title: B728a-WT_H2O2_LabA_Rep2

source_name: Pseudomonas syringae B728a wild type, Oxidative stress


title: CXCR5-KO mouse #6837, EµTCL (pure tumor cells)

status: Public on Sep 01 2014

type: RNA

city: Münster

first: Michael

last: Grau

state: Nordrhein-Westfalen

address: Albert-Schweitzer-Campus 1

department: Faculty of Medicine

country: Germany

institute: University of Münster

hyb_protocol: Affymetrix Hybridization Protocol (Proprietary protocol information available at http://www.affymetrix.com/estore/browse/products.jsp?productId=131467&categoryId=35807#1_1)

scan_protocol: Affymetrix Scan Protocol (Proprietary protocol information available at http://www.affymetrix.com/Auth/support/downloads/manuals/wash_stain_scan_cartridge_arrays_manual.pdf)

data_processing: Raw CEL data were RMA background corrected and then quantile-normalized and baseline-equalized between measurement groups. Probes were aggregated to Entrez Gene probesets as defined by the custom CDF [MoGene11stv1_Mm_ENTREZG_14.1.0] described in [PMID 16284200] via median polish.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Emu-Tcl1 transgenic CXCR5-KO-mouse

label_protocol: Affymetrix Labeling Protocol (Proprietary protocol information available at http://www.affymetrix.com/estore/browse/products.jsp?productId=prod110002&categoryId=35699#1_1)

growth_protocol: CD5+CD19+ tumor cells isolated from spleens of diseased mice. MZB cells isolated from spleens of healthy WT mice. B1 cells isolated form peritoneal cavity of healthy WT animals.

extract_protocol: Cells were isolated from mice, stained with respective antibodies and subsequently sorted by FACS

tag: strain background

tag: genotype/variation

value: Emu-Tcl1 transgenic CXCR5-KO

tag: disease class

value: EµTCL

tag: cell type

value: CD5+CD19+ tumor cells

tag: tumor load (in percent)

tag: measurement group


title: B728a-WT_H2O2_LabA_Rep1

city: Ames

first: Gwyn

middle: A

last: Beattie

state: IA

address: 207 Science I

department: Dept of Plant Pathology & Microbiology

country: USA

institute: Iowa State University

description: Washed, late log-phase cells were incubated in HMM medium amended H2O2 to a final concentration of 0.5 mM and 2.5x109 CFU/ml for 15 min at 25°C.

hyb_protocol: Hybridization was performed by Roche NimbleGen Inc., Reykjavík, Iceland, 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:
Expression values were generated from the raw fluorescent readings for each probe (.pair files) using quantile normalization (Bolstad et al., 2003, Bioinformatics, 19:185), and the Robust Multichip Average (RMA) algorithm (Irizarry et al., 2003, Nucleic Acids Res. 31: e15 and Irizarry et al., 2003, Biostatistics 4:249) by Roche NimbleGen Inc.
A linear model analysis of the data was conducted for each feature (ORF or predicted sRNA), and this model analysis included data from nine additional B728a mutants subjected to each stress treatment (data for the mutants are not included here).  Each linear model included fixed effects for replications, treatments, strains, and treatment-by-strain interactions, as well as a fixed intercept parameter and one random error effect for each observation. LIMMA analysis (Smyth, 2004, Stat Appl Genet Mol Biol 3:Art 3) was applied to share information across genes when estimating error variances. This was done separately for distinct groups of treatments that had similar absolute median residuals. The resulting variance estimates were used to calculate Welch t-statistics and corresponding P-values among all pairwise treatment comparisons of interest. For each comparison of interest, q-values were estimated from the corresponding distribution of P-values (Nettleton et al., 2006, J Agr Biol Envir St 11:337-356).

organism: Pseudomonas syringae

label_protocol: Labeling was performed by Roche NimbleGen Inc., Reykjavík, Iceland, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Cells were grown on solid King’s B medium containing rifampin (50 μg/ml).  Cells were transferred to liquid HMM and subcultured twice in HMM with aeration via shaking at 25°C.  HMM medium contained 0.2% D-fructose, 0.2% D-mannitol, 0.2% succinate, 10 mM L-glutamine, 10 µM FeCl3, 10 µM N-(β-ketocaproyl)-L-homoserine lactone (AHL), 50 mM potassium phosphate buffer, 7.6 mM (NH4)2SO4, 1.7 mM MgCl2, and 1.7 mM NaCl.   When the cells reached late-log phase (5x108 CFU/ml), they were collected by centrifugation at 5,000xg for 10 min.

extract_protocol: In the in vitro treatments, RNA was stabilized using RNAprotect Bacteria Reagent (Qiagen Inc., Valencia, CA).  In the in planta treatments, RNA was stabilized using an acidic phenol RNA stabilizing solution due to the large volumes required.  Total RNA was extracted from the cells using a Qiagen RNeasy mini kit and DNA was removed using the on-column DNase I digestion with subsequent DNase I removal.  RNA integrity was evaluated using an Agilent 2100 bioanalyzer.

treatment_protocol:
For the in vitro treatments, the HMM-grown cells were resuspended in HMM medium lacking L-glutamine, FeCl3, AHL and (NH4)SO4, designated HMM-FeN medium.  The cells were washed in HMM-FeN and resuspended in HMM-FeN to a final density of 2.5x109 CFU/ml.  Aliquots were transferred to 5 test tubes and diluted to 2.5x108 CFU/ml with either 1) HMM medium, 2) HMM medium with NaCl to a final concentration of 0.23 M, 3) HMM medium with H2O2 to a final concentration of  0.5 mM, 4) HMM medium lacking FeCl3 but with N,N’-di(2-hydroxybenzyl)ethylenediamin-N,N’-diacetic acid monohydrochloride hydrate (HBED) to a final concentration of 100 µM, or 5) HMM medium lacking L-glutamine, (NH4)SO4 and AHL; these were designated as the basal medium, osmotic stress, Apoplastic growth, iron limitation and nitrogen limitation treatments, respectively. At the end of the treatments, the cells were immediately diluted with an RNA stabilizing agent, harvested by centrifugation, and stored as cell pellets at -20°C.  All treatments were performed at 25°C with aeration via shaking.  Two of the in vitro samples are missing; these are the B728a ∆rpoS cells in the basal medium (replicate 2) and the B728a ∆retS cells exposed to low N (replicate 2).
For the in planta treatments, the HMM-grown cells were suspended in water, which contained 0.01% of the biosurfactant Silwet L-77, to a density of 1x106 CFU/ml for B728a, ΔahlR, ΔaefR, ΔgacS, ΔsalA, and ΔretS, to a density of 1x107 CFU/ml for ΔrpoS and ΔalgU, to a density of 1x108 CFU/ml for ΔhrpL, and to a density of 1x109 CFU/ml for ΔrpoN. The higher inoculum densities were to compensate for the reduced growth of the mutants in planta and to ensure sufficient RNA recovery.  One of the in planta treatment samples is missing: the B728a ∆rpoN cells recovered from the apoplast (replicate 2).
To establish epiphytic populations, the HMM-grown cells were suspended in water containing 0.01% of the biosurfactant Silwet L-77 to a density of 1x106 CFU/ml for B728a, ΔahlR, ΔaefR, ΔgacS, ΔsalA, and ΔretS, to a density of 1x107 CFU/ml for ΔrpoS and ΔalgU, to a density of 1x108 CFU/ml for ΔhrpL, and to a density of 1x109 CFU/ml for ΔrpoN. The higher inoculum densities were to compensate for the reduced growth of the mutants in planta and to ensure sufficient RNA recovery.  The bacteria were spray inoculated onto leaves.  Plants were incubated for 24 h in a 95% RH mist chamber, at which time the chamber was partially opened until the water on the leaves had visibly evaporated and was then re-sealed to allow incubation without active humidification for another 48 h.  The incubations were at 25°C with ambient but not supplemental lighting.  A total of 400 to 600 primary leaves were collected, immediately submerged in an RNA stabilizing solution, sonicated for 10 min, and then physically removed from the solution.
To establish apoplastic populations, the HMM-grown cells were suspended in water, which contained 0.01% of the biosurfactant Silwet L-77, to the same densities as for the epiphytic treatment, with the exception of the ΔrpoS mutant, for which 106 cells/ml were used. The bacteria were introduced by vacuum infiltration into leaves that were submerged in the inoculum.  Plants were incubated for 48 h under plant growth lights with a 12-h photoperiod.  A total of 40 to 80 leaves were collected and immediately submerged in an RNA stabilizing solution.  The leaves were cut into squares (~ 3x3 mm2) while submerged, and the plant tissues and liquid were sonicated for 10 min.  The solution was filtered through Whatman filter paper #1, with repeated filter changes.
For both in planta treatments, the cells in the suspension (epiphytic cells) or filtrate (apoplastic cells) were collected by centrifugation, suspended in the residual supernatant, separated from plant debris by filtration through a 5-µm filter with repeated filter changes, again harvested by centrifugation, and stored as cell pellets at -20°C.

tag: genotype

value: Wild type

tag: strain


title: Colorectal Normal Tissue-073011-01NS-Affymetrix Human Exon 1.0 ST

city: Riyadh

first: Sathish

last: Periyasamy

state: Select a State or Province

department: Bioinformatics

country: Saudi Arabia

institute: NGHA

description: RMA expression value derived from AltAnalyze; core-exon analysis

hyb_protocol: GeneChip® Hybridization Wash and Stain Kit (cat # 900720) was procured from Affymetrix and used according the manufacturers protocol.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing: Data Processing using AltAnalyze Software. The default recommended settings by Altanalyze was used to analyze the data

label: Biotin

organism: Homo sapiens

source_name: Colorectal Normal Tissue

label_protocol: Gene Chip WT Terminal Labelling and Controls Kit (cat # 951024) was procured from Affymetrix and used according the manufacturers protocol.

growth_protocol: NONE (Tissue samples were used)

extract_protocol: RNA was isolated from <30mg of biopsy and surgery derived tissues using Macherey Nagel (Germany) Trio Kit. Both DNA and RNA were extracted in the same protocol accoding to manufacturers protocol.

treatment_protocol: not applicable

value: Adjacent Normal

tag: gender

value: Female

tag: age

tag: tissue

value: Colon & Rectum

tag: tnm

tag: Stage

value: Not Available


title: Colorectal Normal Tissue-092611-01NB-Affymetrix Human Exon 1.0 ST

value: II


title: Mm_Mouse_16t_6

city: Amsterdam

first: Oskar

last: Bruning

address: Science Park 904

department: SILS

country: Netherlands

institute: University of Amsterdam

hyb_protocol: Each hybridization mixture was made up from 750 ng Test (Cy3) and 750 µg Reference (Cy5) sample.  Samples were dried and 1.98 µl of water was added. The hybridization cocktail was made according to the manufacturer’s instructions (Nimblegen Arrays User’s Guide – Gene Expression Arrays Version 5.0, Roche Nimblegen). 5.22 µl from this mix was added to each sample. The samples were incubated for 5 min at 65°C and 5 min at 42°C prior to loading. Hybridization samples were loaded onto 12x135k custom designed microarrays against E. coli (OID 38205, Design 120315). Microarrays were hybridized for 18 hours at 42°C with the NimbleGen Hybridization System 4 (Roche Nimblegen).

scan_protocol: the slides were washed according to the Nimblegen Arrays User’s Guide – Gene Expression Arrays Version 5.0 and scanned in an ozone-free room with a Agilent DNA microarray scanner G2565CA (Agilent Technologies). Feature extraction was performed with NimbleScan v2.6 (Roche Nimblegen).

data_processing: The raw data from all arrays was subjected to multiple quality control checks, i.e. visual inspection of the scans, testing against criteria for foreground and background signals, testing for consistent performance of the labeling dyes, checking for spatial effects through pseudo-color plots, and inspection of pre- and post-normalized data with box plots, ratio-intensity (RI) plots and PCA plots. Within array normalization was performed using LOESS. Between array normalization was run on the Cy3-channel by summarizing (Gene id's) the intensity values of the probes in a probe set using the robust multi-array average (RMA) algorithm.

label_protocol: Per test sample, 5 µg total RNA combined with 1 µg random octamers (Biolegio) in 4.5 µl was heated to 65°C for 10 min to denature the RNA and was allowed to cool in an ice-waterbath for 10 min. This 4.5 µl was made to 10 µl with a first strand mastermix containing final concentrations of 50 mM Tris-Cl (pH 8.3), 3 mM MgCl2, 75 mM KCl, 200 mM Raffinose (Sigma-Aldrich), 0.015% Triton X-100, 30 ng Actinomycin-D (Sigma-Aldrich), 0.01M DTT, 0.5 mM dGAC, 0.35 mM dUTP, 0.15 mM dUTP-Cy3 (test) or dUTP-Cy5 (common reference) (GE Healthcare) and 200U SuperScript-II (Life Technologies).  This mixture was incubated for 2 min at 25°C, 120 min at 42°C and 15 min at 70°C. Finally, 1.5 µl of 2.5M NaOH was added to hydrolyze the remaining RNA by heating for 10 min at 70°C. 8.5 µl 2M MOPS was added for neutralization and the labeled cDNA was purified with the E.Z.N.A. MicroElute RNA Clean-up Kit (Omega Biotek). Dye incorporation and cDNA yield was measured on the NanoDrop ND-1000 (Thermo Scientific) yielding 2-2.5 µg per sample and a FOI > 10 pmol/µg. The common reference was made by an equimolar pool of all test samples (5 µg per sample) and subsequently labeled as the test samples with Cy5 incorporation.

growth_protocol: Wild-type (WT; p53+/+) mice were used for UV exposure studies. All mice used were males of 7-10 weeks of age and at least 10 times backcrossed in SKH hairless strain. Mice received normal feed and water ad libitum.

extract_protocol: At different time points after UV-B exposure, both treated and untreated mice were anaesthetized by isoflurane. 1.5mm biopsies were sampled from the back.  by punching a half moon shape on folded skin. Biopsies were immediately snap frozen in liquid nitrogen and stored at -80°C until further processing. Total RNA was isolated using the RNeasy mini kit (Qiagen, Valencia, CA). RNA was assessed for quality with the Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).

treatment_protocol: All mouse treatments have been approved by the institute's Experimental Animal Ethical Committee and carried out in accordance with national legislation. Mice were UVB irradiated at different doses (90, 180, 360, 450, 720 J/m2) in a chamber containing Phillips TL12 lamps. Control mice were mock treated.

tag: treatment

value: skin

value: Wild-type (WT; p53+/+)

tag: time (hours)

tag: mouse


title: Mm_Mouse_15t_9


title: 2_14_2

city: Blacksburg

first: Fernando

middle: H

last: Biase

state: VA

address: 175 West Campus Drive

department: School of Animal Sciences

institute: Virginia Tech

data_processing: Raw Ct values = 999 were converted to 0 (zero). Relative quantification of gene expression (log2 space) was obtained by subtracting the Ct values from the baseline value of 22. Values < 0 (zero) were converted to 0 (zero).

label: EvaGreen

source_name: pre-implantatio embryo

label_protocol: The cells and pools were subjected to reverse transcription with SuperScript®VILO™ cDNA Synthesis kit (Life Technologies) as recommended by the manufacturer. DELTAgene™ Assays were custom designed for 94 genes associated with embryo development or regulation of gene expression, and two controls. The cDNA from cells and pools were subjected to specific target amplification for 20 cycles. Pre-amplified template was diluted and subjected to primer specific amplification with SooFast™EvaGreen®Supermix (Biorad) on 96.96 array chip and BiomarkHD™ System (Fluidigm).

extract_protocol: Cell was lysed by freezing at -80  Celcius degree


title: B728a-WT_NaCl_LabA_Rep2

description: Washed, late log-phase cells were incubated in HMM medium amended with NaCl to a final concentration of 0.23 M and 2.5x109 CFU/ml for 15 min at 25°C.

source_name: Pseudomonas syringae B728a wild type, Osmotic stress


title: 2_9_2


title: 2_10_1


title: Mm_Mouse_7t_24

value: 90 UV-B J/m2


title: 2_9_1


title: B728a-WT_NaCl_LabA_Rep1


title: 2_8_2


title: 2_11_2


title: Colorectal Normal Tissue-030613-01TB-Affymetrix Human Exon 1.0 ST

source_name: Colorectal Tumor Tissue

value: Tumor

value: IV


title: Colorectal Normal Tissue-072511-01NB-Affymetrix Human Exon 1.0 ST

value: Male

value: III


title: Mm_Mouse_12t_1


title: Mm_Mouse_9t_48


title: 2_8_1


title: B728a-WT_Basal medium_LabA_Rep1

description: Washed, late log-phase cells were incubated in basal HMM medium (2.5x109 CFU/ml) for 15 min at 25°C.

source_name: Pseudomonas syringae B728a wild type, Basal medium


title: low-dose penicillin high fat diet 30 week liver, biological replicate1

city: Buffalo

first: Jiho

last: Sohn

state: New York

address: 3435 Main Street, 644 Biomedical Research Building

department: Oral Biology

institute: SUNY Buffalo

description: Gene expression from liver at week 30

hyb_protocol: standard procedures recommended by Affymetrix was used

data_processing: The raw microarray data was normalized by the Robust Multi-Array (RMA) method using Affy package in Bioconductor

source_name: liver

growth_protocol: All mice were started on normal chow (13.5% fat kcal). At 17 weeks of age, half of the mice were switched to high fat diet (45% fat kcal). Livers were collected at age 30 weeks.

extract_protocol: RNeasy Mini Kit (Qiagen, Valencia CA)

treatment_protocol: C57BL6J  mice received low-dose penicillin through their drinking water (6.7 mg/L), control mice did not receive antibiotics.

value: low-dose pennicillin

value: 30 weeks

tag: diet

value: D12451:45% kCAL from fat


title: B728a-WT_Basal medium_LabA_Rep2


title: Colorectal Normal Tissue-070911-01NB-Affymetrix Human Exon 1.0 ST


title: low-dose penicillin high fat diet 30 week liver, biological replicate3

description: Gene expression from liver at week 30

scan_protocol: standard procedures recommended by Affymetrix was used


title: control_6

city: Aurora

first: Calies

last: Menard-Katcher

state: CO

department: Pediatrics

institute: University of Colorado School of Medicine

data_processing:
Raw data was normalized by means of calculated normalization factors based on sum of positive controls and sum of microRNA counts per NanoString Technologies.
MicroRNA with counts greater than background (average - 2 standard deviations) were considered detectable.

source_name: Esophageal mucosa

extract_protocol: Total RNA was isolated using mirVana miRNA Isolation Kit, with phenol by Life Technologies. RNA was eluted in 100 uL of the kit elution buffer.

value: male

tag: eos/hpf


title: Mm_Mouse_6t_48

value: 0 UV-B J/m2


title: 2_7_2


title: control_5


title: Colorectal Normal Tissue-060612-01NB-Affymetrix Human Exon 1.0 ST

value: Adjacent Normal


title: 2_7_1


title: low-dose penicillin high fat diet 30 week liver, biological replicate2

description: Gene expression from liver at week 30

label_protocol: standard procedures recommended by Affymetrix was used


title: Mm_Mouse_8t_12


title: control_4


title: Mm_Mouse_14t_6


title: control high fat diet 30 week liver, biological replicate1

description: Gene expression from liver at week 30

value: control


title: Mm_Mouse_11t_48


title: 2_6_1


title: 2_6_2


title: control high fat diet 30 week liver, biological replicate2

description: Gene expression from liver at week 30


title: CXCR5-KO mouse #9048, EµTCL (pure tumor cells)

tag: strain background

tag: genotype/variation

value: Emu-Tcl1 transgenic CXCR5-KO

value: EµTCL

value: CD5+CD19+ tumor cells


title: control_2

value: female


title: control_1


title: low-dose penicillin normal chow 30 week liver, biological replicate3

description: Gene expression from liver at week 30

value: normal chow (NC, Purina Mills International Diet # 5001, 13.5% kcal from fat),


title: 2_5_2

tag: cell type


title: Colorectal Normal Tissue-033112-01NB-Affymetrix Human Exon 1.0 ST

value: Sigmoid

value: II


title: control_3


title: Mm_Mouse_13t_3

value: skin

value: Wild-type (WT; p53+/+)


title: Mm_Mouse_10t_0


title: Colorectal Normal Tissue-032713-01NB-Affymetrix Human Exon 1.0 ST

value: Male

value: Colon & Rectum

value: Not Available

value: IV


title: Colorectal Normal Tissue-032612-01NB-Affymetrix Human Exon 1.0 ST

value: Female


title: Mm_Mouse_5t_0

value: 0 UV-B J/m2


title: Mm_Mouse_13t_9


title: Mm_Mouse_11t_3


title: 2_4_1


title: low-dose penicillin normal chow 30 week liver, biological replicate2

description: Gene expression from liver at week 30

value: low-dose pennicillin

value: 30 weeks


title: control normal chow 30 week liver, biological replicate 3

description: Gene expression from liver at week 30

value: control


title: control normal chow 30 week liver, biological replicate 2

description: Gene expression from liver at week 30


title: eoe_4

value: male


title: Colorectal Normal Tissue-030613-01NB-Affymetrix Human Exon 1.0 ST

value: Adjacent Normal


title: Colorectal Normal Tissue-031912-01NB-Affymetrix Human Exon 1.0 ST

value: Recto-sigmoid


title: 2_3_2


title: Mm_Mouse_7t_9

value: 90 UV-B J/m2


title: control high fat diet 30 week liver, biological replicate3

description: Gene expression from liver at week 30

value: D12451:45% kCAL from fat


title: NCS+

city: Houston

first: Cecil

last: Han

state: TX

address: 7777 knight road

department: Cancer Biology Department

institute: MD Anderson Cancer Center

description: NCS treated

data_processing: data pre-processing, normalization and statistical analysis were performed using Exiqon GenEx qPCR software

label: SYBR Green

label_protocol: microRNA was synthesized by Exiqon RT kit according to manufacture instruction

growth_protocol: Human U2OS cell were cultured in DMEM 5% FBS , cells were infected by shDDX1 and shcontrol lentivirus and selected with puromycin 2ug/ml

extract_protocol: Total RNA was extracted by Trizol (ambion)

treatment_protocol: NCS (500 ng/ml) treated for 6 hours to U2OS

tag: cell line

value: NCS 500ng/6 hr treated


title: 2_2_2


title: low-dose penicillin 8 week ileum, biological replicate 4

description: Gene expression from ileum at week 8

source_name: terminal ileum

growth_protocol: C57BL6 mice were weaned at 4 weeks of age onto normal chow, then switched to a high fat diet (45% kcal from fat) at 6 weeks of age. Livers were collected at 8 weeks of age

treatment_protocol: Control mice did not receive antibiotics, LDP mice received low-dose penicillin (6.7 mg/L),  from birth.  Mice were started on normal chow diet and switched to high fat diet at week 6.

value: 8 weeks


title: 2_5_1


title: Colorectal Normal Tissue-010912-01NB-Affymetrix Human Exon 1.0 ST

value: Colon

value: II


title: Mm_Mouse_6t_6

value: skin

value: Wild-type (WT; p53+/+)


title: eoe_1

value: female


title: NCS-

description: NCS non-treated


title: low-dose penicillin 8 week ileum, biological replicate 3

description: Gene expression from ileum at week 8

value: Male


title: eoe_5


title: Mm_Mouse_14t_12


title: control normal chow 30 week liver, biological replicate 1

description: Gene expression from liver at week 30

value: normal chow (NC, Purina Mills International Diet # 5001, 13.5% kcal from fat),


title: Mm_Mouse_8t_48


title: Colorectal Normal Tissue-042413-01NB-Affymetrix Human Exon 1.0 ST

value: Female

value: Colon & Rectum

value: Not Available


title: low-dose penicillin 8 week ileum, biological replicate 2

description: Gene expression from ileum at week 8

value: low-dose pennicillin


title: 2_1_2


title: shDDX1

description: DDX1 shRNA

tag: infection

value: DDX1 shRNA


title: 2_2_1


title: shNS

description: control shRNA

value: control shRNA


title: 2_1_1


title: Colorectal Normal Tissue-010213-01NB-Affymetrix Human Exon 1.0 ST

value: Adjacent Normal

value: IIIB


title: 1-POOL 10


title: Colorectal Normal Tissue-011112-01NB-Affymetrix Human Exon 1.0 ST

value: IV


title: 1-POOL 50


title: 1_11_1

value: zygote


title: Mm_Mouse_9t_24

tag: genotype


title: low-dose penicillin 8 week ileum, biological replicate 1

description: Gene expression from ileum at week 8

value: 8 weeks

tag: strain

value: D12451:45% kCAL from fat


title: control 8 week ileum, biological replicate 2

description: Gene expression from ileum at week 8

value: control

tag: gender


title: Mm_Mouse_10t_1

value: skin

value: Wild-type (WT; p53+/+)


title: Mm_Mouse_15t_48


title: control 8 week ileum, biological replicate 1

description: Gene expression from ileum at week 8

tag: age

value: Male


title: 1_12_1


title: Mm_Mouse_5t_48

value: 0 UV-B J/m2

tag: tissue


title: 1_10_1


title: Mm_Mouse_16t_1


title: Mm_Mouse_12t_0


title: K662_CEBPA_replicate4

city: Rome

first: Alessandro

last: Fatica

address: P.le Aldo Moro 5

department: Biology and Biotechnology "C. Darwin"

country: Italy

institute: Sapienza University of Rome

description: Gene expression after 48 hrs Dox in K562 CEBPA rep 4

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies).

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences.

source_name: K562 CEBPA 48hrs Dox replicate 4

label_protocol: To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).

growth_protocol: K562 cell lines were cultured at 37°C under an atmosphere containing 5% CO2 in RPMI 1640 medium supplemented with 1x Penicillin/Streptomicin solution, 1x L-glutamine and 10% Fetal Bovine Serum.

extract_protocol: RNA was prepared using the Rneasy kit (Qiiagen)

treatment_protocol: Doxycycline (Dox) were purchased from Sigma and utilized at a concentration of 200 ng/ml for 48 hours

value: leukemia


title: Mouse prostate epithelial cells Ccnd1-/- Replicate 2

first: Mathew

middle: Casimiro

last: Casimiro

state: United States

address: 233 South 10th St, Rm 1035

department: 233 South 10th St, Rm 1035

institute: Thomas Jefferson University

hyb_protocol: 15µg of cRNA was fractionated to produce fragments between 35–200 bp using 5x Fragmentation buffer provided in the Cleanup Module, followed by hybridization for 18 hrs. Arrays then were washed and stained using Genechip Fluidic Station 450, and hybridization signals were amplified using antibody amplification with goat IgG (Sigma-Aldrich) and anti-streptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.

data_processing: The data were analyzed and normalized by Robust Multi-array Average (RMA) algorithm.

source_name: Mouse prostate gland

label_protocol: The double stranded cDNA was used as a template to generate biotinylated cRNA using Bioarray HighYield RNA Transcription Labeling Kit (Enzo) and the labeled cRNA purified by GeneChip Sample Cleanup Module (Affymetrix)

growth_protocol: PECs were cultured in F-12 media supplemented with 10% FBS , Insulin 5ug/ml, EGF 10ng/ml, Hydrocortisone 1ug/ml, transferrin 5ng/ml,  bovine pituitary extract 15ug/ml, 1X pen-strep, 1 X Gentamicin

extract_protocol: Total RNA extracted using Trizol reagent (Invitrogen) as per manufacturers' guidelines.

treatment_protocol: No specific treatment protocol

value: FvB

tag: transgenic mouse


title: 1_9_1


title: Mm_Mouse_16t_0


title: Mouse prostate epithelial cells Ccnd1-/- Replicate 1


title: Mouse prostate epithelial cells Ccnd1-/- Replicate 3


title: control 8 week ileum, biological replicate 3

description: Gene expression from ileum at week 8


title: 1_8_1


title: K662_CEBPA_replicate3

description: Gene expression after 48 hrs Dox in K562 CEBPA rep 3

source_name: K562 CEBPA 48hrs Dox replicate 3


title: Mm_Mouse_14t_48


title: Colorectal Normal Tissue-042412-01NB-Affymetrix Human Exon 1.0 ST

value: Female

value: Recto-sigmoid

tag: tnm

tag: Stage

value: III


title: K662_CEBPA_replicate2

description: Gene expression after 48 hrs Dox in K562 CEBPA rep 2

source_name: K562 CEBPA 48hrs Dox replicate 2


title: Mouse prostate epithelial cells Ccnd1+/+ Replicate 3


title: 1_7_1


title: 1_6_1


title: Mm_Mouse_10t_6

tag: treatment

tag: time (hours)


title: Mm_Mouse_7t_48

value: 90 UV-B J/m2

tag: mouse


title: Mouse prostate epithelial cells Ccnd1+/+ Replicate 2


title: K662_CTR_replicate4

description: Gene expression after 48 hrs Dox in K562 control rep 4

source_name: K562 CTR 48hrs Dox replicate 4


title: eoe_2

value: male

tag: eos/hpf


title: eoe_3


title: 2_3_1


title: 1_5_1


title: 2_4_2


title: 40ºC_#2

city: Kodaira

first: Hirohiko

last: Hohjoh

state: Tokyo

address: 4-1-1 Ogawahigashi

country: Japan

institute: National Institute of Neuroscience, NCNP

description: 40ºC treated sample #2. Normalized data are in the Matrix(2) sheet.

hyb_protocol: Hybridization was carried out with the Genopal®-MICM DNA chips (Mitsubishi Rayon) for detection of mouse miRNAs in 100 µl of hybridization buffer [6 x SSC, 0.2% SDS and 1 µg of heat-denatured labeled RNAs] at 42℃ overnight using a hybridization chamber specific for the Genopal®-DNA chip (Mitsubishi Rayon).

scan_protocol: After hybridization, the DNA chips were washed twice in 2xSSC containing 0.2% SDS at 50℃ for 20 min followed by washing in 2xSSC at 50℃ for 10 min, and then hybridization signals were examined by means of a DNA chip reader adopting multi-beam excitation technology according to the manufacturer’s instructions (Yokogawa Electric Corporation).

data_processing: Hybridization signal intensity of each miRNA was normalized to that of the external control oligonucleotides provided by Mitsubishi Rayon.

source_name: HeLa cell

label_protocol: Isolated small-sized RNAs (~1 µg) were subjected to direct labeling with a fluorescent dye using a PlatinumBright 647 Infrared nucleic acid labeling kit (KREATECH), according to the manufacturer’s instructions. After fluorescent labeling, the labeled RNAs were purified from free fluorescent substrates by the KREApure columns (KREATECH) and used in hybridization.

growth_protocol: Cells were grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum, 100 units/ml penicillin, and 100 mg/ml streptomycin at 37ºC in 5% CO2 humidified chamber.

extract_protocol: Total RNAs were extracted from various tissues using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. For preparation of cellular miRNAs, 20 µg of each isolated total RNA was mixed with 5 µl of the external control oligonucleotides provided by Mitsubishi Rayon, and subjected to isolation of small-sized RNAs containing miRNAs using an RNeasy MinElute Cleanup kit (Qiagen).

treatment_protocol: Cell were subjected to a mild hyperthermia at 40ºC for 12h.

tag: Sex

value: female

value: HeLa


title: Mm_Mouse_12t_12


title: 1_4_1

value: zygote


title: 40ºC_#1

description: 40ºC treated sample #1. Normalized data are in the Matrix(2) sheet.


title: 1_3_1


title: Mm_Mouse_8t_0


title: Mouse prostate epithelial cells Ccnd1+/+ Replicate 1


title: K662_CTR_replicate3

description: Gene expression after 48 hrs Dox in K562 control rep 3

source_name: K562 CTR 48hrs Dox replicate 3


title: 37ºC_#1

description: 37ºC treated sample #1. Normalized data are in the Matrix(2) sheet.


title: 1_1_1


title: K662_CEBPA_replicate1

description: Gene expression after 48 hrs Dox in K562 CEBPA rep 1

source_name: K562 CEBPA 48hrs Dox replicate 1


title: 37ºC_#2

description: 37ºC treated sample #2. Normalized data are in the Matrix(2) sheet.


title: 1_2_1


title: serum_inactive_eoe_5

description: inactive disease

data_processing: Data was normalized using the median threshold cycle (Ct) of each array and individual miRNA levels were calculated as 2^(Ctmedian – CtmiRNA).

label: SYBR green

label_protocol: Three uL of total serum RNA was used as input in a 7.5 uL reverse transcription reaction. Twelve cycles of cDNA pre-amplification was then performed using 2.5 uL of the RT reaction product according to manufacturer’s instructions.

extract_protocol: Total RNA was isolated using mirVana miRNA Isolation Kit, with phenol by Life Technologies. 3 uL of a spike solution containing exogenous miR-302a, miR-302d, and miR-372 (5 pM, 5 pM, and 10 pM, respectively) were added as positive controls. RNA was eluted in 100 uL of the kit elution buffer.


title: serum_inactive_eoe_4

description: inactive disease


title: 10_MLN8237-1

city: Essen

first: Alexander

last: Schramm

address: Hufelandstr. 55

department: Childrens Hospital

institute: University Hospital Essen

description:
10_MLN8237-1_(Mouse430_2)
Cell line from MYCN-driven murine neuroblastoma.

hyb_protocol: Hybridisation to murine arrays (Mouse430_2 ) was performed according to the manufacturer's recommendations (Affymetrix).

scan_protocol: Scanning of chips was performed using a GeneArray scanner (Agilent).

data_processing: Data were normalised using the RMA algorithm implemented in Partek Genomics Suite 6.6 (Partek, Inc.) using the default settings.

source_name: mNB-A1, MLN8237

label_protocol: Biotin labelling was performed according to the manufacturer's recommendations (Affymetrix).

growth_protocol: Cells were cultured in RPMI medium supplemented with 10% FCS, penicillin (100 U/ml), streptomycin (100 µg/ml), 1% N2 and 2% B27.

extract_protocol: Total mRNA was isolated from cells using the QIAGEN miRNeasy Mini Kit.

treatment_protocol: Cells were seeded onto 6-well plates and treated with DMSO (0.005%), 500 nM JQ1 (BPS Bioscience) or 500 nM MLN8237 (Axon Medchem) for 24 h.

tag: strain/background

value: mixed C57BL/6 x 129X1/SvJ

value: MYCN-driven neuroblastoma


title: K662_CTR_replicate2

description: Gene expression after 48 hrs Dox in K562 control rep 2

source_name: K562 CTR 48hrs Dox replicate 2

tag: cell type


title: serum_inactive_eoe_3

description: inactive disease


title: 12_MLN8237-3

description:
12_MLN8237-3_(Mouse430_2)
Cell line from MYCN-driven murine neuroblastoma.

tag: cell line


title: 8_JQ1-2

description:
8_JQ1-2_(Mouse430_2)
Cell line from MYCN-driven murine neuroblastoma.

source_name: mNB-A1, JQ1


title: low-dose penicillin normal chow 30 week liver, biological replicate1

description: Gene expression from liver at week 30

value: low-dose pennicillin

value: 30 weeks

tag: diet

value: normal chow (NC, Purina Mills International Diet # 5001, 13.5% kcal from fat),


title: K662_CTR_replicate1

description: Gene expression after 48 hrs Dox in K562 control rep 1

source_name: K562 CTR 48hrs Dox replicate 1


title: serum_inactive_eoe_2

description: inactive disease


title: 11_MLN8237-2

description:
11_MLN8237-2_(Mouse430_2)
Cell line from MYCN-driven murine neuroblastoma.


title: serum_inactive_eoe_1

description: inactive disease


title: 7_JQ1-1

description:
7_JQ1-1_(Mouse430_2)
Cell line from MYCN-driven murine neuroblastoma.


title: 5_DMSO-5

description:
5_DMSO-5_(Mouse430_2)
Cell line from MYCN-driven murine neuroblastoma.

source_name: mNB-A1, DMSO

value: DMSO


title: 561965A11 - 71_WATER_24H_REP3 vs 77_TREATMENT5_24H_REP3

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: Biological question (15 lines max): Identification of grape genes regulated in response to resistance inducer treatments. This transcriptomic analysis should provide insight in the mode of action of the compounds under study and yield generic data relevant to grape defense reaction.

hyb_protocol: 77_TREATMENT5_24H_REP3 Cy5 / 71_WATER_24H_REP3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

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

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Vitis vinifera

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, total RNA  . (PT-SIGMA-01_30-10-2012_T.pdf)

growth_protocol: caulin leaf - peat+perlite (4:1). RH 65%. 20+/-2°C. Daylight + HQI light

treatment_protocol: Name:T5_24H - compound based treatment - plant defense activation ,water:.

tag: variety

value: cv. Marselan

value: herbaceous grape cutting

treatment_protocol: Name:WATER_24H - compound based treatment - water,water:.


title: 561965A10 - 76_TREATMENT4_24H_REP3 vs 71_WATER_24H_REP3

hyb_protocol: 71_WATER_24H_REP3 Cy5 / 76_TREATMENT4_24H_REP3 Cy3 : 30mmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:T4_24H - compound based treatment - plant defense activation ,water:.


title: serum_eoe_5

description: active disease


title: Mm_Mouse_6t_0

value: 0 UV-B J/m2

value: skin

tag: genotype

value: Wild-type (WT; p53+/+)


title: Mm_Mouse_13t_24


title: serum_eoe_4

description: active disease

tag: gender


title: Mm_Mouse_9t_3


title: Mm_Mouse_15t_24


title: Mm_Mouse_5t_24


title: Mm_Mouse_11t_9


title: 2_DMSO-2

description:
2_DMSO-2_(Mouse430_2)
Cell line from MYCN-driven murine neuroblastoma.


title: 9_JQ1-3

description:
9_JQ1-3_(Mouse430_2)
Cell line from MYCN-driven murine neuroblastoma.


title: serum_eoe_3

description: active disease


title: serum_eoe_2

description: active disease


title: serum_eoe_1

description: active disease


title: Mm_Mouse_10t_12


title: 1_DMSO-1

description:
1_DMSO-1_(Mouse430_2)
Cell line from MYCN-driven murine neuroblastoma.


title: 561965A12 - 77_TREATMENT5_24H_REP3 vs 71_WATER_24H_REP3

hyb_protocol: 71_WATER_24H_REP3 Cy5 / 77_TREATMENT5_24H_REP3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: age


title: Mm_Mouse_9t_9

tag: tissue


title: H460R-3

city: Columbus

first: Alessandra

last: Drusco

state: Ohio

address: 460 W 12th Ave

institute: The Ohio State University

description: MiRNA expression from acquired TRAIL-resistant cells

hyb_protocol: The samples were hybridized with a panel of miRNA:tag-specific nCounter capture and barcoded reporter probes. Hybridization reactions were performed with 5µl of the 5-fold diluted sample preparation reaction. All hybridization reactions were incubated at 64°C for a minimum of 18 h. Hybridized probes were purified using the nCounter Prep Station (NanoString Technologies) following the manufacturer’s instructions

scan_protocol: For each assay, a high density scan (600 fields of view) was performed.

data_processing: Nanostring data were normalized by using the Top-100 expressed miRNA normalization as implemented by the Nanostring nSolver software. P-values were calculated using the LIMMA package (Linear Models for Microarray Data) from the Bioconductor R project. The heatmap was generated by the Hierarchical Clustering module of GenePattern software based on normalized miRNA expression data.

source_name: TRAIL-resistant H460 cells

label_protocol: All sample preparations were performed according to the manufacturer’s instructions (NanoString Technologies). Preparation of small RNA samples involves the ligation of a specific DNA tag onto the 3’ end of each mature miRNA. These tags are designed to normalize the Tm’s of the miRNAs as well as to provide a unique identification for each miRNA species in the sample. Following the ligation reaction, excess tags and bridges were removed,

growth_protocol: The cells were grown with RPMI supplemented 10% FBS at 37C

extract_protocol: Trizol extraction was performed following the manufacturer's instructions.

treatment_protocol: NSCLC H460 cells  were  treated  with TRAIL daily for a period of 6 months.

tag: genotype/variation

value: acquired TRAIL-resistance


title: Mm_Mouse_5t_3


title: WT cells, replicate 5

city: New York

first: Prokopios Alexandros

last: Polyzos

address: 413 E 69th St

institute: Weill Cornell Medicine

description:
WT5.CEL (unavailable due to loss from servers)
WT pancreatic cells

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

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

data_processing:
DNA microarray analyses were performed with R. MAS5.0 normalization and log2 transformation was used. Differentially expressed genes were called if FC ≥1.5 and p<0.05.
MAS5.0 raw intenisty and ABS_CALL (Flag). Probes with raw intensity below 50 were considered 'Absent'. Probes with 'Marginal' or 'Present' flag were considered 'Present'

source_name: WT cells, replicate 5

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

growth_protocol: 30 day old bitransgenic Pdx1-cre/Kras*A mice and their wild type siblings were sacrificed and their pancreata were excized for total RNA  extraction.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions and further purified with the RNAeasy kit from QIAGEN

treatment_protocol: The Pdx1-cre/Kras*A is a standart genetic mouse model based on cre lox recombination, therefore no treatment was utilized.

value: WT

value: pancreatic cells


title: 561965A07 - 71_WATER_24H_REP3 vs 75_TREATMENT3_24H_REP3

hyb_protocol: 75_TREATMENT3_24H_REP3 Cy5 / 71_WATER_24H_REP3 Cy3 : 30pmol.

treatment_protocol: Name:T3_24H - compound based treatment - plant defense activation ,water:.


title: Mm_Mouse_8t_6

value: 90 UV-B J/m2


title: 4_DMSO-4

description:
4_DMSO-4_(Mouse430_2)
Cell line from MYCN-driven murine neuroblastoma.


title: 561965A02 - 72_ADJ_24H_REP3 vs 71_WATER_24H_REP3

hyb_protocol: 71_WATER_24H_REP3 Cy5 / 72_ADJ_24H_REP3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:ADJUVANT_24H - compound based treatment - control,adjuvant:.


title: Mm_Mouse_14t_0


title: 561965A09 - 71_WATER_24H_REP3 vs 76_TREATMENT4_24H_REP3

hyb_protocol: 76_TREATMENT4_24H_REP3 Cy5 / 71_WATER_24H_REP3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: WT cells, replicate 2

description:
WT2.CEL (unavailable due to loss from servers)
WT pancreatic cells

source_name: WT cells, replicate 2


title: 561965A08 - 75_TREATMENT3_24H_REP3 vs 71_WATER_24H_REP3

hyb_protocol: 71_WATER_24H_REP3 Cy5 / 75_TREATMENT3_24H_REP3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: H460R-2


title: WT cells, replicate 1

description:
WT1.CEL (unavailable due to loss from servers)
WT pancreatic cells

source_name: WT cells, replicate 1


title: H460R-1


title: H460S-3

description: MiRNA expression from control cell

source_name: TRAIL-sensitive H460 cells

value: control


title: WT cells, replicate 4

description:
WT4.CEL (unavailable due to loss from servers)
WT pancreatic cells

source_name: WT cells, replicate 4


title: 561965A06 - 74_TREATMENT2_24H_REP3 vs 71_WATER_24H_REP3

hyb_protocol: 71_WATER_24H_REP3 Cy5 / 74_TREATMENT2_24H_REP3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:T2_24H - compound based treatment - plant defense activation ,water inoculation:.


title: 561965A01 - 71_WATER_24H_REP3 vs 72_ADJ_24H_REP3

hyb_protocol: 72_ADJ_24H_REP3 Cy5 / 71_WATER_24H_REP3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: H460S-2

description: MiRNA expression from control cell


title: Mm_Mouse_11t_0

hyb_protocol: Each hybridization mixture was made up from 750 ng Test (Cy3) and 750 µg Reference (Cy5) sample.  Samples were dried and 1.98 µl of water was added. The hybridization cocktail was made according to the manufacturer’s instructions (Nimblegen Arrays User’s Guide – Gene Expression Arrays Version 5.0, Roche Nimblegen). 5.22 µl from this mix was added to each sample. The samples were incubated for 5 min at 65°C and 5 min at 42°C prior to loading. Hybridization samples were loaded onto 12x135k custom designed microarrays against E. coli (OID 38205, Design 120315). Microarrays were hybridized for 18 hours at 42°C with the NimbleGen Hybridization System 4 (Roche Nimblegen).


title: Mm_Mouse_12t_48


title: 561891A12 - 63_TREATMENT5_24H_REP2 vs 57_WATER_24H_REP2

hyb_protocol: 57_WATER_24H_REP2 Cy5 / 63_TREATMENT5_24H_REP2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: no treatment


title: 561965A05 - 71_WATER_24H_REP3 vs 74_TREATMENT2_24H_REP3

hyb_protocol: 74_TREATMENT2_24H_REP3 Cy5 / 71_WATER_24H_REP3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Pancreatic tumor cells, replicate 5

description:
Panc5.CEL (unavailable due to loss from servers)
Pancreatic Tumor

source_name: Pancreatic tumor cells, replicate 5

value: bitransgenic Pdx1-cre/Kras*A

value: pancreatic tumor


title: Pancreatic tumor cells, replicate 4

description:
Panc4.CEL (unavailable due to loss from servers)
Pancreatic Tumor

source_name: Pancreatic tumor cells, replicate 4


title: 561891A11 - 57_WATER_24H_REP2 vs 63_TREATMENT5_24H_REP2

hyb_protocol: 63_TREATMENT5_24H_REP2 Cy5 / 57_WATER_24H_REP2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 561891A09 - 57_WATER_24H_REP2 vs 62_TREATMENT4_24H_REP2

hyb_protocol: 62_TREATMENT4_24H_REP2 Cy5 / 57_WATER_24H_REP2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: WT cells, replicate 3

description:
WT3.CEL (unavailable due to loss from servers)
WT pancreatic cells

source_name: WT cells, replicate 3


title: 561891A10 - 62_TREATMENT4_24H_REP2 vs 57_WATER_24H_REP2

hyb_protocol: 57_WATER_24H_REP2 Cy5 / 62_TREATMENT4_24H_REP2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Mm_Mouse_6t_12

treatment_protocol: All mouse treatments have been approved by the institute's Experimental Animal Ethical Committee and carried out in accordance with national legislation. Mice were UVB irradiated at different doses (90, 180, 360, 450, 720 J/m2) in a chamber containing Phillips TL12 lamps. Control mice were mock treated.


title: 561891A08 - 61_TREATMENT3_24H_REP2 vs 57_WATER_24H_REP2

hyb_protocol: 57_WATER_24H_REP2 Cy5 / 61_TREATMENT3_24H_REP2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 6_DMSO-6

description:
6_DMSO-6_(Mouse430_2)
Cell line from MYCN-driven murine neuroblastoma.

hyb_protocol: Hybridisation to murine arrays (Mouse430_2 ) was performed according to the manufacturer's recommendations (Affymetrix).

value: mixed C57BL/6 x 129X1/SvJ

value: MYCN-driven neuroblastoma


title: Mm_Mouse_15t_0


title: Mm_Mouse_16t_48


title: Mm_Mouse_11t_24


title: Pancreatic tumor cells, replicate 3

description:
Panc3.CEL (unavailable due to loss from servers)
Pancreatic Tumor

source_name: Pancreatic tumor cells, replicate 3


title: Mm_Mouse_6t_1


title: Pancreatic tumor cells, replicate 2

description:
Pan21.CEL (unavailable due to loss from servers)
Pancreatic Tumor

source_name: Pancreatic tumor cells, replicate 2


title: H460S-1

description: MiRNA expression from control cell


title: Mm_Mouse_7t_3


title: Pancreatic tumor cells, replicate 6

description:
Panc6.CEL (unavailable due to loss from servers)
Pancreatic Tumor

source_name: Pancreatic tumor cells, replicate 6


title: 561891A07 - 57_WATER_24H_REP2 vs 61_TREATMENT3_24H_REP2

description: Biological question (15 lines max): Identification of grape genes regulated in response to resistance inducer treatments. This transcriptomic analysis should provide insight in the mode of action of the compounds under study and yield generic data relevant to grape defense reaction.

hyb_protocol: 61_TREATMENT3_24H_REP2 Cy5 / 57_WATER_24H_REP2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 3_DMSO-3

description:
3_DMSO-3_(Mouse430_2)
Cell line from MYCN-driven murine neuroblastoma.


title: Mm_Mouse_13t_48


title: Mm_Mouse_15t_3


title: 561891A05 - 57_WATER_24H_REP2 vs 60_TREATMENT2_24H_REP2

hyb_protocol: 60_TREATMENT2_24H_REP2 Cy5 / 57_WATER_24H_REP2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 561891A06 - 60_TREATMENT2_24H_REP2 vs 57_WATER_24H_REP2

hyb_protocol: 57_WATER_24H_REP2 Cy5 / 60_TREATMENT2_24H_REP2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Mm_Mouse_10t_48


title: HMB45DAP_2

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

country: South Korea

institute: GreenGene Biotech Inc.

description: Panicle 5-day-after pollination, HMB4 over-expression, biological replicate 2

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

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Oryza sativa Japonica Group

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

growth_protocol: Seeds of non-transgenic (Oriza sativa L. japonica cultivar Ilmi) and over-expression line were geminated on soil and grown in greenhouse (16-hr-light/ 8-hr-dark cycle). At the age of 1-month, plants were transferred to pot and grown outside of greenhouse under natural conditions.

extract_protocol: Total RNAs were extracted using TriReagent (Molecular Research Center, Inc.).

treatment_protocol: Panicles were collected based on size i.e. 1-3, 8-15, and 20.5-22 cm as P1, P8 and P21; respectively. Moreover, panicles at 5-day-after-pollination 5DAP, was also collected to analyze the developing seed. Leaves (L) at the stage of 4-week before heading which was around the date of panicle initiation was used at reference.

tag: cultivar

value: Oryza sativa L. cv. Ilmi

value: Panicle 5-day-after pollination

value: HMB4 over-expression


title: 561891A03 - 57_WATER_24H_REP2 vs 59_TREATMENT1_24H_REP2

hyb_protocol: 59_TREATMENT1_24H_REP2 Cy5 / 57_WATER_24H_REP2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:T1_24H - compound based treatment - plant defense activation ,water inoculation:.

value: cv. Marselan


title: Tumor 8

description:
MYCN-driven murine neuroblastoma
LSL-MYCN; Dbh-iCre mice spontaneously develop neuroblastomas.

hyb_protocol: Hybridisation to human arrays was performed according to the manufacturers recommendations (Affymetrix)

scan_protocol: Scanning of chips was performed using a GeneArray scanner (Agilent)

data_processing: data were normalised using the RMA implementation in Partek Genomics Suite 6.6.

source_name: tumor - superior cervical ganglion

label_protocol: Biotin labelling was performed according the manufacturers recommendations (Affymetrix)

extract_protocol:
Untreated tumors were excised from euthanised mice
Total mRNA was isolated from tumor tissue using QIAGEN RNeasy Mini Kit.

value: LSL-MYCN;Dbhi-Cre

tag: tumor

value: tumor - superior cervical ganglion


title: 561891A04 - 59_TREATMENT1_24H_REP2 vs 57_WATER_24H_REP2

hyb_protocol: 57_WATER_24H_REP2 Cy5 / 59_TREATMENT1_24H_REP2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: herbaceous grape cutting


title: HMB45DAP_1

description: Panicle 5-day-after pollination, HMB4 over-expression, biological replicate 1


title: Mm_Mouse_7t_0

tag: treatment

value: 0 UV-B J/m2

value: skin

value: Wild-type (WT; p53+/+)


title: Mm_Mouse_12t_6

tag: time (hours)


title: HMB4P21cm_2

description: Panicle size 20.5-22 cm, HMB4 over-expression, biological replicate 2

value: Panicle size 20.5-22 cm


title: 561891A02 - 58_ADJ_24H_REP2 vs 57_WATER_24H_REP2

hyb_protocol: 57_WATER_24H_REP2 Cy5 / 58_ADJ_24H_REP2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: HMB4P21cm_1

description: Panicle size 20.2-22 cm, HMB4 over-expression, biological replicate 1

value: Panicle size 20.2-22 cm


title: HMB4P8cm_1

description: Panicle size 8-15cm, HMB4 over-expression, biological replicate 1

value: Panicle size 8-15cm


title: Tumor 3

source_name: tumor - adrenal

value: tumor - adrenal


title: HMB4P8cm_2

description: Panicle size 8-15cm, HMB4 over-expression, biological replicate 2


title: Pancreatic tumor cells, replicate 1

description:
Panc1.CEL (unavailable due to loss from servers)
Pancreatic Tumor

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

source_name: Pancreatic tumor cells, replicate 1

value: bitransgenic Pdx1-cre/Kras*A

value: pancreatic tumor


title: Tumor 5


title: Mm_Mouse_13t_0

hyb_protocol: Each hybridization mixture was made up from 750 ng Test (Cy3) and 750 µg Reference (Cy5) sample.  Samples were dried and 1.98 µl of water was added. The hybridization cocktail was made according to the manufacturer’s instructions (Nimblegen Arrays User’s Guide – Gene Expression Arrays Version 5.0, Roche Nimblegen). 5.22 µl from this mix was added to each sample. The samples were incubated for 5 min at 65°C and 5 min at 42°C prior to loading. Hybridization samples were loaded onto 12x135k custom designed microarrays against E. coli (OID 38205, Design 120315). Microarrays were hybridized for 18 hours at 42°C with the NimbleGen Hybridization System 4 (Roche Nimblegen).

tag: mouse


title: Tumor 4


title: Tumor 7


title: Mm_Mouse_14t_1


title: Tumor 6


title: HMB4P1cm_2

description: Panicle size 1-3cm, HMB4 over-expression, biological replicate 2

value: Panicle size 1-3cm


title: Tumor 2


title: 561856A12 - 49_TREATMENT5_24H_REP1 vs 43_WATER_24H_REP1

hyb_protocol: 43_WATER_24H_REP1 Cy5 / 49_TREATMENT5_24H_REP1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 561891A01 - 57_WATER_24H_REP2 vs 58_ADJ_24H_REP2

hyb_protocol: 58_ADJ_24H_REP2 Cy5 / 57_WATER_24H_REP2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 561856A11 - 43_WATER_24H_REP1 vs 49_TREATMENT5_24H_REP1

hyb_protocol: 49_TREATMENT5_24H_REP1 Cy5 / 43_WATER_24H_REP1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: HMB4P1cm_1

description: Panicle size 1-3cm, HMB4 over-expression, biological replicate 1

value: Oryza sativa L. cv. Ilmi


title: MEFs_uv0.75_t30

data_processing: The raw data from all arrays was subjected to multiple quality control checks, i.e. visual inspection of the scans, testing against criteria for foreground and background signals, testing for consistent performance of the labeling dyes, checking for spatial effects through pseudo-color plots, and inspection of pre- and post-normalized data with box plots, ratio-intensity (RI) plots and PCA plots. Within array normalization was performed using LOESS. Between array normalization was run on the Cy3-channel by summarizing (Gene id's)  the intensity values of the probes in a probe set using the robust multi-array average (RMA) algorithm.

source_name: MEFs treated uv (0.75j/s) RNA harvest 30 minutes

growth_protocol: Primary MEFs were isolated from E13.5 embryos in a C57BL/6 background (backcrossed for more than F8 generations). MEFs were cultured in Dulbecco's modified Eagle medium (Invitrogen, Breda, The Netherlands) containing 10% fetal bovine serum (Biocell, Rancho Dominguez, CA), 1% nonessential amino acids (Invitrogen, Breda, The Netherlands), penicillin (0.6 μg/ml), and streptomycin (1 μg/ml) at 37°C and under 5% CO2, 3% O2 conditions. The experiment was performed with early-passage MEFs (prior to passage five). FBS.

extract_protocol: Total RNA was isolated using the RNeasy mini kit (Qiagen, Valencia, CA). RNA was assessed for quality with the Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).

treatment_protocol: MEFs (p53 +/+) were expanded and plated at 3.5x105 cells per 6-cm plate. Six hours later , cells were washed with phosphate-buffered saline and exposed to UV-C light at different doses (0.25, 0.75, 2.25, 6.7, 20.0 J/m2). Control samples were mock treated. At several time points after treatment (10 min, 30 min, 1 hr, 3 hr, 6 hr, 12 hr, 24 hr, 48 hr), MEFs were rinsed with phosphate-buffered saline and collected in 350 μl RLT buffer (enclosed in the RNeasy mini kit; see “RNA isolation”).

value: MEFs

tag: strain


title: MEFs_uv0.75_t180

source_name: MEFs treated uv (0.75j/s) RNA harvest 180 minutes


title: HMB4L1_2

description: Leaf at the floral initiation stage, HMB4 over-expression, biological replicate 2

value: Leaf at the floral initiation stage

value: HMB4 over-expression


title: 561856A10 - 48_TREATMENT4_24H_REP1 vs 43_WATER_24H_REP1

hyb_protocol: 43_WATER_24H_REP1 Cy5 / 48_TREATMENT4_24H_REP1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: cv. Marselan


title: MEFs_uv0_t2880

source_name: MEFs treated uv (0j/s) RNA harvest 2880 minutes


title: MEFs_uv0.25_t60

source_name: MEFs treated uv (0.25j/s) RNA harvest 60 minutes


title: Tumor 1

value: LSL-MYCN;Dbhi-Cre


title: IM5DAP_2

description: Panicle 5-day-after pollination, non-transgenic, biological replicate 2

value: Panicle 5-day-after pollination

value: non-transgenic


title: Normoxia+IL-6

city: Hangzhou

first: Bo

last: yang

state: Zhejiang

address: 866 YUHANGTANG ROAD

department: College of Pharmaceutical Sciences

country: China

institute: Zhejiang University

description: Gene expression data from RAW264.7 cells which were exposed to normoxic condition for 4 days in the presence IL-6

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45℃ on Affymetrix Mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChipR Scanner 3000.

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: RAW264.7 cells

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

growth_protocol: RAW264.7 cells were maintained in DMEM containing 10% fetal bovine serum and 100U per ml of penicillin-streptomycin.

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

treatment_protocol: RAW264.7 cells were exposed to normoxic or hypoxic conditions for 4 days in the presence or absence of IL-6

value: normoxia + IL-6


title: IMP21cm_2

description: Panicle size 20.5-22 cm, non-transgenic, biological replicate 2


title: HMB4L1_1

description: Leaf at the floral initiation stage, HMB4 over-expression, biological replicate 1


title: 561856A06 - 46_TREATMENT2_24H_REP1 vs 43_WATER_24H_REP1

description: Biological question (15 lines max): Identification of grape genes regulated in response to resistance inducer treatments. This transcriptomic analysis should provide insight in the mode of action of the compounds under study and yield generic data relevant to grape defense reaction.

hyb_protocol: 43_WATER_24H_REP1 Cy5 / 46_TREATMENT2_24H_REP1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: herbaceous grape cutting


title: Hypoxia+IL-6

description: Gene expression data from RAW264.7 cells which were exposed to  hypoxic condition for 4 days in the presence of IL-6

value: hypoxia + IL-6


title: 561856A07 - 43_WATER_24H_REP1 vs 47_TREATMENT3_24H_REP1

hyb_protocol: 47_TREATMENT3_24H_REP1 Cy5 / 43_WATER_24H_REP1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:WATER_24H - compound based treatment - water,water:. Name: - compound based treatment - plant defense activation ,water:.


title: IM5DAP_1

description: Panicle 5-day-after pollination, non-transgenic, biological replicate 1


title: 561856A05 - 43_WATER_24H_REP1 vs 46_TREATMENT2_24H_REP1

hyb_protocol: 46_TREATMENT2_24H_REP1 Cy5 / 43_WATER_24H_REP1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: MEFs_uv0.25_t360

source_name: MEFs treated uv (0.25j/s) RNA harvest 360 minutes


title: MEFs_uv6.7_t180

source_name: MEFs treated uv (6.7j/s) RNA harvest 180 minutes


title: wildtype islet rep1

city: Shanghai

first: Weiping

middle: J

last: Zhang

address: 800 Xiangyin Road

department: Pathophysiology

institute: Second Military Medical University

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

scan_protocol: GeneChips were scanned using  the Affymetrix GeneArray TM Scanner 3000.

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 500.

source_name: adult control islets

treatment_protocol: After collagenase digestion, islets were hand-picked under the dissecting scope and recovered by overnight culture, followed by snap-freezing in liquid nitrogen before storage at -80C.

value: Islet

value: wildtype

value: 2-3 month-old

value: mixed background


title: b cell-specific ZBTB20 knockout islet Rep1

source_name: adult b-ZB20KO islets

value: b cell-specific ZBTB20 knockout


title: Hypoxia control

description: Gene expression data from RAW264.7 cells which were exposed to hypoxic condition for 4 days

value: hypoxia control


title: Normoxia control

description: Gene expression data from RAW264.7 cells which were exposed to normoxic condition for 4 days

value: normoxia control


title: 561856A04 - 45_TREATMENT1_24H_REP1 vs 43_WATER_24H_REP1

hyb_protocol: 43_WATER_24H_REP1 Cy5 / 45_TREATMENT1_24H_REP1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: IMP21cm_1

description: Panicle size 20.2-22 cm, non-transgenic, biological replicate 1

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

value: Oryza sativa L. cv. Ilmi

value: Panicle size 20.2-22 cm


title: MEFs_uv2.25_t720

source_name: MEFs treated uv (2.25j/s) RNA harvest 720 minutes

value: MEFs


title: MEFs_uv6.7_t1440

source_name: MEFs treated uv (6.7j/s) RNA harvest 1440 minutes


title: 561856A03 - 43_WATER_24H_REP1 vs 45_TREATMENT1_24H_REP1

hyb_protocol: 45_TREATMENT1_24H_REP1 Cy5 / 43_WATER_24H_REP1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: cv. Marselan


title: IMP8cm_2

description: Panicle size 8-15cm, non-transgenic, biological replicate 2

value: Panicle size 8-15cm


title: MEFs_uv2.25_t30

source_name: MEFs treated uv (2.25j/s) RNA harvest 30 minutes


title: MEFs_uv20_t60

source_name: MEFs treated uv (20j/s) RNA harvest 60 minutes


title: MEFs_uv20_t10

source_name: MEFs treated uv (20j/s) RNA harvest 10 minutes


title: MCF7-G, estradiol treated, replicate 1

first: Craig

middle: Joseph

last: Burd

state: OH

address: 460 W. 12th Ave. Rm 920 BRT

department: Molecular Genetics

hyb_protocol: Samples were hybridized using Herring sperm DNA, acetylated BSA , BioArray Eukaryotic Hybridization Controls (ENZO Life Sciences). 65 C for 5 minutes, 99 C for 5 min, 45 C for 5 minutes. Centrifuge top speed for 5 minutes. Hybridize 16 h at 45C at 60 rpm.  Fluidics washing is FS450_001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G using AGCC

data_processing: Data was normalized using the Expression Console Software

source_name: MCF7 cells chronically cultured in GEN

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit

growth_protocol: Cells were grown in phenol-red free DMEM containing 5% charcoal/dextran treadted FBS for 72 hours

extract_protocol: RNA was isolated using Total RNA isolation Nucleospin® RNA II kit (Macherey-Nagel

treatment_protocol: Cells were treated with either ethanol of 10 nM estradiol for 3 hours.

value: estradiol treated


title: MCF7-G, estradiol treated, replicate 2


title: IMP8cm_1

description: Panicle size 8-15cm, non-transgenic, biological replicate 1

value: non-transgenic


title: 561856A02 - 44_ADJ_24H_REP1 vs 43_WATER_24H_REP1

hyb_protocol: 43_WATER_24H_REP1 Cy5 / 44_ADJ_24H_REP1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: MCF7-G, ethanol treated, replicate 2

value: ethanol treated


title: IMP1cm_2

description: Panicle size 1-3cm, non-transgenic, biological replicate 2

value: Panicle size 1-3cm


title: IML1_2

description: Leaf at the floral initiation stage, non-transgenic, biological replicate 2

value: Leaf at the floral initiation stage


title: MCF7-G, ethanol treated, replicate 1


title: IMP1cm_1

description: Panicle size 1-3cm, non-transgenic, biological replicate 1