title: seedling 5, Zhenshan 97, biological rep2

description:
Z16B
Gene expression data of the mixture of seedling of 5, 15, 30, 60 min after hormone KT treatment


title: seedling 4, Zhenshan 97, biological rep2

status: Public on Jan 20 2010

type: RNA

city: Wuhan

first: Weibo

last: Xie

state: Hubei

address: Luoshi Road

department: College of Life Science and Technology

country: China

institute: Huazhong Agricultural University

description:
Z15B
Gene expression data of the mixture of seedling of 5, 15, 30, 60 min after hormone GA3 treatment

hyb_protocol: Microarray hybridization were conducted by the CapitalBio Corporation (Beijing, China) according to the Affymetrix standard protocols (Affymetrix GeneChip Expression Analysis Technical Manual)

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: The probe intensity files (.cel files) for expression profiles were read into R. Background correction, quantile normalization and summarization were performed using the RMA method in Bioconductor affy package.

label: biotin

molecule: total RNA

organism: Oryza sativa Indica Group

source_name: seedling at trefoil stage, treated by GA3, Zhenshan 97

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol.

growth_protocol: Rice seeds were soaked in fresh water until germination. Then the germinated rice seeds were planted in a seed bed in mid-May, and seedling of 20 days old were transplanted to the field and managed according to normal agricultural conditions in the experimental farm of Huazhong Agricultural University, Wuhan, China.

extract_protocol: Total RNA extraction was performed using Trizol, according to the manufacturer's instructions.

treatment_protocol: Untreated.

tag: subspecies

value: indica

tag: variety

value: Zhenshan 97


title: E_2, exon-level analysis

city: Boston

first: Jianlong

last: Sun

state: MA

address: 1 Blackfan Street

department: Hematology/Oncology

country: USA

institute: Boston Children's Hospital

description: Exon RMA expression value derived from Arrayassist software (Stratagene); core-exon analysis; genome build hg18.

hyb_protocol: Hybridization service was provided by Expression Analysis Inc. (Durham, NC).  Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) according to manufacturer's instructions.

scan_protocol: Scan service was provided by Expression Analysis Inc. (Durham, NC) and was performed according to manufacturer's instructions (Affymetrix).

data_processing: The exon array data were analyzed using ArrayAssist (Stratagene) and GeneSpring GX 10 (Agilent) with default settings.  The CEL files were imported and the triplicates from the same siRNA treatment were assigned into the same group.  Probe sets at the Core level were summarized by using the ExonPLIER algorithm.  Quantile normalization was performed and antigenomic probes were used as background probes.  For variance stabilization, the number of 16 was added to probe set intensity values before transformation to a log2 scale.  Once the summarized dataset was obtained, a series of analysis were applied to assess the quality of the samples, hybridization procedures, and actual data. Through these analyses, one of the siNELF-B samples was found to be an outlier, and data from the three arrays of the siNELF-B group were therefore excluded from subsequent analysis.  Probe sets below the noise level was filtered out by the Detection Above Background (DABG) analysis.  A transcript was retained if one of its probe sets had p-value < 0.05 in at least 6 of the remaining 12 arrays.  Gene level expression was estimated with the same algorithm from all probe sets in each transcript.  A splicing index was then calculated for all probe sets using siControl samples as the reference group.  Pairwise analysis was conducted to compare all groups with the siControl reference group using unpaired T test.  Transcripts that were commonly changed in siNELF-A, -C, and –E groups with fold change > 1.5 and p-value < 0.05 were selected as the differentially expressed genes.  And probe sets with absolute value of differential splicing index > 1 and p-value < 0.05 were selected as the alternatively spliced probe sets.  The list of probe sets with significant splicing index was further filtered to retain those with at least two non-overlapping probes and unique hybridization pattern.

organism: Homo sapiens

source_name: breast cancer cell line, siNELF-E

label_protocol: Sample label service was provided by Expression Analysis Inc. (Durham, NC).  1 ug of total RNA from each sample was used to generate labeled probes for array hybridization.  Quality of isolated RNA was first measured by Bioanalyzer QC Assay (Agilent).  Ribosomal RNA was then removed with the RiboMinus Kit (Invitrogen) and the reduction efficiency was verified by capillary electrophoresis.  Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: siRNA transfected T47D cells are grown in DMEM with 10% FBS.

extract_protocol: Total RNA is extracted with Trizol reagent (Invitrogen) following manufacturer's protocol.

treatment_protocol: Transfection of the siRNA duplex into T47D cells was carried out by using RNAiMAX reagent (Invitrogen, Carlsbad, CA) according to manufacturer’s instructions.  Briefly, 1.5 x 10^6 cells in a 10 cm culture dish were transfected with 10 nM of siRNA duplex with 15 ul of RNAiMAX reagent.  Growth medium was replenished 48 hours after transfection, and cells were allowed to grow for additional 48 hours before harvest.

tag: cell line

tag: cell type

value: breast cancer

tag: sirna

value: siNELF-E


title: plumule 2, Zhenshan 97, biological rep1

source_name: plumule, dark, Zhenshan 97


title: C_2, exon-level analysis

source_name: breast cancer cell line, siNELF-C

value: siNELF-C


title: plumule 2, Zhenshan 97, biological rep2


title: 60 min post-1.2uM Mitomycin C 4098316042_F_MMC2_non-BRCA1/2_Pool 2

city: Brisbane

first: Logan

last: Walker

state: QLD

address: PO RBH

country: Australia

institute: Queensland Institute of Medical Research

description: Equal quantities of RNA pooled from 3 samples

hyb_protocol: Standard Illumina protocols were followed for hybridisation, washing and staining of Human-Ref8 V2 Beadchips.

scan_protocol: Slides were scanned with an Illumina Beadarray reader at a factor of 2

data_processing: The data were normalised using quantile normalisation with Beadarray in R

source_name: Lymphoblastoid cell line, 60 min post-1.2uM Mitomycin C

label_protocol: 450 ng of RNA was amplified with the Illumina Totalprep RNA amplification kit (Applied Biosystems)

growth_protocol: lymphoblastoid cell lines were removed from liquid nitrogen and grown for a minimum of 1 week prior to treatment. LCLs were cultered in RPMI 1640 media with 10% serum supreme, and 1% penicillin-streptomycin

extract_protocol: RNA was extracted immediately after the post-treatement culture period using an RNeasy mini kit (Qiagen)

treatment_protocol: 5 hrs prior to treatment, cells were normalised to 500,000 cells/ml. 5 ml cells were untreated, irradiated, or treated with mitomycin C.

tag: gender

value: Female

value: EBV-transformed lymphoblastoid cell line

tag: patient group

value: non-BRCA1/2 mutation

tag: pool number

value: Pool 2

tag: pooled sample #1 mutation

tag: pooled sample #2 mutation

tag: pooled sample #3 mutation

tag: treatment

value: 1.2 uM Mitomycin C

tag: post-treatment culture period

value: 60 min


title: 120 min post-0.4uM Mitomycin C 4098316042_G_MMC3_non-BRCA1/2_Pool 2

source_name: Lymphoblastoid cell line, 120 min post-0.4uM Mitomycin C

value: 0.4 uM Mitomycin C

value: 120 min


title: C_1, exon-level analysis


title: B_3, exon-level analysis

source_name: breast cancer cell line, siNELF-B

value: siNELF-B


title: untreated 4098316042_C_untreated_non-BRCA1/2_Pool 2

source_name: Lymphoblastoid cell line, untreated

value: no treatment


title: germinating seed, Zhenshan 97, biological rep1

source_name: germinating seed, 72 hours after soaking in water, Zhenshan 97


title: 120 min post-1.2uM Mitomycin C 4098316042_H_MMC4_non-BRCA1/2_Pool 2

source_name: Lymphoblastoid cell line, 120 min post-1.2uM Mitomycin C


title: B_2, exon-level analysis


title: callus 8, Zhenshan 97, biological rep1

source_name: callus, 6 h after Agrobacterium infection, Zhenshan 97


title: germinating seed, Zhenshan 97, biological rep2


title: radicle 1, Zhenshan 97, biological rep1

source_name: radicle, light, Zhenshan 97


title: callus 8, Zhenshan 97, biological rep2


title: sheath 1, Zhenshan 97, biological rep2

source_name: mature leaf sheath of the rice plants with developing panicle whose length is less than 1mm, Zhenshan 97


title: panicle 4, Zhenshan 97, biological rep2

source_name: developing panicle with length between 40 and 50mm, Zhenshan 97


title: plumule 1, Zhenshan 97, biological rep1

source_name: plumule, light, Zhenshan 97


title: radicle 1, Zhenshan 97, biological rep2


title: plumule 1, Zhenshan 97, biological rep2


title: 60 min post-0.4uM Mitomycin C 4098316042_E_MMC1_non-BRCA1/2_Pool 2

source_name: Lymphoblastoid cell line, 60 min post-0.4uM Mitomycin C

value: 0.4uM Mitomycin C


title: callus 7, Zhenshan 97, biological rep1

source_name: callus, 1 h after Agrobacterium infection, Zhenshan 97


title: A_3, exon-level analysis

source_name: breast cancer cell line, siNELF-A

value: siNELF-A


title: GL3_3, exon-level analysis

source_name: breast cancer cell line, control

value: siControl against luciferase


title: callus 7, Zhenshan 97, biological rep2

value: indica

value: Zhenshan 97


title: A_2, exon-level analysis

value: breast cancer


title: 60 min post-10 Gy IR 4098316042_D_IR_non-BRCA1/2_Pool 2

source_name: Lymphoblastoid cell line, 60 min post-10 Gy IR

value: 10 Gy gamma radiation


title: A_1, exon-level analysis


title: wt_wt(iso)_rep2

status: Public on May 31 2010

city: Duesseldorf

first: Antje

last: Lindecke

address: Universitaetsstr. 1

department: BMFZ

country: Germany

institute: Universitaet Duesseldorf

hyb_protocol: Hybridization was done in a humidity chamber at 42°C for 16 h. Hybridization buffer contains 50% FA, 5xSSC, 0.1%SDS.

scan_protocol: The GenePix 4000B laser scanner (Axon Inc., USA) was used for visualising fluorescence  signals and the GenePix Pro software (V 6.0) was used to calculate fluorescence intensities.

data_processing: Raw data were intensity dependent normalized using the lowess function in GenePix Acuity4.0

organism: Mus musculus

source_name: heart WT isoproterenol

label_protocol: Labelled cDNA probes were synthesized from 20 µg of total RNA. Reverse transcription was carried out in a 30 µl reaction volume with 0.5 µg oligo-dT18-primer, 10 mM DTT, 20 U RNaseOut, 200 µM of each (dATP, dCTP, dGTP), 80 µM dTTP, 40 µM Cy3-/Cy5-dUTP (Amersham Pharmacia Biosciences, Freiburg, Germany), 200 U of Superscript III (Invitrogen, Karlsruhe, Germany). The labelled cDNA was purified using QIAquick PCR purification columns (Qiagen GmbH, Hilden, Germany) according to manufacturers protocol.

growth_protocol: Mice were kept under conventional conditions and had access to tap water and rodent chow diet ad libitum.

extract_protocol: Total RNA was isolated form heart tissue using the TRIzol reagent (Invitrogen, Karlsruhe, Germany) according to the manufacture’s instruction. Additionally, a cleanup step with the RNeasy Kit (Qiagen GmbH, Hilden, Germany) was performed. The integrity of total RNA was checked by capillary electrophoresis (2100 Bioanalyzer, Agilent Technologies, Inc. Palo Alto, CA,  U.S.A.).

treatment_protocol: The isoproterenol application (4 mg *kg -1 *d -1 ) was done via osmotic minipump over two weeks

tag: strain

value: NMRI

tag: tissue

value: heart

source_name: heart WT vehicle


title: callus 5, Zhenshan 97, biological rep2

source_name: callus, 5 days after regeneration, Zhenshan 97


title: B_1, exon-level analysis

source_name: breast cancer cell line, siNELF-B


title: 120 min post-0.4uM Mitomycin C 4098316058_G_MMC3_non-BRCA1/2_Pool 1

source_name: Lymphoblastoid cell line, 120 min post-0.4uM Mitomycin C

value: Female

value: EBV-transformed lymphoblastoid cell line

value: non-BRCA1/2 mutation

value: Pool 1


title: callus 4, Zhenshan 97, biological rep1

source_name: callus, at screening stage, Zhenshan 97


title: 60 min post-1.2uM Mitomycin C 4098316058_F_MMC2_non-BRCA1/2_Pool 1

source_name: Lymphoblastoid cell line, 60 min post-1.2uM Mitomycin C

value: 1.2 uM Mitomycin C

value: 60 min


title: callus 6, Zhenshan 97, biological rep1

source_name: callus, right before Agrobacterium infection, Zhenshan 97


title: callus 6, Zhenshan 97, biological rep2


title: callus 2, Zhenshan 97, biological rep1

source_name: callus, 15 days after induction at 31℃, Zhenshan 97


title: callus 4, Zhenshan 97, biological rep2


title: untreated 4098316058_C_untreated_non-BRCA1/2_Pool 1

source_name: Lymphoblastoid cell line, untreated


title: 13969146 - col0 light-2 vs det1 light-2

status: Public on May 01 2010

city: Evry

first: Delphine

last: Gey

address: 2 rue Gaston Crémieux

department: URGV

country: France

institute: INRA

description: - Identification of the genes deregulated in det1-1 when seedlings grow in light or in dark (dark increase morphological differences between det1-1 and wild-type) - Expression profile of seedlings grown in dark then exposed to light

hyb_protocol: det1 light-2 Cy5 / col0 light-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

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

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

organism: Arabidopsis thaliana

source_name: det1 light-2

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

growth_protocol: plantlet - MS 1X without sucrose light: 100 micromol/m2/s

extract_protocol: det1 light-2:11.4ug.

treatment_protocol: no treatment

value: col-0 mutant (det1-1)

tag: dev.stage (boyes et al. plant cell 2001)

source_name: col0 light-2

extract_protocol: col0 light-2:11ug.


title: 120 min post-1.2uM Mitomycin C 4098316058_H_MMC4_non-BRCA1/2_Pool 1

source_name: Lymphoblastoid cell line, 120 min post-1.2uM Mitomycin C

value: 120 min


title: callus 3, Zhenshan 97, biological rep2

source_name: callus, 15 days after subculture, Zhenshan 97


title: callus 5, Zhenshan 97, biological rep1


title: callus 2, Zhenshan 97, biological rep2


title: 60 min post-0.4uM Mitomycin C 4098316058_E_MMC1_non-BRCA1/2_Pool 1

source_name: Lymphoblastoid cell line, 60 min post-0.4uM Mitomycin C

value: 0.4uM Mitomycin C


title: callus 1, Zhenshan 97, biological rep2

source_name: callus, 15 days after induction, Zhenshan 97


title: callus 3, Zhenshan 97, biological rep1


title: panicle 3, Minghui 63, biological rep3, technical rep2

source_name: developing panicle with length between 10 and 15 mm, Minghui 63

value: Minghui 63


title: GL3_2, exon-level analysis

source_name: breast cancer cell line, control

value: siControl against luciferase


title: GL3_1, exon-level analysis


title: panicle 3, Minghui 63, biological rep3, technical rep1

value: indica


title: callus 1, Zhenshan 97, biological rep1

value: Zhenshan 97


title: 120 min post-1.2uM Mitomycin C 4098316049_H_MMC4_BRCA2_Pool 3

value: BRCA2 mutation

value: Pool 3


title: untreated 4098316049_C_untreated_BRCA2_Pool 3

value: no treatment


title: panicle 3, Minghui 63, biological rep2, technical rep2


title: panicle 2, Minghui 63, biological rep2, technical rep2

source_name: developing panicle with length between 3 and 5 mm, Minghui 63


title: panicle 3, Minghui 63, biological rep2, technical rep1


title: 60 min post-10 Gy IR 4098316058_D_IR_non-BRCA1/2_Pool 1

source_name: Lymphoblastoid cell line, 60 min post-10 Gy IR

value: 10 Gy gamma radiation


title: 120 min post-0.4uM Mitomycin C 4098316049_G_MMC3_BRCA2_Pool 3

value: Female

value: 0.4 uM Mitomycin C


title: panicle 3, Minghui 63, biological rep1, technical rep2


title: panicle 3, Minghui 63, biological rep1, technical rep1


title: 60 min post-1.2uM Mitomycin C 4098316049_F_MMC2_BRCA2_Pool 3

value: EBV-transformed lymphoblastoid cell line


title: panicle 2, Minghui 63, biological rep1, technical rep2


title: panicle 1, Minghui 63, biological rep3, technical rep2

source_name: developing panicle with length less than 1mm, Minghui 63


title: panicle 2, Minghui 63, biological rep3, technical rep2


title: panicle 2, Minghui 63, biological rep3, technical rep1


title: panicle 1, Minghui 63, biological rep2, technical rep2


title: 60 min post-10 Gy IR 4098316049_D_IR_BRCA2_Pool 3


title: 60 min post-0.4uM Mitomycin C 4098316049_E_MMC1_BRCA2_Pool 3


title: panicle 2, Minghui 63, biological rep2, technical rep1


title: panicle 1, Minghui 63, biological rep3, technical rep1


title: untreated 4098316044_C_untreated_BRCA2_Pool 2

value: Pool 2

value: BRCA2 2000_2003 del TTTA (STOP 612)

value: BRCA2 4365_4369 del GATTA (STOP 1400)


title: panicle 2, Minghui 63, biological rep1, technical rep1


title: panicle 1, Minghui 63, biological rep2, technical rep1


title: panicle 1, Minghui 63, biological rep1, technical rep2


title: sham male wildtype mice replicate 4

city: Berlin

first: Henning

last: Witt

address: Ihnestrasse 65

department: Hans Lehrach

institute: Max Planck Institute for Molecular Genetics

description: Sham operated male wildtype mice.

hyb_protocol: 15 ug of each cRNA sample was hybridized for 16 hours at 45°C to Affymetrix GeneChip arrays. Following the hybridization arrays were washed and stained with streptavidin-phycoerythrin using a fluidics station in accordance with the Affymetrix protocol.

scan_protocol: Affymetrix GeneChip System confocal scanner 2500

data_processing: Analysis of microarray data was performed using the Affymetrix Microarray Suite Version 5.0 software and Data Mining Tool 3.0. For normalization, all array experiments were scaled to a target intensity of 500.

source_name: male, wildtype, sham

label_protocol: The amplification and labeling of the RNA samples were carried out according to the manufacturer's instructions (Affymetrix, Santa Clara, CA). Briefly, total RNA was quantified by UV-spectroscopy and its quality was checked by analysis on a LabChip (BioAnalyzer, AGILENT Technologies, Santa Clara, CA). In the presence of an oligo(dT)24 primer containing a T7 RNA polymerase promoter (TIBMOL Biol, Berlin, Germany) one to three micrograms of total RNA were used for the synthesis of double-stranded cDNA (SuperScript transcriptase, Life Technologies, Inc., Carlsbad, CA). Labeled complementary RNA (cRNA) was prepared from double-stranded cDNA by in vitro transcription using the GeneChip RNA transcript labeling kit (Affymetrix, Santa Clara, CA). After cleanup (Qiagen, Hilden, Germany), the biotin-labeled cRNA was fragmented by alkaline treatment [40 mmol/L Tris-acetate (pH 8.2), 100 mmol//L potassium acetate, and 50 mmol//L magnesium acetate] at 94°C for 35 minutes.

extract_protocol: TRIzol Reagent (Invitrogen), standard protocol

treatment_protocol: sham operated

value: C57Bl6 mice

value: male

tag: age

value: 10 weeks

value: cardiac left ventricle


title: sham male wildtype mice replicate 2

description: Sham operated male wildtype mice.


title: sham male wildtype mice replicate 3

description: Sham operated male wildtype mice.


title: 120 min post-1.2uM Mitomycin C 4098316044_H_MMC4_BRCA2_Pool 2

value: 1.2 uM Mitomycin C

value: 120 min


title: seedling 2, Minghui 63, biological rep3, technical rep2

source_name: seedling at trefoil stage, Minghui 63

tag: subspecies

value: indica

value: Minghui 63


title: sham male wildtype mice replicate 1

description: Sham operated male wildtype mice.


title: seedling 2, Minghui 63, biological rep2, technical rep2

tag: variety


title: seedling 2, Minghui 63, biological rep1, technical rep2


title: sham female wildtype mice replicate 4

description: Sham operated female wildtype mice.

source_name: female, wildtype, sham

value: female


title: seedling 2, Minghui 63, biological rep2, technical rep1


title: 60 min post-1.2uM Mitomycin C 4098316044_F_MMC2_BRCA2_Pool 2

source_name: Lymphoblastoid cell line, 60 min post-1.2uM Mitomycin C

tag: cell line

value: BRCA2 mutation

value: 60 min


title: panicle 1, Minghui 63, biological rep1, technical rep1


title: sham female wildtype mice replicate 3

description: Sham operated female wildtype mice.


title: 60 min post-0.4uM Mitomycin C 4098316044_E_MMC1_BRCA2_Pool 2

value: Female

value: 0.4uM Mitomycin C


title: 120 min post-0.4uM Mitomycin C 4098316044_G_MMC3_BRCA2_Pool 2

source_name: Lymphoblastoid cell line, 120 min post-0.4uM Mitomycin C

value: EBV-transformed lymphoblastoid cell line

value: 0.4 uM Mitomycin C


title: 60 min post-10 Gy IR 4098316044_D_IR_BRCA2_Pool 2

value: Pool 2

value: BRCA2 2000_2003 del TTTA (STOP 612)

value: 10 Gy gamma radiation


title: seedling 2, Minghui 63, biological rep1, technical rep1


title: seedling 2, Minghui 63, biological rep3, technical rep1


title: untreated 4098316051_C_untreated_BRCA2_Pool 1

source_name: Lymphoblastoid cell line, untreated

value: Pool 1

value: no treatment


title: sham female wildtype mice replicate 1

description: Sham operated female wildtype mice.

value: C57Bl6 mice

value: 10 weeks

value: cardiac left ventricle


title: sham female wildtype mice replicate 2

description: Sham operated female wildtype mice.


title: seedling 1, Minghui 63, biological rep3, technical rep2

source_name: seedling, 3 days after sowing, Minghui 63

value: indica


title: 120 min post-1.2uM Mitomycin C 4098316051_H_MMC4_BRCA2_Pool 1

value: 1.2 uM Mitomycin C

value: 120 min


title: hypertrophic male wildtype mice replicate 4

description: Hypertrophy was induced by transverse aortic constriction in male wildtype mice.

source_name: male, wildtype, transverse aortic constriction

treatment_protocol: transverse aortic constriction

value: male


title: seedling 1, Minghui 63, biological rep2, technical rep2

value: Minghui 63


title: seedling 1, Minghui 63, biological rep3, technical rep1


title: seedling 1, Minghui 63, biological rep2, technical rep1


title: leaf 4, Minghui 63, biological rep1

source_name: flag leaf, 14 days after pollination, Minghui 63


title: hypertrophic male wildtype mice replicate 1


title: hypertrophic male wildtype mice replicate 3


title: leaf 4, Minghui 63, biological rep2


title: seedling 1, Minghui 63, biological rep1, technical rep2


title: 60 min post-10 Gy IR 4098316051_D_IR_BRCA2_Pool 1

value: Female

value: BRCA2 mutation

value: 60 min


title: hypertrophic female wildtype mice replicate 4

description: Hypertrophy was induced by transverse aortic constriction in female wildtype mice.

source_name: female, wildtype, transverse aortic constriction

value: female


title: seedling 1, Minghui 63, biological rep1, technical rep1


title: 60 min post-1.2uM Mitomycin C 4098316051_F_MMC2_BRCA2_Pool 1

value: EBV-transformed lymphoblastoid cell line


title: spikelet, Minghui 63, biological rep2

source_name: spikelet, 3 days after flowering, Minghui 63


title: endosperm 1, Minghui 63, biological rep2

source_name: endosperm, 7 days after pollination, Minghui 63


title: endosperm 2, Minghui 63, biological rep1

source_name: endosperm, 14 days after pollination, Minghui 63


title: hypertrophic female wildtype mice replicate 3


title: 120 min post-0.4uM Mitomycin C 4098316051_G_MMC3_BRCA2_Pool 1

value: 0.4 uM Mitomycin C


title: 60 min post-0.4uM Mitomycin C 4098316051_E_MMC1_BRCA2_Pool 1

source_name: Lymphoblastoid cell line, 60 min post-0.4uM Mitomycin C

value: 0.4uM Mitomycin C


title: endosperm 3, Minghui 63, biological rep1

source_name: endosperm, 21 days after pollination, Minghui 63


title: untreated 4098316050_C_untreated_BRCA1_Pool 3

value: BRCA1 mutation

value: Pool 3


title: endosperm 3, Minghui 63, biological rep2


title: hypertrophic female wildtype mice replicate 2

value: C57Bl6 mice


title: endosperm 2, Minghui 63, biological rep2


title: hypertrophic male wildtype mice replicate 2

value: 10 weeks


title: palea/lemma, Minghui 63, biological rep2

source_name: palea/lemma, just before heading date, Minghui 63


title: 120 min post-0.4uM Mitomycin C 4098316050_G_MMC3_BRCA1_Pool 3


title: endosperm 1, Minghui 63, biological rep1


title: stamen, Minghui 63, biological rep1

source_name: stamen, just before heading date, Minghui 63


title: spikelet, Minghui 63, biological rep1


title: hypertrophic female wildtype mice replicate 1

value: cardiac left ventricle


title: stamen, Minghui 63, biological rep2

value: indica


title: sham male estrogen receptor beta knockout mice replicate 4

description: Sham operated male estrogen receptor beta knockout mice.

source_name: male, estrogen receptor beta knockout, sham


title: sham male estrogen receptor beta knockout mice replicate 3


title: panicle 5, Minghui 63, biological rep1

source_name: mature panicle, heading stage, Minghui 63


title: panicle 5, Minghui 63, biological rep2


title: 120 min post-1.2uM Mitomycin C 4098316050_H_MMC4_BRCA1_Pool 3

source_name: Lymphoblastoid cell line, 120 min post-1.2uM Mitomycin C

value: 1.2 uM Mitomycin C


title: palea/lemma, Minghui 63, biological rep1


title: untreated 4098316040_C_untreated_BRCA1_Pool 2

value: Pool 2

value: BRCA1 184_185 ins TT (STOP 23)

value: no treatment


title: 60 min post-10 Gy IR 4098316050_D_IR_BRCA1_Pool 3

source_name: Lymphoblastoid cell line, 60 min post-10 Gy IR

value: Female

value: 10 Gy gamma radiation


title: 60 min post-1.2uM Mitomycin C 4098316050_F_MMC2_BRCA1_Pool 3

source_name: Lymphoblastoid cell line, 60 min post-1.2uM Mitomycin C

value: 60 min


title: stem 2, Minghui 63, biological rep1

source_name: stem, heading stage, Minghui 63

value: Minghui 63


title: stem 1, Minghui 63, biological rep2

source_name: stem, just before heading date, Minghui 63


title: 60 min post-0.4uM Mitomycin C 4098316050_E_MMC1_BRCA1_Pool 3

value: EBV-transformed lymphoblastoid cell line


title: leaf 3, Minghui 63, biological rep1

source_name: flag leaf, just before heading date, Minghui 63


title: sham male estrogen receptor beta knockout mice replicate 2

value: male


title: leaf 3, Minghui 63, biological rep2


title: sham female estrogen receptor beta knockout mice replicate 4

description: Sham operated female estrogen receptor beta knockout mice.

source_name: female, estrogen receptor beta knockout, sham

value: female


title: sham male estrogen receptor beta knockout mice replicate 1


title: stem 1, Minghui 63, biological rep1


title: panicle 4, Minghui 63, biological rep2

source_name: developing panicle with length between 40 and 50mm, Minghui 63


title: 120 min post-1.2uM Mitomycin C 4098316040_H_MMC4_BRCA1_Pool 2

value: BRCA1 mutation

value: 120 min


title: stem 2, Minghui 63, biological rep2


title: 120 min post-0.4uM Mitomycin C 4098316040_G_MMC3_BRCA1_Pool 2

source_name: Lymphoblastoid cell line, 120 min post-0.4uM Mitomycin C

value: 0.4 uM Mitomycin C


title: 60 min post-1.2uM Mitomycin C 4098316040_F_MMC2_BRCA1_Pool 2


title: sheath 2, Minghui 63, biological rep2

source_name: mature leaf sheath of the rice plants with developing panicle whose length is between 40 and 50 mm, Minghui 63


title: 60 min post-10 Gy IR 4098316040_D_IR_BRCA1_Pool 2


title: 60 min post-0.4uM Mitomycin C 4098316040_E_MMC1_BRCA1_Pool 2

value: 0.4uM Mitomycin C


title: panicle 4, Minghui 63, biological rep1


title: sham female estrogen receptor beta knockout mice replicate 3

value: C57Bl6 mice

value: 10 weeks

value: cardiac left ventricle


title: sheath 2, Minghui 63, biological rep1

value: indica


title: sham female estrogen receptor beta knockout mice replicate 1


title: leaf 2, Minghui 63, biological rep1

source_name: mature leaf blade of the rice plants with developing panicle whose length is between 40 and 50 mm, Minghui 63


title: sheath 1, Minghui 63, biological rep1

source_name: mature leaf sheath of the rice plants with developing panicle whose length is less than 1mm, Minghui 63


title: sham female estrogen receptor beta knockout mice replicate 2


title: sheath 1, Minghui 63, biological rep2


title: root, Minghui 63, biological rep2

source_name: root of the seedling with 2 tillers, Minghui 63


title: root, Minghui 63, biological rep1


title: leaf 1, Minghui 63, biological rep1

source_name: mature leaf blade of the rice plants with developing panicle whose length is less than 1mm, Minghui 63


title: untreated 4098316045_C_untreated_BRCA1_Pool 1

source_name: Lymphoblastoid cell line, untreated

value: Pool 1

value: BRCA1 2138 del A (STOP 700)


title: leaf 2, Minghui 63, biological rep2


title: hypertrophic male estrogen receptor beta knockout mice replicate 3

description: Hypertrophy was induced by transverse aortic constriction in male estrogen receptor beta knockout mice.

source_name: male, estrogen receptor beta knockout, transverse aortic constriction

treatment_protocol: Hypertrophy was induced with transverse aortic constriction (9 weeks).


title: hypertrophic male estrogen receptor beta knockout mice replicate 4


title: leaf 1, Minghui 63, biological rep2


title: 120 min post-1.2uM Mitomycin C 4098316045_H_MMC4_BRCA1_Pool 1

value: Female

value: 1.2 uM Mitomycin C


title: hypertrophic male estrogen receptor beta knockout mice replicate 2


title: hypertrophic female estrogen receptor beta knockout mice replicate 3

description: Hypertrophy was induced by transverse aortic constriction in female estrogen receptor beta knockout mice.

source_name: female, estrogen receptor beta knockout, transverse aortic constriction


title: shoot, Minghui 63, biological rep1

source_name: shoot of the seedling with 2 tillers, Minghui 63


title: seedling 5, Minghui 63, biological rep1

description:
M16A
Gene expression data of the mixture of seedling of 5, 15, 30, 60 min after hormone KT treatment

source_name: seedling at trefoil stage, treated by KT, Minghui 63


title: hypertrophic female estrogen receptor beta knockout mice replicate 4


title: shoot, Minghui 63, biological rep2


title: 60 min post-1.2uM Mitomycin C 4098316045_F_MMC2_BRCA1_Pool 1

source_name: Lymphoblastoid cell line, 60 min post-1.2uM Mitomycin C

value: 60 min


title: seedling 5, Minghui 63, biological rep2

description:
M16B
Gene expression data of the mixture of seedling of 5, 15, 30, 60 min after hormone KT treatment

value: Minghui 63


title: seedling 4, Minghui 63, biological rep2

description:
M15B
Gene expression data of the mixture of seedling of 5, 15, 30, 60 min after hormone GA3 treatment

source_name: seedling at trefoil stage, treated by GA3, Minghui 63


title: seedling 4, Minghui 63, biological rep1

description:
M15A
Gene expression data of the mixture of seedling of 5, 15, 30, 60 min after hormone GA3 treatment


title: 60 min post-0.4uM Mitomycin C 4098316045_E_MMC1_BRCA1_Pool 1

source_name: Lymphoblastoid cell line, 60 min post-0.4uM Mitomycin C

value: EBV-transformed lymphoblastoid cell line


title: hypertrophic female estrogen receptor beta knockout mice replicate 2


title: seedling 3, Minghui 63, biological rep1

description:
M14A
Gene expression data of the mixture of seedling of 5, 15, 30, 60 min after hormone NAA treatment

source_name: seedling at trefoil stage, treated by NAA, Minghui 63


title: seedling 3, Minghui 63, biological rep2

description:
M14B
Gene expression data of the mixture of seedling of 5, 15, 30, 60 min after hormone NAA treatment


title: hypertrophic male estrogen receptor beta knockout mice replicate 1

value: male


title: E_3, gene-level analysis

description: Gene RMA expression value derived from Arrayassist software (Stratagene); core-exon analysis; genome build hg18.

source_name: breast cancer cell line, siNELF-E

tag: cell type

value: breast cancer

value: siNELF-E


title: plumule 2, Minghui 63, biological rep1

source_name: plumule, dark, Minghui 63


title: radicle 1, Minghui 63, biological rep2

source_name: radicle, light, Minghui 63


title: E_2, gene-level analysis

tag: sirna


title: 60 min post-10 Gy IR 4098316045_D_IR_BRCA1_Pool 1

source_name: Lymphoblastoid cell line, 60 min post-10 Gy IR

tag: gender

value: BRCA1 mutation

value: 10 Gy gamma radiation


title: plumule 1, Minghui 63, biological rep1

source_name: plumule, light, Minghui 63


title: radicle 2, Minghui 63, biological rep2

source_name: radicle, dark, Minghui 63


title: radicle 1, Minghui 63, biological rep1


title: hypertrophic female estrogen receptor beta knockout mice replicate 1

value: female


title: radicle 2, Minghui 63, biological rep1


title: E_1, gene-level analysis


title: plumule 2, Minghui 63, biological rep2


title: B_3, gene-level analysis

source_name: breast cancer cell line, siNELF-B

value: siNELF-B


title: C_1, gene-level analysis

source_name: breast cancer cell line, siNELF-C

value: siNELF-C


title: callus 5, Minghui 63, biological rep2

source_name: callus, 5 days after regeneration, Minghui 63


title: germinating seed, Minghui 63, biological rep2

source_name: germinating seed, 72 hours after soaking in water, Minghui 63


title: B_1, gene-level analysis


title: callus 4, Minghui 63, biological rep1

source_name: callus, at screening stage, Minghui 63


title: plumule 1, Minghui 63, biological rep2


title: germinating seed, Minghui 63, biological rep1


title: C_3, gene-level analysis


title: C_2, gene-level analysis


title: callus 1, Minghui 63, biological rep2

source_name: callus, 15 days after induction, Minghui 63


title: callus 3, Minghui 63, biological rep2

source_name: callus, 15 days after subculture, Minghui 63


title: B_2, gene-level analysis


title: A_1, gene-level analysis

source_name: breast cancer cell line, siNELF-A

value: siNELF-A


title: callus 5, Minghui 63, biological rep1

value: indica


title: callus 3, Minghui 63, biological rep1


title: callus 4, Minghui 63, biological rep2


title: callus 2, Minghui 63, biological rep1

source_name: callus, 15 days after induction at 31℃, Minghui 63


title: GL3_1, gene-level analysis

source_name: breast cancer cell line, control

value: siControl against luciferase


title: 120 min post-0.4uM Mitomycin C 4098316045_G_MMC3_BRCA1_Pool 1

source_name: Lymphoblastoid cell line, 120 min post-0.4uM Mitomycin C

tag: patient group

value: Pool 1

value: BRCA1 2138 del A (STOP 700)

value: 0.4 uM Mitomycin C

value: 120 min


title: callus 2, Minghui 63, biological rep2

value: Minghui 63


title: NEMO Protoarray replicate 2

type: protein

city: Dublin

first: Beau

last: Fenner

address: 123 Saint Stephen's Green

country: Ireland

institute: Royal College of Surgeons in Ireland

description: Human NF-kappaB essential modulator (NEMO)

hyb_protocol: 10 µg of biotinylated NEMO was combined with probiing buffer (PBS, pH 7.4, 0.05% Triton X-100, 5% glycerol, 1% BSA, 5 mM MgCl2) and applied to a Protorrary previously blocked in blocking buffer (PBS, 1% BSA, 0.1% Tween 20). Protoarray was incubated at 4°C with gentle shaking for 1 h followed by washing in fresh probing buffer. Sample detection was performed by adding streptavidin-Alexa Fluor 647 in incubating the Protoarray in the dark for 30 min, followed by several more washes. The array was then dried at room temperature prior to scanning.

scan_protocol: Scanned on a Perkin Elmer ScanArray ExpressHT

data_processing: Scanned spot signals were normalized using internal Protoarray control proteins and Z scores subsequently determined based on comparisons of mean signals for each spot pair to the mean spot intensity for the array. Z scores greater than 3.0 were considered significant

molecule: protein

source_name: Biotinylated full-length NEMO protein

label_protocol: NEMO biotinylated using Invitrogen Protoarray Biotinylation and Purification modules

extract_protocol: GSH-sepharose 4b purification followed by thrombin cleavage of GST tag

tag: protein

value: NEMO expressed in E. coli BL21(DE3) as GST fusion protein in pGEX-4T

tag: purification

value: Protein purified using GSH-sepharose 4b (GE Life Sciences)

tag: post-purification

value: GST tag removed by thrombin digestion and subsequent spin filtration


title: GL3_3, gene-level analysis

value: breast cancer


title: A_3, gene-level analysis


title: GL3_2, gene-level analysis


title: A_2, gene-level analysis


title: callus 1, Minghui 63, biological rep1


title: rectus_abdomins_no_cancer_19

status: Public on Jan 19 2010

city: Stirling

first: Iain

last: Gallagher

address: Room 4B133 Cottrell Building, University of Stirling, Airthrey Road

department: Faculty of Health Sciences and Sport

country: United Kingdom

institute: University of Stirling

hyb_protocol: As per standard Affymetrix protocol.

scan_protocol: Scanning was carried out according to Affymetrix directions.

data_processing: All arrays were processed using the Microarray Suite version 5.0 (MAS 5.0) algorithm to a global scaling intensity of 100. Data were filtered using present/absent calls. Probes called absent by MAS 5.0 across all arrays were discarded. Normalization was carried out using RMA in the bioconductor suite (www.bioconductor.org) version 2.1.

source_name: rectus abdomins muscle no cancer

label_protocol: As per standard Affymetrix protocol.

extract_protocol: Muscle was homogenized in Trizol with a Mini-Beadbeater-8 homogenizer and RNA extraction carried out using Trizol protocol (Invitrogen). Hybridization, washing, staining and scanning of the arrays were performed according to manufacturer's instructions (Affymetrix).

value: rectus abdominus

tag: disease status

value: no cancer

tag: weightloss

tag: crp

tag: age (years)

value: Male

tag: body mass index (bmi)


title: rectus_abdomins_UGI_cancer_17

source_name: rectus abdomins muscle UGI cancer

tag: tissue

value: upper GI cancer


title: rectus_abdomins_UGI_cancer_14


title: GST control Protoarray replicate 1

description: Glutathione S-transferase control protein

hyb_protocol: 10 µg of biotinylated GST was combined with probiing buffer (PBS, pH 7.4, 0.05% Triton X-100, 5% glycerol, 1% BSA, 5 mM MgCl2) and applied to a Protorrary previously blocked in blocking buffer (PBS, 1% BSA, 0.1% Tween 20). Protoarray was incubated at 4°C with gentle shaking for 1 h followed by washing in fresh probing buffer. Sample detection was performed by adding streptavidin-Alexa Fluor 647 in incubating the Protoarray in the dark for 30 min, followed by several more washes. The array was then dried at room temperature prior to scanning.

organism: Escherichia coli

source_name: Biotinylated GST protein

label_protocol: GST biotinylated using Invitrogen Protoarray Biotinylation and Purification modules

extract_protocol: GSH-sepharose 4b purification

value: GST expressed in E. coli BL21(DE3) from pGEX-4T-3


title: rectus_abdomins_no_cancer_2


title: NEMO Protoarray replicate 1


title: rectus_abdomins_UGI_cancer_18


title: rectus_abdomins_UGI_cancer_10


title: rectus_abdomins_no_cancer_1

value: Female


title: rectus_abdomins_UGI_cancer_15


title: rectus_abdomins_UGI_cancer_9


title: rectus_abdomins_UGI_cancer_5


title: rectus_abdomins_UGI_cancer_16


title: rectus_abdomins_UGI_cancer_12


title: rectus_abdomins_UGI_cancer_6


title: rectus_abdomins_UGI_cancer_3


title: rectus_abdomins_UGI_cancer_7


title: rectus_abdomins_UGI_cancer_2


title: rectus_abdomins_UGI_cancer_8


title: rectus_abdomins_UGI_cancer_11


title: rectus_abdomins_UGI_cancer_1


title: rectus_abdomins_UGI_cancer_13


title: rectus_abdomins_UGI_cancer_4


title: HepG2_sample11

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

description: Stanford-Meyers

data_processing: Raw CEL files were processed using Affymetrix Expression Console Software using RMA-Core-DABG

label_protocol: 1ug of total RNA was labeled according to Standard Affymetrix WT protocol for Exon 1.0 ST arrays

extract_protocol: total RNA was extracted from cell pellets using Trizol protocol or RNEasy protocol

treatment_protocol: cells were supplied as frozen pellets, pellets in trizol, pellets in RNA later or pellets in RLT buffer


title: HepG2_sample12

description: Ualbany-Tenenbaum

hyb_protocol: Standard Affymetrix WT protocol for Exon 1.0 ST arrays


title: HeLa-S3_sample9

description: Ualbany-Tenenbaum

scan_protocol: Standard Affymetrix WT protocol for Exon 1.0 ST arrays


title: HepG2_sample13

description: Ualbany-Tenenbaum


title: HeLa-S3_sample10

description: Ualbany-Tenenbaum


title: HeLa-S3_sample8

description: Stanford-Meyers


title: HeLa-S3_sample6

description: Broad-Bernstein


title: HeLa-S3_sample7

description: Broad-Bernstein


title: shCDK8_Time_0_2

city: Boulder

first: Aaron

last: Donner

state: CO

department: Molecular Cellular and Developmental Biology

institute: University of Colorado Boulder

description: Gene expression data from serum-starved shCDK8 HCT116 cells

hyb_protocol: Samples were hybridized to Affymetrix GeneChip® Human Gene 1.0 ST arrays using an Affymetrix GeneChip® Hybridization Oven 640.  Each array was washed and stained using a GeneChip® Hybridization, Wash and Stain kit (Invitrogen) and an Affymetrix Fluidics station 450.

scan_protocol: Arrays were scanned with an Affymetrix scanner 3000 7G.

data_processing: CEL files were imported into SpotFire (TIBCO), normalized using Robust Multi-chip Average (RMA) and analyzed using the Spotfire Decision Site.

source_name: HCT116 colon cancer cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA.

growth_protocol: HCT116 cells were routinely passaged in 10% FBS McCoy's 5A medium . Cells were serum-starved for 40 hours in McCoy's

extract_protocol: Total RNA was isolated using RNeasy kit from Qiagen per the manufacturers protocol.

treatment_protocol: Serum-starved Control and shCDK8 expressing HCT116 cells were either not treated or treated with 10%FBS McCoy's 5A for 30 minutes in duplicate before RNA was isolated as below.

tag: short-hairpin rna


title: shCDK8_Time_30_2

description: Gene expression data from serum-starved shCDK8 HCT116 cells treated with 10% FBS McCoy's 5A for 30 minutes


title: Control_Time_30_2

description: Gene expression data from serum-starved shControl HCT116 cells treated with 10% FBS McCoy's 5A for 30 minutes

value: shControl


title: Control_Time_30_1


title: Control_Time_0_1

description: Gene expression data from serum-starved shControl HCT116 cells


title: HEB-deficient (HEBKO) DP cells, biological rep 2

status: Public on Jan 16 2010

city: La Jolla

first: Louise

last: D'Cruz

state: CA

address: 9500 Gilman Drive

institute: UCSD

description: Gene expression data from HEB-deficient double-positive thymocytes

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed using Expression File Creator module on Gene Pattern Suite and RMA as normalization method.

source_name: HEB-deficient double positive cells sorted from thymus of 8 week old mouse

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

growth_protocol: thymuses were harvested from individual mice, single cell suspensions were made and cells were stained with antibodies for CD4 and CD8 before sorting.

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

treatment_protocol: cells were stored in 5% BGS+ PBS prior to FACS

value: thymus

tag: genotype

value: HEBflox/flox cd4-cre+

tag: age

value: 8 weeks


title: 2nd design mouse embryonic stem cells untreated

type: genomic

city: Bethesda

first: Jing

last: Huang

state: MD

institute: National Cancer Institute

description: Hybridized to Agilent's mouse promoter array (2nd design)

hyb_protocol: Per Agilent's ChIP-on-chip protocol (Version 10.0), 5ug of labeled input and IP DNA were mixed and hybridized to a mouse promoter microarray (Agilent, G4490A) in an oven at 65 degree with rotation at 20 rpm.

scan_protocol: After washing, the microarrays were scanned with Agilent DNA microarray scanner.

data_processing: Features were extracted with Feature Extraction software (Agilent, version 10.0). Data analysis was performed with DNA Analytics software (Agilent, version 4.0). The genomic BSs of p53 were identified with a Whitehead Per-Array Neighborhood Mode with high confidence.

molecule: genomic DNA

source_name: ES, R1E embryonic stem cells

label_protocol: Per Agilent's genomic DNA labeling protocol, dUTP-Cy3 and –Cy5 dyes were used to label 2ug input and IP DNA, respectively.

growth_protocol: R1E cells were grown in mESC growth medium, Knockout DMEM (KO-DMEM), 15% Fetal Bovine Serum, 100mM MEM non-essential amino acids, 0.1mM 2-mercaptoethanol, 2mM L-glutamine and 1X penicillin-streptomycin (All from Invitrogen) plus 1000 units/ml leukemia inhibitory factor (Lif, Millipore)

extract_protocol: Cell pellets were collected by centrifuging at 3,000rpm for 5 minutes followed by washing with Lysis Buffer 1 (50mM Hepes-KOH, pH 7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) and Lysisi Buffer 2 (10mM Tris-HCl, pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA). Precipitated chromatin was then resuspended in Lysis Buffer 3 (10mM Tris-HCl, pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and sonciated with a Misonix XL2020 for total of 16 cycles of 30-second on and 1-minute off. 50ul clear whole cell extract was saved as input. After immunoprecipitation with 10ug p53 antibody (M19, Santa Cruz) using Protein G Dynal beads (Invitrogen), reverse cross-link was performed at 65 degree overnight. RNA and protein were digested with RNase A and Proteinase K treatment, respectively, and DNA was purified using ethanol precipitation method. Ligation-mediated PCR was carried out to amplify the input and IP DNA.

treatment_protocol: R1E cells were untreated (control)  for 8 hours in growth medium plus 1000 units/ml Lif. Briefly, 50 million R1E cells were fixed with 1% formaldehyde at room temperature for 10 minutes. Fixation was quenched by adding glycine to a final concentration of 125mM.

tag: cell line

value: R1E cells

tag: reference

value: input

tag: antibody

value: p53 IP DNA


title: shCDK8_Time_30_1


title: 2nd design mouse embryonic stem cells adriamycin-treated

treatment_protocol: R1E cells were treated with 0.5 micromolar adriamycin  for 8 hours in growth medium plus 1000 units/ml Lif. Briefly, 50 million R1E cells were fixed with 1% formaldehyde at room temperature for 10 minutes. Fixation was quenched by adding glycine to a final concentration of 125mM.


title: Control_Time_0_2


title: E2A/HEB-deficient (DKO) DP cells, biological rep 2

description: Gene expression data from E2A-deficient HEB-deficient double-positive thymocytes

source_name: E2A and HEB deficient double positive cells sorted from thymus of 8 week old mouse

value: E2Aflox/flox HEBflox/flox cd4-cre+


title: E2A/HEB-deficient (DKO) DP cells, biological rep 1


title: 1st design mouse embryonic stem cells untreated

description: Hybridized to Agilent's mouse promoter array (1st design)


title: 1st design mouse embryonic stem cells adriamycin-treated


title: shCDK8_Time_0_1


title: HEB-deficient (HEBKO) DP cells, biological rep 1


title: E2A/HEB-deficient (DKO) DP cells, biological rep 3


title: sh3293 (to target ERBB3) T47D cell line, replicate 2

city: Rehovot

first: Amit

last: Zeisel

address: Weizmann Institute

department: Physics of complex systems

country: Israel

institute: Weizmann Institute of Science

hyb_protocol: According to the Affymetrix manual.

scan_protocol: According to the Affymetrix manual.

data_processing: PLIER (no normalization, only summarization) + Lowess.

label_protocol: According to the Affymetrix manual.

growth_protocol: T47D cells were grown in DMEM medium (Gibco Life Technologies, Paisley, UK) supplemented with 10% v/v heat-inactivated fetal calf serum, sodium pyruvate and a mixture of antibiotics (penicillin and streptomycin) at 37 °C and 5% CO2. Cells were then infected with lentiviral particles carrying the indicated shRNA particles at MOI=5 in the presence of 8mg/ml of polybrene. Cells were thereafter selected using puromycin and their RNA was extracted.

extract_protocol: Standard procedures.


title: sh2608 (to target ERBB3) T47D cell line, replicate 2


title: E2A-deficient (E2AKO) DP cells, biological rep 2

description: Gene expression data from E2A-deficient double-positive thymocytes

source_name: E2A-deficient double positive cells sorted from thymus of 8 week old mouse

value: E2Aflox/flox Cd4-cre+


title: wild-type DP cells, biological rep 2

description: Gene expression data from wild-type double-positive thymocytes

source_name: wild-type double positive cells sorted from thymus of 8 week old mouse

value: wild-type cd4-cre+


title: E2A-deficient (E2AKO) DP cells, biological rep 1


title: F.candida_Heat_Shock_rep3

city: Amsterdam

first: Benjamin

last: Nota

state: Noord Holland

address: Plesmanlaan 125

department: Research Facilities

country: Netherlands

institute: Sanquin

description: No additional information available.

hyb_protocol: Agilent Gene Expression Hybridization Kit (Agilent Technologies) was used for hybridization, which was done at 65°C for 17 hours rotating at 4 rpm in an incubator. After hybridization the arrays were washed using Gene Expression Wash Buffer Kit (Agilent Technologies).

scan_protocol: The arrays were scanned on an Agilent DNA microarray scanner (Agilent Technologies), and fluorescence intensities were measured with Feature Extraction (9.1.3.1) Software (Agilent Technologies).

data_processing: Pre-processing and normalization was done using the limma (2.14.5) package in the R (2.7.1) software environment (http://www.R-project.org/), which consisted of Edward’s background correction (set off = 30) and global loess normalization. For each channel the median background intensity was substracted from the mean signal (foreground) intensity.

organism: Folsomia candida

source_name: F.candida, Reference

label_protocol: 500 ng input was used for amplification and labeling with the Agilent Low-Input Fluorescent Linear Amplification Kit (Agilent Technologies), according to the manufacturer’s guidelines with slightest modification that the transcription (labeling) reactions were done in half amounts of volume. Furthermore, no spike-in controls were added. Labeled/amplified cRNA was purified using RNeasy (Qiagen).

extract_protocol: Total RNA was extracted from all animals (~30) per jar, using SV Total RNA isolation System (Promega).

treatment_protocol: Approximately thirty animals of F.candida ('Berlin' Strain), age 25 days old, were acclimated at 20 C for two days, in a jar containing ~30g of LUFA 2.2 soil. Then the animals were extracted from the jar, pooled, and RNA was isolated. This is a reference (control) sample.

tag: strain

value: Berlin

source_name: F.candida, Heat shock

treatment_protocol: Approximately thirty animals of F.candida ('Berlin' Strain), age 25 days old, were acclimated at 20 C for two days, in a jar containing ~30g of LUFA 2.2 soil. Then the jars were exposed, in a waterbath, to 30 C for 30 min. The animals were extracted from the jar, pooled, and RNA was isolated. This is a treated (Heat shock) sample.


title: sh3293 (to target ERBB3) T47D cell line, replicate 1


title: wild-type DP cells, biological rep 1


title: sh2608 (to target ERBB3) T47D cell line, replicate 1


title: shEGFP T47D cell line, replicate 2

description: GFPb

source_name: T47D, shEGFP

value: shEGFP T47D

tag: sample type

value: control


title: Dog-tumor-394

city: Athens

first: Jie

last: Tang

state: GA

address: 120 Green St

department: Institute of Bioinformatics

institute: University of Georgia

description: Oligo array CGH Tumor 394/Normal 394

hyb_protocol: Using NimbleGen Hybridization System (following the NimbleGen official Manual)

scan_protocol: scanning two-color NimbleGen arrays with GenePix 4000B Scanner and associated software(following the NimbleGen official Manual)

data_processing: Analyzing the data with the segMNT algorithm (following the NimbleGen official Manual)

organism: Canis lupus familiaris

source_name: DNA from colon tumor tissue of dog 394

label_protocol: labeling test samples with Cy3 following the NimbleGen official Manual, see more at NimbleGen website.

extract_protocol: Genomic DNA was extracted from the dissected tissues using a Qiagen Tissue DNeasy purification kit (exactly following the kit manual)

tag: stage

value: Adenocarcinoma

source_name: DNA from colon normal tissue of dog 394

label_protocol: labeling reference samples with Cy5 following the NimbleGen official Manual, see more at NimbleGen website.

value: DNA from colon normal tissue of dog 394


title: F.candida_Heat_Shock_rep1

description: No additional information available.


title: Liver S compound 28µmol/kg technical replicate 6

city: Croissy-sur-Seine

first: Aurélie

last: Cotillard

address: 125 chemin de ronde

institute: Institut de Recherches Servier

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice. Technical replicate 6 of 6. Db/db mice treated with 28µmol/kg of S compound

hyb_protocol: Samples were incubated at 60°C for 30 minutes and then hybridized for 17 hours at 65°C in a 10 rpm rotary oven. Slides were then washed in buffer 1 and 2, according to manufacturer’s specification.

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5).

data_processing: Agilent Feature Extraction Software (v 9.5) was used for background subtraction and LOWESS normalization (GE2-v5_95_Feb07 protocol). Rosetta Resolver (v 7.1) was used for the dye-swap combination.

source_name: Pool of db/db control mice

label_protocol: Total RNA samples were labelled using Agilent low RNA input linear amplification Kit, according to the manufacturer's protocols. 500ng of liver and IAT total RNA were reversed transcribed by MMLV reverse transcriptase. Amplification and labelling were done by T7-polymerase transcription. Test and reference cRNA were labelled with cyanine Cy5 or Cy3-CTP dyes.

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

treatment_protocol: Per os treatment for 18 days

value: Liver

value: BKS Cg-m+/+ Leprdb/J

source_name: db/db mouse treated with 28µmol/kg of S compound


title: F.candida_Heat_Shock_rep2

description: No additional information available.


title: F.candida_Heat_Shock_rep4

description: No additional information available.


title: shEGFP T47D cell line, replicate 1

description: GFPa


title: T47D cell line, replicate 2

description: WTb

source_name: T47D, WT


title: T47D cell line, replicate 1

description: WTa


title: Dog-tumor-88012

description: Oligo array CGH Tumor 88012/Normal 88012

source_name: DNA from colon tumor tissue of dog 88012

value: Adenoma

source_name: DNA from colon normal tissue of dog 88012


title: Dog-tumor-125

description: Oligo array CGH Tumor 125/Normal 125

source_name: DNA from colon tumor tissue of dog 125

source_name: DNA from colon normal tissue of dog 125

value: DNA from colon normal tissue of dog 125


title: wild-type DP cells, biological rep 3

value: thymus


title: Dog-tumor-896

description: Oligo array CGH Tumor 896/Normal 896

source_name: DNA from colon tumor tissue of dog 896

source_name: DNA from colon normal tissue of dog 896

value: DNA from colon normal tissue of dog 896


title: Liver S compound 28µmol/kg technical replicate 4

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice. Technical replicate 4 of 6. Db/db mice treated with 28µmol/kg of S compound


title: Liver S compound 28µmol/kg technical replicate 5

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice. Technical replicate 5 of 6. Db/db mice treated with 28µmol/kg of S compound


title: Liver S compound 28µmol/kg technical replicate 3

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice. Technical replicate 3 of 6. Db/db mice treated with 28µmol/kg of S compound


title: Liver S compound 28µmol/kg technical replicate 1

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice. Technical replicate 1 of 6. Db/db mice treated with 28µmol/kg of S compound


title: Liver rosiglitazone 28µmol/kg technical replicate 5

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice. Technical replicate 5 of 6. Db/db mice treated with 28µmol/kg of rosiglitazone

source_name: db/db mouse treated with 28µmol/kg of rosiglitazone


title: Dog-tumor-209439

description: Oligo array CGH Tumor 209439/Normal 209439

source_name: DNA from colon tumor tissue of dog 209439

source_name: DNA from colon normal tissue of dog 209439


title: Liver S compound 28µmol/kg technical replicate 2

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice. Technical replicate 2 of 6. Db/db mice treated with 28µmol/kg of S compound


title: Liver rosiglitazone 28µmol/kg technical replicate 6

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice. Technical replicate 6 of 6. Db/db mice treated with 28µmol/kg of rosiglitazone


title: Liver rosiglitazone 28µmol/kg technical replicate 4

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice. Technical replicate 4 of 6. Db/db mice treated with 28µmol/kg of rosiglitazone


title: Dog-tumor-212227

description: Oligo array CGH Tumor 212227/Normal 212227

source_name: DNA from colon tumor tissue of dog 212227

value: Leiomyosarcoma

source_name: DNA from colon normal tissue of dog 212227


title: Liver rosiglitazone 28µmol/kg technical replicate 1

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice. Technical replicate 1 of 6. Db/db mice treated with 28µmol/kg of rosiglitazone


title: Dog-tumor-48

description: Oligo array CGH Tumor 48/Normal 48

source_name: DNA from colon tumor tissue of dog 48

source_name: DNA from colon normal tissue of dog 48

value: DNA from colon normal tissue of dog 48


title: IAT S compound 280µmol/kg biological replicate 1

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 1 of 6. Db/db mice treated with 280µmol/kg of S compound

value: Inguinal adipose tissue

source_name: db/db mouse treated with 280µmol/kg of S compound


title: IAT S compound 280µmol/kg biological replicate 6

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 6 of 6. Db/db mice treated with 280µmol/kg of S compound

source_name: Pool of db/db control mice


title: IAT S compound 84µmol/kg biological replicate 6

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 6 of 6. Db/db mice treated with 84µmol/kg of S compound

source_name: db/db mouse treated with 84µmol/kg of S compound


title: IAT S compound 280µmol/kg biological replicate 3

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 3 of 6. Db/db mice treated with 280µmol/kg of S compound


title: Liver rosiglitazone 28µmol/kg technical replicate 2

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice. Technical replicate 2 of 6. Db/db mice treated with 28µmol/kg of rosiglitazone


title: IAT S compound 280µmol/kg biological replicate 2

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 2 of 6. Db/db mice treated with 280µmol/kg of S compound


title: Dog-tumor-78709

description: Oligo array CGH Tumor 78709/Normal 78709

source_name: DNA from colon tumor tissue of dog 78709

source_name: DNA from colon normal tissue of dog 78709


title: IAT S compound 280µmol/kg biological replicate 4

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 4 of 6. Db/db mice treated with 280µmol/kg of S compound


title: IAT S compound 84µmol/kg biological replicate 5

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 5 of 6. Db/db mice treated with 84µmol/kg of S compound


title: IAT S compound 280µmol/kg biological replicate 5

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 5 of 6. Db/db mice treated with 280µmol/kg of S compound


title: Dog-tumor-8888302

description: Oligo array CGH Tumor 8888302/Normal 8888302

source_name: DNA from colon tumor tissue of dog 8888302

value: Metastatic Mast cell tumor

source_name: DNA from colon normal tissue of dog 8888302


title: IAT S compound 84µmol/kg biological replicate 3

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 3 of 6. Db/db mice treated with 84µmol/kg of S compound


title: IAT S compound 28µmol/kg biological replicate 5

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 5 of 6. Db/db mice treated with 28µmol/kg of S compound

source_name: db/db mouse treated with 28µmol/kg of S compound


title: IAT S compound 84µmol/kg biological replicate 2

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 2 of 6. Db/db mice treated with 84µmol/kg of S compound


title: Dog-tumor-81705

description: Oligo array CGH Tumor 81705/Normal 81705

source_name: DNA from colon tumor tissue of dog 81705

source_name: DNA from colon normal tissue of dog 81705


title: Human-tumor

description: Oligo array CGH Tumor 2551/Normal 2551

source_name: DNA from colon tumor tissue of human 2551

source_name: DNA from colon normal tissue of human 2551


title: IAT S compound 84µmol/kg biological replicate 4

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 4 of 6. Db/db mice treated with 84µmol/kg of S compound


title: IAT S compound 28µmol/kg biological replicate 2

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 2 of 6. Db/db mice treated with 28µmol/kg of S compound


title: IAT S compound 28µmol/kg biological replicate 6

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 6 of 6. Db/db mice treated with 28µmol/kg of S compound


title: IAT S compound 28µmol/kg biological replicate 1

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 1 of 6. Db/db mice treated with 28µmol/kg of S compound


title: IAT S compound 28µmol/kg biological replicate 4

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 4 of 6. Db/db mice treated with 28µmol/kg of S compound


title: IAT S compound 28µmol/kg biological replicate 3

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 3 of 6. Db/db mice treated with 28µmol/kg of S compound


title: IAT S compound 84µmol/kg biological replicate 1

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 1 of 6. Db/db mice treated with 84µmol/kg of S compound


title: IAT rosiglitazone 280µmol/kg biological replicate 6

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 6 of 6. Db/db mice treated with 280µmol/kg of rosiglitazone

source_name: db/db mouse treated with 280µmol/kg of rosiglitazone


title: IAT rosiglitazone 280µmol/kg biological replicate 5

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 5 of 6. Db/db mice treated with 280µmol/kg of rosiglitazone


title: IAT rosiglitazone 280µmol/kg biological replicate 1

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 1 of 6. Db/db mice treated with 280µmol/kg of rosiglitazone


title: IAT rosiglitazone 280µmol/kg biological replicate 2

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 2 of 6. Db/db mice treated with 280µmol/kg of rosiglitazone


title: IAT rosiglitazone 280µmol/kg biological replicate 4

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 4 of 6. Db/db mice treated with 280µmol/kg of rosiglitazone


title: IAT rosiglitazone 280µmol/kg biological replicate 3

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 3 of 6. Db/db mice treated with 280µmol/kg of rosiglitazone


title: IAT rosiglitazone 84µmol/kg biological replicate 6

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 6 of 6. Db/db mice treated with 84µmol/kg of rosiglitazone

source_name: db/db mouse treated with 84µmol/kg of rosiglitazone


title: IAT rosiglitazone 84µmol/kg biological replicate 2

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 2 of 6. Db/db mice treated with 84µmol/kg of rosiglitazone


title: Area X, singing 3hr, Replicate 5

city: Durham

first: Osceola

last: Whitney

state: NC

address: Research Drive, Bryan Research Building, Room 401E

department: Neurobiology

institute: Duke University Medical Center

description:
Gene expression after singing
54 male zebra finch birds were isolated overnight in sound attenuation chambers on a 12/12 light:dark cycle with ad lib access to food and water.

hyb_protocol: Labeled cDNA was dried in a speed-vac and resuspended in 25ul of hybridization buffer that contained 16% formamide, and 1X Agilent Blocking buffer. Samples were then denatured at 95 degrees for 3 mins and 18uLs of each samples was loaded to each array. Each micrroarray slide contained 4 arrays (4X44K) that were hybridized using a special A4 clamp to hold Agilent 4 x 44K arrays in Maui A4 mixers. The mixer was held at 55oC for at least 20 hrs, with the humidity chamber positioned over arrays.The following day, slides were rinsed in pre-heated (42oC). They were then shaken in Agilent Wash 1 buffer solution at RT X 1min and then Agilent Wash 2 at 37C for 1min. The slides were then slowly removed from the Wash buffer to minimize droplet formation.

scan_protocol: Slides were scanned immediately after washing on the GenePix 4000 Microarray Scanner and Agilent's Feature Extraction Software v9.5.1 using one color scan setting for 4x44k array slides (Scan resolution was 5um, Dye channel was set to 532 [Green] and PMT to 520).

data_processing: The data was normalized with variance stabilization for one-color data based on Huber et al 2002 [PMID 12169536].  Microarrays with a low percentage of probes above background and high standard deviation from the median were removed.

organism: Taeniopygia guttata

source_name: Area X, singing 3hr

label_protocol: 2.2 ugs of purified cDNA was labeled and fragmented using FL-Ovation Cy3 labeling and fragmentation kit according to the manufacturers instructions (Nugen). 2.2 ugs of purified cDNA was labeled and fragmented using FL-Ovation Cy3 labeling and fragmentation kit according to the manufacturers instructions (Nugen).   Dye incorporation and cDNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the Picopure RNA Extraction kit (Molecular Devices, Sunnyvale, CA) following the manufacturer's recommendations.  The protocol includes an on-column DNase digestion.  RNA was quantified using a NanoDrop-1000 spectrophotometer (Nanodrop Wilmington, DE) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). From 1.5-2ng of total RNA, amplified cDNA was prepared using the WT-Ovation Pico System (Nugen, San Carlos, CA) according to the manufacturer's instructions.

treatment_protocol: In the morning before singing or immediately after singing for 0.5, 1, 2, 3, 4, 5, 6, or 7hrs, brains were quickly dissected. For the singing groups, we used birds that sang continuously >25 bouts per 0.5 hours.

value: Brain

tag: gender

value: Male

value: >120 days


title: IAT rosiglitazone 84µmol/kg biological replicate 3

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 3 of 6. Db/db mice treated with 84µmol/kg of rosiglitazone


title: IAT rosiglitazone 84µmol/kg biological replicate 1

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 1 of 6. Db/db mice treated with 84µmol/kg of rosiglitazone


title: Area X, singing 4hr, Replicate 1

source_name: Area X, singing 4hr


title: IAT rosiglitazone 84µmol/kg biological replicate 4

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 4 of 6. Db/db mice treated with 84µmol/kg of rosiglitazone


title: IAT rosiglitazone 84µmol/kg biological replicate 5

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 5 of 6. Db/db mice treated with 84µmol/kg of rosiglitazone


title: IAT rosiglitazone 28µmol/kg biological replicate 6

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 6 of 6. Db/db mice treated with 28µmol/kg of rosiglitazone

source_name: db/db mouse treated with 28µmol/kg of rosiglitazone


title: Liver rosiglitazone 28µmol/kg technical replicate 3

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice. Technical replicate 3 of 6. Db/db mice treated with 28µmol/kg of rosiglitazone


title: IAT rosiglitazone 28µmol/kg biological replicate 5

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 5 of 6. Db/db mice treated with 28µmol/kg of rosiglitazone


title: IAT rosiglitazone 28µmol/kg biological replicate 4

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 4 of 6. Db/db mice treated with 28µmol/kg of rosiglitazone


title: Area X, singing 3hr, Replicate 4


title: Area X, singing 3hr, Replicate 1


title: Area X, singing 3hr, Replicate 3


title: Area X, singing 3hr, Replicate 2


title: Area X, singing 2hr, Replicate 3

source_name: Area X, singing 2hr


title: IAT rosiglitazone 28µmol/kg biological replicate 3

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 3 of 6. Db/db mice treated with 28µmol/kg of rosiglitazone

source_name: Pool of db/db control mice


title: Area X, singing 2hr, Replicate 5


title: IAT rosiglitazone 28µmol/kg biological replicate 2

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 2 of 6. Db/db mice treated with 28µmol/kg of rosiglitazone


title: Area X, singing 2hr, Replicate 4


title: Liver S compound 280µmol/kg biological replicate 6

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 6 of 6. Db/db mice treated with 280µmol/kg of S compound

source_name: db/db mouse treated with 280µmol/kg of S compound


title: Area X, singing 1hr, Replicate 4

source_name: Area X, singing 1hr


title: Area X, singing 2hr, Replicate 1


title: Liver S compound 280µmol/kg biological replicate 5

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 5 of 6. Db/db mice treated with 280µmol/kg of S compound


title: Liver S compound 84µmol/kg biological replicate 2

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 2 of 6. Db/db mice treated with 84µmol/kg of S compound

source_name: db/db mouse treated with 84µmol/kg of S compound


title: Liver S compound 84µmol/kg biological replicate 5

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 5 of 6. Db/db mice treated with 84µmol/kg of S compound


title: Area X, singing 1hr, Replicate 5


title: Area X, singing 1hr, Replicate 1


title: Liver S compound 84µmol/kg biological replicate 6

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 6 of 6. Db/db mice treated with 84µmol/kg of S compound


title: Area X, singing 1hr, Replicate 2


title: Area X, singing 0.5hr, Replicate 5

source_name: Area X, singing 0.5hr


title: IAT rosiglitazone 28µmol/kg biological replicate 1

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 1 of 6. Db/db mice treated with 28µmol/kg of rosiglitazone


title: Liver S compound 280µmol/kg biological replicate 3

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 3 of 6. Db/db mice treated with 280µmol/kg of S compound


title: Area X, singing 2hr, Replicate 2

description:
Gene expression after singing
54 male zebra finch birds were isolated overnight in sound attenuation chambers on a 12/12 light:dark cycle with ad lib access to food and water.


title: Liver S compound 84µmol/kg biological replicate 3

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 3 of 6. Db/db mice treated with 84µmol/kg of S compound


title: Liver S compound 84µmol/kg biological replicate 4

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 4 of 6. Db/db mice treated with 84µmol/kg of S compound


title: Liver S compound 280µmol/kg biological replicate 4

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 4 of 6. Db/db mice treated with 280µmol/kg of S compound


title: Area X, singing 1hr, Replicate 3


title: Area X, singing 0.5hr, Replicate 2


title: Area X, silent 1hr,  Replicate 6

source_name: Area X, silent 1hr


title: Liver S compound 280µmol/kg biological replicate 1

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 1 of 6. Db/db mice treated with 280µmol/kg of S compound


title: Area X, singing 0.5hr, Replicate 4


title: Liver S compound 280µmol/kg biological replicate 2

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 2 of 6. Db/db mice treated with 280µmol/kg of S compound


title: Liver S compound 84µmol/kg biological replicate 1

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 1 of 6. Db/db mice treated with 84µmol/kg of S compound


title: Area X, singing 0.5hr, Replicate 1


title: Area X, singing 0.5hr, Replicate 3


title: Liver S compound 28µmol/kg biological replicate 4

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 4 of 6. Db/db mice treated with 28µmol/kg of S compound

source_name: db/db mouse treated with 28µmol/kg of S compound


title: Area X, silent 1hr,  Replicate 1

description:
Silent control sample for gene expression after singing
54 male zebra finch birds were isolated overnight in sound attenuation chambers on a 12/12 light:dark cycle with ad lib access to food and water.


title: Area X, silent 1hr,  Replicate 5


title: Liver S compound 28µmol/kg biological replicate 6

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 6 of 6. Db/db mice treated with 28µmol/kg of S compound


title: Area X, silent 1hr,  Replicate 4


title: Liver S compound 28µmol/kg biological replicate 5

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 5 of 6. Db/db mice treated with 28µmol/kg of S compound


title: Liver rosiglitazone 280µmol/kg biological replicate 5

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 5 of 6. Db/db mice treated with 280µmol/kg of rosiglitazone


title: Liver rosiglitazone 280µmol/kg biological replicate 4

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 4 of 6. Db/db mice treated with 280µmol/kg of rosiglitazone


title: Liver S compound 28µmol/kg biological replicate 3

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 3 of 6. Db/db mice treated with 28µmol/kg of S compound


title: Area X, singing 7hr, Replicate 5

source_name: Area X, singing 7hr


title: Area X, singing 7hr, Replicate 4


title: Liver S compound 28µmol/kg biological replicate 2

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 2 of 6. Db/db mice treated with 28µmol/kg of S compound


title: Area X, silent 1hr,  Replicate 3


title: Area X, singing 7hr, Replicate 1


title: Liver S compound 28µmol/kg biological replicate 1

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 1 of 6. Db/db mice treated with 28µmol/kg of S compound


title: Area X, singing 7hr, Replicate 2


title: 13852143 - pER8 25+ 2 vs pER8 25- 2

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

description: Are there some genes deregulated by the p25 viral protein.

hyb_protocol: pER8 25- 2 Cy5 / pER8 25+ 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: root - Media=MS255	 Temperature=21°C - 17°C	 Light=16h - 8h

treatment_protocol: Name:Induction - gene induction - compound addition,estradiol:quantity 10mM time 5hour . Bedding out of the plants from a plate to an other plate that contains the compound, and then root extraction 5 hours later.

tag: ecotype

value: columbia

tag: genome/variation

value: mutant (per8::P25-)

tag: developmental stage (boyes et al. plant cell 2001)

value: mutant (per8::P25+)


title: Area X, silent 1hr,  Replicate 2


title: Liver rosiglitazone 280µmol/kg biological replicate 6

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 6 of 6. Db/db mice treated with 280µmol/kg of rosiglitazone


title: 13852248 - pER8 GFP- 2 vs pER8 GFP+ 2

hyb_protocol: pER8 GFP+ 2 Cy5 / pER8 GFP- 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: pER8 GFP+ 2

value: mutant (per8::GFP+)

source_name: pER8 GFP- 2

value: mutant (per8::GFP-)


title: 13852249 - pER8 GFP+ 2 vs pER8 GFP- 2

hyb_protocol: pER8 GFP- 2 Cy5 / pER8 GFP+ 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Area X, singing 6hr, Replicate 4

description:
Gene expression after singing
54 male zebra finch birds were isolated overnight in sound attenuation chambers on a 12/12 light:dark cycle with ad lib access to food and water.

source_name: Area X, singing 6hr


title: 13852244 - pER8 GFP- 1 vs pER8 GFP+ 1

hyb_protocol: pER8 GFP+ 1 Cy5 / pER8 GFP- 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: pER8 GFP+ 1

source_name: pER8 GFP- 1


title: 13852142 - pER8 25- 2 vs pER8 25+ 2

hyb_protocol: pER8 25+ 2 Cy5 / pER8 25- 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13852247 - pER8 GFP+ 1 vs pER8 GFP- 1

hyb_protocol: pER8 GFP- 1 Cy5 / pER8 GFP+ 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13852149 - 25 6F 2 vs WT 6F 2

hyb_protocol: WT 6F 2 Cy5 / 25 6F 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: WT 6F 2

value: wild type

value: mutant (p25)


title: Liver rosiglitazone 280µmol/kg biological replicate 2

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 2 of 6. Db/db mice treated with 280µmol/kg of rosiglitazone

value: Liver

value: BKS Cg-m+/+ Leprdb/J

source_name: db/db mouse treated with 280µmol/kg of rosiglitazone


title: Area X, singing 6hr, Replicate 3


title: Liver rosiglitazone 280µmol/kg biological replicate 3

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 3 of 6. Db/db mice treated with 280µmol/kg of rosiglitazone


title: 13852147 - 25 6F 1 vs WT 6F 1

hyb_protocol: WT 6F 1 Cy5 / 25 6F 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: WT 6F 1


title: 13852148 - WT 6F 2 vs 25 6F 2

hyb_protocol: 25 6F 2 Cy5 / WT 6F 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13852140 - pER8 25- 1 vs pER8 25+ 1

hyb_protocol: pER8 25+ 1 Cy5 / pER8 25- 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13852144 - WT 4F 2 vs 25 4F 2

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

source_name: WT 4F 2


title: 13852146 - WT 6F 1 vs 25 6F 1

hyb_protocol: 25 6F 1 Cy5 / WT 6F 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Liver rosiglitazone 280µmol/kg biological replicate 1

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 1 of 6. Db/db mice treated with 280µmol/kg of rosiglitazone

source_name: Pool of db/db control mice


title: Area X, singing 6hr, Replicate 2


title: Liver rosiglitazone 84µmol/kg biological replicate 5

description: Analysis used the pool of db/db mice as control samples for comparison to the treated mice.Biological replicate 5 of 6. Db/db mice treated with 84µmol/kg of rosiglitazone

source_name: db/db mouse treated with 84µmol/kg of rosiglitazone


title: Area X, singing 6hr, Replicate 1