title: 7h-DBA 280

city: Ottawa

first: Julie

last: Buick

state: Ontario

address: 50 Colombine Driveway

department: Mechanistic Studies Division

country: Canada

institute: Health Canada

description: Co-hybridized with negative vehicle control pool (DMSO +S9)

hyb_protocol: Labelled cRNA samples (325 ng of cyanine-3 labelled cRNA and 325 ng of cyanine-5 labelled cRNA) were hybridized to Agilent SurePrint G3 Human GE 8x60K oligonucleotide microarrays (Agilent Catalogue No: G4851A, Agilent Microarray Design ID: 028004; Agilent Technologies, Mississauga, ON, Canada) at 65oC for 17 hours.

scan_protocol: Slides were washed according to the manufacturer’s specifications and scanned using an Agilent G2505C DNA Microarray Scanner at 3 μm resolution. Agilent Feature Extraction (version 11.0.1.1) was used for data extraction purposes from the generated image files and to generate QC reports for each array.

data_processing: The log2 of the ratio using the median signal intensities were normalized using lowess using the transform.madata function in the maanova library in R.  After normalization the log2 ratios for the dye swap were averaged yielding a ratio representing the treatment relative to the vehicle control.

source_name: TK6 lymphoblastoid cell line

label_protocol: Gene expression profiles were generated using a two-colour dye swap design [Kerr and Churchill, 2001]. Microarray analysis was conducted on all time points from the definitive studies (n=3 per concentration and time point), along with the corresponding pooled vehicle and positive controls. Agilent Low-Input Quick Amp Labelling kits were used to ultimately generate cyanine-3 and cyanine-5 labelled cRNA from 100 ng of total RNA, according to the manufacturer’s instructions (Agilent Technologies, Mississauga, ON, Canada).

growth_protocol: TK6 cells, a human lymphoblastoid cell line, were obtained from American Type Culture Collection (ATCC# CRL-8015; ATCC, Manassas, VA, USA). TK6 cells were maintained as described elsewhere [Ellinger-Ziegelbauer et al., 2009]. Briefly, cells were cultured and maintained in RPMI 1640 medium containing 10% heat inactivated horse serum, in addition to 0.1% pluronics, sodium pyruvate and antibiotics (penicillin at 20 units/ml and streptomycin at 20 µg/ml) at 37 ± 1oC and 6 ± 1% CO2 in air. Immediately prior to chemical exposure, cells were seeded at a density of 4 (± 0.5) x 105 cells/ml in twelve-well plates with a final volume of 3 ml per well. Given that TK6 cells are not metabolically competent cells and that the test chemicals require metabolic activation to form reactive metabolites, all cellular exposures were conducted in the presence of 2% aroclor-induced rat liver S9 (Moltox, Boone, NC, USA) with NADPH generating system cofactors, except for furan which was co-exposed with 5%-ethanol-induced rat liver S9. The in vitro cellular exposures were performed by Integrated Laboratory Systems, Inc. (ILS; Research Triangle Park, NC, USA), in addition to the associated cytotoxicity and genotoxicity testing.

extract_protocol: Following chemical exposures, total RNA was isolated from treated and control TK6 cells between 7 and 8 hours post-exposure. An RNeasy Mini Kit (Qiagen, Toronto, ON, Canada) was used to isolate and purify total RNA using the spin technology protocol with an on-column DNase I digestion, following the manufacturer’s instructions. Total RNA was quantified and assessed for purity and integrity using a NanoDrop® ND-1000 spectrophotometer and an Agilent 2100 Bioanalyzer. Only high quality total RNA samples, with RNA Integrity Numbers (RINs) ranging from 8.0 to 10 and A260/280 absorbance ratios ≥2.0 were used for gene expression analysis.

treatment_protocol: TK6 cells were exposed to 3 concentrations of each test chemical as follows: 0.75, 1.5 and 2 µg/ml for 2-aminoanthracene; 1, 3.2 and 10 mM for acetaminophen; 1, 5 and 20 µM for cyclophosphamide; 1, 20 and 280 µg/ml for dibenz[a,h]antracene; 1, 5 and 10 mM for dimethylnitrosamine; 2, 3 and 5 mM for furan; 10, 50 and 300 µM for 2-nitrofluorene; 8, 40 and 100 µg/ml phenanthrene; and 1, 3.2 and 10 mM for sucrose. Separate plates were used for exposures to vehicle and positive controls (VC (+S9), and BaP(+S9), respectively). Cells were co-exposed to each chemical (+S9) for four hours, then the media was replaced and cells were collected 3 to 4 hours later. All exposures were done in the presence of 2% aroclor-induced rat liver S9 with NADPH generating system cofactors to act as a metabolic activation system (MAS), as TK6 cells do not have inherent metabolic capacity (except for the direct-acting positive control and its associated negative and vehicle controls), except for furan which was co-exposed with 5% ethanol-induced S9. Exponentially growing cells were exposed to each chemical for 4 ± 0.5 hours. At the end of each 4h exposure, the exposed and control TK6 cells for each time point were removed by centrifugation and the cells were rinsed in PBS. The cells were then re-suspended in 3 ml of media and re-incubated for an additional 3 to 4 hours before being harvested for RNA extraction. Cells dedicated for the purposes of RNA extraction were collected from each well (4 ± 0.5 x 106 cells), pelleted by centrifugation and flash frozen in liquid nitrogen. Cells were stored at -80oC until RNA extraction was performed.

tag: concentration

value: 280 µg/ml


title: infected_with_VD_4

status: Public on Aug 25 2016

type: RNA

city: Buenos Aires

first: Natalia

middle: Anahí

last: Juiz

address: 2490, Vuelta de Obligado

country: Argentina

institute: INGEBI-CONICET

description: Replicate 4

hyb_protocol: 1500 ng of labeled cRNA samples were hybridized to each Mouse WG-6 v2.0 Expression Beadchip for 17h at 58°C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA). Detection of array signal was carried out using Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the bead array manual. Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions.

data_processing: Raw data were extracted using the software provided by the manufacturer (Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)).   Array probes transformed by logarithm and normalized by quantile method.  Statistical significance of the expression data was determined using LPE test and fold change in which the null hypothesis was that no difference exists among groups. False discovery rate (FDR) was controlled by adjusting p value using Benjamini-Hochberg algorithm. For a DEG set, Hierarchical cluster analysis was performed using complete linkage and Euclidean distance as a measure of similarity.   Gene-Enrichment and Functional Annotation analysis for significant probe list was performed using DAVID (http://david.abcc.ncifcrf.gov/home.jsp).  All data analysis and visualization of differentially expressed genes was conducted using R 3.1.2 (www.r-project.org).

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Mouse Placenta

label_protocol: 500 ng of total RNA was reverse-transcribed to cDNA using a T7 oligo(dT) primer. Second-strand cDNA was synthesized, in vitro transcribed, and labeled with biotin-NTP.

growth_protocol: Adult C57BL/6J female mice and pregnant. Animals were maintained in rooms at 24°C with 40% humidity and a 12 hour light/dark cycle and were provided food and water adlibitum until used.

extract_protocol: Total RNA was extracted from placentas using the TRIzol® reagent (Invitrogen, Carlsbad, CA) according to manufacturer's instructions, treated with RQ1 RNase-Free DNase (Promega, Madison, USA) and stored at −80°C until used.

treatment_protocol: To obtain chronically infected mice, 4 inbred females between 6 and 8 weeks old were inoculated by the intradermoplantar (idp) route with 500 bloodstream trypomastigotes of K98 or with 50 bloodstream trypomastigotes of VD, because higher inocula of VD are lethal for this mouse strain by the intraperitoneal route. Parasitemia was measured weekly by counting in a Neubauer chamber the number of parasites obtained from the tail vein blood diluted (1/10) in red blood cell lysis solution (Tris–NH4 Cl 0.83% pH 7.2). Chronic phase was considered when no parasites were detected in chamber (around 3 weeks post-infection). At day 30 post-infection two females were housed with 1 uninfected male per cage. To assess the day of fertilization, the vaginal plug was macroscopically searched [14], being the day of vaginal plug appearance considered as day 0.5 of pregnancy. A third group of 4 uninfected females of the same age and weight were used as control. On day 18.5±1 of pregnancy, dams were euthanized and samples of maternal blood were taken by cardiac puncture and stored in EDTA solution until processed. Finally, entire placentas from the naturally mated crosses were removed and placed in RNAlater® solution (Applied Biosystems, Foster City, CA).

tag: strain

tag: gender

value: female

tag: tissue

value: placenta

tag: agent

value: Trypanosoma cruzi VD


title: Lung tissue_S4

city: Barcelona

first: Ricardo

last: Bastos

address: Rosellón  149-153

department: Cell Biology, Neurosciences and Immunology

country: Spain

institute: IDIBAPS/University of Barcelona

hyb_protocol: Biotin-labeled cRNA was cleanup and quantified and subsequently it was fragmented by metal-induced hydrolysis (GeneChip Sample Cleanup Module, Affymetrix Inc). Hybridization was performed with GeneChip® Hybridization Wash and Stain Kit (Affymetrix Inc) according to manufactures instructions.

scan_protocol: GeneChips were scanned using the GeneChip®Scanner 3000 7G (Affymetrix Inc)

data_processing: Expression measures were normalized and summarized using the GC content adjusted-Robust Multiarray Analysis (GC-RMA) methodology

organism: Homo sapiens

source_name: Peripheral lung tissue,  smoker

label_protocol: cRNA amplification and biotin labeling was synthesized from 2ug cDNA by means of an in vitro transcription reaction in the presence of T7 RNA Polymerase and of biotinylated nucleotide analog/ribonucleotide mix (GeneChip IVT labeling Kit, Affymetrix Inc, Santa Clara, CA)

extract_protocol: RNA was prepared from grossly homogenous pieces of tissue (100-200 mg) with an RNeasy Midi kit (Qiagen, Valencia, CA)  according to the manufactures instructions

value: Peripheral lung tissue

tag: phenotype

value: healthy smoker


title: infected_with_VD_3

description: Replicate 3

scan_protocol: Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions


title: control_uninfected_1

description: Replicate 1

value: Uninfected


title: Lung tissue_S6


title: Lung tissue_S3


title: Lung tissue_S9


title: 7h-DBA 20

value: 20 µg/ml

tag: cell line


title: infected_with_K98_2

description: Replicate 2

value: Trypanosoma cruzi K98


title: infected_with_VD_2

description: Replicate 2


title: control_uninfected_3

description: Replicate 3


title: control_uninfected_4

description: Replicate 4


title: control_uninfected_2

description: Replicate 2


title: Lung tissue_S5


title: infected_with_K98_3

description: Replicate 3


title: infected_with_K98_4

description: Replicate 4


title: 7h-DBA 1

value: 1 µg/ml


title: 7h-BaP5

value: 10 µg/ml


title: 7h-PHEN 100

value: 100 µg/ml


title: Lung tissue_S2


title: 7h-DMN 1

value: 1 mM


title: Lung tissue_NS9

source_name: Peripheral lung tissue,  nonsmoker

value: Nonsmoker


title: 7h-PHEN 40

value: 40 µg/ml


title: 7h-BaP4


title: 7h-DMN 5

value: 5 mM


title: 7h-2AA 1.5

value: 1.5 µg/ml


title: Lung tissue_S1


title: 7h-DMN 10

value: 10 mM


title: 7h-2AA 0.75


title: 7h-BaP2


title: 7h-BaP3


title: 7h-ACET 10


title: Lung tissue_NS5


title: Lung tissue_NS6


title: Lung tissue_NS4


title: Lung tissue_NS8


title: 7h-SUC 1

description: Co-hybridized with negative vehicle control pool (H2O +S9)


title: 7h-2NF 300


title: Lung tissue_NS7


title: 7h-2AA 2

value: 2.0 µg/ml


title: Lung tissue_NS2


title: Lung tissue_NS3


title: 7h-ACET 3.2


title: 7h-ACET 1


title: 7h-2NF 50

value: 50 µM


title: 7h-CP 5

value: 5 µM


title: Lung tissue_NS1

value: Peripheral lung tissue


title: 7h-2NF 10

value: 10 µM


title: 7h-FUR 3

value: 3 mM


title: H19 block 2

city: Milan

first: Fabio

last: Martelli

address: via morandi 30

country: Italy

institute: IRCCS-Policlinico San Donato

hyb_protocol: The obtained cRNAs were hybridized on a HumanHT-12 v4 Expression BeadChip according to the Standard Illumina hybridization protocol.

scan_protocol: Scanned and the background subtracted intensities were generated by GenomeStudio Software, according to the standard Illumina scanning protocol.

data_processing: Between arrays normalization (quantile) and differential expression analysis were performed by limma package (Bioconductor, RStudio v 0.98.501).

source_name: HAOEC

label_protocol: Biotinylated cRNA was prepared using the Ambion Illumina RNA amplification kit.

growth_protocol: HAOEC were grown in EGM-2 (Lonza) containing 2% FBS.

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

treatment_protocol: HAOEC were transfected with 50 nM of antisense LNA™ GapmeRs customer-designed for H19 or Negative control A (Exiqon).

tag: experiment type

value: H19 GAPmer

tag: experiment id

tag: cell type

value: HAOEC


title: Control 2

value: Negative Control


title: Hypoxia 2

source_name: HUVEC

growth_protocol: HUVEC were grown in EGM-2 (Lonza) containing 2% FBS.

treatment_protocol: HUVEC were exposed to 1% oxygen for 24 or 48 hours.

value: HUVEC


title: 7h-FUR 2

value: 2 mM


title: 7h-FUR 5


title: 7h-CP 20

value: 20 µM


title: Hypoxia 1


title: Ctrl 2


title: 7h-CP 1

value: 1 µM


title: Hypoxia 4


title: Hypoxia 3


title: 7h-SUC 10


title: RNA from mouse liver 440

city: Sydney

first: Samantha

last: Solon-Biet

state: NSW

address: The University of Sydney

department: Charles Perkins Centre

country: Australia

institute: University of Sydney

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on the Affymetrix Mouse Gene ST 2.1 Array plate. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Bioconductor package for R

source_name: Total RNA from mouse liver 440

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: Mice were placed on one of 25 different diets from 3 weeks of age and fed ad libitum. Mice were maintained 3 per cage at 24-26C.

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions using the Qiagen AllPrep DNA/RNA/Protein Mini Kit

treatment_protocol: Mice were placed on one of 25 different diets from 3 weeks of age and fed ad libitum. Mice were left to age until 15 months old and culled for analyses of tissues

value: liver

tag: macronutrient in p/c/f

value: Gene expression data from mouse 440 High energy 42/29/29


title: H19 block 1


title: RNA from mouse liver 122

source_name: Total RNA from mouse liver 122

value: Gene expression data from mouse 122 Medium energy 42/29/29


title: RNA from mouse liver 418

source_name: Total RNA from mouse liver 418

value: Gene expression data from mouse 418 Medium energy 33/47/20


title: RNA from mouse liver 409

source_name: Total RNA from mouse liver 409

value: Gene expression data from mouse 409 High energy 23/38/38


title: Control 1


title: RNA from mouse liver 165

source_name: Total RNA from mouse liver 165

value: Gene expression data from mouse 165 High energy 14/29/57


title: RNA from mouse liver 438

source_name: Total RNA from mouse liver 438

value: Gene expression data from mouse 438 High energy 14/57/29


title: RNA from mouse liver 198

source_name: Total RNA from mouse liver 198

value: Gene expression data from mouse 198 High energy 33/20/47


title: Ctrl 1


title: RNA from mouse liver 385

source_name: Total RNA from mouse liver 385

value: Gene expression data from mouse 385 High energy 23/65/12


title: 7h-SUC 3.2


title: RNA from mouse liver 435

source_name: Total RNA from mouse liver 435

value: Gene expression data from mouse 435 High energy 5/48/48


title: RNA from mouse liver 154

source_name: Total RNA from mouse liver 154

value: Gene expression data from mouse 154 Medium energy 42/29/29


title: RNA from mouse liver 402

source_name: Total RNA from mouse liver 402

value: Gene expression data from mouse 402 High energy 14/29/57


title: RNA from mouse liver 426

source_name: Total RNA from mouse liver 426

value: Gene expression data from mouse 426 High energy 5/75/20


title: RNA from mouse liver 381

source_name: Total RNA from mouse liver 381

value: Gene expression data from mouse 381 Medium energy 33/47/20


title: RNA from mouse liver 124

source_name: Total RNA from mouse liver 124

value: Gene expression data from mouse 124 Medium energy 23/38/38


title: RNA from mouse liver 387

source_name: Total RNA from mouse liver 387

value: Gene expression data from mouse 387 Medium energy 14/57/29


title: RNA from mouse liver 128

source_name: Total RNA from mouse liver 128

value: Gene expression data from mouse 128 High energy 5/75/20


title: RNA from mouse liver 434

source_name: Total RNA from mouse liver 434

value: liver

value: Gene expression data from mouse 434 High energy 5/48/48


title: RNA from mouse liver 135

source_name: Total RNA from mouse liver 135

value: Gene expression data from mouse 135 High energy 5/48/48


title: RNA from mouse liver 420

source_name: Total RNA from mouse liver 420

value: Gene expression data from mouse 420 Medium energy 33/20/47


title: 02_C4BP_1

city: Lund

first: Petter

last: Storm

address: Sölvegatan 19, BMC A11

department: Developmental and Regenerative Neurobiology

country: Sweden

institute: Lund University

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using Expression Console software. Probe intensities, gene level expression were summarized and then quantile normalized.

organism: Rattus norvegicus

source_name: DMSO

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

growth_protocol: The INS-1 cells were grown as 5 separate clones for 10 passages before plating in a 12-well plate (Nunc) at 100.000 cells per well and grown in complete RPMI 1640 medium to 70% confluency for approximately 48 h.

extract_protocol: RNA extraction and purification was done according to Qiagen RNeasy kit protocol.

treatment_protocol: The cells were then challenged by adding 300 ug/ml monomeric IAPP alone or together with C4BP (300 ug/ml). DMSO (1%) as well as C4BP (300 ug/ml) alone were used as controls.

value: beta-cell line

tag: treated with

value: 1% DMSO (control)


title: RNA from mouse liver 211

source_name: Total RNA from mouse liver 211

value: Gene expression data from mouse 211 Low energy 42/29/29


title: mRNA levels 40min after release from G1 with EdU dye flip, rep2

type: mixed

city: Montpellier

first: Marta

last: Radman-Livaja

address: 1919 route de Mende

department: IGMM

country: France

institute: CNRS

description: cDNA_CY3/gDNA_Cy5_40minEdU replicate 2

hyb_protocol: Labeled probes (a mixture of Cy3 labeled cDNA/genomic DNA and Cy5 labeled genomic DNA/cDNA) were hybridized onto an Agilent yeast 8x15 gene expression array.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an InnoScan 710 MicroArray scanner (Innopsys) at 5 micron resolution and processed with the Mapix software.

data_processing: After background correction and removal of flagged values, data was block normalized by dilation and log base 2 ratios (Cy3/Cy5) were calculated to produce the values given in the data table.

organism: Saccharomyces cerevisiae

source_name: cDNA late S-phase +EdU

label_protocol: We used ~30 µg of total RNA for each expression array. RNA was reverse transcribed using oligodTs (0.15µg/µl each) as primers. Reactions (0.5mM dNTP (N=A,G,C), 0.2mMdTTP and 0.3mM amino-allyl dUTP (SIGMA), 6µg/ml Actinomycine D (SIGMA), 10mMDTT, 1XFS buffer and 10U/µl Superscript III (Life Technologies)) were incubated at 50°C for 2hrs. RNA was then degraded with NaOH at 65°C (10µl 1N NaOH and 10µl 0.5M EDTA into 30µl reactions), the solution was neutralized with HEPES pH=7.5 (25µl 1M stock) and the buffer was exchanged for water in Amicon30 centricon spin columns. The resulting cDNA was dye-coupled with Cy5 or Cy3 NHS-esters and purified as described previously (Liu et al., 2005). Genomic DNA labeling: 2ug (quantified in the Qubit fluorimeter) PV1 G1 genomic DNA in Klenow NEB buffer, 0.3 µg/µl random hexamers, 0.12 mM dNTP (N=A,G,T),0.06mM dCTP and 0.06mM Cy5 or Cy3 conjugated dCTP (GE healthcare), and 1U/µl Klenow enzyme (NEB); incubated 2hrs at 37°C and cleaned up in Amicon-30 centricon spin columns.

growth_protocol: Cells were grown overnight at 30°C in Synthetic Complete- URA + Dextrose media to OD 0.3. After 3.75hrs of incubation at 30°C with alpha factor (0.25μg/ml), cells were pelleted and transferred into preheated and premixed SCD-URA+ or - 10μM EdU (Carbosynth) as indicated, with freshly added 20μg/ml pronase (Sigma).

extract_protocol: Genomic DNA was isolated from G1 arrested flash frozen cell pellets with Phenol/Chloroform, and sonicated with the Bioruptor Pico cup sonicator (200µl at 200ng/ µl, 30”ON 30”OFF at 4°C). Total RNA was isolated from frozen PV1 cell pellets with Trizol. Frozen cell pellets were resuspended directly in Trizol and bead beated in the Bullet Blender (Next Advance). RNA was then purified and DNaseI treated with the RNeasy Column purification kit (Qiagen).

treatment_protocol: 50ml aliquots were flash frozen in liquid nitrogen before and 32 and 40min after release from G1 arrest.

tag: genotype/variation

value: MATa ade2-1 trp1-1 can1-1000 leu2-3,112 his3-11,15 GAL psi+ RAD5+ ura3::URA3/GPD-TK(7x) AUR1c::ADH-hENT1 bar1D::KANR

tag: growth phase

value: late S-phase

tag: treatment

value: EdU

molecule: genomic DNA

source_name: G1 genomic DNA


title: mRNA levels 40min after release from G1 dye flip, rep2

description: cDNA_CY3/gDNA_Cy5_32min replicate 2

source_name: cDNA mid S-phase

value: mid S-phase


title: 7h-PHEN 8

source_name: TK6 lymphoblastoid cell line

value: 8 µg/ml


title: RNA from mouse liver 213

source_name: Total RNA from mouse liver 213

value: Gene expression data from mouse 213 Low energy 23/38/38


title: 13_IAPP_4

value: 300 ug/ml C4b-binding protein (C4BP)


title: mRNA levels 32min after release from G1 with EdU dye flip, rep2

description: cDNA_CY3/gDNA_Cy5_32minEdU replicate 2

source_name: cDNA mid S-phase +EdU


title: 05_IAPP_2

source_name: IAPP + C4BP

value: 300 ug/ml IAPP + 300 ug/ml C4b-binding protein (C4BP)


title: RNA from mouse liver 130

source_name: Total RNA from mouse liver 130

value: Gene expression data from mouse 130 High energy 5/20/75


title: mRNA levels 32min after release from G1 dye flip, rep2

description: cDNA_CY3/gDNA_Cy5_40min replicate 2

source_name: cDNA late S-phase


title: 12_DMSO_3


title: 07_C4BPD_2


title: 19_C4BPD_5

source_name: IAPP

value: 300 ug/ml monomeric islet amyloid polypeptide (IAPP)


title: RNA from mouse liver 201

source_name: Total RNA from mouse liver 201

value: liver

value: Gene expression data from mouse 201 High energy 14/29/57


title: RNA from mouse liver 156

source_name: Total RNA from mouse liver 156

value: Gene expression data from mouse 156 Medium energy 23/38/38


title: RNA from mouse liver 218

source_name: Total RNA from mouse liver 218

value: Gene expression data from mouse 218 High energy 23/65/12


title: mRNA levels 40min after release from G1 with EdU, rep2

description: gDNA_Cy3/cDNA_CY5_40minEdU replicate 2


title: mRNA levels 32min after release from G1 with EdU, rep2

description: gDNA_Cy3/cDNA_CY5_32minEdU replicate 2


title: mRNA levels 32min after release from G1, rep2

description: gDNA_Cy3/cDNA_CY5_40min replicate 2


title: mRNA levels 40min after release from G1, rep2

description: gDNA_Cy3/cDNA_CY5_32min replicate 2


title: RNA from mouse liver 150

source_name: Total RNA from mouse liver 150

value: Gene expression data from mouse 150 Medium energy 33/20/47


title: RNA from mouse liver 199

source_name: Total RNA from mouse liver 199

value: Gene expression data from mouse 199 High energy 5/48/48


title: 03_C4BPD_1

value: beta-cell line


title: 16_DMSO_4


title: RNA from mouse liver 195

source_name: Total RNA from mouse liver 195

value: Gene expression data from mouse 195 High energy 33/47/20


title: 06_C4BP_2

source_name: DMSO

value: 1% DMSO (control)


title: RNA from mouse liver 129

source_name: Total RNA from mouse liver 129

value: Gene expression data from mouse 129 High energy 5/20/75


title: RNA from mouse liver 142

source_name: Total RNA from mouse liver 142

value: Gene expression data from mouse 142 Low energy 60/20/20


title: mRNA levels 32min after release from G1 dye flip, rep1

description: cDNA_CY3/gDNA_Cy5_40min replicate 1

value: MATa ade2-1 trp1-1 can1-1000 leu2-3,112 his3-11,15 GAL psi+ RAD5+ ura3::URA3/GPD-TK(7x) AUR1c::ADH-hENT1 bar1D::KANR

value: late S-phase

source_name: G1 genomic DNA


title: mRNA levels 32min after release from G1 with EdU dye flip, rep1

description: cDNA_CY3/gDNA_Cy5_32minEdU replicate 1

value: mid S-phase

value: EdU


title: mRNA levels 40min after release from G1 with EdU dye flip, rep1

description: cDNA_CY3/gDNA_Cy5_40minEdU replicate 1

source_name: cDNA late S-phase +EdU


title: 10_C4BP_3

value: 300 ug/ml C4b-binding protein (C4BP)


title: RNA from mouse liver 419

source_name: Total RNA from mouse liver 419

value: Gene expression data from mouse 419 Medium energy 33/20/47


title: mRNA levels 32min after release from G1 with EdU, rep1

description: gDNA_Cy3/cDNA_CY5_32minEdU replicate 1

source_name: cDNA mid S-phase +EdU


title: RNA from mouse liver 126

source_name: Total RNA from mouse liver 126

value: liver

value: Gene expression data from mouse 126 High energy 60/20/20


title: mRNA levels 40min after release from G1 with EdU, rep1

description: gDNA_Cy3/cDNA_CY5_40minEdU replicate 1


title: RNA from mouse liver 194

source_name: Total RNA from mouse liver 194

value: Gene expression data from mouse 194 High energy 60/20/20


title: 11_C4BPD_3


title: mRNA levels 40min after release from G1 dye flip, rep1

description: cDNA_CY3/gDNA_Cy5_32min replicate 1

source_name: cDNA mid S-phase


title: RNA from mouse liver 141

source_name: Total RNA from mouse liver 141

value: Gene expression data from mouse 141 Low energy 60/20/20


title: 08_DMSO_2


title: 14_C4BP_4

source_name: IAPP

value: 300 ug/ml monomeric islet amyloid polypeptide (IAPP)


title: RNA from mouse liver 127

source_name: Total RNA from mouse liver 127

value: Gene expression data from mouse 127 High energy 5/75/20


title: 15_C4BPD_4

source_name: IAPP + C4BP

value: beta-cell line

value: 300 ug/ml IAPP + 300 ug/ml C4b-binding protein (C4BP)


title: 01_IAPP_1


title: 04_DMSO_1


title: RNA from mouse liver 193

source_name: Total RNA from mouse liver 193

value: Gene expression data from mouse 193 Medium energy 23/38/38


title: RNA from mouse liver 140

source_name: Total RNA from mouse liver 140

value: Gene expression data from mouse 140 High energy 23/38/38


title: mRNA levels 32min after release from G1, rep1

description: gDNA_Cy3/cDNA_CY5_40min replicate 1

source_name: cDNA late S-phase


title: 09_IAPP_3


title: 20_DMSO_5


title: RNA from mouse liver 125

source_name: Total RNA from mouse liver 125

value: Gene expression data from mouse 125 High energy 60/20/20


title: RNA from mouse liver 120

source_name: Total RNA from mouse liver 120

value: Gene expression data from mouse 120 Medium energy 14/57/29


title: 17_IAPP_5


title: RNA from mouse liver 138

source_name: Total RNA from mouse liver 138

value: Gene expression data from mouse 138 High energy 14/57/29


title: RNA from mouse liver 136

source_name: Total RNA from mouse liver 136

value: Gene expression data from mouse 136 High energy 14/29/57


title: RNA from mouse liver 104

source_name: Total RNA from mouse liver 104

value: Gene expression data from mouse 104 Low energy 60/20/20


title: RNA from mouse liver 118

source_name: Total RNA from mouse liver 118

value: Gene expression data from mouse 118 Medium energy 14/29/57


title: mRNA levels 40min after release from G1, rep1

description: gDNA_Cy3/cDNA_CY5_32min replicate 1

source_name: G1 genomic DNA

value: MATa ade2-1 trp1-1 can1-1000 leu2-3,112 his3-11,15 GAL psi+ RAD5+ ura3::URA3/GPD-TK(7x) AUR1c::ADH-hENT1 bar1D::KANR

value: mid S-phase


title: RNA from mouse liver 160

source_name: Total RNA from mouse liver 160

value: liver

value: Gene expression data from mouse 160 High energy 5/75/20


title: RNA from mouse liver 192

source_name: Total RNA from mouse liver 192

value: Gene expression data from mouse 192 Medium energy 42/29/29


title: Oviductal_Tumor_sample6

city: Ann Arbor

first: Rork

last: Kuick

state: MI

address: University of Michigan, SPH II, 1415 Washington Heights, Room M2533

country: USA

institute: University of Michigan

hyb_protocol: Following fragmentation, cDNA was hybridized for 20 hr at 48C to Affymetrix Mouse Genome 2.1 ST arrays.

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system.

data_processing: Data was analyzed using the affy package implemented in the R-statistical environment version 3.1.1. RMA was used to estimate log2 transformed expression values for each probe-set.

source_name: Right side tumor from tamoxifen treated Ovgp1-iCre-ERT2;Apc fl/fl;Pten fl/fl  mouse 10455

label_protocol: 250-400 ng total RNA was reverse-transcribed, amplified and labeled, with the Affy Plus kits.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen), and purified using Rneasy columns (Qiagen). Quality was checked with an Agilent 2100 Bioanalyzer.

tag: Sex

value: female


title: Ovarian_Tumor_sample4

source_name: Right side tumor from Ovgp1-iCre-ERT2;Apc fl/fl;Pten fl/fl  mouse 10438 injected with AdCre


title: Ovarian_Tumor_sample2

source_name: Right side tumor from Ovgp1-iCre-ERT2;Apc fl/fl;Pten fl/fl  mouse 10162 injected with AdCre


title: Oviductal_Tumor_sample1

source_name: Left side tumor from tamoxifen treated Ovgp1-iCre-ERT2;Apc fl/fl;Pten fl/fl  mouse 10405


title: Ovarian_Tumor_sample3

source_name: Right side tumor from Ovgp1-iCre-ERT2;Apc fl/fl;Pten fl/fl  mouse 10286 injected with AdCre


title: Normal_Ovary_sample4

source_name: Two normal ovaries from  Ovgp1-iCre-ERT2;Apc fl/fl;Pten fl/fl mouse 10523


title: Oviductal_Tumor_sample2

source_name: Right side tumor from tamoxifen treated Ovgp1-iCre-ERT2;Apc fl/fl;Pten fl/fl  mouse 10406


title: Oviductal_Tumor_sample4

source_name: Left side tumor from tamoxifen treated Ovgp1-iCre-ERT2;Apc fl/fl;Pten fl/fl  mouse 10437


title: Oviductal_Tumor_sample3

source_name: Right side tumor from tamoxifen treated Ovgp1-iCre-ERT2;Apc fl/fl;Pten fl/fl  mouse 10436


title: Ovarian_Tumor_sample5

source_name: Left side tumor from Ovgp1-iCre-ERT2;Apc fl/fl;Pten fl/fl  mouse 10438 injected with AdCre


title: RNA from mouse liver 131

source_name: Total RNA from mouse liver 131

value: Gene expression data from mouse 131 High energy 33/47/20


title: Ovarian_Tumor_sample1

source_name: Left side tumor from Ovgp1-iCre-ERT2;Apc fl/fl;Pten fl/fl  mouse 10273 injected with AdCre


title: Oviductal_Tumor_sample5

source_name: Left side tumor from tamoxifen treated Ovgp1-iCre-ERT2;Apc fl/fl;Pten fl/fl  mouse 10453


title: RNA from mouse liver 408

source_name: Total RNA from mouse liver 408

value: Gene expression data from mouse 408 High energy 23/38/38


title: Normal_Ovary_sample2

source_name: Two normal ovaries from  Ovgp1-iCre-ERT2;Apc fl/fl;Pten fl/fl mouse 10467


title: Endometrium_Day 4_Replicate 3

city: Clayton

first: Moshe

last: Olshansky

state: Vic

address: 19 Innovation Walk (Bldg 76)

department: Microbiology

institute: Monash University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: First the data was re-annotated using illuminaHumanv4.db bioconductor R package. This included exclusion of “bad” probes and assignment of probes to correct genes (see Barbosa-Morais et al. (2010) A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data. Nucleic Acids Research). The reannotated data were analysed using RUV-inv (Gagnon-Bartsch JA, Jacob L, Speed TP. Removing unwanted variation from high dimensional data with negative controls. Statistics Technical Reports, Department of Statistics, University of California, Berkley, USA. 2013; Gagnon-Bartsch JA, Speed TP. Using control genes to correct for unwanted variation in microarray data. Biostatistics. 2012;13(3):539-552).   This method does not include a traditional normalisation step, and therefore only matrices of original and reannotated, but still non-normalised data are provided.

label: Biotin

source_name: Endometrium, day 4 of menstruation

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was collected into RNALater and RNA extracted with Trizol reagent, followed by column extraction  with AmbionPure Link kit in accordance with the manufacturers protocol and eluting in 50μl.  RNA was quantified using the nanodrop 2000 (thermo Scientific).

value: Female


title: Endometrium_Day 4_Replicate 4


title: Endometrium_Day 4_Replicate 2


title: Endometrium_Day 4_Replicate 5


title: Normal_Ovary_sample1

source_name: Two normal ovaries from  Ovgp1-iCre-ERT2;Apc fl/fl;Pten fl/fl mouse 10466


title: Normal_Ovary_sample3

source_name: Two normal ovaries from  Ovgp1-iCre-ERT2;Apc fl/fl;Pten fl/fl mouse 10522


title: Endometrium_Day 4_Replicate 1


title: Endometrium_Day 4_Replicate 6


title: Endometrium_Day 3_Replicate 8

source_name: Endometrium, day 3 of menstruation


title: Endometrium_Day 3_Replicate 3


title: Endometrium_Day 3_Replicate 7


title: Endometrium_Day 3_Replicate 6


title: Endometrium_Day 3_Replicate 2


title: Endometrium_Day 3_Replicate 4


title: Endometrium_Day 3_Replicate 5


title: Endometrium_Day 2_Replicate 8

source_name: Endometrium, day 2 of menstruation


title: Endometrium_Day 2_Replicate 7


title: KO PBS-3

city: Xuzhou

first: Bin

last: Pan

state: Jiangsu

address: #99 West Huaihai Road

department: Hematology

country: China

institute: The Affiliated Hospital of Xuzhou Medical University

description: Gene expression after incubation with PBS for 4 hrs

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8x60K Microarray Ver2.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: macrophages, GPR15KO, PBS, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Murine macrophages were isolated from abdominal cavity of mice, and were cultured in DMEM (Thermo Fisher Scientific, Waltham, MA, USA) medium supplied with 10% FBS (Biowest, Nuaillé, France).

extract_protocol: Total RNA from macrophages were extracted using a TRIzol-chloroform based method. RNA quality was measured using a NanoDrop 2000 Spectrophotometers (Thermo Fisher Scientific).

treatment_protocol: Abdominal macrophages from WT and GPR15 KO mice were stimulated with LPS (100 ng/ml) for 4 hrs.

value: Abdominal cavity

value: macrophages

tag: genotype

tag: stimulation

value: PBS


title: Endometrium_Day 3_Replicate 9


title: Endometrium_Day 2_Replicate 6


title: Endometrium_Day 2_Replicate 9


title: KO LPS-1

description: Gene expression after incubation with LPS (100 ng/ml) for 4 hrs

source_name: macrophages, GPR15KO, LPS, replicate 1

tag: strain

value: LPS


title: KO LPS-3

source_name: macrophages, GPR15KO, LPS, replicate 3


title: KO PBS-1

source_name: macrophages, GPR15KO, PBS, replicate 1


title: KO PBS-2

source_name: macrophages, GPR15KO, PBS, replicate 2


title: KO LPS-2

source_name: macrophages, GPR15KO, LPS, replicate 2


title: Endometrium_Day 3_Replicate 1

tag: gender


title: WT LPS-2

source_name: macrophages, wild type, LPS, replicate 2

tag: tissue

value: wildtype


title: Endometrium_Day 2_Replicate 4


title: Endometrium_Day 2_Replicate 3


title: WT PBS-3

source_name: macrophages, wild type, PBS, replicate 3


title: WT LPS-3

source_name: macrophages, wild type, LPS, replicate 3


title: Endometrium_Day 2_Replicate 5


title: Endometrium_Day 2_Replicate 2


title: Endometrium_Day 2_Replicate 1


title: WT LPS-1

source_name: macrophages, wild type, LPS, replicate 1


title: WT PBS-1

source_name: macrophages, wild type, PBS, replicate 1


title: WT PBS-2

source_name: macrophages, wild type, PBS, replicate 2


title: CVI, AR imbibed (AR_ME12.3)

status: Public on Aug 24 2016

city: Wageningen

first: Leónie

last: Bentsink

address: Droevendaalsesteeg 1

country: Netherlands

institute: Wageningen University

description:
AR_ME12.3
CVI, dissected seed

hyb_protocol: CVI samples: The GeneChip (#900720) HWS kit was used for hybridisation, washing and staining of the cartridges.

scan_protocol: Scanning of the arrays was performed using the Affimetrix 3000G scanner.

data_processing: The GeneChip data were analyzed using the R statistical programming environment and Bioconductor packages. The data were normalized using the RMA algorithm using a custom chip definition file (.cdf) from the CustomCDF project [66] (Ath1121501_At_TAIRG.cdf v18.0.0, released 23rd January 2014 obtained via http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/).

organism: Arabidopsis thaliana

source_name: After-ripened seeds imbibed in water for 12h

label_protocol: CVI: RNA was processed and cRNA synthesized by use of the 3’ IVT-Express Labeling Kit (#901229).

growth_protocol: For the transcriptome analysis of CVI, plants were grown in three replicates on rockwool supplemented with a standard nutrient solution.

extract_protocol: CVI samples: RNA of the RAD samples was isolated with the Absolutely RNA Nanoprep kit (Agilent Technologies), RNA of the MCE and dry seed samples was isolated by an alternative method based on the hot borate isolation protocol and additionally cleaned up with NucleoSpin RNA Clean-Up XS (Macherey-Nagel).

treatment_protocol: CVI samples: RNA was extracted from whole dry seeds and dissected seeds that were imbibed for 3, 7, 12 and 24 hours in water.

tag: ecotype

value: CVI

tag: plant stage

value: After-ripened seeds

tag: protocol

value: After-ripened seeds imbibed in water

tag: time

value: seed

tag: tissue compartment

value: MCE (micropylar and chalazal endosperm)


title: CVI, AR imbibed (AR_RAD3.3)

description:
AR_RAD3.3
CVI, dissected seed

source_name: After-ripened seeds imbibed in water for 3h

value: RAD (radicle and hypocotyl)


title: CVI, AR imbibed (AR_RAD12.3)

description:
AR_RAD12.3
CVI, dissected seed


title: CVI, AR imbibed (AR_ME24.3)

description:
AR_ME24.3
CVI, dissected seed

source_name: After-ripened seeds imbibed in water for 24h


title: CVI, AR imbibed (AR_RAD7.3)

description:
AR_RAD7.3
CVI, dissected seed

source_name: After-ripened seeds imbibed in water for 7h


title: CVI, AR imbibed (AR_ME3.3)

description:
AR_ME3.3
CVI, dissected seed


title: CVI, AR imbibed (AR_RAD24.3)

description:
AR_RAD24.3
CVI, dissected seed


title: CVI, AR imbibed (AR_ME7.2)

description:
AR_ME7.2
CVI, dissected seed


title: Pericyte PDGF-BB treated 1 day rep3

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

institute: Karolinska Institutet

description: Pericytes were isolated and treated with PDGF-BB or control for 5 days

hyb_protocol: Samples were hybridized with the Affymetrix Mouse Gene 1.0 ST Array according the instructions of the manufacturer

scan_protocol: Arrays were scanned using the GeneArray Scanner 3000 according to the instructions from the manufacturer.

data_processing: Data were extracted and normalized using a custom CDF and Robust Multi-array Average (RMA) in R (r-project.org) with default settings.

source_name: Mouse pericytes

label_protocol: Single round labeling recommended by manufacturer.

growth_protocol: Pericytes were isolated and maintained as described (Cao, R., et al. VEGFR1-mediated pericyte ablation links VEGF and PlGF to cancer-associated retinopathy. Proc Natl Acad Sci U S A 107, 856-861 (2010).)

extract_protocol: RNAeasy (Qiagen)

treatment_protocol: Treatment with PDGF-BB (100 ng/ml) for 1 day, 5 days or control

tag: cell type

value: Pericyte

tag: condition

value: PDGF-BB for 1 day


title: Pericyte PDGF-BB treated 1 day rep2


title: CVI, AR imbibed (AR_ME7.3)

description:
AR_ME7.3
CVI, dissected seed


title: Pericyte PDGF-BB treated 5 days rep3

value: PDGF-BB for 5 days


title: CVI, AR imbibed (AR_ME24.2)

description:
AR_ME24.2
CVI, dissected seed


title: Pericyte PDGF-BB treated 5 days rep2


title: Pericyte control rep2

value: Control


title: CVI, AR imbibed (AR_ME12.2)

description:
AR_ME12.2
CVI, dissected seed


title: Pericyte control rep3


title: CVI, AR imbibed (AR_ME3.2)

description:
AR_ME3.2
CVI, dissected seed


title: Pericyte PDGF-BB treated 5 days rep1


title: Pericyte PDGF-BB treated 1 day rep1


title: CVI, AR imbibed (AR_RAD24.2)

description:
AR_RAD24.2
CVI, dissected seed


title: Pericyte control rep1


title: CVI, AR imbibed (AR_RAD12.2)

description:
AR_RAD12.2
CVI, dissected seed


title: CVI, AR imbibed (AR_RAD3.2)

description:
AR_RAD3.2
CVI, dissected seed


title: CVI, AR imbibed (AR_ME12.1)

description:
AR_ME12.1
CVI, dissected seed


title: CVI, AR imbibed (AR_ME24.1)

description:
AR_ME24.1
CVI, dissected seed


title: CVI, AR imbibed (AR_RAD7.2)

description:
AR_RAD7.2
CVI, dissected seed


title: 18_C4BP_5

source_name: DMSO

tag: cell line

value: beta-cell line

tag: treated with

value: 1% DMSO (control)


title: RNA from mouse liver 162

source_name: Total RNA from mouse liver 162

value: liver

tag: macronutrient in p/c/f

value: Gene expression data from mouse 162 High energy 33/20/47


title: CVI, AR imbibed (AR_ME7.1)

description:
AR_ME7.1
CVI, dissected seed


title: CVI, AR imbibed (AR_RAD3.1)

description:
AR_RAD3.1
CVI, dissected seed


title: CVI, AR dry seeds (AR_DRY.2)

description:
AR_DRY.2
CVI, whole seed

source_name: After-ripened dry seeds

value: After-ripened dry seeds

value: control

value: whole seeds


title: CVI, D dormant (FR_ME12.3)

description:
FR_ME12.3
CVI, dissected seed

source_name: Dormant seeds imbibed in water for 12h

value: CVI

value: Dormant seeds

value: Dormant seeds imbibed in water


title: CVI, D dormant (FR_ME7.3)

description:
FR_ME7.3
CVI, dissected seed

source_name: Dormant seeds imbibed in water for 7h

value: seed


title: CVI, AR imbibed (AR_ME3.1)

description:
AR_ME3.1
CVI, dissected seed

value: After-ripened seeds

value: After-ripened seeds imbibed in water

value: MCE (micropylar and chalazal endosperm)


title: CVI, AR imbibed (AR_RAD24.1)

description:
AR_RAD24.1
CVI, dissected seed

value: RAD (radicle and hypocotyl)


title: CVI, AR dry seeds (AR_DRY.1)

description:
AR_DRY.1
CVI, whole seed


title: CVI, D dormant (FR_RAD7.3)

description:
FR_RAD7.3
CVI, dissected seed


title: CVI, AR imbibed (AR_RAD12.1)

description:
AR_RAD12.1
CVI, dissected seed


title: CVI, D dormant (FR_ME3.3)

description:
FR_ME3.3
CVI, dissected seed

source_name: Dormant seeds imbibed in water for 3h


title: CVI, AR dry seeds (AR_DRY.3)

description:
AR_DRY.3
CVI, whole seed


title: CVI, D dormant (FR_RAD12.3)

description:
FR_RAD12.3
CVI, dissected seed


title: CVI, D dormant (FR_ME24.2)

description:
FR_ME24.2
CVI, dissected seed

source_name: Dormant seeds imbibed in water for 24h


title: CVI, D dormant (FR_ME24.3)

description:
FR_ME24.3
CVI, dissected seed


title: CVI, D dormant (FR_ME12.2)

description:
FR_ME12.2
CVI, dissected seed


title: CVI, AR imbibed (AR_RAD7.1)

description:
AR_RAD7.1
CVI, dissected seed


title: CVI, D dormant (FR_ME7.2)

description:
FR_ME7.2
CVI, dissected seed


title: CVI, D dormant (FR_RAD24.2)

description:
FR_RAD24.2
CVI, dissected seed


title: CVI, D dormant (FR_RAD24.3)

description:
FR_RAD24.3
CVI, dissected seed


title: CVI, D dormant (FR_RAD7.2)

description:
FR_RAD7.2
CVI, dissected seed


title: CVI, D dormant (FR_ME24.1)

description:
FR_ME24.1
CVI, dissected seed


title: CVI, D dormant (FR_ME3.2)

description:
FR_ME3.2
CVI, dissected seed


title: YMW based diet, biological rep2

first: Soumya

middle: Kanti

last: Kar

state: I am not in the U.S. or Canada

address: De Elst1

department: Animal Science Group

institute: WUR

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA, USA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.36.1).

source_name: Yellow meal worm (YMW) based diet, fed for four week, ileum

label_protocol: Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: Male C57BL/6J mice, aged 3 weeks, were purchased from Harlan (Horst, the Netherlands), and housed in a light and temperature-controlled animal facility of Wageningen University (12:12 h light/dark cycle, 20±2 °C). Mice had free access to feed and water.

extract_protocol: Total RNA was isolated using the RNeasy kit (Qiagen) with a DNase digestion step according to the manufacturer's protocol. RNA quality was assessed using RNA 6000 nanochips on the Agilent 2100 bioanalyzer (Agilent Technologies, Amsterdam, the Netherlands). RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Mice were fed CAS based diet for 1 week. After this adaptation period, mice were stratified according to their body weight and allocated to the control (SBM), SDPP and CAS based diet group (n=5) or WGM, DWP ans YMW diet group (n=6, ). After 4 weeks dietary intervention, mice were anesthetized using isoflurane and sacrificed by cervical dislocation. Ileum was removed, mucosal scrapings were collected, snap-frozen in liquid nitrogen and stored at −80°C (scrapings).

value: Ileum

value: Male

tag: age (wk)


title: CVI, D dormant (FR_ME12.1)

description:
FR_ME12.1
CVI, dissected seed


title: CVI, D dormant (FR_RAD3.3)

description:
FR_RAD3.3
CVI, dissected seed


title: SDPP based diet, biological rep5

source_name: Spray dried plasma protein (SDPP) based diet, fed for four week, ileum

tag: Sex


title: CVI, D dormant (FR_RAD12.2)

description:
FR_RAD12.2
CVI, dissected seed


title: CVI, D dormant (FR_RAD3.2)

description:
FR_RAD3.2
CVI, dissected seed


title: CVI, D dormant (FR_ME7.1)

description:
FR_ME7.1
CVI, dissected seed


title: CVI, D dormant (FR_RAD3.1)

description:
FR_RAD3.1
CVI, dissected seed


title: YMW based diet, biological rep5


title: CVI, D dormant (FR_RAD12.1)

description:
FR_RAD12.1
CVI, dissected seed


title: CVI, D dormant (FR_RAD7.1)

description:
FR_RAD7.1
CVI, dissected seed


title: CVI, D dry seeds (FR_DRY.3)

description:
FR_DRY.3
CVI, whole seed

source_name: Dormant dry seeds

value: Dormant dry seeds


title: YMW based diet, biological rep6


title: SDPP based diet, biological rep3


title: YMW based diet, biological rep4


title: CVI, D dry seeds (FR_DRY.2)

description:
FR_DRY.2
CVI, whole seed


title: SDPP based diet, biological rep4


title: CVI, D dry seeds (FR_DRY.1)

description:
FR_DRY.1
CVI, whole seed


title: SDPP based diet, biological rep1


title: CVI, D dormant (FR_RAD24.1)

description:
FR_RAD24.1
CVI, dissected seed


title: CVI, D dormant (FR_ME3.1)

description:
FR_ME3.1
CVI, dissected seed


title: SDPP based diet, biological rep2


title: WGM based diet, biological rep5

source_name: Wheat gluten (WGM) based diet, fed for four week, ileum


title: WGM based diet, biological rep6


title: DWP based diet, biological rep4

source_name: Delactosed whey powder (DWP) based diet, fed for four week, ileum


title: SBM based diet, biological rep1

source_name: Soybean (SBM) based diet, fed for four week, ileum


title: WGM based diet, biological rep4


title: DWP based diet, biological rep2


title: WGM based diet, biological rep3


title: YMW based diet, biological rep3


title: DWP based diet, biological rep1


title: ExN6h-Rep2-LeafRegion4

city: Vienna

first: Angelika

middle: B

last: Czedik-Eysenberg

address: Dr-Bohr-Gasse 3

country: Austria

institute: Gregor-Mendel-Institute

hyb_protocol: default affymetrix protocol (conducted by Atlas biolabs, Berlin)

data_processing: Affymetrix gene expression values were normalized by the Robust multi-arrays average (RMA) algorithm using the software Robin  (Lohse et al., 2010). Three samples (one replicate from leaf region 3 time point 1, one replicate from region 4 time point 1 and one replicate from region 4 time point 3) were excluded from further analysis based on atypical behavior in the Robin quality controls.

organism: Zea mays

source_name: maize leaf, extended night 6h, mature leaf part

growth_protocol: 700μE PAR, 14hours light/10 hours dark cycles, temperature settings 25°C/22°C (the effective day temperature at the plant level is ~29°C), 70% air humidity.

extract_protocol: Quiagen RNAEasy plant mini kit, DTT instead of ß-mercaptoethanol

treatment_protocol: Extension of the night be kepeping night conditions in the plants chamber

tag: sampling time point

value: extended night 6h (ExN 6h)

tag: leaf region

value: R4:mature eleaf region


title: ED-Rep3-LeafRegion3

scan_protocol: default affymetrix protocol (conducted by Atlas biolabs, Berlin)

source_name: maize leaf, end of day, elongation zone

value: end of day (ED)

value: R3:elongation zone, 3-4.5cm above ligule


title: DWP based diet, biological rep3

tag: strain


title: CAS based diet, biological rep3

source_name: Casein (CAS) based diet, fed for four week, ileum


title: CAS based diet, biological rep4


title: CAS based diet, biological rep2


title: CAS based diet, biological rep5


title: DWP based diet, biological rep6


title: WGM based diet, biological rep2


title: SBM based diet, biological rep5


title: SBM based diet, biological rep3


title: CAS based diet, biological rep1


title: SBM based diet, biological rep4


title: WGM based diet, biological rep1


title: ED-Rep3-LeafRegion4

source_name: maize leaf, end of day, mature leaf part

label_protocol: default affymetrix protocol (conducted by Atlas biolabs, Berlin)

value: R4:mature leaf region


title: ExN24h-Rep3-LeafRegion1

source_name: maize leaf, extended night 24h, division zone

tag: genotype

value: genotype SL (KWS Einbeck)

value: extended night 24h (ExN 24h)

value: R1:division zone, 0-1.5cm above ligule


title: ExN14h-Rep3-LeafRegion4

source_name: maize leaf, extended night 14h, mature leaf part

value: extended night 14h (ExN 14h)


title: SBM based diet, biological rep2

tag: tissue


title: ExN24h-Rep2-LeafRegion4

source_name: maize leaf, extended night 24h, mature leaf part


title: ExN6h-Rep3-LeafRegion3

source_name: maize leaf, extended night 6h, elongation zone


title: ExN24h-Rep3-LeafRegion3

source_name: maize leaf, extended night 24h, elongation zone


title: YMW based diet, biological rep1


title: ExN14h-Rep1-LeafRegion1

source_name: maize leaf, extended night 14h, division zone


title: ExN6h-Rep3-LeafRegion4


title: ExN14h-Rep1-LeafRegion3

source_name: maize leaf, extended night 14h, elongation zone


title: ExN14h-Rep3-LeafRegion3


title: ExN24h-Rep2-LeafRegion3


title: ExN6h-Rep3-LeafRegion1

source_name: maize leaf, extended night 6h, division zone


title: ExN14h-Rep3-LeafRegion1


title: DWP based diet, biological rep5


title: ExN14h-Rep2-LeafRegion3


title: ExN14h-Rep1-LeafRegion4


title: ExN24h-Rep3-LeafRegion4


title: ExN24h-Rep2-LeafRegion1


title: ExN14h-Rep2-LeafRegion1


title: ExN14h-Rep2-LeafRegion4


title: LNCaP-MBD2 KD-replicate 3

type: genomic

city: Darlinghurst

first: Elena

last: Zotenko

address: 384 Victoria St.

department: Genomics and Epigenetics

institute: Garvan Institute of Medical Research

description: LNCaP cells, MBD2 knockdown

hyb_protocol: Bisulfite converted DNA was hybridized to an Illumina HumanMethylation450 BeadChip (HM450K) and run on an Illumina HiScan System (Illumina, CA, USA) according to the manufacturer’s instructions (performed at the Australian Genome Research Facility, Melbourne)

scan_protocol: Standard Illumina protocol.

data_processing: Raw intensity data was processed and background normalized using preprocessIllumina function from Bioconductor minfi package.

label: Cy5 and Cy3

source_name: LNCaP cells, MBD2 knockdown

label_protocol: Standard Illumina protocol.

growth_protocol: LNCaP prostate cancer cells were cultured in T-Medium with 10% heat-inactivated FCS and 1% penicillin/streptomycin (Invitrogen).  The cells were grown at 37C in 5% C02 atmosphoere and split 1:3 every 4-5 days.

extract_protocol: Genomic DNA was extracted fromcell lines using QIAamp DNA minikit (Qiagen).

treatment_protocol: LNCaP prostate cancer cells were stably transfected with ShRNA directed against MBD2 (Acc. No. AF072242.1) or  scrambled shRNA controls  in the siLentGene-2 Vector (Promega). Stable trnasfectants were selected by neomycin resistance.

value: LNCaP

tag: transfection

value: shRNA directed against MBD2


title: LNCaP-scrambled shRNA-replicate 3

description: LNCaP cells, stable scrambled shRNA control

value: scrambled shRNA control


title: ExN6h-Rep2-LeafRegion3


title: ExN6h-Rep2-LeafRegion1


title: ExN6h-Rep1-LeafRegion4


title: ExN6h-Rep1-LeafRegion3


title: ExN6h-Rep1-LeafRegion1


title: EN-Rep3-LeafRegion4

source_name: maize leaf, end of night, mature leaf part

value: end of night (EN)


title: LNCaP-MBD2 KD-replicate 1

description: LNCaP cells, MBD2 knockdown


title: LNCaP-scrambled shRNA-replicate 1

source_name: LNCaP cells, stable scrambled shRNA control


title: ExN24h-Rep1-LeafRegion3


title: ExN24h-Rep1-LeafRegion4


title: EN-Rep3-LeafRegion3

source_name: maize leaf, end of night, elongation zone


title: ExN24h-Rep1-LeafRegion1


title: sE23_C_NS

city: Xi’an

first: Huiyun

last: Xu

state: Shanxi

address: 127 West Youyi Road,Xi’an Shaanxi,710072,P.R.China

department: School of Life Sciences

institute: Northwestern Polytechnical University

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings. Raw data were normalized by Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

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

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

growth_protocol: In an incubator at 37°C with 5 percent CO2 for 30 mins

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

treatment_protocol: treated by irrelevant rabbit IgG antibody (CWBIO, Beijing, China, 1:50 dilution) in an incubator at 37°C with 5 percent CO2 for 30 mins, then separated into 4 groups: control (C), 1g, 2g and μg groups Fantibody (1:50 dilution, 28 µg/ml) was added into the media in 35 mm culture dish for 30 min. Cells of +(-)E2-1g,  +(-)E2-2g and  +(-)E2-μg groups were cultured in the given positions on HMGE platform, while cells of E2-C group were cultured in the same incubator with C group

value: osteocytic cells

tag: subjected to

value: normal cell incubator (control)

tag: incubated with

value: hemichannel-blocking antibody Cx43(E2)


title: sE23_ug_NS

value: high magneto-gravitational environment (HMGE; ug)


title: sE23_2g_NS

value: high magneto-gravitational environment (HMGE; 2g)


title: EN-Rep3-LeafRegion1

source_name: maize leaf, end of night, division zone


title: sE23_1g_NS

value: high magneto-gravitational environment (HMGE; 1g)


title: EN-Rep2-LeafRegion4


title: LNCaP-MBD2 KD-replicate 2

description: LNCaP cells, MBD2 knockdown


title: LNCaP-scrambled shRNA-replicate 2


title: EN-Rep1-LeafRegion3


title: EN-Rep1-LeafRegion4


title: sE22_C_NS


title: EN-Rep2-LeafRegion1


title: sE22_ug_NS


title: EN-Rep2-LeafRegion3


title: sE22_1g_NS


title: EN-Rep1-LeafRegion1


title: ED-Rep2-LeafRegion4

value: end of day (ED)

value: R4:mature eleaf region


title: sE21_C_NS


title: ED-Rep2-LeafRegion3

value: R3:elongation zone, 3-4.5cm above ligule


title: sE21_1g_NS


title: ED-Rep3-LeafRegion1

source_name: maize leaf, end of day, division zone

value: genotype SL (KWS Einbeck)


title: sE21_ug_NS


title: ED-Rep2-LeafRegion1


title: sE22_2g_NS


title: s3_2g_NS


title: ED-Rep1-LeafRegion3

source_name: maize leaf, end of day, elongation zone


title: ED-Rep1-LeafRegion1


title: s3_C_NS


title: 4B(+/+)

city: Tokushima

first: Hisashi

last: Nagamoto

address: 463-10 Kagasuno, Kawauchi-cho

country: Japan

institute: Otsuka Pharmaceutical Co., Ltd.

hyb_protocol: Following fragmentation, 12.5 μg of cRNA were hybridized for 16 hr at 45ºC on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: lung

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.3 μg total RNA (GeneChip 3’ IVT Express Kit Affymetrix).

growth_protocol: Mice other than C57 were originally prepared in Stanford University (Proc Natl Acad Sci USA. 1999;96(21):11998-2003, Proc Natl Acad Sci USA. 2002;99(11):7628-33). These mice were backcrossed to C57 mice for at least 11 generations before use. After birth, mice were maintained under the condition with specific pathogen-free and free access to chow and tap water.

extract_protocol: Lung tissues (5 lungs/strain) were quickly frozen in liquid nitrogen, and were pulverized under liquid nitrogen. A portion of the frozen lung powder was used to prepare RNA by RNeasy Plus Kit (QIAGEN) according to the manufacturer's instructions. After checking the degree of refining of RNA preparations by Bioanalyser (2100 Bioanalyzer, Agilent), three of five samples were selected to be mixed to prepare the representative RNA samples for each strain.

treatment_protocol: All mice were naïve (no mice were subjected to elastase treatment.)

tag: genetic background

value: female, C57BL/6 × 129/Ola as background, and backcrossed to C57BL/6J for at leaset 11 generations


title: 4D(-/-)


title: s3_1g_NS


title: s2_C_NS


title: ED-Rep1-LeafRegion4

source_name: maize leaf, end of day, mature leaf part

value: R4:mature leaf region


title: s2_2g_NS


title: sE21_2g_NS


title: 4B(-/-)


title: s3_ug_NS


title: 4D(+/+)


title: s2_ug_NS


title: C57

value: female, C57BL/6J


title: s1_ug_NS


title: lymphatic medullary sinus, biological replicate 7

city: Turku

first: Kati

last: Elima

address: Tykistökatu 6

department: MediCity

country: Finland

institute: University of Turku

hyb_protocol: Cy3-labeled cDNAs were hybridized overnight (17h, 65C) to an Agilent Whole Mouse Genome Oligo Microarrays 8x60K using Agilent's recommended hybridization chamber and oven. The microarrys were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at rt followed by a second wash with preheated Agilent Gene Expression Wash buffer 2 (37C) for 1 min.

scan_protocol: Signals were detected using Agilent's Microarray Scanner System. The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files.

data_processing: The signal intensities from the raw data lists were background corrected and normalized by dividing the intensity values by their median. The normalized intensities were log2-transformed.

source_name: lymphatic endothelial cells, FACS

label_protocol: Cy3-labeling was performed according to Miltenyi Biotec's undisclosed protocol

extract_protocol: LCM: LNs were collected in SUPERase-In, placed onto a layer of OCT, Alexa fluor 488 anti-mouse CD31 and PE-Texas red anti-mouse F4/80 antibodies were applied to the frozen sections of lymph nodes. After washing the sections were dehydrated. LCMP was conducted on a PALM micro beam instrument to isolate CD31 labeled LEC cells. Micro-dissected cells were collected in adhesive caps. Altogether 50 cells were collected/experiment into Superamp lysis buffer. FACS sorting: LNs were digested in PBS containing liberase TM research grade and DNase I. For cell sorting the following antibodies were used: lineage (CD3e, CD11b, CD45R/B220, Erythroid Cells, Ly-6G and Ly-6C) cocktail,anti-CD73, and anti –podoplanin 7-AAD was used to exclude dead cells.1200 cells were sorted into fetal calf serum coated FACS tubes containing RPMI-1640 and 20% FCS. The samples were centrifuged and resuspended in SuperAmp Lysis Buffer.

value: lymphatic medullary sinus

value: lymphatic endothelial cells, FACS


title: lymphatic medullary sinus, biological replicate 6


title: s1_2g_NS


title: s1_C_NS


title: s2_1g_NS


title: subcapsular sinus, biologic replicate 6

value: subcapsular sinus


title: S42_1

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

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

source_name: hippocampal neurons_S42

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Sprague Dawley

tag: tissue/cell type

value: primary rat hippocampal neurons

value: S42; scrambled Ab42


title: subcapsular sinus, biologic replicate 7

tag: cell type


title: lymphatic medullary sinus, biological replicate 5

source_name: lymphatic endothelial cells, LCM

value: lymphatic endothelial cells, LCM


title: S42_3


title: lymphatic medullary sinus, biological replicate 4


title: S40_3

source_name: hippocampal neurons_S40

value: S40; scrambled Ab40


title: s1_1g_NS

value: osteocytic cells


title: S40_1


title: F42_3

source_name: hippocampal neurons_F42

value: F42; fibrillar Ab42


title: subcapsular sinus, biologic replicate 1


title: F40_1

source_name: hippocampal neurons_F40

value: F40; fibrillar Ab40


title: lymphatic medullary sinus, biological replicate 1


title: F40_2


title: subcapsular sinus, biologic replicate 3


title: F42_2


title: lymphatic medullary sinus, biological replicate 3


title: F42_1


title: XL42_3

source_name: hippocampal neurons_XL42

value: XL42; cross-linked Ab42 oligomers


title: subcapsular sinus, biologic replicate 5


title: XL42_2


title: subcapsular sinus, biologic replicate 4


title: lymphatic medullary sinus, biological replicate 2


title: XL40_3

source_name: hippocampal neurons_XL40

value: XL40; cross-linked Ab40 oligomers


title: XL40_2


title: subcapsular sinus, biologic replicate 2


title: T42_2

source_name: hippocampal neurons_T42

value: T42; low molecular weight Ab42


title: T42_3


title: XL40_1


title: T40_1

source_name: hippocampal neurons_T40

value: T40; low molecular weight Ab40


title: cont_1

source_name: hippocampal neurons_control

value: none (control)


title: cont_2


title: cont_3


title: LNCaP-MBD2 KD-replicate 2

description: LNCaP cells, MBD2 knockdown

hyb_protocol: Labeling and hybridization were performed according to Affymetrix GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual

scan_protocol: Scanning was done on an affymetrix GeneChip Scanner 7G.

data_processing: Arrays were normalised within each batch using RMA function from Bioconductor oligo package. Only probes that were annotated in RefSeq or GenBank (according to the Affymetrix annotation release 32) were included in downstream analyses. Differentially expressed (DE) genes were determined using Bioconductor limma package, with the linear model including a covariate representing batch, resulting in 134 up-regulated and 103 down-regulated genes (unadjusted p-value < 0.05; log-fold change > 0.58).

molecule: cytoplasmic RNA

source_name: LNCaP cells, MBD2 knockdown

label_protocol: Biotin

extract_protocol: Cytoplasmic RNA was isolated using Trizol reagent (Ambion, 15596-018) according to the manufacturer’s protocol.

value: LNCaP

value: shRNA directed against MBD2


title: LNCaP-scrambled shRNA-replicate 2

source_name: LNCaP cells, stable scrambled shRNA control

value: scrambled shRNA control


title: Granny_Smith_Green_2

status: Public on Aug 23 2016

city: San Michele all'Adige

first: Fabrizio

last: Costa

state: N/A = Not Applicable

address: Via Mach 1

department: Center Agriculture Food Environment

institute: University of Trento

hyb_protocol: Four μg of purified aRNA were subsequently hybridized on the array according to manufacturer’s instruction. After hybridization, microarray slides were scanned using an AxoGenePix 4400A (Molecular Device)

scan_protocol: Densitometric analysis were performed by GenePixPro 7 software (provided with the instrument)

data_processing: Probe signals were considered when higher than negative control values plus twice the standard deviation. Data were normalized by quantile normalization and differentially expressed genes were identified with Linear Model Microarray Analysis (LIMMA), considering a False Discovery rate (FDR) < 0.05. All values were log transformed (base 2) and genes with an absolute fold change > 1 and P-value ² 0.05 were considered as differentially expressed in pairwise comparison

organism: Malus domestica

label_protocol: For the transcriptome analysis carried out with iRIPE, 2 _g of RNA were further amplified and labeled using the RNA ampULSE kit (GEA-022, Kreatech)

growth_protocol: Plants were manteined following standard agronomical techniques for pruning, thinning and pest-disease control

extract_protocol: Total RNA was isolated from fruit cortex tissue of three biological replicates with the Spectrum Total RNA kit (Sigma). RNA quantity and quality was controlled with a Nanodrop ND-8000 (Thermo Scientific, USA) and an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

treatment_protocol: 1ppm of 1-methylcyclopropene (1-MCP) was applied after harvest overnight

tag: cultivar

value: Granny Smith

tag: developmental stage

value: Green (3 cm diameter)

value: fruit cortex


title: LNCaP-scrambled shRNA-replicate 3

tag: cell line


title: Granny_Smith_Green_1


title: LNCaP-MBD2 KD-replicate 3

description: LNCaP cells, MBD2 knockdown


title: TH-MYCN 791 sphere cells

city: Augusta

first: Justin

last: Choi

state: GA

address: 1410 Laney Walker Blvd.

department: Cancer Center

institute: Georgia Regents University

description: 791 sphere

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Data were normalized, significance determined by ANOVA, and fold change calculated with the Partek Genomics Suite (Partek Inc., St. Louis, MO).

label: TdT

source_name: TH-MYCN sphere cells

label_protocol: TdT-labled cRNA were prepared with an Affymetrix GeneChip WT Terminal labeling kit

growth_protocol: Neuroblastoma tumors were removed from TH-MYCN mice, minced, and mechanically dissociated into single cells by using a cell strainer (70 µm, Fisher Scientific 22363548). Red blood cells were lysed in ACK buffer (150 mM NH4Cl, 10 mM KHCO3, 0.1 mM EDTA, pH 7.3), and dead cells were removed by passing through Ficoll-Paque Plus (GE Healthcare 17-1440-02). The remaining viable cells were primary tumor cells. Sphere cells were obtained by culturing primary tumor cells in the neural crest cell medium (Etchevers, H. (2011). Primary culture of chick, mouse or human neural crest cells. Nat Protoc 6, 1568-1577).

extract_protocol: Total RNA was isolated from the cell samples using Trizol (Invitrogen), and RNA quality and quantity was assessed using a Agilent BioAnalyzer and a Nanodrop Spectrophotometer.

treatment_protocol: No treatment

value: TH-MYCN

value: Neuroblastoma tumor

value: neuroblastoma spheres

tag: culture age

value: day57 culture


title: TH-MYCN 816 sphere cells

description: 816 sphere

value: day50 culture


title: Granny_Smith_Flower_2

value: Flower

value: flower


title: Golden_Delicious_PostHarvest_1-MCP_3

value: Golden Delicious

value: PostHarvest treated with 1-MCP


title: Golden_Delicious_PostHarvest_1-MCP_2


title: Granny_Smith_Fruitlet_1

value: Fruitlet


title: LNCaP-MBD2 KD-replicate 1

description: LNCaP cells, MBD2 knockdown


title: TH-MYCN 787 sphere cells

description: 787 sphere

value: day36 culture


title: TH-MYCN 787 primary tumor cells

description: 787 tumor

source_name: TH-MYCN primary tumor cells

value: primary neuroblastoma tumor cells


title: Granny_Smith_Fruitlet_2


title: Granny_Smith_Fruitlet_3


title: Granny_Smith_Flower_3


title: Granny_Smith_Flower_1


title: TH-MYCN 816 primary tumor cells

description: 816 tumor


title: LNCaP-scrambled shRNA-replicate 1

value: LNCaP


title: TH-MYCN 791 primary tumor cells

description: 791 tumor


title: T42_1

value: Sprague Dawley

value: primary rat hippocampal neurons

tag: treated with

value: T42; low molecular weight Ab42


title: Golden_Delicious_PostHarvest_Ctrl_3

value: PostHarvest control

value: fruit cortex


title: T40_2

value: T40; low molecular weight Ab40


title: T40_3


title: Golden_Delicious_Harvest_3

value: Harvest


title: Golden_Delicious_PostHarvest_Ctrl_2


title: Golden_Delicious_PostHarvest_Ctrl_1


title: Golden_Delicious_PostHarvest_1-MCP_1


title: Golden_Delicious_Harvest_2


title: Golden_Delicious_Breaker_3

value: Breaker


title: Golden_Delicious_Harvest_1


title: Golden_Delicious_Breaker_2


title: Golden_Delicious_Breaker_1


title: Golden_Delicious_Mature_Green_2

value: Mature Green (6-8 cm diameter)


title: Granny_Smith_PostHarvest_Ctrl_2

value: Granny Smith


title: Granny_Smith_PostHarvest_Ctrl_3


title: Granny_Smith_PostHarvest_1-MCP_2


title: Granny_Smith_PostHarvest_Ctrl_1


title: Golden_Delicious_Mature_Green_1


title: Golden_Delicious_Fruitlet_1


title: Golden_Delicious_Green_3

value: Green (3 cm diameter)


title: Granny_Smith_Harvest_2


title: Granny_Smith_Harvest_3


title: Golden_Delicious_Flower_3

value: Golden Delicious

value: Flower

value: flower


title: Golden_Delicious_Flower_2


title: Golden_Delicious_Flower_1


title: Granny_Smith_PostHarvest_1-MCP_3

value: PostHarvest treated with 1-MCP


title: Golden_Delicious_Green_1


title: Golden_Delicious_Fruitlet_2

value: Fruitlet


title: Golden_Delicious_Fruitlet_3


title: Granny_Smith_Breaker_3


title: Granny_Smith_Harvest_1


title: Granny_Smith_Breaker_2


title: Granny_Smith_Mature_Green_3


title: Golden_Delicious_Mature_Green_3


title: Golden_Delicious_Green_2


title: Granny_Smith_Mature_Green_2


title: Granny_Smith_PostHarvest_1-MCP_1


title: Granny_Smith_Mature_Green_1


title: Granny_Smith_Breaker_1


title: Granny_Smith_Green_3


title: 3 mg/kg cisplatin kidney at day 26, biological rep3

city: Wuppertal

first: Heidrun

middle: Christine

last: Ellinger-Ziegelbauer

address: Aprather Weg 18a

country: Germany

institute: Bayer Pharma AG

description: Gene expression of kidney cortex homogenate from rats 26 days after administration of 3mg/kg cisplatin

hyb_protocol: Following fragmentation, 12.5 µg of aRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 running th Prime_450 protocol.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using GeneData Expressionist® Pro Refiner. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: kidney cortex enriched homogenate from rats treated with 3 mg/kg cisplatin

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 500 ng high quality total kidney RNA (GeneChip® 3 IVT Express Kit).

growth_protocol: All animal experiments were performed according to the German guidelines for care and use of laboratory animals. Male Han Wistar rats, 8 weeks old, were purchased from Charles River laboratories (Sulzbach, Germany). Animals were individually housed in type III makrolon cages, with a 12h light-dark cycle. Standard rodent chow pellets and water were provided ad libitum.

extract_protocol: On days 3, 5, 8 and 26 rats were euthanized and the kidneys were removed for histopathological examination and RNA isolation. Kidney tissue for RNA isolation was placed in RNAlater (Qiagen; Hilden, Germany), incubatedand for 12h at 4°C and then stored at -80°C. Total kidney RNA was isolated with the RNeasy Mini Kit (Qiagen; Hilden, Germany) from 70 mg kidney tissue (cortex enriched),  according to the manufacturer’s instructions. The quality of isolated RNA was assessed using Bioanalyzer Small RNA Kits (Agilent; Santa Clara, CA) and the quantity was determined with a spectrophotometer.

treatment_protocol: Male Han Wistar rats (8 weeks old) were randomly grouped (n = 6) and dosed once i.p. with 0, 1 or 3 mg/kg body weight cis-diamminedichloroplatinum (II) (cisplatin; Sigma Aldrich, Germany) diluted in 0.9% saline. Control groups received appropriate volumes of saline.

value: Han Wistar [Crl:WI(Han)]

tag: gender

value: male

value: kidney


title: 3 mg/kg cisplatin kidney at day 8, biological rep1

description: Gene expression of kidney cortex homogenate from rats 8 days after administration of 3mg/kg cisplatin


title: 3 mg/kg cisplatin kidney at day 8, biological rep4


title: 3 mg/kg cisplatin kidney at day 26, biological rep4


title: 3 mg/kg cisplatin kidney at day 3, biological rep5

description: Gene expression of kidney cortex homogenate from rats 3 days after administration of 3mg/kg cisplatin


title: 1 mg/kg cisplatin kidney at day 26, biological rep4

description: Gene expression of kidney cortex homogenate from rats 26 days after administration of 1mg/kg cisplatin

source_name: kidney cortex enriched homogenate from rats treated with 1 mg/kg cisplatin


title: 3 mg/kg cisplatin kidney at day 26, biological rep1


title: 3 mg/kg cisplatin kidney at day 8, biological rep3


title: 3 mg/kg cisplatin kidney at day 3, biological rep2


title: 3 mg/kg cisplatin kidney at day 5, biological rep3

description: Gene expression of kidney cortex homogenate from rats 5 days after administration of 3mg/kg cisplatin


title: 3 mg/kg cisplatin kidney at day 5, biological rep2


title: 3 mg/kg cisplatin kidney at day 26, biological rep2


title: 3 mg/kg cisplatin kidney at day 5, biological rep5


title: 3 mg/kg cisplatin kidney at day 3, biological rep3


title: 3 mg/kg cisplatin kidney at day 3, biological rep4


title: 1 mg/kg cisplatin kidney at day 26, biological rep5


title: 3 mg/kg cisplatin kidney at day 8, biological rep5


title: 1 mg/kg cisplatin kidney at day 26, biological rep3


title: 3 mg/kg cisplatin kidney at day 8, biological rep2


title: 1 mg/kg cisplatin kidney at day 26, biological rep2


title: 3 mg/kg cisplatin kidney at day 26, biological rep5


title: 1 mg/kg cisplatin kidney at day 8, biological rep5

description: Gene expression of kidney cortex homogenate from rats 8 days after administration of 1mg/kg cisplatin


title: 3 mg/kg cisplatin kidney at day 5, biological rep1


title: 1 mg/kg cisplatin kidney at day 8, biological rep4


title: 3 mg/kg cisplatin kidney at day 5, biological rep4


title: 1 mg/kg cisplatin kidney at day 26, biological rep1


title: 1 mg/kg cisplatin kidney at day 8, biological rep3


title: 3 mg/kg cisplatin kidney at day 3, biological rep1


title: 1 mg/kg cisplatin kidney at day 8, biological rep2


title: 1 mg/kg cisplatin kidney at day 5, biological rep3

description: Gene expression of kidney cortex homogenate from rats 5 days after administration of 1mg/kg cisplatin


title: 1 mg/kg cisplatin kidney at day 8, biological rep1


title: 1 mg/kg cisplatin kidney at day 5, biological rep2


title: 1 mg/kg cisplatin kidney at day 3, biological rep4

description: Gene expression of kidney cortex homogenate from rats 3 days after administration of 1mg/kg cisplatin


title: 1 mg/kg cisplatin kidney at day 3, biological rep1


title: 1 mg/kg cisplatin kidney at day 3, biological rep5


title: 1 mg/kg cisplatin kidney at day 3, biological rep3


title: 1 mg/kg cisplatin kidney at day 5, biological rep1


title: 1 mg/kg cisplatin kidney at day 3, biological rep2


title: Mouse Co-Cultured Cortical Neuron and Cortical Precursor, Biological Replicate 2

city: Toronto

first: Freda

last: Miller

state: ON

address: 686 Bay St

institute: Hospital for Sick Children

description:
Gene expression of co-cultured cortical precursors and cortical neurons
Mix2

hyb_protocol: Affymetrix Mouse Gene 2.0 ST arrays were washed, stained and scanned according to the Fluidics Protocol FS450_0002 using 5.5 ug of cDNA

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed using the oligo package of Bioconductor in R. The data were background corrected, normalized with quantile normalization, transformed into the log2 scale, and summarized into probesets using the Robust Multichip Analysis (RMA) method.

source_name: Wild-type CD1 mouse co-cultured E13 cortical precursors and E16 cortical neurons

label_protocol: cDNA was prepared using the Ambion WT Expression Kit using 100 ng of total RNA

growth_protocol: Cortical neuron cultures were prepared from wild-type CD1 E16 embryos and cultured for 4 days. Cortical precursor cultures were prepared from wild-type CD1 E13 embryos and cultured for 1 day. Co-cultured cortical neuron and cortical precursor cultures were prepared by first preparing cortical neurons from wild-type CD1 E16 embryos, culturing for 4 days and then adding cortical precursors prepared from wild-type CD1 E13 embryos to the cortical neurons for 1 day.

extract_protocol: Total RNA was extracted using the Ambion RiboPure RNA purification kit

treatment_protocol: Cortical neurons cultured for 5 total days. Cortical precursors cultured for 1 day. Co-cultured cortical neuron and cortical precursors cultured for 5 and 1 total days respectively.

tag: genotype/variation

value: WT

value: Co-cultured Cortical Neuron and Cortical Precursor


title: Control kidney at day 26, biological rep4

description: Gene expression of kidney cortex homogenate from control rats day 26

source_name: kidney cortex enriched homogenate from control rats


title: Mouse Cortical Precursor, Biological Replicate 3

description:
Gene expression of cultured cortical precursors
CP3

source_name: Wild-type CD1 mouse E13 cortical precursors

value: Cortical Precursor


title: Control kidney at day 26, biological rep1


title: Control kidney at day 26, biological rep3


title: Mouse Co-Cultured Cortical Neuron and Cortical Precursor, Biological Replicate 1

description:
Gene expression of co-cultured cortical precursors and cortical neurons
Mix1


title: Control kidney at day 8, biological rep3

description: Gene expression of kidney cortex homogenate from control rats day 8


title: SW48

city: Edinburgh

first: Romina

last: Briffa

state: Lothian

address: Crewe Road South

department: Division of Pathology

country: United Kingdom

institute: University of Edinburgh

hyb_protocol: Labeled DNA samples were hybridized to the NimbleGen aCGH array for 72 h at 42°C, according to the manufacturer's instructions (NimbleGen, Madison, USA).

scan_protocol: The slides were loaded in the NimbleGen MS 200 Microarray Scanner (Roche). The MS 200 Data Collection software was launched and the green and red lasers were switched on.  The default scan parameters were used. A pre-scan was conducted at 40µm resolution.  The slides were subsequently scanned at a 2µm resolution.

data_processing: The array data were exported, processed and analyzed using NimbleScan v2.6. Arrays were processed using manufacturer's standard settings with NimbleScan v2.6 segMNT.

source_name: Control (Reference) DNA

label_protocol: One µg of each genomic DNA test sample was labeled with Cy5 using a Cy5-random nonamer, whereas one µg of each genomic DNA reference sample was labeled with Cy3 using a Cy3-random nonamer

extract_protocol: Genomic DNA was extracted from each cell line using DNeasy Blood and Tissue Kit (Qiagen, Cat.No. 69504).  When the cells reached 70-80% confluence, cells were removed from the Petri dish using a cell scraper (BD FalconTM, Cat. no. 353085).  The manufacturer's protocol was followed.

tag: diagnosis

value: normal

value: colorectal cancer

tag: sensitivity to 5 fu

value: less

tag: sensitivity to l-ohp

value: high

tag: sensitivity to bez235

value: insensitive


title: Mouse Co-Cultured Cortical Neuron and Cortical Precursor, Biological Replicate 3

description:
Gene expression of co-cultured cortical precursors and cortical neurons
Mix3

tag: strain


title: DLD-1

value: sensitive


title: Control kidney at day 8, biological rep5

tag: tissue


title: Control kidney at day 8, biological rep1


title: Control kidney at day 5, biological rep5

description: Gene expression of kidney cortex homogenate from control rats day 5


title: Control kidney at day 8, biological rep4


title: Mouse Cortical Precursor, Biological Replicate 2

description:
Gene expression of cultured cortical precursors
CP2


title: Control kidney at day 8, biological rep2


title: Mouse Cortical Precursor, Biological Replicate 1

description:
Gene expression of cultured cortical precursors
CP1


title: Control kidney at day 26, biological rep2


title: Mouse Cortical Neuron, Biological Replicate 2

description:
Gene expression of cultured cortical neurons
CN2

source_name: Wild-type CD1 mouse E16 cortical neurons

value: Cortical Neuron


title: Mouse Cortical Neuron, Biological Replicate 3

description:
Gene expression of cultured cortical neurons
CN3


title: Control kidney at day 5, biological rep4


title: Control kidney at day 5, biological rep3


title: Control kidney at day 5, biological rep2


title: Mouse Cortical Neuron, Biological Replicate 1

description:
Gene expression of cultured cortical neurons
CN1


title: HT29


title: Control kidney at day 5, biological rep1


title: Control kidney at day 3, biological rep4

description: Gene expression of kidney cortex homogenate from control rats day 3


title: Colo320DM


title: NCI H508

source_name: NCI H508

value: NCI H508


title: Control kidney at day 3, biological rep3


title: NCI H716

source_name: NCI H716

value: NCI H716


title: T84


title: Control kidney at day 3, biological rep2


title: SW837


title: Colo201


title: HCT116


title: SK CO 1

source_name: SK CO 1

value: SK CO 1


title: LoVo

source_name: LoVo

value: LoVo


title: SW480


title: Control kidney at day 3, biological rep5

value: Han Wistar [Crl:WI(Han)]


title: LS411N


title: Control kidney at day 3, biological rep1

value: male


title: mammosphere pSuper

city: Tokyo

first: REI

last: MIMOTO

address: 3-25-8 Nishishinbashi, Minato-ku

department: Biochemistry

institute: The Jikei University School of Medicine

hyb_protocol: cRNA was hybridized to Affymetrix Human Gene 1.0 ST array, washed and stained according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner

data_processing: The data were analyzed with median polish summarization and quantile normalization by Affymetrix® Power Tool version 1.15.0 software, and obtained normalized intensity values.

source_name: mammosphere pSuper

label_protocol: The cRNA was amplified, labeled using GeneChip WT Terminal Labeling and Control Kit according to the manufacturer's instructions.

extract_protocol: Total RNA extraction was performed using TRIsure(Nippon genetics) following the manufacture's instructuion.

treatment_protocol: To keep stable transfectants, MCF-7 cells were cultured in the presence of puromycyn (1µg/ml).

value: mammosphere

tag: infection

value: pSuper vector


title: HCT116 p53-/-


title: pSuper-contol

source_name: pSuper-contol


title: HCT116 Dicer intermediate cells

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description: Intermediate levels of Dicer protein expression

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: HCT116 cells

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: DMEM with 10% FBS with or without tetracycline

extract_protocol: Standard Trizol Reagent for the RNA extraction.

treatment_protocol: For Hct tet100 cells, Dicer gene disrupted HCT116 cells were transduced with tet-on Dicer gene and cultured with 100 pg/ml tetracycline for more than one week.

value: Colon carcinoma


title: mammosphere shRNA-DYRK2

source_name: mammosphere shRNA-DYRK2

value: pSuper vector + shRNA-DYRK2


title: HCT116 Dicer disrupted cells

description: Dicer null cells


title: sdh2△/△ cells vs SC5314 cells (Grown in Spider Medium) Replicate 3

city: Beijing

first: Dedong

last: Li

state: Beijing

address: Fuxing Road 28

department: department of clinical pharmacology

institute: PLA General Hospital

description: Biological replicate 3 of 3. Control Candida albicans, grown in Spider medium for 1 h.

hyb_protocol: standard CapitalBio Methods

scan_protocol: standard Luxscan 10K (CapitalBio) protocol

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed. Two hybridizations were performed by using a reversal fluorescent strategy in one test and control and the other hybridization without performing reversal fluorescent.

organism: Candida albicans

source_name: Candida albicans

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-labe

growth_protocol: Strains were propagated in yeast-peptone-dextrose (YPD) medium (1% w/v yeast extract, 2% w/v peptone, 2% w/v dextrose).

extract_protocol: Total RNA was isolated by the hot phenol method.

treatment_protocol: Candida albicans cells were added to the culture medium (Spider medium) with the suspensions at 5×10^6 cells/ml. Following incubating statically at 37 °C at 1 h, the cells were collected and stored in liquid nitrogen.

tag: treatment

value: Grown in Spider

tag: genotype

tag: passage

value: Yeast-form cells incubated statically in Spider medium at 37 °C for 1h

value: Candida albicans sdh2△/△

value: Candida albicans SC5314

tag: age

value: 1 h


title: sdh2△/△ cells vs SC5314 cells (Grown in Spider+Glucose Medium) Replicate 1

description: Biological replicate 1 of 3. Control Candida albicans, grown in Spider+Glucose medium for 1 h.

treatment_protocol: Candida albicans cells were added to the culture medium (Spider medium supplemented with 100mM glucose) with the suspensions at 5×10^6 cells/ml. Following incubating statically at 37 °C at 1 h, the cells were collected and stored in liquid nitrogen.

value: Grown in Spider+Glucose Medium

tag: cell type

value: Yeast-form cells incubated statically in Spider+Glucose medium at 37 °C for 1h


title: sdh2△/△ cells vs SC5314 cells (Grown in Spider+Glucose Medium) Replicate 3

description: Biological replicate 3 of 3. Control Candida albicans, grown in Spider+Glucose medium for 1 h.


title: sdh2△/△ cells vs SC5314 cells (Grown in Spider Medium) Replicate 1

description: Biological replicate 1 of 3. Control Candida albicans, grown in Spider medium for 1 h.


title: sdh2△/△ cells vs SC5314 cells (Grown in Spider+Glucose Medium) Replicate 2

description: Biological replicate 2 of 3. Control Candida albicans, grown in Spider+Glucose medium for 1 h.


title: sdh2△/△ cells vs SC5314 cells (Grown in Spider Medium) Replicate 2

description: Biological replicate 2 of 3. Control Candida albicans, grown in Spider medium for 1 h.


title: shRNA-DYRK2


title: WT_WW30m_replicate2

city: Jena

first: Klaus

last: Gase

address: Hans-Knoell-Strasse 8

department: Molecular Ecology

institute: Max-Planck-Institute for Chemical Ecology

description: Gene expression after 30 min of elicitation with Wounding + Water

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent platform GPL21138 for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) and at 37°C with GE Wash buffer 2 (Agilent) as outlined in the One-Color Microarray-Based Gene Expression Analysis manual (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Data was acquired with the Agilent Scan Control software (version A.7.0.1 for the B scanner) and extracted using the Agilent Feature Extraction software (version 9.5). Quantile normalization and log2 transformation was performed for all raw microarray data using the R package “Agi4x44PreProcess”. All probes with signal within 95% confidence interval of the signal of negative control probes were discared from down-stream analysis.  All replicated probes were averaged.

organism: Nicotiana attenuata

source_name: wild type plant leaves, 30 min, Wounding + Water elicitation, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp labeling kit (Agilent, Santa Clara, CA) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Hilden, Germany).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Seeds from N. attenuata wild type and ir-AOC plants were grown in the glasshouse under high-pressure sodium lamps (200-300 µmol s-1 m-2 light) with a day/night cycle of 16 h(26-28°C)/8 h(22-24°C) and 45 to 55% humidity.

extract_protocol: Total RNA was extracted from leaves using the Plant RNeasy kit (Qiagen, Hilden, Germany) and its quality checked by spectrophotometry (NanoDrop, Wilmington, DE). Genomic DNA was removed by DNAse treatment following commercial instructions (Turbo DNase; Ambion, Europe), RNA was cleaned up with RNeasy MinElute columns (Qiagen) and the RNA quality was checked with the RNA 6000 Nano kit (Agilent, Santa Clara, CA) using an Agilent 2100 Bioanalyzer (Agilent).

treatment_protocol: For elicitation treatment, leaves were wounded by rolling a fabric-pattern wheel three times on each side of the midvein and the wounds were supplemented with 20 microliters of FAC diluted 1/5 (v/v) in water.

value: wild type

value: elicitation with Wounding + Water

value: leaves


title: WT_FAC30m_replicate3

description: Gene expression after 30 min of elicitation with Wounding + FAC

source_name: wild type plant leaves, 30 min, Wounding + FAC elicitation, replicate 3

value: elicitation with Wounding + FAC


title: 18h +Isotype control sample 2

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in Partek Genomic Suite

source_name: 18h +Isotype control sample 2

label_protocol: Biotinylated cRNA were prepared with the TargetAmpTM Nano-gTM Biotin-aRNA Labeling Kit

extract_protocol: Total RNA from all cell samples was isolated using TRIzol Reagent (Invitrogen).

value: DesTCR mice (Tg(KB5.C20-TCR))

value: 8-16 weeks

value: splenic DesTCR T cells


title: WT_FAC30m_replicate1

source_name: wild type plant leaves, 30 min, Wounding + FAC elicitation, replicate 1


title: 4h +Isotype control sample 3

description: replicate 3

source_name: 4h +Isotype control sample 3


title: 4h +FcMR sample 3

description: replicate 3

source_name: 4h +FcMR sample 3


title: WT_WW30m_replicate1

source_name: wild type plant leaves, 30 min, Wounding + Water elicitation, replicate 1


title: 48h +FcMR sample 3

description: replicate 3

source_name: 48h +FcMR sample 3


title: 0h sample 5

description: replicate 5

source_name: 0h sample 5


title: WT_FAC30m_replicate2

source_name: wild type plant leaves, 30 min, Wounding + FAC elicitation, replicate 2


title: 0h sample 6

description: replicate 6

source_name: 0h sample 6


title: irAOC_WW30m_replicate3

source_name: irAOC plant leaves, 30 min, Wounding + Water elicitation, replicate 3

value: irAOC