 0320-35

growth_protocol: When the rats is 8 weeks old, the same dose of sodium citrate buffer, single intraperitoneal injection, then they were raised without blood sugar control for 10 weeks before the ligation of left anterior descending coronary artery, and then they were again raised without blood sugar control for 1 weeks after the ligation before sacrifice.


title: WT ESC (J1)

source_name: WT ESC (J1)


title: WT ESC (B21)

source_name: WT ESC (B21)


title: WT EB (J1)

source_name: WT EB (J1)


title: 0320-a38

hyb_protocol: available at manufacturer's web site www.affymetrix.com

growth_protocol: When the rats is 8 weeks old, the same dose of sodium citrate buffer, single intraperitoneal injection, then they were raised without blood sugar control for 10 weeks before the ligation of left anterior descending coronary artery, and then they were again raised without blood sugar control for 4 weeks after the ligation before sacrifice.


title: control_non_infected

status: Public on Aug 31 2009

type: protein

city: Rochester

first: Kenneth

middle: L.

last: Johnson

state: MN

address: 200 First Street S.W.

institute: Mayo Clinic

data_processing: Extract_msn (Bioworks 3.2) was used to create dta files, all dta files from within each LC-MS/MS data file were concatenated and converted to mgf format.  Each mgf file was searched against the human, bovine, vaccinia excerpt from Jan. 2007 SwissProt database.  The search database also contained appended entries for common contaminants (keratins and trypsin) and randomized decoy entries.  Searched using Sequest, Mascot, and X!Tandem search engines.  Precursor Tol.=7 ppm, Fragment tol.= 0.6 Da, no enzyme specificity.  Database contained 46000 entries, including the decoy proteins.  Search results from each LC-MS/MS analysis were combined using Scaffold into one common report.  Score thresholds for positive identification were established by calculating a false positive rate (FPR) by the formula; ((# matches to decoy peptide x 2) / total number of matches).

molecule: protein

organism:
Homo sapiens
Bos taurus

source_name: human B cells

growth_protocol: Epstein-Barr virus (EBV)-transformed B cells (European Collection of Cell Cultures - ECACC number 86052111, Salisbury, Wiltshire, UK), homozygous for HLA-A*0201, -B*1501, and -C*03, were of human origin and used as antigen presenting cells.  The New York City Board of Health (NYCBOH) vaccine-strain of vaccinia virus (Dryvax) was cultured in HeLa cells in Dulbecco's modified Eagles's medium, supplemented with 5% fetal calf serum (FCS).

extract_protocol:
Class I HLA molecules were purified from B cell lysates by immunoaffinity.  Cells were lysed with a buffer of 20 mM Tris, pH 8.0, 150 mM NaCl, 1% CHAPS, and 1 mM Pefabloc.  The clarified supernatants were passed over a column of monoclonal antibody (W6/32, specific to HLA-A, -B, and -C alleles) bound to protein A-Sepharose.  The HLA/peptide complexes were eluted from the column and the complexes disrupted with 0.2 N acetic acid, pH 2.7.  Peptides were separated from the HLA molecules by ultrafiltration with a 10kDa molecular mass cutoff filter.

Digestion protocol:
No digestion; these are naturally processed peptides

Separation method:
The peptide pool was first desalted on a 1mm by 10mm reversed phase cartridge.  Peptides were then fractionated using off-line strong cation exchange (SCX), followed by multiple 1D-LC-MS/MS injections from each SCX fraction.  SCX separations were done on a Polysulfoethyl-aspartamide cartridge column, using a gradient of 5mM potassium phosphate, pH 3.0, into 0.4 M KCl in 5 mM potassium phosphate.  Each mobile phase contained 20% acetonitrile.  2 minute fractions were collected and vacuum centrifuged to dryness. nLC-MS/MS used a 15cm by 75um C18 column, 2%-40%B over 60 min., then to 95%B over the next 10 min.  Mob. phase A= water/acetonitrile/formic acid, 98/2/0.2 by volume, and mob. phase B= acetonitrile/water/formic acid, 90/10/0.2 by volume.

Mass Spectrometer:
LTQ-Orbitrap; 60,000 RP survey scan, followed by top 5 LTQ CAD MS/MS; 2-3 injections per fraction: singly charged precursors from m/z 750-1500, and doubly or triply charged ions from m/z 375-750, precursor dynamic exclusion=45s.

treatment_protocol: Cells were infected with live vaccinia virus at a multiplicity of infection (moi) of 0.1 plaque-forming-units/cell for two hours and were further maintained for 24-30 hours in RPMI-1640 supplemented with 8% FCS.  Approximately 1x109 cells were pooled and lysed for purification of the HLA/class I peptide complexes.

tag: B cells not infected with vaccinia virus


title: instrument_blanks

description: Since the analyses are a series of SCX fractions from the same peptide preparations, the blanks serve to demonstrate the amount of carryover, but have essentially no effect on conclusions regarding the results, since subsequent analyses are of different fractions from the same sample.

organism:
Homo sapiens
Bos taurus
Orthopoxvirus vaccinia

tag: instrument carryover


title: 0320-A26

growth_protocol: When the rats is 8 weeks old, STZ 65mg/kg, single intraperitoneal injection, then they were raised without blood sugar control for 10 weeks before the ligation of left anterior descending coronary artery, and then they were again raised without blood sugar control for 4 weeks after the ligation before sacrifice.


title: vaccinia_virus_infected

description: Note that vaccinia-infected B cells will still continue to present (primarily) a wide variety of peptides originating from endogenous proteins; this data set contains evidence for more than 5000 peptides.  The challenge is in detecting and identifying the peptides that originate from the pathogen (vaccinia virus) in the presence (background) of this large number of endogensous 'self' peptides.

organism:
Homo sapiens
Orthopoxvirus vaccinia

extract_protocol:
Class I HLA molecules were purified from B cell lysates by immunoaffinity.  Cells were lysed with a buffer of 20 mM Tris, pH 8.0, 150 mM NaCl, 1% CHAPS, and 1 mM Pefabloc.  The clarified supernatants were passed over a column of monoclonal antibody (W6/32, specific to HLA-A, -B, and -C alleles) bound to protein A-Sepharose.  The HLA/peptide complexes were eluted from the column and the complexes disrupted with 0.2 N acetic acid, pH 2.7.  Peptides were separated from the HLA molecules by ultrafiltration with a 10kDa molecular mass cutoff filter.
Digestion protocol:
No digestion; these are naturally processed peptides
Separation method:
The peptide pool was first desalted on a 1mm by 10mm reversed phase cartridge.  Peptides were then fractionated using off-line strong cation exchange (SCX), followed by multiple 1D-LC-MS/MS injections from each SCX fraction.  SCX separations were done on a Polysulfoethyl-aspartamide cartridge column, using a gradient of 5mM potassium phosphate, pH 3.0, into 0.4 M KCl in 5 mM potassium phosphate.  Each mobile phase contained 20% acetonitrile.  2 minute fractions were collected and vacuum centrifuged to dryness. nLC-MS/MS used a 15cm by 75um C18 column, 2%-40%B over 60 min., then to 95%B over the next 10 min.  Mob. phase A= water/acetonitrile/formic acid, 98/2/0.2 by volume, and mob. phase B= acetonitrile/water/formic acid, 90/10/0.2 by volume.
Mass Spectrometer:
LTQ-Orbitrap; 60,000 RP survey scan, followed by top 5 LTQ CAD MS/MS; 2-3 injections per fraction: singly charged precursors from m/z 750-1500, and doubly or triply charged ions from m/z 375-750, precursor dynamic exclusion=45s.

tag: human B cells infected with vaccinia virus


title: 0320-a20

scan_protocol: available at manufacturer's web site www.affymetrix.com

growth_protocol: When the rats is 8 weeks old, STZ 65mg/kg, single intraperitoneal injection, then they were raised without blood sugar control for 10 weeks before the ligation of left anterior descending coronary artery, and then they were again raised without blood sugar control for 2 weeks after the ligation before sacrifice.

value: 20 weeks


title: 0320-a7

growth_protocol: When the rats is 8 weeks old, the same dose of sodium citrate buffer, single intraperitoneal injection, then they were raised without blood sugar control for 10 weeks before the ligation of left anterior descending coronary artery, and then they were again raised without blood sugar control for 2 weeks after the ligation before sacrifice.


title: Glucose-limited chemostat in presence of ADA strain DS17690 -3

status: Public on Aug 01 2009

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

hyb_protocol: Probe preparation and Target hybridization Double stranded cDNA synthesis was carried out using 10 ug of total RNA and the components of the One Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, USA). The double-stranded cDNA was purified with the GeneChip® Sample Cleanup Module (Affymetrix/Qiagen) followed by in vitro transcription and labeling using the GeneChip® IVT labeling Kit (Affymetrix). Finally, labeled cRNA was purified (GeneChip® Sample Cleanup Module, Affymetrix/Qiagen) prior to fragmentation. 15 µg of fragmented, biotinylated cRNA was hybridized to the P. chrysogenum MicroArrays (a proprietary GeneChip®, DSM_PENa520255F) at 45 °C for 16 h as described in the Affymetrix users' manual. Washing and staining of arrays were performed using the GeneChip® Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner 3000.

data_processing: Data analysis Acquisition and quantification of array images were performed using Affymetrix GeneChip® Operating Software (GCOS version 1.2). CHP file targeted at 100.

label: SAPE (Streptavidin Phycoerythrin)

organism: Penicillium chrysogenum

source_name: Chemostat culture

growth_protocol:
Chemostat cultivation Aerobic glucose-limited chemostat cultivation was performed at 25 °C in 3 - L turbine stirred bioreactors (Applikon, Schiedam, The Netherlands) with a working volume of 1.8 L. The pH was maintained at 6.5 via automated addition of 2 M NaOH (ADI 1030 biocontroller, Applikon, Schiedam, The Netherlands). The fermenter was sparged with air at a flow rate of 0.9 L•min-1 using a Brooks mass-flow controller (Brooks Instruments, Hatfield, USA) and stirred at 750 rpm. The dissolved-oxygen concentration was continuously monitored with an oxygen electrode (Applisens, Schiedam, The Netherlands). Continuous cultivation was initiated after 50-60 hours of batch cultivation. The feed medium was supplied continuously by a peristaltic pump (Masterflex, Cole Parmer, USA) and the dilution rate was set at 0.03 h-1 for all chemostat experiments. Effluent was removed discontinuously by means of a special overflow device, which has been described previously (Harris, D.M., et al. Enzymic analysis of NADPH metabolism in Penicillium chrysogenum: presence of a mitochondrial NADPH dehydrogenase in beta-lactam-producing cultures. Metab. Eng. 8, 91-101 (2006)). The time interval between effluent removals was fixed in such a way that each time approximately 1 % of the culture volume was removed. To prevent excessive foaming, silicone antifoam (10 % vol/vol, BDH) was discontinuously added at timed intervals.
Media The mineral medium was set at pH 5.5 with KOH pellets and contained per liter of demineralised water 7.5 g glucose, 3.5 g (NH4)2SO4, 0.8 g KH2PO4, 0.5 g MgSO4•7H2O, 10 mL of a trace element solution. The trace element solution contained 15 g•L-1 Na2EDTA•2H2O, 0.5 g•L-1 Cu2SO4•5H2O, 2 g•L-1 ZnSO4•7H2O, 2 g•L-1 MnSO4•H2O, 4 g•L-1 FeSO4•7H2O, and 0.5 g•L-1 CaCl2•2H2O and was set at pH 6.0 by adding NaOH pellets. Glucose was heat-sterilized separately (110 °C) and added to the medium in a concentration of 7.5 g•L-1. After filter sterilization and during the chemostat experiments the medium vessel was mixed continuously by a magnetic stirrer.
Production of ad6APA was induced by adding 5.0 g•L-1 adipic acid (ADA) to the medium

extract_protocol: Sampling and RNA extraction procedures 60 mL of culture broth was sampled and rapidly filtered over a glass fiber filter (Type A/E, Pall Life Sciences, East Hills, USA). The filter with mycelium was wrapped in aluminum foil, quenched in liquid nitrogen and subsequently stored at -80 °C until further use. For total RNA extraction half of the pellet was grounded by mortar and pestle under constant cooling with liquid nitrogen. The powder was dissolved in 5 mL of Trizol reagent (Invitrogen) and 1 mL chloroform (Sigma) and mixed well. The two phases were separated by centrifugation (4600 g, 15 minutes). Total RNA was isolated using a phenol-chloroform extraction method, which consisted of two extraction steps in acid-phenol/chloroform/isoamyl alcohol (5:1, pH 4.8, Ambion), followed by a chloroform extraction step. Each time the phases were separated by centrifugation (4600 g, 15 minutes). Total RNA was precipitated for 30 minutes at -20°C in 96% ethanol and 0.3 M sodium acetate. The RNA was collected by centrifugation at 23000 g for 15 minutes and dissolved in RNAse free H2O.

treatment_protocol: Liquid nitrogen quenching

tag: Penicillium chrysogenum DS17690 Penicillin G high producing prototrophic strain (Harris, D.M., et al. Enzymic analysis of NADPH metabolism in Penicillium chrysogenum

value: presence of a mitochondrial NADPH dehydrogenase in beta-lactam-producing cultures. Metab. Eng. 8, 91-101 (2006). DS17690 is derived from the strain improvement program of DSM after several classical mutagenesis rounds and is an offspring of the sequenced Wisconsin 54-1255 strain.


title: ACE1, 24hour palmitate exposure, biol rep 1

status: Public on Jun 05 2009

city: Los Angeles

first: Jason

middle: Thaddeus

last: Dean

address: 420 Westwood Plaza

department: Chemical and Biomolecular Engineering

institute: UCLA

description: Gene expression data from wild type HepG2 cell line after 24 hour 300uM palmiate exposure.

hyb_protocol: 10 ug of fragmented target cRNA was hybridized at 45 degrees C with rotation for 16 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix HG_U133A 2 array. The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The results were quantified and analyzed using GCOS 1.2 software using default values (Scaling, Target Signal Intensity = 500; Normalization, All Probe Sets; Parameters, all set at default values).

source_name: Human hepatocyte HepG2 cell line, stably transfected with pBudaceAB

label_protocol: 15ug of  biotin-tagged cRNA was fragmented to an average strand length of 100 bases (range 35-200 bases) following prescribed protocols.

growth_protocol: pBudaceAB transfected HepG2 cell line grown in DMEM augmented with 300uM palmitate.

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

treatment_protocol: Cells were plated in 10cm plate at 70% confluency.  Cells were washed with PBS and then given DMEM augmented with 300uM palmitate for 24 hours, at which point total RNA was harvested.

tag: HepG2 cell line stably transfected with pBudaceAB

tag: Experiments done before pasage 10


title: male vs 72hrs - Replicate 2

status: Public on Jun 01 2009

city: Cambridge

first: Dean

last: Baker

address: Department of Genetics, Downing Street

country: United Kingdom

institute: University of Cambridge

description: Gene Expression during the Egg Development of Drosophila melanogaster.

hyb_protocol: Genomics Solution GeneTAC hybridisation station with Ocimum hybridisation buffer. Hybridisation and washing described in detail at http://www.flychip.org.uk/protocols/hybridisation/hyb_oligoMWG.php

scan_protocol: Axon 4000B scanner using standard protocols (http://www.flychip.org.uk/protocols/imaging/scanning2.php)

data_processing: Spot finding and quantitation via the Dapple package. Normalization of M-values within each slides using the print-tip loess method and between all slides using quantile normalization of intensity values.

organism: Drosophila melanogaster

source_name: male

label_protocol: Standard Klenow labelling of double stranded DNA (http://www.flychip.org.uk/protocols/gene_expression/klenow.php) using 3 to 5 microgrammes of total RNA.

extract_protocol: 10 adult abdomens were dissected and transferred into an eppendorf tube containing 600ul TRIzol. Tissues were stored at -80 C until homogenization and RNA extraction.

tag: total RNA from adult abdomens


title: WT EB (B21)

source_name: WT EB (B21)


title: WT1, 24hour palmitate exposure, biol rep 1

source_name: Human hepatocyte HepG2 cell line

growth_protocol: Wild type HepG2 cell line grown in DMEM augmented with 300uM palmitate.

tag: Wild type HepG2 cell line


title: 48hrs vs 24hrs - Replicate 2


title: Glucose-limited chemostat in presence of ADA strain DS17690 -1

scan_protocol: Probe preparation and Target hybridization Double stranded cDNA synthesis was carried out using 10 ug of total RNA and the components of the One Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, USA). The double-stranded cDNA was purified with the GeneChip® Sample Cleanup Module (Affymetrix/Qiagen) followed by in vitro transcription and labeling using the GeneChip® IVT labeling Kit (Affymetrix). Finally, labeled cRNA was purified (GeneChip® Sample Cleanup Module, Affymetrix/Qiagen) prior to fragmentation. 15 µg of fragmented, biotinylated cRNA was hybridized to the P. chrysogenum MicroArrays (a proprietary GeneChip®, DSM_PENa520255F) at 45 °C for 16 h as described in the Affymetrix users' manual. Washing and staining of arrays were performed using the GeneChip® Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner 3000.


title: female vs male - Replicate 2

source_name: female


title: WT2, 24hour palmitate exposure, biol rep 2


title: TKO EB (2-55-2)


title: TKO EB (14-14-4)


title: 24hrs vs Diapause - Replicate 2

source_name: Diapause


title: male vs female


title: ACE2, 24hour palmitate exposure, biol rep 2


title: male vs female - Replicate 2


title: 48hrs vs 72hrs - Replicate 2


title: 72hrs vs male - Replicate 2


title: Diapause vs female - Replicate 2


title: 48hrs vs 72hrs


title: Glucose-limited chemostat in presence of ADA strain DS17690 -2

label_protocol: Probe preparation and Target hybridization Double stranded cDNA synthesis was carried out using 10 ug of total RNA and the components of the One Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, USA). The double-stranded cDNA was purified with the GeneChip® Sample Cleanup Module (Affymetrix/Qiagen) followed by in vitro transcription and labeling using the GeneChip® IVT labeling Kit (Affymetrix). Finally, labeled cRNA was purified (GeneChip® Sample Cleanup Module, Affymetrix/Qiagen) prior to fragmentation. 15 µg of fragmented, biotinylated cRNA was hybridized to the P. chrysogenum  MicroArrays (a proprietary GeneChip®, DSM_PENa520255F) at 45 °C for 16 h as described in the Affymetrix users' manual. Washing and staining of arrays were performed using the GeneChip® Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner 3000.


title: 24hrs vs 48hrs - Replicate 2


title: Diapause vs 24hrs - Replicate 2


title: 72hrs vs 48hrs - Replicate 2


title: Diapause vs 24hrs


title: 48hrs vs 24hrs


title: female vs male


title: 24hrs vs 48hrs


title: female vs Diapause - Replicate 2


title: 24hrs vs Diapause


title: 72hrs vs 48hrs


title: 72hrs vs male


title: EL4_CHX_unstim_rep3

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

country: Australia

institute: University of Canberra

description: Unstimulated, CHX treated EL4 cells

hyb_protocol: As per standard Affymetrix protocol for the Mouse 1.0ST arrays.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing: Quantile normalisation and Robust Multichip Average (RMA) background correction adjusting for probe sequence (Partek Software) was used to generate gene expression levels from the Mouse Gene 1.0ST arrays.

source_name: Unstimulated, CHX treated EL4 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol for the Mouse 1.0ST arrays from 100ng total RNA.

growth_protocol: EL-4 were cultured in RPMI 1640 medium with 10 mM HEPES, 10% fetal calf serum (FCS; CSL, Australia), 120 microg/ml penicillin, and 16 microg/ml gentamycin.

extract_protocol: Total RNA was isolated using TRI-reagent as per manufacturers instructions

treatment_protocol: EL4 cells were pre-treated with either 10microg/mL cycloheximide (CHX) in DMSO or DMSO for 30 min and stimulated with PMA (10 ng/ml phorbol myristate acetate) and Ionomcyin (1 microM) for 0h or 4h

tag: Treatment

value: Cycloheximide

value: Unstimulated

tag: cell line


title: EL4_DMSO_PMAIoM_rep3

description: 4h Stimulated, DMSO treated EL4 cells

source_name: 4h PMA/IoM Stimulated, DMSO treated EL4 cells

value: DMSO

value: PMA and Ionomycin


title: EL4_CHX_PMAIoM_rep3

description: 4h Stimulated, CHX treated EL4 cells

source_name: 4h PMA/IoM Stimulated, CHX treated EL4 cells


title: Lens_c57 Wild Type_10 days_rep2

status: Public on May 01 2009

city: Chicago

first: Nalin

last: Kumar

state: IL

address: 1855 West Taylor Street

department: Ophthalmology and Visual Sciences

institute: University of Illinois at Chicago

description: Lens_c57 Wild Type_10 days_rep2

hyb_protocol: Hybridized to Mu74Av2 gene chips (Affymetrix, Santa Clara, CA) according to the manufacturer�s instructions.

scan_protocol: Scanned on a chip reader (Affymetrix, Santa Clara, CA). Affymetrix Microarray Suite (MS) 5.0 is used for data analysis.

data_processing: MAS5.0, scaled to 500

label: biotin-labeled oligonucleotide

source_name: lens, 10 days old

label_protocol: Total RNA was used for reverse transcription synthesis of double-stranded cDNA with a commercial system (Superscript Choice System; Invitrogen-Gibco, Carlsbad, CA). The purified, double-stranded cDNA was then used for in vitro transcription, incorporating biotin-labeled NTPs with an RNA transcript labeling kit (BioArray High Yield; Enzo Biochem, New York, NY). The cRNA was then purified, fragmented, mixed with manufacturer-supplied control polynucleotides (a biotin-labeled oligonucleotide and four control cRNA sequences)

growth_protocol: Rnase-free medium

extract_protocol: Lens of mice were transferred immediately into extraction reagent (TRIzol, Invitrogen-Gibco, Rockville, MD) on ice, and stored at -80�C. 20-30 lenses from each group were pooled, and total RNA was isolated according to the manufacturer�s protocol. Isolated RNA was further purified with a kit (Rneasy; Qiagen,Valencia, CA). RNA integrity was verified by visualization of the 28S and 18S ribosomal RNA bands.

tag: Strain

value: both

value: 10 days

value: lens


title: EL4_DMSO_PMAIoM_rep1

description: 4h Stimulated, DMSO treated EL4 cells


title: EL4_DMSO_unstim_rep2

description: Unstimulated, DMSO treated EL4 cells

source_name: Unstimulated, DMSO treated EL4 cells


title: EL4_DMSO_unstim_rep3

description: Unstimulated, DMSO treated EL4 cells


title: Lens_c57 alpha3Cx46 Knock out_10 days_rep1


title: male vs 72hrs


title: Lens_129 alpha3Cx46 Knock out_10 days_rep2


title: Lens_129 Wild Type_10 days_rep2

description: Lens_129 Wild Type_10 days_rep2


title: EL4_CHX_PMAIoM_rep2

description: 4h Stimulated, CHX treated EL4 cells


title: EL4_CHX_unstim_rep2

description: Unstimulated, CHX treated EL4 cells


title: Diapause vs female


title: EL4_DMSO_PMAIoM_rep2

description: 4h Stimulated, DMSO treated EL4 cells


title: EL4_CHX_PMAIoM_rep1

description: 4h Stimulated, CHX treated EL4 cells


title: female vs Diapause


title: Pineal_LD_ZT14

city: Tel Aviv

first: Yoav

last: Gothilf

address: Sherman Building, Room 405

department: Neurobiology, Faculty of Life Sciences

country: Israel

institute: Tel Aviv University

description: Gene expression data from zebrafish pineal

hyb_protocol: The target cRNA generated from each sample was fragmented and 15 micogram of the fragmented cRNA was added to the hybridization cocktail which includes in addition to the fragmented target, probe array controls (pre-mixed biotin-labeled bioB, bioC, bioD and cre, in staggered concentrations, ready to be added directly to the hybridization cocktail. These controls facilitate monitoring of the hybridization process for troubleshooting), BSA, and herring sperm DNA. It was then hybridized to the probe array during a 16-hour incubation at 45 deg (C). The array was then washed and stained  on the Affymetrix  fluidic station (using Streptavidin-Phycoerythrin which binds to the biotinylated UTP and CTP incorporated previously in the hybridized cRNA).

scan_protocol: The stained array was scanned on the Affymetrix scanner (450).

data_processing: The GCOS (Gene Operating System) generates the numerical data from the scanned intensities using the MAS 5 software (MicroArray suite 5.0; Affymetrix).

organism: Danio rerio

source_name: pineal at ZT14, 12-h light/12-h dark cycle

label_protocol: Double-strand cDNA was generated from 10-100 ng of mRNA by using a T7-linked oligo(dT) primer (Affymetrix). After second-strand synthesis, in vitro transcription was performed with MEGAscript® T7 Kit (Ambion, Inc.). The cRNA (600ng) was then used for second cycle first-strand cDNA (Affymetrix) by using a T7-linked oligo(dT) primer (Affymetrix). After 2nd cycle - second-strand synthesis, in vitro transcription was again performed; this time biotinylated UTP and CTP (Affymetrix) were incorporated in the cRNA, resulting in approximately 1800-fold amplification of labeled RNA.

growth_protocol: Adult zebrafish were raised in a light- and temperature-controlled recirculation water system under a 12-h light/12-h dark cycle at 28 °C and fed twice a day.

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions (RNeasy, Qiagen).

treatment_protocol: Fish were anesthetized in 1.5 mM Tricane (Sigma) and sacrificed by decapitation, and pineal glands were removed under a fluorescent dissecting microscope. 12 pineal glands were collected and pooled at each time point and at each light condition.

tag: Tg(aanat2:EGFP)Y8 transgenic zebrafish

value: adult (3-6 months)

value: males and females


title: Pineal_LD_ZT10

source_name: pineal at ZT10, 12-h light/12-h dark cycle

tag: Gender


title: Pineal_LD_ZT2b

source_name: pineal at ZT2b, 12-h light/12-h dark cycle

tag: Age


title: Lens_c57 alpha3Cx46 Knock out_10 days_rep2

tag: Tissue


title: Pineal_LD_ZT18

source_name: pineal at ZT18, 12-h light/12-h dark cycle


title: EL4_CHX_unstim_rep1

description: Unstimulated, CHX treated EL4 cells


title: EL4_DMSO_unstim_rep1

description: Unstimulated, DMSO treated EL4 cells


title: Pineal_DD_ZT6

source_name: pineal at ZT6, constant darkness


title: planktonic_stationary_rep3

status: Public on Apr 01 2009

city: Sapporo

first: Akinobu

last: Ito

address: North-13, West-8, Kitaku

department: Graduate School of Engineering

country: Japan

institute: Hokkaido University

description: Planktonic sample

hyb_protocol: The labeled cRNA was fragmented, and 10 µg of the fragmented cRNA was hybridized to E. coli Antisense Genome Array (Affymetrix) For 16 hours at 45ºC according to the Affymetrix protocols.

scan_protocol: Affymetrix protocols

data_processing: Normalization was performed with dchip software using the Invariant Set Normalization method. Sample “At 1” was used as the baseline array.

source_name: planktonic stationary phase in MOPS media with 0.2% glucose

label_protocol: The mRNA was purified from extracted total RNA with MICROBExpressTM (Ambion, Austin, TX) by removing the 16S and 23S ribosomal RNAs. The purified mRNA was polyadenylated with Poly(A) Polymerase (PAP), primed with an oligo(dT) primer bearing a T7 promoter by using MessageAmpTM II-Bacteria (Ambion). The second strand cDNA was synthesized from the obtained first strand cDNA. The cRNA was synthesized from the obtained second strand cDNA and biotin-labeled with GeneChip® Expression 3’-Amplification Reagents for IVT Labeling (Affymetrix, Santa Clara, CA).

growth_protocol: Samples were grown in MOPS minimal media with 0.2% glucose.

extract_protocol: Samples were RNA-stabilized with Qiagen RNAProtect Bacterial Reagent, and total RNA was isolated with Qiagen RNeasy mini kit (Qiagen).

value: Escherichia coli MG1655


title: Lens_129 alpha3Cx46 Knock out_10 days_rep1


title: Pineal_DD_ZT10

source_name: pineal at ZT10, constant darkness


title: biofilm_maturation_rep3

description: Biofilm sample on glass surface

source_name: maturation process during biofilm formation in MOPS media with 0.2% glucose


title: Lens_c57 Wild Type_10 days_rep1

description: Lens_c57 Wild Type_10 days_rep1


title: Pineal_DD_ZT14

source_name: pineal at ZT14, constant darkness


title: Pineal_LD_ZT22

source_name: pineal at ZT22, 12-h light/12-h dark cycle


title: planktonic_stationary_rep1

description: Planktonic sample


title: planktonic_stationary_rep2

description: Planktonic sample


title: Pineal_DD_ZT18

source_name: pineal at ZT18, constant darkness


title: Pineal_DD_ZT22

source_name: pineal at ZT22, constant darkness


title: biofilm_maturation_rep2

description: Biofilm sample on glass surface


title: Lens_129 Wild Type_10 days_rep1

description: Lens_129 Wild Type_10 days_rep1

hyb_protocol: Hybridized to Mu74Av2 gene chips (Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions.

extract_protocol: Lens of mice were transferred immediately into extraction reagent (TRIzol, Invitrogen-Gibco, Rockville, MD) on ice, and stored at -80ºC. 20-30 lenses from each group were pooled, and total RNA was isolated according to the manufacturer’s protocol. Isolated RNA was further purified with a kit (Rneasy; Qiagen,Valencia, CA). RNA integrity was verified by visualization of the 28S and 18S ribosomal RNA bands.


title: Pineal_LD_ZT6

source_name: pineal at ZT6, 12-h light/12-h dark cycle