title: Myoblasts_1d_old-4, biological rep8

source_name: Human myoblasts, extracted from the quadriceps of old woman; day 1 (baseline)


title: Healthy volunteer [GRDS0027_HV26_1]

status: Public on Jun 01 2015

type: RNA

city: Sophia Antipolis

first: Isabelle

last: Carlavan

address: 2400 route des colles

department: Research

country: France

institute: Galderma R&D

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix Gene Chip Scanner 3000.

data_processing: The data were analyzed with Expression Console (Affymetrix) with RMA normalization.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Human skin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA).

extract_protocol: miRNeasy (Qiagen) RNA extraction was performed according to the manufacturer's instructions.

tag: group

value: Healthy volunteer


title: Healthy volunteer [GRDS0027_HV2_2]


title: Myoblasts_old-AZA-untreated-1, biological rep1

city: Washington

first: Svetlana

last: Ghimbovschi

state: DC

address: 111 Michigan Ave., NW

department: Research Center for Genetic Medicine

country: USA

institute: Children's National Medical Center

description: mRNA gene expression data from Human myoblasts

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised (quantile normalisation),  and background was subtructed in Illumina Genome Studio program

source_name: Human old myoblasts, AZA untreated

label_protocol: Biotinylated cRNA were prepared with Illumina® TotalPrep™ -96 RNA Amplification Kit (Ambion, Austin, TX).

growth_protocol: The myoblasts were expanded in proliferative medium: DMEM supplemented with 20% FBS and then differentiated  in DMEM for 3 days.

extract_protocol: Cell pellete (myoblasts) were subjected to total RNA isolation procedure using  mirVana™ miRNA Isolation Kit (Applied Biosystems/Ambion, Austin, TX). Concentration of each RNA sample was determined by NanoDrop® spectrophotometer ND-1000 (NanoDrop Technologies, Wilmington, DE). The quality of RNA samples was assessed with Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA).

treatment_protocol: no treatment

tag: lab id

tag: Sex

value: female

tag: age


title: Myoblasts_1d_young-2, biological rep2

source_name: Human myoblasts, extracted from the quadriceps of young woman; day 1 (baseline)


title: Myoblasts_3d_old-2, biological rep5

source_name: Human myoblasts, extracted from the quadriceps of old woman; day 3 of differentiation


title: Myoblasts_1d_old-3, biological rep7


title: Myoblasts_1d_young-4, biological rep4


title: Healthy volunteer [GRDS0027_HV1_1]


city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient FM0309

hyb_protocol: Sample was hybridized on an Agilent microarray (G4470B) at 55°C for 17 hr in a rotating oven.

scan_protocol: Image at 5 um resolution was generated using an Agilent scanner G2505B and the Feature Extraction 10.7.3.1 software (Agilent Technologies) was used to obtain the microarray raw-data.

data_processing: The raw gTotalGeneSignal has been recalculated using the procedures described in Agilent Feature Extraction Software version 10.1 manual. Non-human probes, miRNAs flagged as “absent” (i.e. expressed below background levels) throughout the whole dataset and miRNAs expired according to Sanger miRBase Release 15 (April 2010) were discarded, and a quantile normalization was applied on raw data using the aroma.light package for Bioconducor. The data were then converted to obtain positive values throughout the dataset, at a minimum value of 1, and log2 transformed.

label_protocol: Labeled miRNAs were obtained from 500 ng of total RNA by ligating 5'-cytidine bisphosphate-Cy3 (pCp-Cy3, Agilent Technologies) in their 3'-ends. To enhance the ligation efficiency of the pCp-Cy3 T4 RNA ligase (Promega, Madison, WI), the total RNA was previously treated with alkaline phosphatase (Amersham, GE Healthcare, Buckinghamshire, UK) at 37°C for 30 min. The labeled RNA was purified on chromatography columns (Micro Biospin 6, Bio-Rad, Hercules, CA)

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

treatment_protocol: Peripheral blood mononuclear cells from B-CLL patients were isolated by Ficoll-Hypaque (Seromed, Biochrom KG, Berlin, Germany) density-gradient centrifugation and the proportion of CD5/CD19/CD23 triple positive B cells in the suspension was determined by direct immunofluorescence performed using a FACS-sort flow cytometer (Becton Dickinson & Co, Sunnyvale, CA) with antibodies to: CD19 FITC/PE, CD23 PE and CD5 Cy-Chrome (Becton Dickinson). If B-CLL cells were less than 90%, T cells, NK cells and monocytes were removed by negative selection using CD3, CD56, CD16, and CD14 monoclonal antibody (mAb) treatment (Becton Dickinson) followed by magnetic beads (Goat Anti-Mouse IgG Dynabeads, Dynal Biotech ASA, Oslo, Norway).

tag: igvh mutational status (fais et al. j clin invest, 1998)

value: mut


title: Myoblasts_1d_old-2, biological rep6


title: Healthy volunteer [GRDS0027_HV1_2]


title: Myoblasts_1d_young-3, biological rep3


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient FI0152


title: Myoblasts_1d_young-1, biological rep1


title: Myoblasts_1d_old-1, biological rep5


title: HROC32

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

institute: Candiolo Cancer Institute, University of Torino

description: CRC cell line

hyb_protocol: Hybridization of cRNAs (750 ng) was carried out using Illumina Human 48k gene chips (Human HT-12 V4 BeadChip)

scan_protocol: Hybridized Beadchips were scanned with the Illumina  BeadArray Reader

data_processing:
Non-normalized data were generated by the Illumina GenomeStudio software version V2011.1 . Data were Loess normalized with the Lumi R package
Signal values and detection p-values as provided by the Illumina Genome Studio software. Normalized signal values as provided by the Lumi R package.

label: Biotin

source_name: HROC32 CRC cell line, standard culture conditions

label_protocol: Synthesis of cDNA and biotinylated cRNA was performed using the IlluminaTotalPrep RNA Amplification Kit (Ambion), according to the manufacturer’s protocol using 500ng of total RNA

growth_protocol: Standard culture conditions for each cell line

extract_protocol: total RNA was extracted using miRNeasy Mini Kit (Qiagen), according to the manufacturer’s protocol, without the separation step between mRNAs and microRNAs

treatment_protocol: No treatment

tag: cell line


title: Myoblasts_3d_old-3, biological rep6


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient FB0332


title: siSTAT3_TAM_24hr_rep03

city: Boston

first: Joseph

middle: Daniel

last: Fleming

state: Massachusetts

address: 240 Longwood Ave

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard University

description:
Gene expression data.
siSTAT3 treated cells. Grown for an additional 24 hrs after tamoxifen treatment (induces transformation).

hyb_protocol: Amplified RNA was given to the Children’s Hospital Boston microarray core facility for hybridization to GeneChip Human Genome U133 Plus 2.0 gene expression arrays (Affymetrix, USA) and imaging. Affymetrix GeneChip Hybridization Oven 640 as per manufacturer recommendations.

scan_protocol: Affymetrix GeneChip Scanner 3000 as per manufacturer recommendations.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: MCF10A-ER-Src, siSTAT3, tamoxifen, 24hr

label_protocol: RNA was prepared for arrays using 3’ IVT Express kit (Affymetrix, USA) as per manufacturer protocol -- 100 ng RNA, 15 amplification cycles.

growth_protocol: A detailed protocol can be found at: www.encodeproject.org/. Briefly, cells were grown in a 5% CO2, humidified, atmosphere at 37C in the following media: 2x 500ml DMEM/F12, 50ml charcoal stripped horse serum (CSHS, 5% final), 10ml pen/strep (1X), 200ul EGF (20ng/ml final), 500ul hydrocortisone (0.5ug/ml final), 100ul Cholera toxin (100ng/ml final) and 1ml Insulin (10ug/ml final).

extract_protocol: RNA was harvested after 4 or 24 hr post treatment.

treatment_protocol: Cells were seeded in 6-well plates containing 25 nM ON-TARGETplus SMARTpool STAT3 or ON-TARGETplus Non-targeting Pool and after 48 hr of growth were treated with ethanol or tamoxifen (1 µM, 4-hydroxytamoxifen) for 4 hr or 24 hr.

tag: sirna type

tag: treatment

value: tamoxifen

tag: time (hrs)


title: Myoblasts_3d_old-1, biological rep4


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient FC0075


title: Myoblasts_3d_young-3, biological rep3

source_name: Human myoblasts, extracted from the quadriceps of young woman; day 3 of differentiation


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient FA0294


title: Myoblasts_3d_young-1, biological rep1

source_name: Human myoblasts, extracted from the quadriceps of young man; day 3 of differentiation

value: male


title: siSTAT3_TAM_24hr_rep02


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient ET0128

value: unmut


title: siSTAT3_TAM_04hr_rep03

description:
Gene expression data.
siSTAT3 treated cells. Grown for an additional 4 hrs after tamoxifen treatment (induces transformation).

source_name: MCF10A-ER-Src, siSTAT3, tamoxifen, 4hr


title: Myoblasts_3d_young-2, biological rep2


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient FA0347


title: VED-3-H

city: Perth

first: Montse

last: Saladie-Foraste

state: Western Australia

address: 35 Stirling Highway; Crawley

department: School of Chemistry and Biochemistry

country: Australia

institute: University of Western Australia

description: SAMPLE 41

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: Raw data were analysed without background subtraction using the oligo package from Bioconductor (http://www.bioconductor.org). Background was corrected by the robust multi-array average (RMA) method. The data were normalized by quantiles, model-fitted using Tukey’s Median Polish method and transformed into log2 values. Differentially expressed genes were extracted using the Bioconductor Microarray Significant Profiles (MaSigPro) R package for the analysis of single and multiseries time course microarray experiments [Conesa et al. 2006]. MaSigPro follows a two step regression strategy to find genes with significant temporal expression changes and significant differences between experimental groups. For our experiments with four time points a cubic regression model (degree = 3) was defined. First, the global model was adjusted by the least-squared technique to identify differentially expressed genes, and significance was assessed by applying a false discovery rate (Q=0.01). Second, a variable selection procedure was applied to find significant variables for each gene, for which a stepwise regression was employed (step.method = two.ways.backward, α=0.01). Then, lists of differentially expressed genes according to each variable were generated (rsq=0.6). After the MaSigPro analysis, a cut-offoflog2 (-fold difference) ≥1 (i.e. at least two-fold difference) was applied to designate genes as differentially expressed. Genes whose expression did not change were excluded to minimize background noise

organism: Cucumis melo

source_name: Vedrantais Harvest fruit Rep3

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Melon (Cucumis melo L.) plants were grown under the same greenhouse conditions as described in [Eduardo et al. 2005].

extract_protocol: Total RNA from three different biological replicates for each stage and genotype was isolated from mesocarp tissue using a Plant RNeasy® Mini Kit (Qiagen, Hilden, Germany). RNA was treated with RNAse free TURBO-DNase I (Turbo-DNA-freeTM Kit; Applied Biosystems, Ambion®, USA) for 30 min at 37 °C, before use as a template for cDNA synthesis. RNA quality was assessed by agarose gel electrophoresis, spectophotometric analysis with a Nanodrop ND-1000 (NanoDrop® Technologies, Wilmington, Delaware) and analysis on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). High-quality RNA samples were reversed transcribed into cDNA using a SuperScript™ double-stranded cDNA synthesis kit (Invitrogen, Carlsbad, CA). The integrity of cDNA was assessed as described above for RNA. A minimum of 2.5 µg of cDNA per sample was supplied for labelling and hybridization on custom-made melon microarrays.

treatment_protocol: Flowers (one per plant) were hand pollinated to precisely determine the stage of development, and fruits were harvested at 15, 25 and 35 Days after Pollination (DAP) and at maturity as determined by fruit abscission in Ved (45 DAP) and Dulce (50 DAP), or by the maximal sucrose content in PI (50 DAP) and PS (55 DAP). For each genotype and sampling time, flesh (mesocarp) was collected from three separate fruits. Samples were taken from the middle of the fruit, avoiding rind, seed and jelly tissues.

tag: cultivar

value: Vedrantais

tag: Stage

value: Harvest

tag: tissue

value: fruit

tag: climacteric status

value: climacteric


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient EG0341


title: VED-3-35d

description: SAMPLE 40

source_name: Vedrantais 35 DAP fruit Rep3

value: 35 DAP


title: VED-3-25d

description: SAMPLE 39

source_name: Vedrantais 25 DAP fruit Rep3

value: 25 DAP


title: siSTAT3_TAM_04hr_rep02


title: VED-3-15d

description: SAMPLE 38

source_name: Vedrantais 15 DAP fruit Rep3

value: 15 DAP


title: siSTAT3_EtOH_24hr_rep02

description:
Gene expression data.
siSTAT3 treated cells. Grown for an additional 24 hrs after control ethanol treatment.

source_name: MCF10A-ER-Src, siSTAT3, ethanol, 24hr

value: ethanol


title: siSTAT3_TAM_04hr_rep01


title: VED-2-H

description: SAMPLE 37

source_name: Vedrantais Harvest fruit Rep2


title: VED-2-35d

description: SAMPLE 36

source_name: Vedrantais 35 DAP fruit Rep2


title: siSTAT3_EtOH_04hr_rep03

description:
Gene expression data.
siSTAT3 treated cells. Grown for an additional 4 hrs after control ethanol treatment.

source_name: MCF10A-ER-Src, siSTAT3, ethanol, 4hr


title: VED-1H

description: SAMPLE 34

source_name: Vedrantais Harvest fruit Rep1


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient EB0042


title: VED-2-15d

description: SAMPLE 35

source_name: Vedrantais 15 DAP fruit Rep2


title: VED-1-25d

description: SAMPLE 32

source_name: Vedrantais 25 DAP fruit Rep1


title: VED-1-35d

description: SAMPLE 33

source_name: Vedrantais 35 DAP fruit Rep1


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient DT0300


title: siSTAT3_EtOH_24hr_rep01


title: siSTAT3_EtOH_04hr_rep02


title: VED-1-15d

description: SAMPLE 31

source_name: Vedrantais 15 DAP fruit Rep1


title: PS-3-H

description: SAMPLE 30

source_name: Piel de sapo Harvest fruit Rep3

value: Piel de Sapo

value: non-climacteric


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient DR0312


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient DG0193


title: siSTAT3_EtOH_04hr_rep01


title: PS-3-35d

description: SAMPLE 29

source_name: Piel de sapo 35 DAP fruit Rep3


title: PS-2-35d

description: SAMPLE 25

source_name: Piel de sapo 35 DAP fruit Rep2


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient DF0319


title: PS-3-25d

description: SAMPLE 28

source_name: Piel de sapo 25 DAP fruit Rep3


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient DG0186


title: siNEG_TAM_24hr_rep03

description:
Gene expression data.
siNEG control treated cells. Grown for an additional 24 hrs after tamoxifen treatment (induces transformation).

source_name: MCF10A-ER-Src, siNEG, tamoxifen, 24hr

value: siNEG


title: PS-1-35d

description: SAMPLE 23

source_name: Piel de sapo 35 DAP fruit Rep1


title: PS-2-H

description: SAMPLE 26

source_name: Piel de sapo Harvest fruit Rep2


title: siNEG_TAM_24hr_rep02


title: siNEG_TAM_24hr_rep01


title: PS-1-15d

description: SAMPLE 22

source_name: Piel de Sapo 15 DAP fruit Rep1


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient DE0279


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient DE0085


title: PS-3-15d

description: SAMPLE 27

source_name: Piel de Sapo 15 DAP fruit Rep3


title: PS-1-H

description: SAMPLE 24

source_name: Piel de sapo Harvest fruit Rep1


title: siNEG_TAM_04hr_rep03

description:
Gene expression data.
siNEG control treated cells. Grown for an additional 4 hrs after tamoxifen treatment (induces transformation).

source_name: MCF10A-ER-Src, siNEG, tamoxifen, 4hr


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient DD0280


title: PI-3H

description: SAMPLE 21

source_name: PI 161375 Harvest fruit Rep3


title: PI-2-H

description: SAMPLE 17

source_name: PI 161375 Harvest fruit Rep2


title: PI-3-35d

description: SAMPLE 20

source_name: PI 161375 35 DAP fruit Rep3


title: PI-3-15d

description: SAMPLE 18

source_name: PI 161375 15 DAP fruit Rep3


title: PI-3-25d

description: SAMPLE 19

source_name: PI 161375 25 DAP fruit Rep3


title: siNEG_TAM_04hr_rep02


title: siNEG_TAM_04hr_rep01


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient DC0371


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient DA0215


title: PI-2-25d

description: SAMPLE 15

source_name: PI 161375 25 DAP fruit Rep2


title: PI-2-35d

description: SAMPLE 16

source_name: PI 161375 35 DAP fruit Rep2


title: siNEG_EtOH_24hr_rep03

description:
Gene expression data.
siNEG control treated cells. Grown for an additional 24 hrs after control ethanol treatment.

source_name: MCF10A-ER-Src, siNEG, ethanol, 24hr


title: PI-2-15d

description: SAMPLE 14

source_name: PI 161375 15 DAP fruit Rep2


title: PI-1-H

description: SAMPLE 13

source_name: PI 161375 Harvest fruit Rep1


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient DA0094


title: siNEG_EtOH_24hr_rep02


title: siNEG_EtOH_24hr_rep01


title: siNEG_EtOH_04hr_rep03

description:
Gene expression data.
siNEG control treated cells. Grown for an additional 4 hrs after control ethanol treatment.

source_name: MCF10A-ER-Src, siNEG, ethanol, 4hr


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient DA0029


title: PI-1-35d

description: SAMPLE 12

source_name: PI 161375 35 DAP fruit Rep1


title: siNEG_EtOH_04hr_rep02


title: DUL-3-35d

description: SAMPLE 9

source_name: Dulce 35 DAP fruit Rep3

value: Dulce


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient CS0290


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient CS0030


title: PI-1-25d

description: SAMPLE 11

source_name: PI 161375 25 DAP fruit Rep1


title: DUL-3-25d

description: SAMPLE 8

source_name: Dulce 25 DAP fruit Rep3


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient CR0297


title: DUL-2-35d

description: SAMPLE 6

source_name: Dulce 35 DAP fruit Rep2


title: DUL-3-H

description: SAMPLE 10

source_name: Dulce Harvest fruit Rep3


title: DUL-2-H

description: SAMPLE 7

source_name: Dulce Harvest fruit Rep2


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient CR0159


title: DUL-2-15d

description: SAMPLE 5

source_name: Dulce 15 DAP fruit Rep2


title: DUL-1-35d

description: SAMPLE 3

source_name: Dulce 35 DAP fruit Rep1


title: DUL-1-25d

description: SAMPLE 2

source_name: Dulce 25 DAP fruit Rep1


title: DUL-1-15d

description: SAMPLE 1

source_name: Dulce 15 DAP fruit Rep1


title: SaOS-2_day14_rep2

city: Bologna

first: Andrea

last: Grilli

state: Italy

address: v. di Barbiano 1/10

department: Laboratory of Experimental Oncology

institute: Rizzoli Orthopaedic Institute

description:
Saos2_g14
SaOS-2 cell lines maintained in differentiation medium for 14 days

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data were analyzed with Bioconductor affy package, using RMA algorithm for normalization and summarization.

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

growth_protocol: Cells were routinely cultured in Iscove's modified Dulbecco's medium (IMDM), supplemented with 100 U/ml penicillin, 100 Î¼g/ml streptomycin, and 10% inactivated fetal bovine serum (FBS) and maintained at 37Â°C in a humidified 5% CO2 atmosphere. 4 days after cell seeding, cells were exposed to specific osteogenic medium and maintained in differentiative conditions up to 21-28 days. Medium was renewed every 4 days. Cultures were harvested at various time points to collect total RNA or proteins.

extract_protocol: Total RNA was extracted by the TRIzol extraction kit (Invitrogen). Quality and quantity of RNA samples were assessed with NanoDrop analysis (NanoDrop Technologies).

treatment_protocol: Stable transfectants expressing CD99 were obtained from the Saos-2 cell lines (Sa/CD99wt22, Sa/CD99wt36) by using calcium-phosphate transfection method. Transfectants were selected in IMDM containing 10% FBS and 500 Î¼g/ml neomycin

tag: cell type

value: osteosarcoma cell line

tag: transfected with

value: none (parental)

tag: time point

value: 14 days


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient FD0404


title: LymphNode_Dog4_Resistant_rep1

city: Tokyo

first: Hirotaka

last: Tomiyasu

state: Not Applicable

address: 1-1-1 Yayoi, Bunkyo-ku

department: Veterinary Internal Medicine

country: Japan

institute: the University of Tokyo

description: Gene expression of lymphoma tissue sample of Dog 4 at resistant phase

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >20.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 1x Agilent Fragmentation buffer and 2x Agilent Gene Expression Blocking Agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 μl of 2x Agilent Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent Canine oligo DNA microarray ver.2 (4×44K) for 17 hours at 65 °C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed with Gene Expression Wash Buffer Kit, then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner G2505C using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5μm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 021193_D_F_20080808) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Canis lupus familiaris

source_name: LymphNode, Dog4, Resistant, rep1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using Low Input Quick Amp Labeling Kit, one-color (Agilent Technologies) and One-Color RNA Spike-In Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was isolated from tumor cell samples using RNeasy Mini Kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. The protocol includes an on-column DNase digestion.  RNA quantity and qualtiy were assessed using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) and RNA integrity numbers were confirmed as above 9.0.

treatment_protocol: Tumor cell samples derived from peripheral lymph nodes were obtained from 4 dogs with lymphoma at both drug-sensitive and drug-resistant phases by fine needle aspiration. The samples had been stored in RNA later (Ambion, Austin, TX) at -20 ºC until batch analysis.

value: lymph node

tag: phenotype

value: B-cell lymphoma

tag: phase

value: drug-resistant

value: Spayed female

tag: breed

value: French Bulldog


title: LymphNode_Dog4_Resistant_rep3

source_name: LymphNode, Dog4, Resistant, rep3

tag: Sex


title: siNEG_EtOH_04hr_rep01


title: SaOS-2_day0_rep2

description:
Saos2_g0
SaOS-2 cell lines maintained in differentiation medium for 0 days

value: 0 day


title: DUL-1-H

description: SAMPLE 4

source_name: Dulce Harvest fruit Rep1

value: Harvest

value: fruit

value: climacteric


title: LymphNode_Dog4_Resistant_rep2

source_name: LymphNode, Dog4, Resistant, rep2

tag: age


title: SaOS-2_day14_rep1

description:
Saos1_g14
SaOS-2 cell lines maintained in differentiation medium for 14 days


title: LymphNode_Dog4_Sensitive_rep3

description: Gene expression of lymphoma tissue sample of Dog 4 at sensitive phase

source_name: LymphNode, Dog4, Sensitive, rep3

value: drug-sensitive


title: SaOS-2_day0_rep1

description:
Saos1_g0
SaOS-2 cell lines maintained in differentiation medium for 0 days


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient CP0109

tag: igvh mutational status (fais et al. j clin invest, 1998)

value: mut


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient CP0104

value: unmut


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient CR0203


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient CM0289


title: LymphNode_Dog4_Sensitive_rep1

source_name: LymphNode, Dog4, Sensitive, rep1


title: LymphNode_Dog4_Sensitive_rep2

source_name: LymphNode, Dog4, Sensitive, rep2


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient CL0317


title: LymphNode_Dog3_Resistant_rep1

description: Gene expression of lymphoma tissue sample of Dog 3 at resistant phase

source_name: LymphNode, Dog3, Resistant, rep1

value: Castrated male


title: LymphNode_Dog3_Sensitive_rep3

description: Gene expression of lymphoma tissue sample of Dog 3 at sensitive phase

source_name: LymphNode, Dog3, Sensitive, rep3


title: LymphNode_Dog3_Resistant_rep3

source_name: LymphNode, Dog3, Resistant, rep3


title: LymphNode_Dog3_Sensitive_rep2

source_name: LymphNode, Dog3, Sensitive, rep2


title: siSTAT3_EtOH_24hr_rep03

description:
Gene expression data.
siSTAT3 treated cells. Grown for an additional 24 hrs after control ethanol treatment.

source_name: MCF10A-ER-Src, siSTAT3, ethanol, 24hr

tag: cell line

value: ethanol


title: LymphNode_Dog2_Resistant_rep2

description: Gene expression of lymphoma tissue sample of Dog 2 at resistant phase

source_name: LymphNode, Dog2, Resistant, rep2

value: Male

value: Doberman


title: LymphNode_Dog3_Sensitive_rep1

source_name: LymphNode, Dog3, Sensitive, rep1


title: Sa/CD99_wt36_day0

description:
wt36_g0
SaOS-2 cell lines stably transfected with CD99 and maintained in differentiation medium for 0 days

value: osteosarcoma cell line


title: Sa/CD99_wt22_day14

description:
wt22_g14
SaOS-2 cell lines stably transfected with CD99 and maintained in differentiation medium for 14 days

value: 14 days


title: LymphNode_Dog3_Resistant_rep2

source_name: LymphNode, Dog3, Resistant, rep2

value: lymph node

value: B-cell lymphoma


title: LymphNode_Dog2_Sensitive_rep3

description: Gene expression of lymphoma tissue sample of Dog 2 at sensitive phase

source_name: LymphNode, Dog2, Sensitive, rep3


title: LymphNode_Dog2_Resistant_rep3

source_name: LymphNode, Dog2, Resistant, rep3

value: drug-resistant


title: LymphNode_Dog2_Resistant_rep1

source_name: LymphNode, Dog2, Resistant, rep1


title: Sa/CD99_wt22_day0

description:
wt22_g0
SaOS-2 cell lines stably transfected with CD99 and maintained in differentiation medium for 0 days


title: Sa/CD99_wt36_day14

description:
wt36_g14
SaOS-2 cell lines stably transfected with CD99 and maintained in differentiation medium for 14 days


title: SaOS-2_day7_rep1

description:
Saos1_g7
SaOS-2 cell lines maintained in differentiation medium for 7 days

value: none (parental)

value: 7 days


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient CM0246


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient CG0204


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient CM0057


title: Sa/CD99_wt22_day7

description:
wt22_g7
SaOS-2 cell lines stably transfected with CD99 and maintained in differentiation medium for 7 days


title: LymphNode_Dog2_Sensitive_rep2

source_name: LymphNode, Dog2, Sensitive, rep2


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient CI0005


title: LymphNode_Dog2_Sensitive_rep1

source_name: LymphNode, Dog2, Sensitive, rep1


title: LymphNode_Dog1_Sensitive_rep3

description: Gene expression of lymphoma tissue sample of Dog 1 at sensitive phase

source_name: LymphNode, Dog1, Sensitive, rep3

value: Shih Tzu


title: SaOS-2_day7_rep2

description:
Saos2_g7
SaOS-2 cell lines maintained in differentiation medium for 7 days


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient CG0166


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient CF0003


title: LymphNode_Dog1_Resistant_rep1

description: Gene expression of lymphoma tissue sample of Dog 1 at resistant phase

source_name: LymphNode, Dog1, Resistant, rep1


title: Sa/CD99_wt36_day7

description:
wt36_g7
SaOS-2 cell lines stably transfected with CD99 and maintained in differentiation medium for 7 days


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient CE0078


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient CE0399


title: LymphNode_Dog1_Resistant_rep2

source_name: LymphNode, Dog1, Resistant, rep2


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient CC0311


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient CD0310


title: LymphNode_Dog1_Resistant_rep3

source_name: LymphNode, Dog1, Resistant, rep3


title: Clockwise shifts_fourteen days recovery_20h_nr364

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

country: Netherlands

institute: Natl. Inst. Public Health & Environment

description: channel #2 in FTR file corresponds to Cy5-labeled common reference

hyb_protocol: Samples were hybridized to Nimblegen Mus musculus 12 x 135 k microarrays (Roche NimbleGen, Germany). This type of microarray contains 44,170 gene probes with three spots per probe.

scan_protocol: Slides were scanned with an Agilent G2565CA DNA microarray scanner. Feature extraction was performed with NimbleScan v2.5 (Roche NimbleGen), resulting in a table containing individual probe signal intensities for both dyes.

data_processing: The raw data were subjected to a set of quality control checks to ensure comparable signal average and distribution. Raw microarray data for gene-coding probes were normalized in R (www.r-project.org) using a four step approach [Pennings et al, PLoS One, 2011. 6(4): p. e18866.]: (1) natural log-transformation, (2) quantile normalization of all scans, (3) correcting the sample spot signal for the corresponding reference spot signal and (4) averaging data from replicate probe spots. The normalized data of 44,170 probes were further analysed in R and Excel (Microsoft Corporation, USA).

organism: Mus musculus

source_name: liver RNA

label_protocol: RNA was processed for gene expression analysis using the methods described in [Pennings et al, PLoS One, 2011. 6(4): p. e18866.]. Experimental samples (each corresponding to RNA from one individual mouse) were labelled with Cy3 and the common reference sample (made by pooling equimolar amounts of RNA from experimental samples) was labelled with Cy5.

growth_protocol: Female FVB mice, 8 to 12 weeks of age, were kept under a normal 12:12 hour light-dark (LD) cycle for approximately three weeks, with Zeitgeber Time 0 (ZT0) corresponding to lights on. Animals were group-housed and food and water were provided ad libitum.

extract_protocol: RNA was extracted from livers (n=4 per time point at baseline and n= 2 per time point for the CCW and CW groups) using the miRNeasy Mini Kit (Qiagen Benelux, Venlo, The Netherlands). RNA concentrations were measured using a NanoDrop ND-1000 Spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA), and RNA quality was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Amstelveen, the Netherlands).

treatment_protocol: Prior to the first shift, animals (n=24) were sacrificed around the clock at four hour intervals (n=4 at each time point). Subsequently, the remaining group of animals underwent six shifts in either a clockwise (CW) or counterclockwise (CCW) rotating light schedule. Specifically, mice were exposed to a phase delay or phase advance of eight hours every five days, respectively. After one shift, six shifts, five days recovery and fourteen days recovery n=30 animals per group were sacrificed around the clock with four hour intervals (n=5 per time point).

tag: strain

value: FVB

tag: light rotation

value: Clockwise shifts

tag: group

value: fourteen days recovery

tag: zeitgeber time

tag: mouse id


title: LymphNode_Dog1_Sensitive_rep2

source_name: LymphNode, Dog1, Sensitive, rep2

tag: tissue

value: drug-sensitive


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient CA0345

value: mut


title: 3293 - mAdbID:99989

city: omaha

first: Javeed

last: Iqbal

state: NE

address: 40th street

department: Pathology and Microbiology

institute: University of Nebraska Medical Center

description: mAdb experiment ID: 99989

hyb_protocol: Affymetrix Hybridization Protocol Other: The labeled cRNAs were hybridized to HG-U133 plus 2.0 Affymetrix GeneChip arrays (Affymetrix). Arrays were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scannning Protocol Other: The chips were scanned with an Affymetrix GeneChip Scanner 3000 and subsequent images analyzed by the use of GCOS 1.4 (Affymetrix).

data_processing:
MAS 5.0 Data Processing Protocol
Calculation Method: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label_protocol:
Affymetrix Labeling Protocol
Other: The total RNAs (1 ug) were amplified and labeled following the one-cycle target labeling protocol (Affymetrix).

extract_protocol:
AllPrep DNA/RNA/isolation Kit
Other: Total RNA was extracted with AllPrep DNA/RNA/isolation Kit (Qiagen), according to the manufacturer's instructions.

tag: gender

value: male

tag: disease state

value: Peripheral T-cell lymphoma (PTCL)

tag: individual


title: Clockwise shifts_fourteen days recovery_12h_nr353


title: LymphNode_Dog1_Sensitive_rep1

source_name: LymphNode, Dog1, Sensitive, rep1

value: Male


title: Clockwise shifts_fourteen days recovery_20h_nr362


title: 3288 - mAdbID:99984

description: mAdb experiment ID: 99984

tag: clinical info

value: Follow up status:alive

value: Follow up years:3.852156057


title: Clockwise shifts_fourteen days recovery_12h_nr352


title: 3292 - mAdbID:99988

description: mAdb experiment ID: 99988


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient CA0160


title: Clockwise shifts_fourteen days recovery_16h_nr358


title: Clockwise shifts_fourteen days recovery_16h_nr357


title: 3289 - mAdbID:99985

description: mAdb experiment ID: 99985


title: 3286 - mAdbID:99963

description: mAdb experiment ID: 99963


title: 3291 - mAdbID:99987

description: mAdb experiment ID: 99987

value: Follow up years:2.206707734


title: 3284 - mAdbID:99961

description: mAdb experiment ID: 99961

value: lymph node


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient CA0101

value: unmut


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient CA0058


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient CC0244


title: Clockwise shifts_fourteen days recovery_8h_nr348


title: 3280 - mAdbID:99957

description: mAdb experiment ID: 99957


title: Clockwise shifts_fourteen days recovery_8h_nr347


title: Clockwise shifts_fourteen days recovery_4h_nr343


title: 3243 - mAdbID:99713

description: mAdb experiment ID: 99713

value: female

value: Follow up status:dead

value: Follow up years:0.093086927


title: 3246 - mAdbID:99716

description: mAdb experiment ID: 99716

value: Follow up years:0.399726215


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient BV0176


title: Clockwise shifts_fourteen days recovery_4h_nr342

value: FVB


title: 3242 - mAdbID:99712

description: mAdb experiment ID: 99712

value: Follow up years:1.040383299


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient BP0326


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient BS0214


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient BR0218


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient BV0229


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient BG0236


title: Clockwise shifts_fourteen days recovery_0h_nr337

value: Clockwise shifts

value: fourteen days recovery


title: 3239 - mAdbID:99710

description: mAdb experiment ID: 99710


title: 3238 - mAdbID:99627

description: mAdb experiment ID: 99627

value: Follow up years:4.31211499


title: Clockwise shifts_five days recovery_16h_nr298

value: five days recovery


title: 3235 - mAdbID:99626

description: mAdb experiment ID: 99626

value: Peripheral T-cell lymphoma (PTCL)

value: Follow up years:2.882956879


title: Clockwise shifts_five days recovery_20h_nr303


title: 3233 - mAdbID:99624

description: mAdb experiment ID: 99624

value: male

value: Follow up status:alive

value: Follow up years:1.180013689


title: 3232 - mAdbID:99623

description: mAdb experiment ID: 99623

value: lymph node


title: Clockwise shifts_fourteen days recovery_0h_nr338


title: Clockwise shifts_five days recovery_20h_nr302


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient BF0316

value: mut


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient BG0163


title: Clockwise shifts_five days recovery_12h_nr293


title: 3231 - mAdbID:99622

description: mAdb experiment ID: 99622

value: female


title: Clockwise shifts_five days recovery_12h_nr292


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient BL0162


title: 3224 - mAdbID:99621

description: mAdb experiment ID: 99621

value: Follow up years:6.338124572


title: 3230 - mAdbID:99525

description: mAdb experiment ID: 99525

value: Follow up years:0.005475702


title: Clockwise shifts_five days recovery_8h_nr288


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient BE0192

value: unmut


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient BF0217


title: Clockwise shifts_five days recovery_8h_nr287

description: channel #2 in FTR file corresponds to Cy5-labeled common reference

value: FVB


title: Clockwise shifts_five days recovery_4h_nr283


title: 3228 - mAdbID:99523

description: mAdb experiment ID: 99523

value: Follow up years:1.166324435


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient BB0238


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient BB0245


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient AS0012


title: Clockwise shifts_five days recovery_0h_nr278

value: Clockwise shifts


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient BC0047


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient AR0242


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient BV0061


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient AR0131


title: Human chronic lymphocytic leukemia patient AR0090

description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient AM0034


title: Clockwise shifts_two shifts_20h_nr242

value: two shifts


title: Clockwise shifts_five days recovery_0h_nr277


title: 3229 - mAdbID:99524

description: mAdb experiment ID: 99524

value: Follow up years:0.199863107


title: 3227 - mAdbID:99522

description: mAdb experiment ID: 99522

value: Follow up years:0.060232717


title: 3222 - mAdbID:99518

description: mAdb experiment ID: 99518

value: Peripheral T-cell lymphoma (PTCL)

value: Follow up years:0.52019165


title: Clockwise shifts_two shifts_12h_nr232


title: Clockwise shifts_two shifts_12h_nr233


title: 3013 - mAdbID:98360

description: mAdb experiment ID: 98360

value: Follow up status:dead

value: Follow up years:0.079397673


title: 3226 - mAdbID:99521

description: mAdb experiment ID: 99521


title: Clockwise shifts_two shifts_20h_nr243


title: Clockwise shifts_two shifts_16h_nr237


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient AM0270


title: Clockwise shifts_two shifts_16h_nr238


title: 3005 - mAdbID:98368

description: mAdb experiment ID: 98368

value: male

value: Follow up years:0.271047228


title: 2376 - mAdbID:99208

description: mAdb experiment ID: 99208

value: lymph node

value: Follow up years:0.030116359


title: Clockwise shifts_five days recovery_4h_nr284

value: five days recovery


title: 3010 - mAdbID:98363

description: mAdb experiment ID: 98363

value: Follow up status:alive

value: Follow up years:4.859685147


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient AM0106

value: mut


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient AM0067

value: unmut


title: 3015 - mAdbID:98358

description: mAdb experiment ID: 98358

value: female

value: Follow up years:2.387405886


title: Clockwise shifts_two shifts_8h_nr228

value: FVB

value: Clockwise shifts

value: two shifts


title: Clockwise shifts_two shifts_4h_nr224


title: Clockwise shifts_two shifts_4h_nr223


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient AG0403


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient AM0220


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient AG0136


title: Clockwise shifts_two shifts_0h_nr218


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient AB0350


title: Clockwise shifts_two shifts_8h_nr227


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient AG0268


title: 2065 - mAdbID:97027

description: mAdb experiment ID: 97027

value: Peripheral T-cell lymphoma (PTCL)

value: Follow up years:2.647501711


title: Lympoblast.10 - mAdbID:126566

description: mAdb experiment ID: 126566


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient AA0284


title: Clockwise shifts_one shift_20h_nr182A

description: channel #2 in FTR file corresponds to Cy5-labeled common reference

value: one shift


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient AC0120


title: Clockwise shifts_two shifts_0h_nr217


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient AA0051


title: AITL.60 - mAdbID:126565

description: mAdb experiment ID: 126565

value: Follow up status:dead

value: Follow up years:1.519166667


title: Clockwise shifts_one shift_16h_nr179A


title: Clockwise shifts_one shift_12h_nr173


title: Clockwise shifts_one shift_8h_nr168


title: Lympoblast.7 - mAdbID:126569

description: mAdb experiment ID: 126569

value: lymph node


title: Clockwise shifts_one shift_12h_nr172


title: Clockwise shifts_one shift_8h_nr167


title: Sabre_Diet_Liver_32

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

country: Germany

institute: FBN Dummerstorf

description: Gene expression data from liver sample of offspring

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42C on Affymetrix GeneChip Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500 and BioConductor.

organism: Sus scrofa

source_name: Liver

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (Expression Analysis Technical Manual, 2009, Affymetrix).

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

value: liver

tag: gestation diet

value: methyl-enriched diet

tag: ontogenetic stage

value: 91 dpc

value: Pietrain


title: Clockwise shifts_one shift_4h_nr163


title: NKt.71 - mAdbID:126558

description: mAdb experiment ID: 126558

value: Follow up years:0.06


title: Clockwise shifts_one shift_4h_nr162


title: Sabre_Diet_Liver_31

tag: breed


title: Clockwise shifts_one shift_0h_nr158A


title: Sabre_Diet_Liver_27

value: control diet


title: Sabre_Diet_Liver_30


title: Sabre_Diet_Liver_29


title: Sabre_Diet_Liver_26


title: Counterclockwise shifts_fourteen days recovery_20h_nr333

value: Counterclockwise shifts

value: fourteen days recovery


title: Sabre_Diet_Liver_28


title: Counterclockwise shifts_fourteen days recovery_16h_nr327

value: FVB


title: Clockwise shifts_one shift_0h_nr157A

value: Clockwise shifts


title: Sabre_Diet_Liver_25


title: Counterclockwise shifts_fourteen days recovery_20h_nr332


title: PTCL.66 - mAdbID:126554

description: mAdb experiment ID: 126554

value: Follow up status:alive

value: Follow up years:0.049166667


title: NKt.57 - mAdbID:126549

description: mAdb experiment ID: 126549

value: Peripheral T-cell lymphoma (PTCL)

value: Follow up years:0.725833333


title: NKt.45 - mAdbID:126550

description: mAdb experiment ID: 126550


title: Counterclockwise shifts_fourteen days recovery_16h_nr328


title: Counterclockwise shifts_fourteen days recovery_12h_nr323


title: Clockwise shifts_one shift_16h_nr178A

value: one shift


title: 2066 - mAdbID:97026

description: mAdb experiment ID: 97026

value: male

value: Follow up years:0.284736482


title: Clockwise shifts_five days recovery_16h_nr297

value: five days recovery


title: Sabre_Diet_Liver_22

value: liver

value: methyl-enriched diet

value: 63 dpc


title: Counterclockwise shifts_fourteen days recovery_8h_nr317


title: Sabre_Diet_Liver_21

value: Pietrain


title: Nkt.48 - mAdbID:126561

description: mAdb experiment ID: 126561

value: lymph node


title: Sabre_Diet_Liver_24

value: control diet

value: 91 dpc


title: Counterclockwise shifts_fourteen days recovery_12h_nr322

value: FVB

value: Counterclockwise shifts

value: fourteen days recovery


title: Sabre_Diet_Liver_23


title: Counterclockwise shifts_fourteen days recovery_4h_nr313


title: Sabre_Diet_Liver_19


title: Sabre_Diet_Liver_18


title: Sabre_Diet_Liver_17


title: Counterclockwise shifts_fourteen days recovery_0h_nr307


title: Counterclockwise shifts_fourteen days recovery_0h_nr309


title: Sabre_Diet_Liver_14


title: Sabre_Diet_Liver_20


title: Counterclockwise shifts_five days recovery_16h_nr269


title: Counterclockwise shifts_five days recovery_20h_nr273


title: Sabre_Diet_Liver_12


title: Sabre_Diet_Liver_16


description: MicroRNA profiling data from Human chronic lymphocytic leukemia patient AS0407

value: mut


title: Counterclockwise shifts_five days recovery_12h_nr262


title: AITL.67 - mAdbID:126522

description: mAdb experiment ID: 126522

value: Peripheral T-cell lymphoma (PTCL)

value: Follow up status:dead

value: Follow up years:9.020833333


title: Counterclockwise shifts_five days recovery_16h_nr268


title: Sabre_Diet_Liver_13


title: Counterclockwise shifts_five days recovery_12h_nr264


title: Counterclockwise shifts_fourteen days recovery_4h_nr312


title: Human chronic lymphocytic leukemia patient AM0034

value: unmut


title: Counterclockwise shifts_fourteen days recovery_8h_nr318


title: Clockwise shifts_one shift_20h_nr183A

value: Clockwise shifts

value: one shift


title: Counterclockwise shifts_five days recovery_8h_nr257

value: five days recovery


title: Sabre_Diet_Liver_11

value: liver


title: Counterclockwise shifts_five days recovery_8h_nr258


title: Sabre_Diet_Liver_9

value: methyl-enriched diet

value: 35 dpc


title: Counterclockwise shifts_five days recovery_4h_nr253


title: Sabre_Diet_Liver_7

value: Pietrain


title: Sabre_Diet_Liver_8


title: Sabre_Diet_Liver_4

value: control diet


title: Counterclockwise shifts_five days recovery_20h_nr272


title: Counterclockwise shifts_five days recovery_4h_nr252


title: Sabre_Diet_Liver_10


title: Counterclockwise shifts_two shifts_20h_nr213

value: two shifts


title: PTCL.55 - mAdbID:126512

description: mAdb experiment ID: 126512

value: lymph node


title: PTCL.34 - mAdbID:126508

description: mAdb experiment ID: 126508

value: Follow up years:0.035833333


title: Sabre_Diet_Liver_6


title: Counterclockwise shifts_two shifts_20h_nr212

value: FVB

value: Counterclockwise shifts


title: Counterclockwise shifts_five days recovery_0h_nr248


title: Sabre_Diet_Liver_1


title: Counterclockwise shifts_five days recovery_0h_nr247


title: Counterclockwise shifts_two shifts_8h_nr198


title: Counterclockwise shifts_two shifts_12h_nr204


title: Sabre_Diet_Liver_2


title: Counterclockwise shifts_two shifts_16h_nr208


title: Counterclockwise shifts_two shifts_16h_nr207


title: Smoke exposure IL33  (RE624_31)

city: Gaithersburg

first: Zheng

last: Liu

address: One Medimmune Way

institute: Medimmune LLC

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on mouse genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Bioconductor package fRMA

source_name: Lung

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 400 ng total RNA  (Expression Analysis Technical Manual, Rev 3, Affymetrix).

extract_protocol: Total RNA isolation using RNeasy Mini Kit (Qiagen cat #: 74104) or RNeasy Protect Mini Kit (Qiagen cat #: 74124) followed by GLOBINclear™ Protocol (Invitrogen cat #: AM1981) according to the manufacturer's instructions.

tag: exposure

value: cigarette smoke

tag: treatment

value: lung


title: Counterclockwise shifts_two shifts_12h_nr203


title: Sabre_Diet_Liver_5


title: Sabre_Diet_Liver_15

value: 63 dpc


title: Smoke exposure IL33  (RE624_30)


title: Counterclockwise shifts_two shifts_4h_nr193


title: 3345 - mAdbID:105970

description: mAdb experiment ID: 105970

value: female

tag: age

value: Peripheral T-cell lymphoma (PTCL)

value: Follow up status:alive

value: Follow up years:11.85489391


title: Smoke exposure IL33  (RE624_29)


title: Sabre_Diet_Liver_3

value: liver


title: Counterclockwise shifts_two shifts_4h_nr192


title: Counterclockwise shifts_two shifts_0h_nr188


title: 3343 - mAdbID:105968

description: mAdb experiment ID: 105968

value: male

value: Follow up status:dead

value: Follow up years:0.788501027


title: Smoke exposure IL33  (RE624_28)


title: Smoke exposure IL33  (RE624_32)


title: Counterclockwise shifts_two shifts_8h_nr197


title: Counterclockwise shifts_one shift_20h_nr152A

value: one shift


title: Counterclockwise shifts_one shift_4h_nr133A


title: Counterclockwise shifts_two shifts_0h_nr187

value: two shifts


title: Counterclockwise shifts_one shift_8h_nr137


title: 3332 - mAdbID:105960

description: mAdb experiment ID: 105960

value: lymph node

value: Follow up years:0.922655715


title: Counterclockwise shifts_one shift_20h_nr153A

value: FVB


title: Smoke exposure PBS  (RE624_23)

value: PBS


title: Smoke exposure IL33  (RE624_27)

value: cigarette smoke


title: Counterclockwise shifts_one shift_16h_nr148

value: Counterclockwise shifts


title: Smoke exposure IL33  (RE624_26)

value: lung


title: Smoke exposure PBS  (RE624_21)


title: 3344 - mAdbID:105969

description: mAdb experiment ID: 105969


title: Smoke exposure PBS  (RE624_20)


title: Smoke exposure PBS  (RE624_24)


title: Smoke exposure PBS  (RE624_18)


title: 3346 - mAdbID:105919

description: mAdb experiment ID: 105919

value: female

value: Follow up years:2.548939083


title: Counterclockwise shifts_one shift_16h_nr147


title: Counterclockwise shifts_one shift_12h_nr143


title: Smoke exposure PBS  (RE624_17)


title: Counterclockwise shifts_one shift_0h_nr128A


title: 3394 - mAdbID:101852

description: mAdb experiment ID: 101852

value: Peripheral T-cell lymphoma (PTCL)

value: Follow up years:0.055833333


title: Control_no shift_20h_nr123

value: none (Control)

value: no shift


title: Counterclockwise shifts_one shift_0h_nr127A


title: Counterclockwise shifts_one shift_12h_nr142


title: Counterclockwise shifts_one shift_4h_nr132A


title: 3405 - mAdbID:101854

description: mAdb experiment ID: 101854

value: male

value: Follow up status:dead

value: Follow up years:0.035


title: Counterclockwise shifts_one shift_8h_nr138

value: one shift


title: Control_no shift_20h_nr126


title: Room Air IL33  (RE624_11)

value: room air


title: Room Air IL33  (RE624_15)


title: 3404 - mAdbID:101851

description: mAdb experiment ID: 101851

value: lymph node

value: Follow up status:alive

value: Follow up years:12.075


title: 3339 - mAdbID:105965

description: mAdb experiment ID: 105965

value: Follow up years:1.492128679


title: 3335 - mAdbID:105961

description: mAdb experiment ID: 105961

value: Follow up years:3.570157426


title: Room Air IL33  (RE624_10)

value: lung


title: Control_no shift_20h_nr122

value: FVB


title: Control_no shift_20h_nr125


title: Room Air IL33  (RE624_13)


title: 3386 - mAdbID:101847

description: mAdb experiment ID: 101847

value: female

value: Follow up years:2.900219298


title: 3403 - mAdbID:101850

description: mAdb experiment ID: 101850

value: Peripheral T-cell lymphoma (PTCL)

value: Follow up years:0.54002193


title: Room Air IL33  (RE624_16)


title: 3401 - mAdbID:101846

description: mAdb experiment ID: 101846

value: Follow up years:0.899122807


title: Room Air IL33  (RE624_14)


title: Smoke exposure PBS  (RE624_19)

value: cigarette smoke

value: PBS


title: 3402 - mAdbID:101848

description: mAdb experiment ID: 101848

value: Follow up status:dead

value: Follow up years:0.693530702


title: Smoke exposure IL33  (RE624_25)


title: Smoke exposure PBS  (RE624_22)


title: Room Air IL33  (RE624_12)

value: room air


title: Control_no shift_16h_nr120

value: none (Control)

value: no shift


title: Room Air IL33  (RE624_9)


title: Room Air PBS  (RE624_3)


title: Room Air PBS  (RE624_8)


title: 3395 - mAdbID:101844

description: mAdb experiment ID: 101844

value: male

value: lymph node

value: Follow up status:alive

value: Follow up years:4.662828947


title: 3396 - mAdbID:101845

description: mAdb experiment ID: 101845

value: Follow up years:3.116776316


title: Control_no shift_16h_nr118

value: FVB


title: Control_no shift_16h_nr117


title: Control_no shift_8h_nr109


title: Control_no shift_16h_nr119


title: Control_no shift_12h_nr115


title: Room Air PBS  (RE624_7)

value: lung


title: Room Air PBS  (RE624_6)


title: Room Air PBS  (RE624_5)


title: Control_no shift_12h_nr114


title: 3375 - mAdbID:101841

description: mAdb experiment ID: 101841

value: Peripheral T-cell lymphoma (PTCL)

value: Follow up years:0.035635965


title: Room Air PBS  (RE624_4)


title: Control_no shift_8h_nr110


title: Room Air PBS  (RE624_1)


title: Control_no shift_4h_nr106


title: Control_no shift_12h_nr113


title: Control_no shift_8h_nr107


title: Control_no shift_12h_nr112


title: Room Air PBS  (RE624_2)


title: 3382 - mAdbID:101833

description: mAdb experiment ID: 101833

value: Follow up years:0.463267544


title: DISTAL COLON - AOM/DSS LATE TREATMENT GROUP - BIOLOGICAL REPLICATE 3

city: HERAKLION

first: ARISTIDES

last: ELIOPOULOS

state: CRETE

address: UNIVERSITY CAMPUS

department: MEDICAL SCHOOL

country: Greece

institute: UNIVERSITY OF CRETE

description: AOM/DSS LATE_distal_03

hyb_protocol: The resultant fragmented and labeled cDNA was added to the hybridization cocktail in accordance with the NuGEN™ guidelines for hybridization onto Affymetrix GeneChip® arrays. Hybridization was performed for 16-18 hours at 45°C in an Affymetrix GeneChip® Hybridization Oven 640.

scan_protocol: The array was washed and stained on the GeneChip® Fluidics Station 450 using the appropriate fluidics script, before being inserted into the Affymetrix autoloader carousel and scanned using the GeneChip® Scanner 3000.

data_processing: The Robust Multichip Algorithm (RMA) in Partek 6.5 with quantile normalisation and median polish was applied to the raw data in order to generate the pre-processed data.

source_name: AOM, 4 DSS CYCLES

label_protocol: Total RNA was amplified using the NuGEN™ WT-Ovation™ FFPE RNA Amplification System / NuGEN™ Ovation™ RNA Amplification System V2. The appropriate amount of amplified single-stranded cDNA was fragmented and labeled using the FL-Ovation™ cDNA Biotin Module V2.

extract_protocol: Homogenization in Trizol

treatment_protocol: Mice were injected intaperitoneally with 10mg/kg body weight azoxymethane (AOM) when their weight was approximately 18-20 g (day 1) and 96 hours later 2.5% DSS was administered in their drinking water for five days, followed by 14 days of regular water. This cycle was repeated once (EARLY TREATMENT GROUP) or three times more (LATE TREATMENT GROUP) before mice were sacrificed on days 42 and 120 respectively. Macroscopic and histological analyses showed dysplasias and intramucosal adenocarcinomas in the distal colon of the late treatment group and areas of dysplasia in the early treatment group.  The proximal part of the colon remained unaffected. At least three (3) animals (biological replicates) were used to isolate tissue from proximal and distal areas of the large intestine under different treatment conditions (early vs late AOM/DSS treatment and untreated controls).

value: distal colon

tag: Sex

value: female


title: 3400 - mAdbID:101835

description: mAdb experiment ID: 101835

value: Follow up status:dead

value: Follow up years:14.52028509


title: DISTAL COLON - AOM/DSS LATE TREATMENT GROUP - BIOLOGICAL REPLICATE 6

description: AOM/DSS LATE_distal_06

tag: strain


title: 3374 - mAdbID:101839

description: mAdb experiment ID: 101839

value: Follow up years:15.47697368


title: Control_no shift_4h_nr102

tag: light rotation

value: none (Control)


title: 3383 - mAdbID:101836

description: mAdb experiment ID: 101836

value: Follow up years:5.814144737


title: Control_no shift_0h_nr99

tag: group

value: no shift


title: DISTAL COLON - AOM/DSS LATE TREATMENT GROUP - BIOLOGICAL REPLICATE 2

description: AOM/DSS LATE_distal_02


title: Control_no shift_4h_nr103

tag: zeitgeber time


title: 3377 - mAdbID:101834

description: mAdb experiment ID: 101834

value: lymph node

value: Follow up years:14.79440789


title: PROXIMAL COLON - AOM/DSS LATE TREATMENT GROUP - BIOLOGICAL REPLICATE 3

description: AOM/DSS LATE_prox_03

value: proximal colon


title: PROXIMAL COLON - AOM/DSS LATE TREATMENT GROUP - BIOLOGICAL REPLICATE 4

description: AOM/DSS LATE_prox_04


title: 3376 - mAdbID:101829

description: mAdb experiment ID: 101829

value: male

value: Follow up years:0.844298246


title: 3380 - mAdbID:101831

description: mAdb experiment ID: 101831

value: Follow up status:alive

value: Follow up years:13.62938596


title: DISTAL COLON - AOM/DSS LATE TREATMENT GROUP - BIOLOGICAL REPLICATE 1

description: AOM/DSS LATE_distal_01


title: Control_no shift_4h_nr104

value: FVB

tag: mouse id


title: 3391 - mAdbID:101827

description: mAdb experiment ID: 101827

tag: tissue

value: Peripheral T-cell lymphoma (PTCL)

value: Follow up years:2.146381579


title: 3390 - mAdbID:101828

description: mAdb experiment ID: 101828

tag: gender

value: female

value: Follow up years:1.33497807


title: DISTAL COLON - AOM/DSS LATE TREATMENT GROUP - BIOLOGICAL REPLICATE 5

description: AOM/DSS LATE_distal_05

value: distal colon


title: Control_no shift_8h_nr108


title: DISTAL COLON - AOM/DSS LATE TREATMENT GROUP - BIOLOGICAL REPLICATE 4

description: AOM/DSS LATE_distal_04


title: PROXIMAL COLON - AOM/DSS LATE TREATMENT GROUP - BIOLOGICAL REPLICATE 2

description: AOM/DSS LATE_prox_02


title: Control_no shift_0h_nr97


title: Control_no shift_0h_nr98


title: PROXIMAL COLON - AOM/DSS LATE TREATMENT GROUP - BIOLOGICAL REPLICATE 1

description: AOM/DSS LATE_prox_01


title: 3492 - mAdbID:101825

description: mAdb experiment ID: 101825

tag: disease state

value: Follow up status:dead

value: Follow up years:0.655153509


title: Control_no shift_0h_nr100

value: none (Control)


title: 3259 - mAdbID:101242

description: mAdb experiment ID: 101242

tag: individual

value: Follow up years:0.073921971


title: DISTAL COLON - AOM/DSS EARLY TREATMENT GROUP - BIOLOGICAL REPLICATE 3

description: AOM/DSS EARLY_distal_03

source_name: AOM, 2 DSS CYCLES


title: PROXIMAL COLON - AOM/DSS EARLY TREATMENT GROUP - BIOLOGICAL REPLICATE 1

description: AOM/DSS EARLY_prox_01


title: PROXIMAL COLON - AOM/DSS EARLY TREATMENT GROUP - BIOLOGICAL REPLICATE 2

description: AOM/DSS EARLY_prox_02


title: DISTAL COLON - AOM/DSS EARLY TREATMENT GROUP - BIOLOGICAL REPLICATE 2

description: AOM/DSS EARLY_distal_02


title: PROXIMAL COLON - AOM/DSS EARLY TREATMENT GROUP - BIOLOGICAL REPLICATE 3

description: AOM/DSS EARLY_prox_03


title: DISTAL COLON - UNTREATED - BIOLOGICAL REPLICATE 6

source_name: UNTREATED


title: DISTAL COLON - UNTREATED - BIOLOGICAL REPLICATE 5


title: 3263 - mAdbID:101239

description: mAdb experiment ID: 101239

value: lymph node

tag: clinical info

value: Follow up years:8.657084189


title: DISTAL COLON - UNTREATED - BIOLOGICAL REPLICATE 3


title: DISTAL COLON - UNTREATED - BIOLOGICAL REPLICATE 4


title: 3266 - mAdbID:101236

description: mAdb experiment ID: 101236

value: Follow up years:0.076659822


title: 3265 - mAdbID:101237

description: mAdb experiment ID: 101237

value: male

value: Follow up years:2.302532512


title: DISTAL COLON - UNTREATED - BIOLOGICAL REPLICATE 2


title: 3268 - mAdbID:101234

description: mAdb experiment ID: 101234

value: Follow up years:0.572210815


title: 3253 - mAdbID:101246

description: mAdb experiment ID: 101246

value: Follow up years:3.041752225


title: PROXIMAL COLON - UNTREATED - BIOLOGICAL REPLICATE 6

value: proximal colon


title: DISTAL COLON - UNTREATED - BIOLOGICAL REPLICATE 1


title: PROXIMAL COLON - UNTREATED - BIOLOGICAL REPLICATE 5


title: DISTAL COLON - AOM/DSS EARLY TREATMENT GROUP - BIOLOGICAL REPLICATE 1

description: AOM/DSS EARLY_distal_01


title: 3271 - mAdbID:101231

description: mAdb experiment ID: 101231

value: Peripheral T-cell lymphoma (PTCL)

value: Follow up years:0.287474333


title: Heterozygous high cytokines, bio rep 1

city: Charlottesville

first: Stephen

last: Turner

state: VA

address: 1670 Discovery Drive

institute: Signature Science, LLC

description: Mus musculus Heterozygous high cytokines, bio rep 1

hyb_protocol: cRNA was hybridized to Affymetric GeneChip Mouse Genome 430 2.0 oligonucleotide arrays.

scan_protocol: Arrays were scanned with an Affymetrix GeneChip Scanner 7G to generate raw intensity data.  Affymetrix .CEL files were processed using R/BioConductor packages for GCRMA-based quantification (gcrma version 2.34.0) with quantile normalization across all 12 samples.  QC metrics including global Principal Components Analysis (PCA) and median distance heatmaps were generated with arrayQualityMetrics version 3.18.0, with no outliers detected. By PCA, db/db islets treated with high concentration cytokines were mildly separated from the other samples, but little other clustering along experimental axes was observed.

data_processing: Data extraction, QC, and RMA normalization were performed with BioConductor software. Probes were annotated using the Bioconductor GEOQuery package.

label_protocol: Biotin-labeled cRNA was prepared from 2 ug of total RNA and then fragmented.

growth_protocol: Islets were isolated from prediabetic 4- or 5-week-old male db/db mice and non-diabetic heterozygous controls using collagenase digestion and Histopaque centrifugation and then incubated overnight in RPMI media before use.

extract_protocol: Islet tissues were extracted for total RNA using a Qiagen RNeasy kit.

treatment_protocol: Islets were exposed for 20 hours to 10 pg/ml IL-1beta + 20 pg/ml IL-6 (low cytokines), 100 pg/ml IL-1beta + 200 pg/ml IL-6 (high cytokines), or left untreated for each strain. Islets were then collected for use in the microarray study. Two replicates for each condition were used, each consisting of equal numbers of islets pooled from 4 mice.

tag: genotype

value: Heterozygous

value: high cytokines

value: islets


title: 3272 - mAdbID:101230

description: mAdb experiment ID: 101230

value: Follow up status:dead

value: Follow up years:0.52019165


title: Heterozygous high cytokines, bio rep 2

description: Mus musculus Heterozygous high cytokines, bio rep 2


title: Db/db low cytokines, bio rep 1

description: Mus musculus Db/db low cytokines, bio rep 1

value: Db/db

value: low cytokines


description: Mus musculus Heterozygous untreated control islets, bio rep 2

value: untreated control islets


title: 3299 - mAdbID:101223

description: mAdb experiment ID: 101223

value: female

value: lymph node

value: Follow up years:0.752908966


description: Mus musculus Db/db untreated control islets, bio rep 2


description: Mus musculus Heterozygous untreated control islets, bio rep 1


title: 3275 - mAdbID:101227

description: mAdb experiment ID: 101227

value: male

value: Follow up status:alive

value: Follow up years:10.48323066


title: 3278 - mAdbID:101225

description: mAdb experiment ID: 101225

value: Follow up years:0.616016427


title: Db/db high cytokines, bio rep 1

description: Mus musculus Db/db high cytokines, bio rep 1


title: Db/db high cytokines, bio rep 2

description: Mus musculus Db/db high cytokines, bio rep 2


title: 3310 - mAdbID:101214

description: mAdb experiment ID: 101214

value: Peripheral T-cell lymphoma (PTCL)

value: Follow up years:1.075975359


title: 3333 - mAdbID:101228

description: mAdb experiment ID: 101228

value: Follow up years:1.256673511


description: Mus musculus Db/db untreated control islets, bio rep 1


title: PROXIMAL COLON - UNTREATED - BIOLOGICAL REPLICATE 4

value: proximal colon


title: 3276 - mAdbID:101226

description: mAdb experiment ID: 101226

value: Follow up years:6.332648871


title: LL417LP3days-LL417LP6hr_Sample35

city: Notre Dame

first: Jacqueline

last: Lopez

state: Indiana

address: 019 Galvin Life Science Center

department: Biology

institute: University of Notre Dame

hyb_protocol: Hybridization and post-hybridization washing using Hybridization Systems Kit (Roche NimbleGen) and Wash Buffer Kit (Roche NimbleGen) per manufacturer's recommendations. http://www.nimblegen.com

scan_protocol: Image acquisition with Axon GenePix 4200 Professional Scanner, 5 micron resolution.

data_processing: Raw signal intensities extracted with NimbleScan 2.4 Software (Roche NimbleGen) as PAIR files.

organism: Daphnia pulex

label_protocol:
target protocol: Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations.  aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA purified with Invitrogen's ChargeSwitch Kit.
quality assessement protocol: Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.
ds cDNA labeled using NimbleGen Dual Color Labeling Kit (Roche NimbleGen) per manufacturer's recommendations. http://www.nimblegen.com

growth_protocol: 20 C, 16:8 light: dark cycle, 1 mg C/L Scenedesmus algae at high or low phoshourus levels

extract_protocol: First, tissue is homogenized with Trizol Reagent (Ambion). Then RNA is extract with phenol and precipitated with Ethanol. The precipitate is captured and washed using Qiagen Rneasy spin column.

tag: exposed to

value: low phosphorus (C:P=120) for 3days

value: whole body

tag: replicate

value: low phosphorus (C:P=120) for 6hrs


title: Heterozygous low cytokines, bio rep 2

description: Mus musculus Heterozygous low cytokines, bio rep 2

value: Heterozygous

value: low cytokines

value: islets


title: 3270 - mAdbID:101232

description: mAdb experiment ID: 101232

value: lymph node

value: Follow up status:dead

value: Follow up years:4.5229295


title: 3306 - mAdbID:101218

description: mAdb experiment ID: 101218

value: male

value: Follow up years:0.008213552


title: PROXIMAL COLON - UNTREATED - BIOLOGICAL REPLICATE 3

value: female


title: Db/db low cytokines, bio rep 2

description: Mus musculus Db/db low cytokines, bio rep 2

value: Db/db


title: PROXIMAL COLON - UNTREATED - BIOLOGICAL REPLICATE 1


title: Heterozygous low cytokines, bio rep 1

description: Mus musculus Heterozygous low cytokines, bio rep 1


title: 3045 - mAdbID:100778

description: mAdb experiment ID: 100778

value: Peripheral T-cell lymphoma (PTCL)

value: Follow up years:0.090410959


title: LL417LP3days-LL417LP6hr_Sample36


title: PROXIMAL COLON - UNTREATED - BIOLOGICAL REPLICATE 2

value: proximal colon


title: 11766_KO_SUL_O2_3d_lung_Rep_3

city: Research Triangle Park

first: Dr. Steven

last: Kleeberger

state: NC

address: 111 T.W. Alexander Drive

institute: NIEHS

hyb_protocol: Arrays were hybridized sixteen hours at 45°C in a rotating hybridization oven using Affymetrix Eukaryotic Target Hybridization Controls and protocol, washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual and stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure

scan_protocol: Affymetrix Scanner 3000

data_processing: Normalized expression of probe level data was calculated using the Robust Multiarray Average function (RMA) implemented in Bioconductor's affy-package

source_name: Nrf2 knockout, left lung, R-sulforaphane, hyperoxia

label_protocol: Standard Affymetrix procedures

growth_protocol: Mice were maintained on a diet of AIN76A and euthanized using sodium pentobarbital, i.p., 104 mg/kg bodyweight

extract_protocol: Total RNA was extracted using the Qiagen Mini RNA plus isolation kit and transcribed to cRNA

treatment_protocol: Lungs were snap-frozen prior to analysis.

value: Lung

value: Nrf2 knockout

tag: pre-exposure

value: R-sulforaphane, 9 uM in 100 ul PBS, 3 days before inhalation exposure

tag: exposure

value: Hyperoxia

tag: route

value: Continuous whole body inhalation

tag: dose

value: 100% oxygen

tag: time of exposure

value: 3 day

tag: genetic background

value: ICR


title: 3047 - mAdbID:100776

description: mAdb experiment ID: 100776

tag: age

value: lymph node

value: Follow up status:dead

value: Follow up years:0.079452055


title: 3269 - mAdbID:101233

description: mAdb experiment ID: 101233

value: male

value: Follow up years:2.113620808


title: LL417LP6hr-LL417LP3days_Sample33

value: low phosphorus (C:P=120) for 6hrs

value: whole body

value: low phosphorus (C:P=120) for 3days


title: 11765_KO_SUL_O2_3d_lung_Rep_2


title: 11764_KO_SUL_O2_3d_lung_Rep_1


title: 3308 - mAdbID:101216

description: mAdb experiment ID: 101216

value: female

value: Peripheral T-cell lymphoma (PTCL)

value: Follow up status:alive

value: Follow up years:5.193702943


title: 11763_KO_SUL_Air_3d_lung_Rep_3

source_name: Nrf2 knockout, left lung, R-sulforaphane, air

value: Lung

value: Nrf2 knockout

value: R-sulforaphane, 9 uM in 100 ul PBS, 3 days before inhalation exposure

value: Air

value: 21% oxygen


title: LL417LP6hr-LL417LP3days_Sample34


title: 2063 - mAdbID:100455

description: mAdb experiment ID: 100455

value: lymph node

value: Follow up years:2.403832991


title: 11761_KO_SUL_Air_3d_lung_Rep_1

value: Continuous whole body inhalation

value: 3 day

value: ICR


title: 3200 - mAdbID:100741

description: mAdb experiment ID: 100741

value: male

value: Follow up status:dead

value: Follow up years:1.804243669


title: LL417HP3days-LL417LP3days_Sample31

value: high phosphorus (C:P=800) for 3days

value: whole body

value: low phosphorus (C:P=120) for 3days


title: 3040 - mAdbID:100236

description: mAdb experiment ID: 100236

value: female

value: Peripheral T-cell lymphoma (PTCL)

value: Follow up years:1.205479452


title: LL417LP3days-LL417HP3days_Sample29


title: 3201 - mAdbID:100740

description: mAdb experiment ID: 100740

value: Follow up status:alive

value: Follow up years:1.94934976


title: 1446 - mAdbID:100456

description: mAdb experiment ID: 100456

value: Follow up years:0.960985626


title: 3294 - mAdbID:100237

description: mAdb experiment ID: 100237

value: lymph node

value: Follow up years:6.915811088


title: 3252 - mAdbID:100436

description: mAdb experiment ID: 100436

value: Follow up years:0.093086927


title: 3326 - mAdbID:100230

description: mAdb experiment ID: 100230


title: LL417LP3days-LL417HP3days_Sample30


title: LL417HP3days-LL417LP3days_Sample32


title: 11760_KO_PBS_O2_3d_lung_Rep_3

source_name: Nrf2 knockout, left lung, PBS, hyperoxia

value: Lung

value: Nrf2 knockout

value: PBS, 100 ul PBS, 3 days before inhalation exposure

value: Hyperoxia

value: Continuous whole body inhalation

value: 100% oxygen

value: 3 day


title: 11755_KO_PBS_Air_3d_lung_Rep_1

source_name: Nrf2 knockout, left lung, PBS, air

value: Air

value: 21% oxygen

value: ICR


title: 11758_KO_PBS_O2_3d_lung_Rep_1


title: 3325 - mAdbID:100229

description: mAdb experiment ID: 100229

value: male

value: Peripheral T-cell lymphoma (PTCL)


title: 11756_KO_PBS_Air_3d_lung_Rep_2


title: 11759_KO_PBS_O2_3d_lung_Rep_2


title: 11757_KO_PBS_Air_3d_lung_Rep_3


title: 11762_KO_SUL_Air_3d_lung_Rep_2

value: R-sulforaphane, 9 uM in 100 ul PBS, 3 days before inhalation exposure


title: LL417LP3days-LL415LP3days_Sample24

value: low phosphorus (C:P=120) for 3days

value: whole body


title: LL415HP3days-LL417HP3days_Sample25

value: high phosphorus (C:P=800) for 3days


title: LL417HP3days-LL415HP3days_Sample28


title: 11754_WT_SUL_O2_3d_lung_Rep_3

source_name: Wildtype left lung, R-sulforaphane, hyperoxia

value: Wildtype


title: 3324 - mAdbID:100228

description: mAdb experiment ID: 100228

value: lymph node

value: Follow up status:alive

value: Follow up years:0.744695414


title: LL415HP3days-LL417HP3days_Sample26


title: 3312 - mAdbID:100224

description: mAdb experiment ID: 100224

value: female


title: LL417HP3days-LL415HP3days_Sample27


title: 11753_WT_SUL_O2_3d_lung_Rep_2

value: Lung

value: Hyperoxia

value: Continuous whole body inhalation


title: LL415LP3days-LL417LP3days_Sample22


title: 3322 - mAdbID:100226

description: mAdb experiment ID: 100226


title: 3311 - mAdbID:100223

description: mAdb experiment ID: 100223


title: 11751_WT_SUL_Air_3d_lung_Rep_3

source_name: Wildtype left lung, R-sulforaphane, air

value: Air

value: 3 day


title: LL417LP3days-LL415LP3days_Sample23


title: 3320 - mAdbID:100222

description: mAdb experiment ID: 100222

value: Follow up status:dead

value: Follow up years:0.065708419


title: 3319 - mAdbID:100221

description: mAdb experiment ID: 100221

value: male

value: Peripheral T-cell lymphoma (PTCL)


title: 11748_WT_PBS_O2_3d_lung_Rep_3

source_name: Wildtype left lung, PBS, hyperoxia

value: PBS, 100 ul PBS, 3 days before inhalation exposure

value: 100% oxygen

value: ICR


title: 11750_WT_SUL_Air_3d_lung_Rep_2

value: Wildtype

value: R-sulforaphane, 9 uM in 100 ul PBS, 3 days before inhalation exposure

value: 21% oxygen


title: 3318 - mAdbID:100220

description: mAdb experiment ID: 100220

value: lymph node


title: 11749_WT_SUL_Air_3d_lung_Rep_1


title: 11747_WT_PBS_O2_3d_lung_Rep_2


title: 11752_WT_SUL_O2_3d_lung_Rep_1


title: LL415LP3days-LL415HP3days_Sample18

value: low phosphorus (C:P=120) for 3days

value: whole body

value: high phosphorus (C:P=800) for 3days


title: LL415HP3days-LL415LP3days_Sample19


title: 11746_WT_PBS_O2_3d_lung_Rep_1

value: Lung

value: Hyperoxia

value: Continuous whole body inhalation


title: 3317 - mAdbID:100219

description: mAdb experiment ID: 100219

value: female

value: Follow up status:alive

value: Follow up years:1.018480493


title: 3314 - mAdbID:100216

description: mAdb experiment ID: 100216

value: Peripheral T-cell lymphoma (PTCL)


title: 11745_WT_PBS_Air_3d_lung_Rep_3

source_name: Wildtype left lung, PBS, air

value: PBS, 100 ul PBS, 3 days before inhalation exposure

value: Air

value: 3 day


title: 11743_WT_PBS_Air_3d_lung_Rep_1

value: Wildtype

value: ICR


title: 11744_WT_PBS_Air_3d_lung_Rep_2

value: 21% oxygen


title: LL417HP6hr-LL417LP6hr_Sample15

value: high phosphorus (C:P=800) for 6hrs

value: low phosphorus (C:P=120) for 6hrs


title: LL417LP6hr-LL417HP6hr_Sample14

value: whole body


title: 3203 - mAdbID:100163

description: mAdb experiment ID: 100163

value: lymph node

value: Follow up years:12.6


title: 3315 - mAdbID:100217

description: mAdb experiment ID: 100217

value: male

value: Follow up status:dead

value: Follow up years:0.440793977


title: 3214 - mAdbID:100164

description: mAdb experiment ID: 100164

value: Follow up years:3.663013699


title: MVs-FR treated BMDM_biological rep2

city: Domzale

first: Simon

last: Horvat

address: Groblje 3

department: Animal Science

country: Slovenia

institute: University of Ljubljana; Biotechnical faculty

description: Gene expression data from BMDMs, treated with fully oxidized microvesicles (MVs-FR) that do not induce MD-2/TLR4 receptor complex

hyb_protocol: 100 ng of total RNA was used for hybridization of Affymetrix Gene Chip Mouse 1.0 ST Arrays according to manufacturer’s instructions (Genechip® Whole Transcript (wt) Sense Ttarget Labeling Assay Manual – P/N 701880 Rev 4).

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

data_processing: The data were analyzed with Affymetrix Expression Console (version 1.2.0.20) using Robust Multi-array Average (RMA) with default analysis settings (global background correction, quantile normalization).

source_name: bone marrow derived macrophages (BMDM), stimulated with MVs-FR (5000 MV/ml) for 4 hours

label_protocol: Total RNA was used to synthesize double-stranded cDNA with random hexamer primers tagged with a T7 promoter sequence. The double-stranded cDNA was subsequently used as a template and amplified by T7 RNA polymerase producing cRNA. In the second cycle of cDNA synthesis, random hexamers were used to prime reverse transcription of the cRNA and dUTP was incorporated to produce single-stranded DNA. This single-stranded DNA sample was then treated with a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) that specifically recognized the unnatural dUTP residues and broke the DNA strand. DNA was labeled by terminal eoxynucleotidyl transferase (TdT) with the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin.

growth_protocol: Bone marrow cells were stimulated with 40 ng/ml M-CSF (eBioscience) for 1 week to produce bone-marrow derived macrophages (BMDMs) before stimulated with LPS, MVs or MVs-FR.

extract_protocol: Total RNA was extracted 4 h after stimulation using RNA extraction kit (PureLink RNA mini kit, Life Technologies) according to supplier’s protocol.RNA quantity and quality were assessed with NanoDrop and Agilent 2100 Bioanalyzer instruments, all samples isolated fulfilled the minimum requirements (OD260/280 and OD230/280 > 1.8) and RIN numbers above 8.5 for microarray hybridization.

treatment_protocol:
Oxidative stress-derived MVs (or MVsA23187) were produced in HEK293 activated with 12 mM calcium ionophore A23187 for 1 h. MVs were isolated by two-time ultracentrifugation at 100000g for 1 h and resuspended in PBS. The MVs concentrations were determined on a Coulter EPICS Altra flow cytometer (Beckman Coulter Electronics) using a known amount of flow-count fluorospheres (Beckman Coulter).
MVs were oxidized by the Fenton reaction, which was performed as described previously (Rodriguez Capote, K., McCormack, F.X. & Possmayer, F. Pulmonary surfactant protein-A (SP-A) restores the surface properties of surfactant after oxidation by a mechanism that requires the Cys6 interchain disulfide bond and the phospholipid binding domain. J Biol Chem 278, 20461-74,2003). Briefly, MVs were preincubated with 0.9 mM CaCl2 at 11ºC for 4 h as described Sun, S.T., Day, E.P. & Ho, J.T. Temperature dependence of calcium-induced fusion of sonicated phosphatidylserine vesicles. Proc Natl Acad Sci U S A 75, 4325-8 (1978) and FR was performed in buffer (0.15 mM NaCl, 2.0 mM Tris-HCl and 1.5 mM CaCl2) and reaction components (0.65 mM FeCl2, 0.65 mM NaEDTA and 30.0 mM H2O2) were added to MV samples. Samples were then incubated at 37ºC for 24 h. .
BMDMs from C57BL/6J strain were stimulated with LPS (100ng/ml), oxidative stress-derived MVs (5000 MV/ml) or MVs-FR (5000 MV/ml) for 4 h.

tag: strain

tag: Sex

tag: tlr4 genotype

value: wild type


title: MVs-FR treated BMDM_biological rep3


title: MVs-FR treated BMDM_biological rep1


title: LL417LP6hr-LL417HP6hr_Sample13

tag: tissue


title: LL417HP6hr-LL417LP6hr_Sample16


title: LL415LP3days-LL415HP3days_Sample17

value: low phosphorus (C:P=120) for 3days

value: high phosphorus (C:P=800) for 3days


title: LL415LP3days-LL417LP3days_Sample21


title: 3313 - mAdbID:100215

description: mAdb experiment ID: 100215

tag: gender

value: female

tag: disease state

value: Peripheral T-cell lymphoma (PTCL)

value: Follow up status:alive

value: Follow up years:3.832991102


title: LL415HP3days-LL415LP3days_Sample20


title: 3202 - mAdbID:100162

description: mAdb experiment ID: 100162

tag: individual

tag: clinical info

value: Follow up years:1.545205479


title: LL417HP6hr-LL415HP6hr_Sample11

tag: genotype

tag: exposed to

value: high phosphorus (C:P=800) for 6hrs


title: LL417HP6hr-LL415HP6hr_Sample12

tag: replicate


title: MVs treated BMDM_biological rep2

description: Gene expression data from BMDMs, treated with MD-2/TLR4 receptor complex-inducing stress-derived microvesicles (MVs)

source_name: bone marrow derived macrophages (BMDM), stimulated with MVs (5000 MV/ml) for 4 hours


title: 2993 - mAdbID:100159

description: mAdb experiment ID: 100159

value: Follow up years:6.309589041


title: LL415HP6hr-LL417HP6hr_Sample9

value: whole body


title: LL417LP6hr-LL415LP6hr_Sample7

value: low phosphorus (C:P=120) for 6hrs


title: 3052 - mAdbID:100150

description: mAdb experiment ID: 100150

value: lymph node

value: Follow up years:0.44109589


title: LL415LP6hr-LL417LP6hr_Sample6


title: LL417LP6hr-LL415LP6hr_Sample8


title: MVs treated BMDM_biological rep3

value: male


title: LL415HP6hr-LL417HP6hr_Sample10


title: 3077 - mAdbID:100161

description: mAdb experiment ID: 100161

value: Follow up years:5.339726027


title: LPS-treated BMDM_biological rep3

description: Gene expression data from BMDMs, treated with lipopolysaccharide (LPS), a ligand for MD-2/TLR4 receptor complex

source_name: bone marrow derived macrophages (BMDM), stimulated with LPS (100ng/ml) for 4 hours


title: MVs treated BMDM_biological rep1


title: LPS-treated BMDM_biological rep2


title: Control BMDM_biological rep3

description: Gene expression data from BMDMs, untreated control

source_name: bone marrow derived macrophages (BMDM), untreated


title: LPS-treated BMDM_biological rep1


title: 2992 - mAdbID:100149

description: mAdb experiment ID: 100149

value: Follow up status:dead

value: Follow up years:1.416438356


title: LL415LP6hr-LL417LP6hr_Sample5


title: 3051 - mAdbID:100142

description: mAdb experiment ID: 100142

value: Follow up years:1.189041096


title: 2991 - mAdbID:100148

description: mAdb experiment ID: 100148

value: Follow up years:12.83013699


title: LL415HP6hr-LL415LP6hr_Sample4


title: 3050 - mAdbID:100141

description: mAdb experiment ID: 100141

value: Follow up years:4


title: 3046 - mAdbID:100138

description: mAdb experiment ID: 100138

value: female

value: Peripheral T-cell lymphoma (PTCL)

value: Follow up years:0.093150685


title: 3049 - mAdbID:100140

description: mAdb experiment ID: 100140

value: Follow up years:0.035616438


title: Control BMDM_biological rep1

value: wild type


title: LL415HP6hr-LL415LP6hr_Sample3

value: high phosphorus (C:P=800) for 6hrs


title: 3043 - mAdbID:100136

description: mAdb experiment ID: 100136

value: Follow up years:0.189041096


title: 400 dpi LCMV Arm, repl.1

city: Aurora

first: Jens

last: Eberlein

state: CO

address: 1775 Aurora Court

department: Anesthesiology

institute: University of Colorado Denver

hyb_protocol: standard Affymetrix procedures

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA.)

data_processing: Samples were evaluated for quality control parameters using Gene Chip Operating System from Affymetrix. CEL files were then imported into GeneSpring (Agilent Technologies) and processed using the RMA algorithm.

source_name: adoptively transferred P14 cells isolated from spleen 400 days after LCMV Arm infection.

label_protocol: Ovation Biotin RNA Amplification and Labeling System, NuGen

growth_protocol: Mice were housed at the University of Colorado vivarium on a standard laboratory chow diet

extract_protocol: DNA-digested total RNA was extracted from highly purified p14 TE and TM using a MinElute kit (Qiagen) and RNA integrity confirmed by PicoChip RNA technology (Agilent) according to the manufacturer’s instructions.

treatment_protocol: 5e4 P14 cells were adoptively transferred into congenic BL6/C57 mice and infected with LCMV Armstrong 24 hours later. P14 cells were isolated at the indicated timepoints after infection using FACS.

tag: cell type

value: P14 CD8+ T cells

tag: infection

value: acute lcmv infection

tag: source tissue

value: spleen

tag: time

value: 400 days after infection with LCMV Armstrong


title: Control BMDM_biological rep2

value: male


title: LL415LP6hr-LL415HP6hr_Sample1

value: low phosphorus (C:P=120) for 6hrs

value: whole body


title: LL415LP6hr-LL415HP6hr_Sample2


title: 400 dpi LCMV Arm, repl.3

tag: genetic background


title: SC3X_LP-SC3X_HP

scan_protocol: Image acquisition with Roche NimbleGen MS200 Scanner, 2 micron resolution.

data_processing: Raw signal intensities extracted with NimbleScan 2.6 Software (Roche NimbleGen) as PAIR files.

tag: clone id

value: ancient (~700-yr-old clone)

tag: dietary group

value: LP (low P; C:P~120)

value: HP (high P; C:P~800)


title: 286 dpi LCMV Arm, repl.3

source_name: adoptively transferred P14 cells isolated from spleen 286 days after LCMV Arm infection.

value: 286 days after infection with LCMV Armstrong


title: 286 dpi LCMV Arm, repl.1


title: 286 dpi LCMV Arm, repl.2


title: 3035 - mAdbID:100064

description: mAdb experiment ID: 100064

value: female

tag: age

value: lymph node

value: Peripheral T-cell lymphoma (PTCL)

value: Follow up status:alive

value: Follow up years:6.736986301


title: 3044 - mAdbID:100137

description: mAdb experiment ID: 100137

value: Follow up years:10.38356164


title: 400 dpi LCMV Arm, repl.2

value: P14 CD8+ T cells


title: SC15A_LP-SC15A_HP

value: contemporary (~10-yr-old clone)


title: 3031 - mAdbID:100061

description: mAdb experiment ID: 100061

value: Follow up status:dead

value: Follow up years:0.306849315


title: SC4B_LP-SC4B_HP


title: 156 dpi LCMV Arm, repl.4

source_name: adoptively transferred P14 cells isolated from spleen 156 days after LCMV Arm infection.

value: acute lcmv infection

value: spleen

value: 156 days after infection with LCMV Armstrong


title: 3032 - mAdbID:100062

description: mAdb experiment ID: 100062

value: male

value: Follow up years:1.649315068


title: 3030 - mAdbID:100060

description: mAdb experiment ID: 100060

value: Follow up years:5.309589041


title: SKBR3 siPontin shp53

city: New Brunswick

first: Emmanuel

middle: S.

last: Zachariah

state: New Jersey

address: 125 Paterson Street

department: CINJ Functional Genomics Facility

institute: Rutgers

description: Gene expression data from Breast cancer cell line with mutant p53 (R175H) with both sh-RNA knockdown of p53 and si-RNA knockdown of Pontin

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr 15ug of cRNA was hybridized for 16hours on the HG-U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

source_name: SKBR3 siPontin shp53

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: SK-BR-3 cells were grown in DMEM with 10%fetal bovine serum in 37C incubator.

extract_protocol: Total RNA was extracted by using Qiagen RNeasy Mini Kit according to the manufacturer's instructions.

treatment_protocol: SK-BR-3 cells were transfected with shp53 or empty vector. After selection with puromycin, sh-RNA expressed cells were further transfect with siPontin. 24hours after transfection cells were collected.

tag: cell line

value: Breast cancer cell line with mutant p53(R175H )

tag: transfected with

value: p53 shRNA and siRNA against Pontin


title: SC15A_HP-SC15A_LP

value: HP (high P; C:P~800)

tag: tissue

value: whole body

value: LP (low P; C:P~120)


title: SC3X_HP-SC3X_LP

value: ancient (~700-yr-old clone)


title: SC4B_HP-SC4B_LP


title: 156 dpi LCMV Arm, repl.3


title: SKBR3 siPontin shcon

description: Gene expression data from Breast cancer cell line with mutant p53 (R175H) with si-RNA knockdown of Pontin

source_name: SKBR3 siPontin shcon

value: siRNA against Pontin


title: SC1X_LP-SC4B_LP


title: SC1X_LP-SC1X_HP


title: SC1X_HP-SC1X_LP


title: 156 dpi LCMV Arm, repl.2

value: P14 CD8+ T cells


title: SC3X_LP-SC15A_LP

value: contemporary (~10-yr-old clone)


title: S. gallolyticus 2

city: Nijmegen

first: Annemarie

last: Boleij

address: Geert Grooteplein 10

institute: Radboud University Nijmegen Medical Centre

description: HT-29 cells incubated with S. gallolyticus (20 bacteria per cell) for 4 hours(G2)

hyb_protocol: 17 hours at 45 degrees in Affymetrix hybridization oven at 60 rpm,washing and staining in  Fluidics station 450 using stain cocktails: SAPE and antibody solution, (protocol FS450_0001)

scan_protocol: GeneChip scanner 3000 7G

data_processing: RMA + GC correction, log2 values from Partek Genomic Suite 6.4

label_protocol: GeneChip WT Terminal Labeling Kit

growth_protocol: Cultured in DMEM, 10% FCS, 2 mM L-glutamine,29 mM HEPES and 1x non essential amino acids

extract_protocol: Rneasy column purification

treatment_protocol: incubation with the indicated bacteria (See SAMPLES) at 20 bacteria per cell

value: adenocarcinoma cells


title: SC4B_LP-SC3X_LP


title: S. macedonicus 2

description: HT-29 cells incubated with S. macedonicus (20 bacteria per cell) for 4 hours(M2)


title: SC15A_LP-SC1X_LP


title: SKBR3 sicon shcon

description: Gene expression data from Breast cancer cell line with mutant p53 (R175H)

source_name: SKBR3 sicon shcon

value: control shRNA


title: Control 2

description: HT-29 cells incubated for 4 hours (C2)

source_name: HT-29 cells_control


title: SKBR3 sicon shp53

description: Gene expression data from Breast cancer cell line with mutant p53 (R175H) with sh-RNA knockdown of p53

source_name: SKBR3 sicon shp53

value: p53 shRNA


title: S. macedonicus 1

description: HT-29 cells incubated with S. macedonicus (20 bacteria per cell) for 4 hours(M1)


title: S. gallolyticus 1

description: HT-29 cells incubated with S. gallolyticus (20 bacteria per cell) for 4 hours(G1)


title: E. faecalis 2

description: HT-29 cells incubated with E. faecalis (20 bacteria per cell) for 4 hours(F2)

source_name: HT-29 cells incubated with E. faecalis


title: Control 1

description: HT-29 cells incubated for 4 hours (C1)


title: SC4B_HP-SC3X_HP


title: 156 dpi LCMV Arm, repl.1

value: acute lcmv infection

value: spleen


title: 8h p.i._1

first: Ronald

last: van Rij

address: Geert Grooteplein 28

institute: Radboud Institute for Molecular Life Sciences - Radboud University Medical Center

description: 8hpi 1

data_processing: RMA Background Correction using Partek software

organism: Drosophila melanogaster

source_name: Drosophila S2 Invitrogen cells

growth_protocol: Drosophila S2 cells (Invitrogen) were cultured at 25°C in Schneider’s Drosophila Media (Gibco) supplemented with 10% heat-inactivated Fetal Calf Serum (PAA), 50 U/mL Penicillin and 50 μg/mL Streptomycin (Gibco)

extract_protocol: Rneasy column purification followed by on-colomn DNAseI treatment, according to the manufacturer's instructions (Qiagen)

treatment_protocol: S2 cells were seeded in 6-well plates in 2mL of Schneider's media, with 2,5.10^6 cells per well. After media removal, 0.5mL of virus inoculum (Multiplicity of Infection = 10) was added. After one hour incubation, inoculums were replaced with 2mL of fresh media.

value: Drosophila S2 Invitrogen cells

value: Drosophila C Virus infection (DCV)


title: 8h p.i._2

description: 8hpi 2


title: aba2/GA20OX1-OE, rep3

city: Taipei

first: Wan-Hsing

last: Cheng

address: 128 Academia Road, Section 2, Nankang

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica, Taiwan

hyb_protocol: Standard Affymetrix hyb protocol; hybridized for 16.5 hr on Affymetrix Arabidopsis ATH1 Genome Array

scan_protocol: by using Affymetrix GeneChip scanner 3000 7G

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Arabidopsis thaliana

source_name: aerial parts of the aba2/GA20OX1-OE, soil-grown for 21 days

label_protocol: Standard Affymetrix label protocol

growth_protocol: Plants were grown in soil at 22℃ under a 16-hr light/8-hr dark regime with a light intensity of approximately 80-100 μmol m-2 s-1 for 21 days.

extract_protocol: Total RNA was isolated from aerial tissues using TRIzol Plus RNA Purification Kit (Life Technologies) according to the manufacturer’s instructions.

treatment_protocol: The aerial parts were used for microarray analysis.

value: rosette


title: aba2/ga20ox1, rep3

source_name: aerial parts of the aba2/ga20ox1 double mutant, soil-grown for 21 days


title: SC3X_HP-SC4B_HP


title: SC15A_HP-SC1X_HP


title: SC1X_HP-SC4B_HP


title: SC15A_LP-SC3X_LP


title: 24h p.i._2

description: 24hpi 2


title: E. faecalis 1

description: HT-29 cells incubated with E. faecalis (20 bacteria per cell) for 4 hours(F1)


title: SC15A_HP-SC3X_HP


title: ABA2-OE, rep3

source_name: aerial parts of the ABA2 overexpression line, soil-grown for 21 days


title: SC3X_LP-SC4B_LP


title: GA20OX1-OE, rep3

source_name: aerial parts of the GA20OX1 overexpression line, soil-grown for 21 days


title: ga20ox1, rep3

source_name: aerial parts of the ga20ox1 mutant, soil-grown for 21 days


title: Mock_2

description: Mock 2

value: mock

value: control


title: SC3X_HP-SC15A_HP

value: HP (high P; C:P~800)


title: Mock_1

description: Mock 1


title: SC1X_HP-SC15A_HP

value: whole body