title: time-course 1, - IWP-2 on days 2 and 3, day 3

description:
time-course 1, differentiating human ES cells induced with FGF + BMP + WNT, no IWP-2 added on days 2 and 3, day 3
SAMPLE 9


title: time-course 2, + IWP-2 on days 1 and 2, day 2

status: Public on Nov 12 2015

type: RNA

city: Münster

first: Boris

last: Greber

address: Von-Esmarch-Str. 54

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

description:
time-course 2, differentiating human ES cells induced with FGF + BMP + WNT, IWP-2 added on days 1 and 2, day 2
SAMPLE 16

hyb_protocol: 18 hours according to manufacturer's instructions (Illumina)

scan_protocol: Default settings on a HiScan SQ (Illumina)

data_processing: Cubic spline normalization with background subtration in GenomeStudio (Illumina)

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: differentiated cell line

label_protocol: Illumina TotalPrep RNA Amplification Kit (Life Technologies); 14h of in-vitro transcription

growth_protocol: Undifferentiated hPSCs were in chemically defined FTDA medium. Differentiation was induced upon replating cells on Matrigel-coated 24-well plates in a defined serum and serum albumin-free medium based on Knockout-DMEM

extract_protocol: Qiagen RNeasy columns with on-column DNA-digestion

treatment_protocol: Insulin was added to the cells on day 0 and withdrawn from day 1 onwards. Specific differentiation-inducing factors were: 10 ng/ml FGF2, 1 ng/ml BMP4, and 1µM CHIR00921 - all added during the first 24 hours of differentiation. WNT inhibitor IWP-2 (µM) was either added or not added on days 2 and 3 (time-course 1) or on days 1 and 2 (time-course 2)

tag: cell type

value: ES

tag: time-point

value: day 2


title: HB2_123_exp11

city: Cambridge

first: Suraj

last: Menon

address: Li Ka Shing Center, Robinson Way

country: United Kingdom

institute: Cambridge Research Institute, Cancer Research UK

description: Human cells with treated with control and GNG12-AS1 siRNA against exon1, exon7 or exon9 to find differentially expressed genes after knock-down of lncRNA GNG12-AS1.

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The bead-level data were preprocessed using BASH (Cairns et al. (2008) Bioinformatics 24(24):2921-2), a function from the beadarray package (Dunning et al (2007) Bioinformatics 23(16):2183-4) in Bioconductor, and also log base 2 transformed and quantile normalised using the beadarray package.

source_name: Human mammary epithelial cells (HB2)

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

growth_protocol: Human mammary epithelial cells (HB2 cell line) were cultured in Dulbecco’s modified Eagle’s medium (DMEM, GIBCO) supplemented with 10% Fetal bovine serum (FBS), 10 ml/l penicillin-streptomycin solution (P/S), 5 mg/ml insulin (Sigma), and 1 mg/ml hydrocortisone (HC, Sigma). The cells were from American Type Culture Collection (ATCC) and were cultured at 37 °C with 5% CO2.

extract_protocol: RNA was extracted and reverse transcribed with the RNeasy Kit and the QuantiTect Reverse Transcription Kit (QIAGEN). Quantitative real-time PCR was performed on a 7900HT Fast Real-Time PCR System (Applied Biosystems) with Fast SYBR Green Master Mix (Invitrogen).

treatment_protocol: The cells were transfected with control siRNA (Life Technologies, 4390084) and GNG12-AS1 siRNAs targeting different exons (exon 1, exon 7 and exon 9, Life Technologies, Silencer select) using DharmaFECT 3 (Thermo-Scientific) transfection reagent following the manufacturer's instructions. RNA was collected 48 hr after transfection. The siRNAs were used at a final concentration of 50 nM.

tag: samplegroup

tag: cell line

value: mammary epithelial


title: time-course 1, + IWP-2 on days 2 and 3, day 4

description:
time-course 1, differentiating human ES cells induced with FGF + BMP + WNT, IWP-2 added on days 2 and 3, day 4
SAMPLE 5

value: day 4


title: time-course 1, day 0

description:
time-course 1, undifferentiated human ES cells (line HuES6)
SAMPLE 1

source_name: cultured cell line

value: day 0


title: HB2_122_exp11


title: time-course 2, day 0

description:
time-course 2, undifferentiated human ES cells (line HuES6)
SAMPLE 14


title: HB2_122_exp9


title: HB2_control_exp11

value: Control_ siRNA


title: HB2_control_exp5


title: time-course 1, day 1

description:
time-course 1, differentiating human ES cells induced with FGF + BMP + WNT, day 1
SAMPLE 2

value: day 1


title: HB2_62_exp9


title: HB2_123_exp9


title: HB2_62_exp7

value: GNG12-AS1 SiRNA_exon1


title: HB2_122_exp1

value: GNG12-AS1 SiRNA_exon7


title: SUM159_control_exp9

source_name: Human breast cancer cell line (SUM159)

growth_protocol: SUM159 cells were cultured in Ham’s F-12 medium (GIBCO) supplemented with 5% FBS, 5 mg/ml insulin, and 1 mg/ml HC. The cells were from American Type Culture Collection (ATCC) and were cultured at 37 °C with 5% CO2.

treatment_protocol: The cells were transfected with control siRNA (Life Technologies, 4390084) and GNG12-AS1 siRNAs targeting different exons (exon 1, exon 7 and exon 9, Life Technologies, Silencer select) using DharmaFECT 1 (Thermo-Scientific) transfection reagent following the manufacturer's instructions. RNA was collected 48 hr after transfection. The siRNAs were used at a final concentration of 50 nM.

value: breast cancer


title: HB2_62_exp1


title: HB2_control_exp9


title: HB2_122_exp3


title: HB2_control_exp3


title: HB2_control_exp1


title: HB2_62_exp3


title: HB2_control_exp7


title: SUM159_62_exp9


title: HB2_122_exp7


title: HB2_123_exp3

value: GNG12-AS1 SiRNA_exon9


title: SUM159_123_exp9


title: HB2_123_exp1


title: HB2_123_exp7


title: SUM159_122_exp8


title: SUM159_123_exp8


title: 31_rrp6

city: Worcester

first: Craig

middle: L

last: Peterson

state: MASSACHUSETTS

address: 373 Plantation Street

department: Program in Molecular Medicine

country: USA

institute: University of Massachusetts Medical School

hyb_protocol: Hybridizations were carried out at 45C for 16 h with 60 rpm rotation. The staining was carried out using the GeneChip Hybridization. Wash and Stain kit with fluidics protocol FS450_0001 in an Affymetrix Fluidics station

scan_protocol: standard protocol

data_processing:
tilingArray package from Bioconductor; R
sup3_MR.txt and normProbeIntensity.txt.gz
sup3_MR.txt contains annotations and processed signal intensities and normProbeIntensity contains the raw probe intensities for all the arrays individually.
Please note that data from previously published work (Tan-Wong et al. 2012) is included in the processed file and includes the column names "wt_gl", "rrp6_gl", "ssu72_rrp6", "ssu72", although we have excluded the corresponding raw data for this.

organism: Saccharomyces cerevisiae

source_name: Budding yeast cells

label_protocol: First-strand cDNA was purified using the MinElute PCR purification kit (Qiagen) and 5 ug were fragmented and labeled using the GeneChip WT Terminal labeling kit (Affymetrix) according to manufacturers protocol. The labelled cDNA samples were denatured in a volume of 300 ul containing 50 pM control oligonucleotide B2 (Affymetrix) and Hybridization mix (GeneChip Hybridization, Wash and Stain kit, Affymetrix) of which 250 ul were hybridized per array (S. cerevisiae yeast tiling array, Affymetrix, PN 520055).Actinomycin D- to ensure strand specificity of the tiling array data (to inhibit second strand synthesis during the amplification step).

growth_protocol: 50ml of yeast grown in YEP + 2% glucose media at 30˚C were harvested at an OD600 of 0.8- 0.1 (log phase). All cultures were from freshly streaked strains from glycerol stocks stored at -80C. All strains were made by yeast dissections to avoid picking up growth suppressors.

extract_protocol: Cells were lysed by vortexing with glass beads in the presence of hot phenol (pH 4.0) and RNA was exrtacted using multiple phenol:chloroform: isoamyl alcohol and chloroform:isoamyl alcohol extractions, followed by ethanol precipitation.

treatment_protocol: Cultures were flash frozen with liquid nitrogen prior to RNA preparation, typically done within the couple of weeks.

tag: cell density

value: Log phase (OD= 1.0)

tag: cell cycle stage

value: Asynchronous

tag: strain


title: 32_rrp6


title: 34_swr1


title: SUM159_control_exp8


title: SUM159_122_exp9


title: 33_swr1


title: SUM159_62_exp8


title: 24_rtt109


title: 25_rtt109


title: SUM159_123_exp7


title: 23_rtt109


title: 22_swr1_rrp6


title: time-course 2, - IWP-2 on days 1 and 2, day 6

description:
time-course 2, differentiating human ES cells induced with FGF + BMP + WNT, no IWP-2 added on days 1 and 2, day 6
SAMPLE 26

value: day 6


title: SUM159_123_exp6


title: 21_swr1_rrp6


title: 30_rrp6


title: SUM159_122_exp7


title: SUM159_62_exp6


title: 20_swr1_rrp6


title: SUM159_122_exp2


title: SUM159_123_exp2


title: 17_swr1_rrp6


title: 15_swr1_rtt109


title: SUM159_122_exp6


title: 16_swr1_rrp6


title: SUM159_62_exp7


title: 14_swr1_rtt109


title: SUM159_122_exp1


title: 12_rtt109_rrp6


title: SUM159_62_exp2


title: SUM159_control_exp6


title: 13_swr1_rtt109


title: 10_rtt109_rrp6


title: 11_rtt109_rrp6


title: SUM159_control_exp2


title: 9_rtt109_rrp6


title: SUM159_123_exp1


title: SUM159_control_exp1


title: SUM159_control_exp7


title: SUM159_62_exp1


title: 7_swr1_rtt109_rrp6


title: S4-Th2-6d rep2

city: Linköping

first: Danuta

last: Gawel

address: Garnisonsvägen

country: Sweden

institute: Linköping University

hyb_protocol: For Th1 and Th2 cells the gene expression microarray analysis was performed using SurePrint G3 Human Gene Expression 8x60K microarray kit, according to the manufacture’s instruction (Agilent Technologies).

scan_protocol: standard Agilent protocol

data_processing: raw data were quantile normalized

source_name: Naïve CD4+ T cells isolated from buffy coat polarised towards Th2 cells.

label_protocol: The cRNA was prepared using a Low Input QuickAmp Labeling Kit.

extract_protocol: RNA was extracted using a miRneasy Mini Kit (Qiagen).

treatment_protocol: Naïve CD4+ T cells were stimulated with plate-bound anti-CD3 (500 ng/mL), soluble anti-CD28 (500 ng/mL), in the presence of IL-12 (5 ng/mL), IL-2 (10 ng/mL) and anti–IL-4 (5 µg/mL) for Th1, IL-4 (10 ng/mL), IL-2 (10 ng/mL) and anti-IL-12 (5 µg/mL) and anti–IFN-g (5 µg/mL) for Th2, TGF-β (1 ng/mL). Cells were cultured for six days in Iscove’s modified Dulbecco medium (IMDM) supplemented with 2 mM L-glutamine (PAA Laboratories, Linz, Austria), 10% heat-inactivated FCS (PAA Laboratories, Linz, Austria), 5 µM β–mercaptoethanol (Sigma-Aldrich, St. Louis, Missouri, USA) and 50 ug/mL gentamicin (Sigma-Aldrich, St. Louis, Missouri, USA). Cells were cultured for 6 days and then re-stimulated with plate-bound anti-CD3 and soluble anti-CD28 in the presence of corresponding polarizing cytokines and antibodies for another 2 days (Zhang et al. 2013).

tag: time


title: 5_swr1_rtt109_rrp6


title: S4-Th2-8d


title: S3-Th1-8d

source_name: Naïve CD4+ T cells isolated from buffy coat polarised towards Th1 cells.


title: S4-Th2-24h


title: S4-Th2-6d rep1


title: S3-Th2-6d rep2


title: 6_swr1_rtt109_rrp6


title: S4-Th2-3d


title: 8_rtt109_rrp6


title: S4-Th2-6h


title: 37_wt

value: wild type


title: S4-Th1-6d


title: S3-Th1-6d


title: 36_wt


title: S4-Th1-6h


title: S4-Th1-8d


title: S3-Th2-3d


title: S4-Th1-24h


title: S3-Th2-24h


title: S4-Naive T

source_name: Naïve CD4+ T cells isolated from buffy coat.

value: Naive T


title: 35_wt


title: S4-Th1-3d


title: S3-Th1-6h


title: S1-Th2-8d


title: S2-Th1-8d


title: S3-Th2-6h


title: S3-Naive T


title: S2-Th2-6h


title: S2-Th2-24h


title: S1-Th2-3d


title: S2-Th2-8d


title: S2-Th1-3d


title: S3-Th2-6d rep1


title: S3-Th1-3d


title: S1-Th1-6d


title: S1-Th2-6d rep2


title: S1-Th1-8d


title: S2-Th2-6d rep2


title: S2-Th1-24h


title: S2-Th1-6h


title: S2-Th2-6d rep1


title: S2-Th1-6d


title: S2-Th2-3d


title: S1-Th2-6h


title: S1-Th2-6d rep1


title: S2-Naive T


title: B152_ES

city: Jerusalem

first: Uri

last: Ben-David

address: Givat-Ram

department: Genetics

country: Israel

institute: Hebrew University

description: gene expression data from undifferentiated pluripotent stem cells

hyb_protocol: Affymetrix protocol, 11ug cRNA

scan_protocol: GeneChip scanner 3000 7G, GeneChip Operating Software v1.4

data_processing: Affymetrix Expression Console MAS5

source_name: B152 undifferentiated cells

label_protocol: 200ng total RNA, Affymetrix protocol

growth_protocol: Cells were grown on gelatin-coated plates using Knockout DMEM supplemented with 15 % FBS (Hyclone), 5% KnockOutTM Serum Replacement (Invitrogen), 1 mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1 mM beta-mercaptoethanol (Sigma) and 8 ng/ml FGF2 (R&D systems)].  Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml).

extract_protocol: total RNA from was isolated using 5 Prime RNA isolation kit

treatment_protocol: total RNA was isolated from undifferentiated pluripotent stem cells grownon on MEFs with standard human ES culture medium

value: Undifferentiated human embryonic stem cells

tag: genotype


title: S1-Th1-24h


title: S1-Th1-3d


title: S1-Naive T


title: hIPS18_WT p5 CM

source_name: HiPS18 undifferentaited cells

treatment_protocol: total RNA was isolated from undifferentiated pluripotent stem cells grown with MEF-conditioned human ES culture medium

value: Undifferentiated human induced pluripotent stem cells


title: S1-Th2-24h


title: S1-Th1-6h


title: B123p15-ES

source_name: B123 undifferentiated cells


title: B105_ ES

source_name: B105 undifferentiated cells


title: B200p13-ES

source_name: B200 undifferentiated cells


title: S_2_v2_2

hyb_protocol: The expression microarray analyses were performed using Agilent SurePrint G3 Human Exon 4x180K Microarrays according to the manufacturer's instructions.

scan_protocol: not provided

source_name: CD4+ T cells isolated from buffy coat polarized towards Th2 cells

label_protocol: The cRNA was prepared using a Low Input QuickAmp Labeling Kit

extract_protocol: RNA was extracted using a miRneasy Mini Kit (Qiagen). The RNA concentrations were analysed with NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies).Cells were also transfected with non-targeting siRNA (Thermo Scientific) or with buffer. An optimized transfection protocol for the Amaxa system has been published (Freeley and Long 2013).

treatment_protocol: CD4+ Naïve T (NT) cells were extracted. Two repeats for four siRNA vectors (J-003746-07, J-003746-08, J-003746-09, and J-003746-10 predicted to target MAF; ThermoFisherScientific Inc, Waltham, MA USA) were performed (Table S6). For the knock downs, “Nuclefector Kits for Human T Cells” (Lonza, Vallensbak Strand, Denmark) were used. The human CD4+ naïve T cells were transfected in a cuvette with 600 nM of the corresponding siRNA with the Amaxa nucleofection program U-014 as previously described (Bruhn et al. 2012). Five hours after the nucleofection cells were washed, activated and polarized towards Th2 for 24 hours.

tag: vector type

tag: subject


title: S_2_v4


title: S_2_v1


title: S_3_NON_1

value: non-targeting


title: S_3_NON_2


title: S_2_v3


title: S_1_v3


title: MeDIP_E9.5 G9aKO-Rep3

type: genomic

city: Illkirch

first: Michael

last: Weber

address: 300 Bd Sebastien Brant

department: UMR7242 Biotechnology and Cell Signalling

country: France

institute: CNRS

description: MeDIP in G9a-/- E9.5 embryos

hyb_protocol: Hybridization was performed according to standard procedures by Roche Nimblegen.

scan_protocol: Scanning was performed according to standard procedures by Roche Nimblegen.

data_processing:
Data processing and calculations were performed with the R computing software (version 3.0.0) as described (Borgel et al. Nature Genetics 2010 42:1093-1100). First, we calculated MeDIP/Input log2 ratios for each oligonucleotide from raw fluorescence values provided by Roche Nimblegen. All datasets were then normalized using an intra-array loess normalization and an inter-array quantile normalization to have equal normal distributions between arrays using the limma package (version 2.18.2).
normalized log2 (MeDIP/Input) ratio after loess normalization and quantile normalization

molecule: genomic DNA

organism: Mus musculus

source_name: MeDIP DNA from E9.5 G9a-/- embryos

label_protocol: Labeling was performed according to standard procedures by Roche Nimblegen.

extract_protocol: Genomic DNA was extracted by proteinase K digestion followed by phenol/chloroform extraction. Sonication of DNA was performed with a Diagenode Bioruptor apparatus. MeDIP was performed on 200 ng sonicated DNA as described (Borgel et al. Nature Genetics 2010 42:1093-1100), using a anti-5mC antibody from Serotec (catalog no. MCA2201, monoclonal clone 33D3, 1mg/ml). Subsequently, 5ng input DNA and the entire MeDIP product were amplified with the Whole Genome Amplification kit (Sigma-Aldrich) following the manufacturer’s instructions.

tag: embryo stage

tag: gender

value: mixed

tag: antibody

value: 5mC (Serotec)

source_name: Input DNA from E9.5 G9a-/- embryos

value: None, input DNA


title: NC rep5

city: Barcelona

first: Jordi

last: Sintes

address: Dr Aiguader 88

department: B cell Biology

country: Spain

institute: IMIM

hyb_protocol: After fragmentation, 600 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wahs buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 5um resolution and 100%PMT

data_processing: The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).  Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

source_name: Blood

label_protocol: 100ng of total RNA from each sample were amplified by Oligo-dT-T7 reverse transcription and labeled by in vitro transcription with T7 RNA polymerase in the presence of Cy3-CTP using the LowInputQuick Amp Labeling kit  (Agilent 5190-2305) and purified using RNAeasy columns (Qiagen, Hilden, Germany)

growth_protocol: No growth

extract_protocol: High Pure RNA Isolation Kit (Roche)

treatment_protocol: Unstimulated

value: circulating neutrophils (NC cells)


title: NC rep6


title: MeDIP_E9.5 G9aKO-Rep1

description: MeDIP in G9a-/- E9.5 embryos


title: S3-Th1-24h


title: S_1_v4


title: MeDIP_E9.5 WT-Rep2

description: MeDIP in WT E9.5 embryos

source_name: MeDIP DNA from E9.5 WT embryos

source_name: Input DNA from E9.5 WT embryos


title: S_1_v1


title: MeDIP_E9.5 G9aKO-Rep2

description: MeDIP in G9a-/- E9.5 embryos


title: MeDIP_E9.5 WT-Rep3

description: MeDIP in WT E9.5 embryos


title: MeDIP_E9.5 WT-Rep1

description: MeDIP in WT E9.5 embryos


title: NC rep2


title: NC rep3


title: S_2_NON_1


title: NBH rep4

source_name: Spleen

value: splenic neutrophils (NBH cells)


title: NC rep1


title: NC rep4


title: S_2_NON_2


title: NBH rep3


title: S_2_v2_1


title: S3-Th2-8d


title: NBH rep1


title: NBH rep5


title: NBH rep2


title: RAM1 control 6h roots biological replicate 3

city: Hannover

first: Helge

last: Küster

address: Herrenhäuser Str. 2

department: Institut für Pflanzengenetik

institute: Leibniz Universität Hannover

description: Gene expression data from Medicago truncatula RAM1 plantlet roots treated with control solution

hyb_protocol: 10 μg of fragmented aRNA was added to a 300-μl hybridization cocktail also containing hybridization controls. 200 μl of the mixture was hybridized on GeneChips for 16 h at 45°C. Standard post hybridization wash and double-stain protocols (FS450_0001; GeneChip HWS kit; Affymetrix, Santa Clara, CA, USA) were used on an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned on an Affymetrix GeneChip scanner 3000 7G.

data_processing: Cel files obtained from Medicago GeneChip hybridizations were analysed using the Robin software (http://mapman.gabipd.org/web/guest/robin). Normalization was performed using the Robust Multichip Average (RMA) algorithm. Intensity values calculated for each probe set were log2-transformed and averaged across all three biological replicates. Log2 differences between the conditions studied were evaluated statistically via Students t-tests implemented in Robin.

organism: Medicago truncatula

label_protocol: RNA was processed for use on Affymetrix (Santa Clara, CA, USA) GeneChip Medicago Genome Arrays, according to the manufacturer’s GeneChip 3’ IVT Express kit user manual. Briefly, 100 ng of total RNA with by a RIN number (Agilent 2100 Bioanalyzer, Agilent, Böblingen, Germany) of at least 9.0 containing spiked-in poly-A+ RNA controls was used in a reverse transcription reaction (GeneChip 3’ IVT Express Kit; Affymetrix) to generate first-strand cDNA. After secondstrand synthesis, double-stranded cDNA was used in a 16 h in vitro transcription (IVT) reaction to generate aRNA (GeneChip 3’ IVT Express Kit; Affymetrix). Size distribution of in vitro transcribed aRNA and fragmented aRNA, respectively, was assessed via an Agilent 2100 Bioanalyzer, using an RNA 6000 Nano Assay.

growth_protocol: Medicago truncatula Gaertn cv Jemalong seeds were surface-sterilized and scarified. Plates with M. truncatula seeds were incubated for 24 hours in the climate chamber (humidity: 70 %; photosynthetic photon flux: 150 μmol m-2 s-1) at a 16 h light (23 °C) and 8 h dark (18 °C) regime. Subsequently, seedlings were moisturized with sterile water (pH 7.0) to allow careful removal of seed coats. In each case, eight seedlings were put on the upper quarter of a 2.5 % (w/v) phytoagar (Duchefa Biochemie, Haarlem, The Netherlands) slant plate (120 x 120 mm; DoctorLab, Jena, Germany). Seedlings used for treatment with Nod-LCOs and corresponding controls were put on plates with NH-mix (Baier et al. 2007). An approximately one cm strap of Whatman paper (Schleicher & Schuell, Dassel, Germany) soaked with appropriate nutrient solutions as described above was used to fix the seedlings on the plates beneath the cotyledons. Three plates at a time were sealed with transparent wrapping foil, which was cut at the upper side to allow gas exchange. The lower half of each plate stack was wrapped with aluminium foil for light protection to allow normal root development. Each triple pack of plates was placed in an approximately 70° angle in the climate chamber for five days.

extract_protocol: Ten root fragments per biological relicate were pooled and ground using lysing matrix D tubes (MP Biomedicals, Illkirch, France) in a FastPrep (MP Biomedicals, Illkirch, France) prior to RNA extraction. Total RNA isolation and DNaseI on-column digestion was performed via RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. RNA preparations were quality-checked both via spectrophotometry (NanoDrop ND-1000, Peqlab, Erlangen, Germany) and capillary electrophoresis (RNA Nano chips, Agilent Bioanalyzer, Agilent, Böblingen, Germany), as recommended by the manufacturers.

treatment_protocol: Plantlets were carefully removed from slant agar plates and placed in 13 mL tubes wrapped with aluminium foil that were cut off at the 8 mL mark, using 10 plantlets per tube (Sarstedt, Nürnbrecht, Germany). Each tube contained 5 mL of the following solutions: Nod-LCO solution (NH-mix of pH 7.5 containing 10-8 M Nod-LCOs), Nod control solution (NH-mix of pH 7.5). After 6 h of incubation in the climate chamber, 10 plantlets per batch were removed from the treatment or control solutions and harvested.

tag: tissue

value: Root

value: Jemalong A17 (RAM1 mutant)

tag: age

value: 10 days


title: RAM1 control 6h roots biological replicate 1

source_name: Medicago truncatula RAM1 plantlet roots treated with control solution


title: Berry_skin_SM-WD-rep1

city: Reno

first: Grant

last: Cramer

state: Nevada

address: 1664 N. Virginia St

department: Biochemistry & Molecular Biology

institute: University of Nevada, Reno

description:
SMD1
This sample is from Vitis vinifera L. cv. Semillon berry skins, under water deficit (stress) conditions. It is the first of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.

hyb_protocol: Labeled cDNA was hybridized to a NimbleGen microarray 090818 Vitis exp HX12 (Roche, NimbleGen Inc., Madison, WI, USA), which contains probes targeted to 29,549 grapevine genes predicted from the V1 annotation of the 12x grapevine genome (http://srs.ebi.ac.uk/), and 19,091 random probes as negative controls.

scan_protocol: Each microarray was scanned using an Axon GenePix 4400A (Molecular Devices, Sunnyvale, CA, USA) at 532 nm (Cy3 absorption peak) and GenePix Pro7 software (Molecular Devices) according to the manufacturer’s instructions.

data_processing: Images were analyzed using NimbleScan v2.5 software (Roche), which produces pair files containing the raw signal intensity data for each probe and calls files with normalized expression data derived from the average of the intensities of the four probes for each gene.

organism: Vitis vinifera

source_name: Vitis vinifera L. cv. Semillon, harvested berry skin, water deficit

label_protocol: cDNA synthesis and labeling reactions were performed according to the NimbleGen Arrays User's Guide (V 3.2).

growth_protocol: Berries from five grapevine (Vitis vinifera L.) cultivars, Cabernet Sauvignon, Merlot, Pinot Noir, Chardonnay and Semillon, were harvested during the fall of 2011 from the University of Nevada, Reno experimental vineyards. The North Vineyard was divided in half and separated into 15 rows (5-well watered; 10-drought stressed), with Chardonnay on the northern half and Cabernet Sauvignon on the southern half. Each row in the North Vineyard maintained 23 vines of each cultivar. The South Vineyard was divided into six blocks (A-F). Each block contained four rows divided into thirds, with 15 vines of a given cultivar in each third. Merlot, Pinot Noir & Semillon vines were grown in each block. Blocks A, C & D were well watered, and blocks B, E & F were treated with water deficit. Rows in each of the experimental vineyards were planted in a north to south orientation, to achieve nearly maximal daily sunlight exposure.

extract_protocol: Skins were separated from harvested berry clusters by squeezing each berry onto a kim wipe to remove pulp before flash freezing with liquid nitrogen for all berries on the clusters of each biological replicate. Separated skins of all the berries of each biological replicate were pooled and ground in a frozen mortar and pestle. Total RNA was extracted from the finely ground skins and pulp in liquid nitrogen using a modified CTAB extraction. The total RNA was further purified using a Qiagen RNeasy Plant Mini Kit according to the manufacturers’ instructions. RNA quality and quantity were determined using a NanoDrop 2000 spectrophotometer (Thermo Scientific) and a Bioanalyzer Chip RNA 7500 series II (Agilent).

treatment_protocol: Vines were drip irrigated with 8 l h-1 emitters and grown under well-watered or water deficit conditions post-fruit set. Mid-day stem water potentials were measured weekly with a pressure chamber (3005 Plant Water Status Console, Soil Moisture Corp., Goleta, CA, USA), as in [31], on fully mature leaves to assess plant water status throughout the growing season [106, 107]; stem water potential measurements were averaged across cultivars, because no significant differences in stem water potentials amongst the cultivars could be detected. Following weekly measurements, water was either applied or withheld in an effort to maintain a mild water deficit treatment at ~ -0.8 MPa and -0.6 MPa for control vines.

tag: cultivar

value: Semillon

tag: vineyard location

value: Reno, NV, USA

tag: year

value: berry skin

tag: treatment

value: water deficit


title: Berry_skin_SM-WW-rep3

description:
SMW3
This sample is from Vitis vinifera L. cv. Semillon berry skins, under well-watered (control) conditions. It is the third of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.

source_name: Vitis vinifera L. cv. Semillon, harvested berry skin, well-watered

value: well-watered


title: Berry_skin_SM-WD-rep6

description:
SMD6
This sample is from Vitis vinifera L. cv. Semillon berry skins, under water deficit (stress) conditions. It is the five of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.


title: Berry_skin_SM-WD-rep4

description:
SMD4
This sample is from Vitis vinifera L. cv. Semillon berry skins, under water deficit (stress) conditions. It is the three of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.


title: Berry_skin_PN-WD-rep5

description:
PND5
This sample is from Vitis vinifera L. cv. Pinot Noir berry skins, under water deficit (stress) conditions. It is the five of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.

source_name: Vitis vinifera L. cv. Pinot Noir, harvested berry skin, water deficit

value: Pinot Noir


title: RAM1 control 6h roots biological replicate 2


title: RAM1 Nod-LCOs 6h roots biological replicate 2

description: Gene expression data from Medicago truncatula RAM1 plantlet roots treated with Nod-LCOs


title: RAM1 Nod-LCOs 6h roots biological replicate 3

source_name: Medicago truncatula RAM1 plantlet roots treated with Nod-LCOs


title: RAM1 Nod-LCOs 6h roots biological replicate 1


title: Berry_skin_SM-WD-rep3

description:
SMD3
This sample is from Vitis vinifera L. cv. Semillon berry skins, under water deficit (stress) conditions. It is the second of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.


title: Berry_skin_SM-WW-rep2

description:
SMW2
This sample is from Vitis vinifera L. cv. Semillon berry skins, under well-watered (control) conditions. It is the second of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.


title: Berry_skin_SM-WW-rep6

description:
SMW6
This sample is from Vitis vinifera L. cv. Semillon berry skins, under well-watered (control) conditions. It is the fifth of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.


title: NSP1 control 6h roots biological replicate 3

description: Gene expression data from Medicago truncatula NSP1 plantlet roots treated with control solution

value: Jemalong A17 (NSP1 mutant)


title: Berry_skin_SM-WD-rep5

description:
SMD5
This sample is from Vitis vinifera L. cv. Semillon berry skins, under water deficit (stress) conditions. It is the four of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.


title: NBH rep6

tag: cell type


title: NSP1 control 6h roots biological replicate 2

source_name: Medicago truncatula NSP1 plantlet roots treated with control solution


title: Berry_skin_PN-WD-rep4

description:
PND4
This sample is from Vitis vinifera L. cv. Pinot Noir berry skins, under water deficit (stress) conditions. It is the four of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.


title: Berry_skin_SM-WW-rep4

description:
SMW4
This sample is from Vitis vinifera L. cv. Semillon berry skins, under well-watered (control) conditions. It is the fourth of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.


title: NSP1 control 6h roots biological replicate 1


title: Berry_skin_PN-WD-rep2

description:
PND2
This sample is from Vitis vinifera L. cv. Pinot Noir berry skins, under water deficit (stress) conditions. It is the second of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.


title: Berry_skin_PN-WD-rep1

description:
PND1
This sample is from Vitis vinifera L. cv. Pinot Noir berry skins, under water deficit (stress) conditions. It is the first of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.


title: Berry_skin_PN-WW-rep4

description:
PNW4
This sample is from Vitis vinifera L. cv. Pinot Noir berry skins, under well-watered (control) conditions. It is the third of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.

source_name: Vitis vinifera L. cv. Pinot Noir, harvested berry skin, well-watered


title: Berry_skin_SM-WW-rep1

description:
SMW1
This sample is from Vitis vinifera L. cv. Semillon berry skins, under well-watered (control) conditions. It is the first of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.


title: Berry_skin_PN-WW-rep5

description:
PNW5
This sample is from Vitis vinifera L. cv. Pinot Noir berry skins, under well-watered (control) conditions. It is the fourth of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.


title: S3-Treg-6d

hyb_protocol: For Th17 and Treg cells the gene expression microarray analysis was performed using SurePrint G3 Human Gene Expression 8x60K v2 microarray kit, according to the manufacture’s instruction (Agilent Technologies)

source_name: Naïve CD4+ T cells isolated from buffy coat polarised towards Treg cells.

extract_protocol: RNA was extracted using a miRneasy Mini Kit (Qiagen). The RNA concentrations were analysed with NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies).

treatment_protocol: Naïve CD4+ T cells were stimulated with TGF-β (1 ng/mL), IL-1β (10 ng/mL), IL-6 (25 ng/mL), IL-21 (25 ng/mL) and IL-23 (25 ng/mL) for Th17, and TGF-β (10 ng/mL) and IL-2 (10 ng/mL) for Treg. Cells were cultured for six days in Iscove’s modified Dulbecco medium (IMDM) supplemented with 2 mM L-glutamine (PAA Laboratories, Linz, Austria), 10% heat-inactivated FCS (PAA Laboratories, Linz, Austria), 5 µM β–mercaptoethanol (Sigma-Aldrich, St. Louis, Missouri, USA) and 50 ug/mL gentamicin (Sigma-Aldrich, St. Louis, Missouri, USA). Cells were cultured for 6 days and then re-stimulated with plate-bound anti-CD3 and soluble anti-CD28 in the presence of corresponding polarizing cytokines and antibodies for another 2 days (Zhang et al. 2013).

value: Treg


title: NSP1 Nod-LCOs 6h roots biological replicate 1

description: Gene expression data from Medicago truncatula NSP1 plantlet roots treated with Nod-LCOs


title: NSP1 Nod-LCOs 6h roots biological replicate 2

source_name: Medicago truncatula NSP1 plantlet roots treated with Nod-LCOs


title: DMI3 control 6h roots biological replicate 2

description: Gene expression data from Medicago truncatula DMI3 plantlet roots treated with control solution

value: Jemalong A17 (DMI3 mutant)


title: CS77P_DiL

source_name: Peripheral blood mononuclear cells (PBMCs)

extract_protocol: Total RNA was extracted using a miRneasy Mini Kit (Qiagen, Valencia, CA, USA).

treatment_protocol: PBMCs were stimulated with allergen extract (ALK-Abelló A/S; 100 μg/ml) or diluent (PBS) in RPMI 1640 supplemented with 2 mM L-glutamine (PAA Laboratories, Linz, Austria), 5% human AB serum (Lonza, Switzerland), 5 µM β–mercaptoethanol (Sigma-Aldrich, St. Louis, Missouri, USA) and 50 µg/mL gentamicin (Sigma-Aldrich, St. Louis, Missouri, USA). After 17 hours of incubation, total CD4+ T cells were enriched from PBMCs by MACS negative sorting.

value: PBMC

tag: disease state

value: allergic rhinitis

tag: subject class

value: Patient

tag: stimulation

value: Diluent


title: Berry_skin_PN-WD-rep3

description:
PND3
This sample is from Vitis vinifera L. cv. Pinot Noir berry skins, under water deficit (stress) conditions. It is the three of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.


title: CS77P_AC

value: Allergen


title: DMI3 Nod-LCOs 6h roots biological replicate 3

description: Gene expression data from Medicago truncatula DMI3 plantlet roots treated with Nod-LCOs

value: Root


title: DMI3 control 6h roots biological replicate 3

source_name: Medicago truncatula DMI3 plantlet roots treated with control solution


title: Berry_skin_PN-WW-rep6

description:
PNW6
This sample is from Vitis vinifera L. cv. Pinot Noir berry skins, under well-watered (control) conditions. It is the fifth of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.


title: Berry_skin_PN-WW-rep2

description:
PNW2
This sample is from Vitis vinifera L. cv. Pinot Noir berry skins, under well-watered (control) conditions. It is the first of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.


title: Berry_skin_PN-WW-rep3

description:
PNW3
This sample is from Vitis vinifera L. cv. Pinot Noir berry skins, under well-watered (control) conditions. It is the second of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.


title: Berry_skin_ME-WD-rep5

description:
MED5
This sample is from Vitis vinifera L. cv. Merlot berry skins, under water deficit (stress) conditions. It is the four of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.

source_name: Vitis vinifera L. cv. Merlot, harvested berry skin, water deficit

value: Merlot


title: S3-Treg-24h

tag: time


title: NSP1 Nod-LCOs 6h roots biological replicate 3

tag: genotype

value: 10 days


title: Berry_skin_ME-WD-rep1

description:
MED1
This sample is from Vitis vinifera L. cv. Merlot berry skins, under water deficit (stress) conditions. It is the first of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.


title: CS33H_AC

value: Healthy


title: CS33H_Dil


title: DMI3 control 6h roots biological replicate 1


title: Berry_skin_ME-WD-rep2

description:
MED2
This sample is from Vitis vinifera L. cv. Merlot berry skins, under water deficit (stress) conditions. It is the second of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.

value: Reno, NV, USA


title: S3-Treg-3d


title: Berry_skin_ME-WD-rep3

description:
MED3
This sample is from Vitis vinifera L. cv. Merlot berry skins, under water deficit (stress) conditions. It is the three of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.

value: berry skin


title: DMI3 Nod-LCOs 6h roots biological replicate 1

source_name: Medicago truncatula DMI3 plantlet roots treated with Nod-LCOs


title: Berry_skin_ME-WW-rep5

description:
MEW5
This sample is from Vitis vinifera L. cv. Merlot berry skins, under well-watered (control) conditions. It is the fifth of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.

source_name: Vitis vinifera L. cv. Merlot, harvested berry skin, well-watered


title: Berry_skin_ME-WD-rep6

description:
MED6
This sample is from Vitis vinifera L. cv. Merlot berry skins, under water deficit (stress) conditions. It is the five of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.

value: water deficit


title: S3-Th17-3d

source_name: Naïve CD4+ T cells isolated from buffy coat polarised towards Th17 cells.


title: DMI3 Nod-LCOs 6h roots biological replicate 2


title: CS11H_AC


title: S3-Treg-6h


title: Berry_skin_ME-WW-rep4

description:
MEW4
This sample is from Vitis vinifera L. cv. Merlot berry skins, under well-watered (control) conditions. It is the fourth of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.

value: well-watered


title: CS71P_AC


title: CS71P_Dil


title: Berry_skin_ME-WW-rep2

description:
MEW2
This sample is from Vitis vinifera L. cv. Merlot berry skins, under well-watered (control) conditions. It is the second of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.


title: S3-Th17-6h


title: S3-Th17-6d


title: S3-Th17-24h


title: NFP control 6h roots biological replicate 3

description: Gene expression data from Medicago truncatula NFP plantlet roots treated with control solution

value: Jemalong A17 (NFP mutant)


title: NFP control 6h roots biological replicate 2

source_name: Medicago truncatula NFP plantlet roots treated with control solution


title: CS11H_Dil


title: S2-Treg-6d


title: NFP Nod-LCOs 6h roots biological replicate 3

description: Gene expression data from Medicago truncatula NFP plantlet roots treated with Nod-LCOs


title: Berry_skin_ME-WW-rep1

description:
MEW1
This sample is from Vitis vinifera L. cv. Merlot berry skins, under well-watered (control) conditions. It is the first of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.


title: NFP control 6h roots biological replicate 1


title: Berry_skin_ME-WW-rep3

description:
MEW3
This sample is from Vitis vinifera L. cv. Merlot berry skins, under well-watered (control) conditions. It is the third of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.


title: S2-Treg-24h


title: NFP Nod-LCOs 6h roots biological replicate 1

source_name: Medicago truncatula NFP plantlet roots treated with Nod-LCOs


title: CS80H_Dil


title: WT control roots 6h biological replicate 2

description: Gene expression data from Medicago truncatula WT plantlet roots treated with control solution

value: Jemalong A17 (WT)


title: Berry_skin_CD-WD-rep6

description:
CDD6
This sample is from Vitis vinifera L. cv. Chardonnay berry skins, under water deficit (stress) conditions. It is the five of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.

source_name: Vitis vinifera L. cv. Chardonnay, harvested berry skin, water deficit

value: Chardonnay


title: Berry_skin_CD-WD-rep2

description:
CDD2
This sample is from Vitis vinifera L. cv. Chardonnay berry skins, under water deficit (stress) conditions. It is the second of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.


title: NFP Nod-LCOs 6h roots biological replicate 2


title: S2-Treg-6h

value: Treg


title: S2-Th17-24h


title: CS76H_AC

value: PBMC


title: CS50P_AC

value: allergic rhinitis


title: Berry_skin_CD-WD-rep5

description:
CDD5
This sample is from Vitis vinifera L. cv. Chardonnay berry skins, under water deficit (stress) conditions. It is the four of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.


title: Berry_skin_CD-WD-rep4

description:
CDD4
This sample is from Vitis vinifera L. cv. Chardonnay berry skins, under water deficit (stress) conditions. It is the three of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.


title: WT control roots 6h biological replicate 3

source_name: Medicago truncatula WT plantlet roots treated with control solution


title: S2-Th17-6d


title: WT roots Nod-LCOs 6h biological replicate 2

description: Gene expression data from Medicago truncatula WT plantlet roots treated with Nod-LCOs


title: CS50P_Dil

value: Patient


title: Berry_skin_CD-WD-rep1

description:
CDD1
This sample is from Vitis vinifera L. cv. Chardonnay berry skins, under water deficit (stress) conditions. It is the first of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.


title: CS80H_AC


title: WT control roots 6h biological replicate 1


title: S2-Th17-3d


title: CS59P_AC


title: CS76H_DiL

value: Diluent


title: Berry_skin_CD-WW-rep6

description:
CDW6
This sample is from Vitis vinifera L. cv. Chardonnay berry skins, under well-watered (control) conditions. It is the fifth of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.

source_name: Vitis vinifera L. cv. Chardonnay, harvested berry skin, well-watered


title: CS59P_Dil


title: Berry_skin_CD-WW-rep3

description:
CDW3
This sample is from Vitis vinifera L. cv. Chardonnay berry skins, under well-watered (control) conditions. It is the third of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.


title: S1-Treg-6d


title: Berry_skin_CS-WD-rep5

description:
CSD5
This sample is from Vitis vinifera L. cv. Cabernet Sauvignon berry skins, under water deficit (stress) conditions. It is the five of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.

source_name: Vitis vinifera L. cv. Cabernet Sauvignon, harvested berry skin, water deficit

value: Cabernet Sauvignon


title: S1-Treg-3d


title: CS57P_AC

value: Allergen


title: Berry_skin_CD-WW-rep2

description:
CDW2
This sample is from Vitis vinifera L. cv. Chardonnay berry skins, under well-watered (control) conditions. It is the second of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.


title: CS57P_Dil


title: Berry_skin_CD-WW-rep1

description:
CDW1
This sample is from Vitis vinifera L. cv. Chardonnay berry skins, under well-watered (control) conditions. It is the first of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.


title: WT roots Nod-LCOs 6h biological replicate 1

source_name: Medicago truncatula WT plantlet roots treated with Nod-LCOs

value: Root


title: Berry_skin_CD-WW-rep4

description:
CDW4
This sample is from Vitis vinifera L. cv. Chardonnay berry skins, under well-watered (control) conditions. It is the fourth of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.


title: S2-Treg-3d


title: S1-Treg-24h


title: WT roots Nod-LCOs 6h biological replicate 3

value: 10 days


title: S2-Th17-6h


title: S1-Treg-6h


title: CS38H_AC

value: Healthy


title: CS38H_Dil


title: NSP1 control 6h roots biological replicate 2

description: Gene expression data from Medicago truncatula NSP1 plantlet roots treated with control solution

growth_protocol: Medicago truncatula Gaertn cv Jemalong seeds were surface-sterilized and scarified. Plates with M. truncatula seeds were incubated for 24 hours in the climate chamber (humidity: 70 %; photosynthetic photon flux: 150 μmol m-2 s-1) at a 16 h light (23 °C) and 8 h dark (18 °C) regime. Subsequently, seedlings were moisturized with sterile water (pH 7.0) to allow careful removal of seed coats. In each case, eight seedlings were put on the upper quarter of a 2.5 % (w/v) phytoagar (Duchefa Biochemie, Haarlem, The Netherlands) slant plate (120 x 120 mm; DoctorLab, Jena, Germany). Seedlings used for treatment with Myc-LCOs and corresponding controls were put on plates with half-strength Hoagland´s solution (Arnon and Hoagland, 1940) set to pH 6.5 with KOH. An approximately one cm strap of Whatman paper (Schleicher & Schuell, Dassel, Germany) soaked with appropriate nutrient solutions as described above was used to fix the seedlings on the plates beneath the cotyledons. Three plates at a time were sealed with transparent wrapping foil, which was cut at the upper side to allow gas exchange. The lower half of each plate stack was wrapped with aluminium foil for light protection to allow normal root development. Each triple pack of plates was placed in an approximately 70° angle in the climate chamber for five days.

treatment_protocol: Plantlets were carefully removed from slant agar plates and placed in 13 mL tubes wrapped with aluminium foil that were cut off at the 8 mL mark, using 10 plantlets per tube (Sarstedt, Nürnbrecht, Germany). Each tube contained 5 mL of the following solutions: sulphated Myc-LCO solution (half-strength Hoagland´s solution of pH 6.5 containing 10-8 M sulphated Myc-LCOs), non-sulphated Myc-LCO solution (half-strength Hoagland´s solution of pH 6.5 containing 10-7 M non-sulphated Myc-LCOs), mixed sulphated and non-sulphated Myc-LCO solution (half-strength Hoagland´s solution of pH 6.5 containing 10-8 M sulphated and 10-7 M non-sulphated Myc-LCOs), Myc control solution (half-strength Hoagland´s solution of pH 6.5). After 6 h of incubation in the climate chamber, 10 plantlets per batch were removed from the treatment or control solutions and harvested.

value: Jemalong A17 (NSP1 mutant)


title: NSP1 control 6h roots biological replicate 3

source_name: Medicago truncatula NSP1 plantlet roots treated with control solution


title: Berry_skin_CS-WD-rep2

description:
CSD2
This sample is from Vitis vinifera L. cv. Cabernet Sauvignon berry skins, under water deficit (stress) conditions. It is the second of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.

value: Reno, NV, USA

value: berry skin


title: NSP1 control 6h roots biological replicate 1


title: CS02P_AC


title: s/nsMyc-LCOs NSP1 6h roots biological replicate 3

description: Gene expression data from Medicago truncatula NSP1 plantlet roots treated with Myc LCOs


title: CS32H_AC


title: s/nsMyc-LCOs NSP1 6h roots biological replicate 2

source_name: Medicago truncatula NSP1 plantlet roots treated with Myc LCOs


title: CS32H_Dil


title: S1-Th17-24h


title: Berry_skin_CS-WD-rep4

description:
CSD4
This sample is from Vitis vinifera L. cv. Cabernet Sauvignon berry skins, under water deficit (stress) conditions. It is the four of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.

value: water deficit


title: Berry_skin_CS-WD-rep3

description:
CSD3
This sample is from Vitis vinifera L. cv. Cabernet Sauvignon berry skins, under water deficit (stress) conditions. It is the three of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.


title: Berry_skin_CS-WD-rep1

description:
CSD1
This sample is from Vitis vinifera L. cv. Cabernet Sauvignon berry skins, under water deficit (stress) conditions. It is the first of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.


title: S1-Th17-3d


title: S1-Th17-6d


title: S1-Th17-6h


title: s/nsMyc-LCOs NSP1 6h roots biological replicate 1


title: Berry_skin_CS-WW-rep6

description:
CSW6
This sample is from Vitis vinifera L. cv. Cabernet Sauvignon berry skins, under well-watered (control) conditions. It is the fifth of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.

source_name: Vitis vinifera L. cv. Cabernet Sauvignon, harvested berry skin, well-watered

value: well-watered


title: S4-Th17-8d


title: nsMyc-LCOs NSP1 6h roots biological replicate 2


title: nsMyc-LCOs NSP1 6h roots biological replicate 3


title: Berry_skin_CS-WW-rep5

description:
CSW5
This sample is from Vitis vinifera L. cv. Cabernet Sauvignon berry skins, under well-watered (control) conditions. It is the fourth of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.


title: sMyc-LCOs NSP1 6h roots biological replicate 3


title: nsMyc-LCOs NSP1 6h roots biological replicate 1


title: CS02P_DiL


title: CS35P_AC


title: S3-Th17-8d


title: S2-Treg-8d

source_name: Naïve CD4+ T cells isolated from buffy coat polarised towards Treg cells.


title: S4-Treg-8d


title: sMyc-LCOs NSP1 6h roots biological replicate 2


title: CS28H_AC

source_name: Peripheral blood mononuclear cells (PBMCs)


title: CS28H_DiL


title: CS35P_Dil


title: S3-Treg-8d


title: Berry_skin_CS-WW-rep4

description:
CSW4
This sample is from Vitis vinifera L. cv. Cabernet Sauvignon berry skins, under well-watered (control) conditions. It is the third of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.


title: Berry_skin_CS-WW-rep3

description:
CSW3
This sample is from Vitis vinifera L. cv. Cabernet Sauvignon berry skins, under well-watered (control) conditions. It is the second of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.


title: Berry_skin_CS-WW-rep2

description:
CSW2
This sample is from Vitis vinifera L. cv. Cabernet Sauvignon berry skins, under well-watered (control) conditions. It is the first of five biological replicates used in this experiment, each from at least two clusters harvested from non-adjacent vines in each block. The timing of harvest for each cultivar was determined by berries sampled for a target ˚Brix to TA ratio of 3.5. The average ˚Brix and TA (g L-1) were 23.3 and 7.1, respectively, with an average ratio of 3.3.


title: TL36-YoungAdult

city: Chiba

first: Masaaki

last: Sunaoshi

state: Chiba

address: 4-9-1 Anagawa, Inage-ku

department: Department of Radiation Effects Research, Institute for Radiological Science

country: Japan

institute: National Institutes for Quantum Science and Technology

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent Oligo aCGH/ChIP-on-Chip Hybridization Kit) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially in wash buffer.

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (v 10.7.3.1)

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and data extraction.

label_protocol: Alu I and Rsa I-restricted DNA (400 ng) derived from ear and lymphoma were labeled by 60 µM Cyanine3-UTP and Cyanine5-UTP, respectively. Exo-Klenow fragment enzyme (Agilent Genomic DNA Enzymatic Labeling kit) was used to label these DNA.

extract_protocol: Genomic DNA was extracted from 38 mouse ears and lymphomas using Maxwell 16 Instrument (Promega). After extraction, DNA was treated with RNase A (Sigma).

treatment_protocol:
breeding protocol: Mice were observed daily until moribund, when thymic enlargement and dyspnea symptoms were recognized, after which they were sacrificed by exsanguination under terminal isofluorane anesthesia and autopsied.
irradiation protocol: Female B6C3F1/Crlj mice were exposed to 1.2 Gy whole-body X-ray irradiation for four consecutive weeks starting at 1, 4 or 8 weeks of age. Mice were irradiated using an X-ray generator (PANTAK Ltd.) at 0.7 Gy/min (200 kVp, 20 mA, with 0.5-mm Cu and 0.5-mm Al filters).

tag: strain

tag: irradiated age

value: Young Adult

value: Thymocytes

value: T cell lymphoma

source_name: Ear obtained from the same individual

value: Ear


title: S2-Th17-8d


title: TL35-YoungAdult


title: CS40H_AC

value: PBMC


title: CS40H_Dil


title: CS03P_AC

value: allergic rhinitis

value: Patient


title: TL34-YoungAdult


title: sMyc-LCOs NSP1 6h roots biological replicate 1


title: RAM1 control 6h roots biological replicate 3

description: Gene expression data from Medicago truncatula RAM1 plantlet roots treated with control solution

value: Jemalong A17 (RAM1 mutant)


title: CS03P_DiL

value: Diluent


title: S1-Th17-8d


title: S4-Treg-6d

value: Treg


title: RAM1 control 6h roots biological replicate 1

source_name: Medicago truncatula RAM1 plantlet roots treated with control solution

value: Root

value: 10 days


title: S4-Treg-6h


title: TL31-YoungAdult


title: s/nsMyc-LCOs RAM1 6h roots biological replicate 2

description: Gene expression data from Medicago truncatula RAM1 plantlet roots treated with Myc LCOs


title: CS27H_AC

value: Healthy

value: Allergen


title: S4-Treg-3d


title: S4-Th17-6d


title: RAM1 control 6h roots biological replicate 2


title: TL32-YoungAdult


title: s/nsMyc-LCOs RAM1 6h roots biological replicate 3

source_name: Medicago truncatula RAM1 plantlet roots treated with Myc LCOs


title: CS27H_Dil


title: CS72P_DiL


title: nsMyc-LCOs RAM1 6h roots biological replicate 2


title: s/nsMyc-LCOs RAM1 6h roots biological replicate 1


title: TL28-Adolescent

value: Adolescent


title: TL29-YoungAdult


title: S4-Treg-24h


title: CS72P_AC


title: CS12P_AC


title: S4-Th17-6h


title: CS12P_DiL


title: CS24H_AC


title: S4-Th17-24h


title: sMyc-LCOs RAM1 6h roots biological replicate 2


title: CS24H_DiL


title: TL33-YoungAdult


title: TL26-Adolescent


title: sMyc-LCOs RAM1 6h roots biological replicate 1


title: nsMyc-LCOs RAM1 6h roots biological replicate 1


title: TL23-Adolescent


title: TL24-Adolescent


title: TL25-Adolescent


title: TL19-Adolescent


title: TL18-Adolescent


title: TL16-Adolescent


title: TL22-Adolescent


title: TL21-Adolescent


title: TL20-Adolescent


title: TL12-Infant

value: Infant


title: TL14-Infant


title: TL17-Adolescent


title: TL13-Infant


title: TL11-Infant


title: TL37-YoungAdult

growth_protocol: Mice were observed daily until moribund, when thymic enlargement and dyspnea symptoms were recognized, after which they were sacrificed by exsanguination under terminal isofluorane anesthesia and autopsied.

treatment_protocol: Female B6C3F1/Crlj mice were exposed to 1.2 Gy whole-body X-ray irradiation for four consecutive weeks starting at 8 weeks of age. Mice were irradiated using an X-ray generator (PANTAK Ltd.) at 0.7 Gy/min (200 kVp, 20 mA, with 0.5-mm Cu and 0.5-mm Al filters).


title: Bifidobacterium, replicate 1 [TFG19]

city: Chicago

first: Thomas

middle: F.

last: Gajewski

state: ILLINOIS

address: 929 E 57th St GCIS W423H

institute: University of Chicago

description: replicate 1

hyb_protocol: The cRNA was hybridized to Illumina MouseRef8v2 arrays using Illumina provided protocols.

scan_protocol: Scanned using an Illumina HiScan.

data_processing: The data were background subtracted and normalized using quantile normalization.

source_name: BM-derived DCs

label_protocol: Total RNA was processed into biotinylated cRNA using the Epicentre TargetAmp™ 2-Round Biotin-aRNA Amplification Kit 3.0 (TAB2R71024).

extract_protocol: Total RNA was isolated using RNeasy® Micro kit (Qiagen). Quality control was performed with Agilent Bioanalyser.

value: 6-8 weeks

value: BM-derived DCs


title: TL38-YoungAdult

value: Young Adult

value: Thymocytes


title: TL15-Infant

value: T cell lymphoma

value: Ear


title: Unstimulated, replicate 2 [TFG2]

description: replicate 2


title: nsMyc-LCOs RAM1 6h roots biological replicate 3


title: Bifidobacterium, replicate 2 [TFG20]

description: replicate 2


title: TL9-Infant


title: S1-Treg-8d


title: TL8-Infant


title: TL7-Infant


title: Tomato_ToMV_inoculated_Rep1

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

country: Italy

institute: University of Verona

description: leaf, ETI response

hyb_protocol: Four micrograms of labelled aRNA was hybridized to the array according to the manufacturer’s recommendations (http://www.combimatrix.com/support_docs.htm). Prehybridization was performed by incubating the arrays with prehybridization solution (6X SSPE, 1% SDS, 0.2% BSA) for 60 minutes at 37 °C. Hybridization was performed at 37°C for 16 hours in hybridization solution (6X SSPE, 0.8% BSA, 12% DI Formamide, 2.5% SDS) using 4 μg of labelled aRNA. Hybridization washings were performed as following: wash with 6X SSPET wash solution (6X SSPE, 0.05% Tween-20), wash with 3X SSPET wash solution (3X SSPE, 0.05% Tween-20), 2 washes with 0.5X SSPET wash solution (0.5X SSPE, 0.05% Tween-20).

scan_protocol: The array was scanned with an Axon GenePix 4400A scanner and GenePix Pro 7 software (MDS Analytical Technologies). Laser was set at 33. PMT gain was set at 500.

data_processing: Raw data was extracted using GenePix Pro 7 software (MDS Analytical Technologies). The data were investigated for quality assessment, preprocessed and normalized using a suitable subset of control probes available in the Combimatix array and a quantile normalization technique.The significance of the differential expression was assessed taking into account the multiple testing setting and controlling the False Discovery Rate (FDR) at level FDR=0.01 and the emprical Bayes moderated t-statistics available in the limma package.

organism: Solanum lycopersicum

label_protocol: Total RNA (1 µg) was amplified and labelled using the RNA ampULSe kit (Kreatech).

extract_protocol: RNA was isolated from whole plants using Rneasy Plant Kit according to the manual instructions (Quiagen Valencia, USA).

treatment_protocol: The inoculation of the tomato plants with F. oxysporum f. sp. lycopersici (Fol) and Tomato Mosaic Virus (ToMV) was made according to the method reported in the CPVO technical protocol TP/044/3.

tag: variety

value: Rosso Delta

value: leaf


title: Unstimulated, replicate 1 [TFG1]

description: replicate 1


title: TL3-Infant


title: TL4-Infant


title: Jackson, replicate 2

description: replicate 2

source_name: Tumor-infilltrating DCs

value: Tumor-infilltrating DCs


title: Tomato_ToMV_inoculated_Rep2

description: leaf, ETI response


title: Tomato_ToMV_not-inoculated_Rep2

description: leaf, ETI response


title: Bifidobacterium, replicate 2

description: replicate 2


title: Taconic, replicate 2

description: replicate 2


title: Tomato_Fol_inoculated_Rep2

description: leaf, ETI response


title: Bifidobacterium, replicate 1

description: replicate 1


title: TL1-Infant


title: Tomato_Fol_inoculated_Rep1

description: leaf, ETI response


title: TL2-Infant


title: Tomato_ToMV_not-inoculated_Rep1

description: leaf, ETI response


title: Jackson, replicate 1

description: replicate 1


title: Tomato_Fol_not-inoculated_Rep2

description: leaf, ETI response


title: sMyc-LCOs RAM1 6h roots biological replicate 3

value: Jemalong A17 (RAM1 mutant)


title: RG2

status: Public on Nov 11 2015

city: Göttingen

first: Judith

last: Besseling

address: Am Faßberg 11

department: Sleep and Waking

institute: Max Planck Institute for Biophysical Chemistry

description: Gene expression non-mendelian F1

hyb_protocol: For hybridization, the Agilent Gene Expression Hybridisation Kit (Agilent Technologies) was used following the manufacturer‘s protocol. The microarray was washed once with the Agilent Gene Expression Wash Buffer 1 for one minute at ambient temperature followed by a second wash with preheated (37°C) Gene Expression Wash Buffer 2 for one minute.

scan_protocol: Fluorescence signals on microarrays were detected by the SureScan Microarray Scanner (Agilent Technologies), generating a 20-bit TIFF file. Agilent’s Feature Extraction software version 11 was used to read and process the TIFF files.

data_processing:
The Feature Extraction software measures feature intensities, flags outlier features, and calculates statistical confidences. Prior to normalization the following processing steps were performed: removal of signals from control probes
, mean of signals from replicate probes
, mean of signals from all probes of a target. Data of all samples were then quantile-normalized using ranked-median quantiles. Statistical parameters were computed after organizing the samples in groups where each group contains biological replicates. A statistical t-test was computed for each gene/feature, which indicates whether the observed values are indeed statistically significant.

organism: Caenorhabditis elegans

source_name: non-mendelian F1 after crossing of parental strains

label_protocol: The Low Input QuickAmp Labeling Kit (Agilent Technologies) was used for generation of fluorescent cRNA

growth_protocol: C. elegans worms were grown on Nematode Growth Medium (NGM) plates seeded with E. coli OP50 at 25° C.

extract_protocol: RNA extraction was done using the QIAGEN RNeasy kit.

treatment_protocol: Worms were transferred to 400 µl Trizol prior to RNA extraction.

value: non-mendelian F1

tag: gender

value: hermaphrodite

value: young adult

value: whole animal


title: RG1

description: Gene expression non-mendelian F1


title: Tomato_Fol_not-inoculated_Rep1

description: leaf, ETI response


title: RG3

description: Gene expression non-mendelian F1


title: R1

description: Gene expression maternal strain

source_name: hermaphrodites of the maternal strain

value: maternal strain


title: R2

description: Gene expression maternal strain


title: Taconic, replicate 1

description: replicate 1


title: R3

description: Gene expression maternal strain


title: O1

description: Gene expression mendelian F1

source_name: co-segregating (mendelian) F1 after crossing of parental strains

value: mendelian F1


title: G3

description: Gene expression paternal strain

source_name: hermaphrodites of the paternal strain

value: parental strain


title: O2

description: Gene expression mendelian F1


title: G2

description: Gene expression paternal strain


title: TL30-YoungAdult


title: O3

description: Gene expression mendelian F1


title: S4-Th17-3d

source_name: Naïve CD4+ T cells isolated from buffy coat polarised towards Th17 cells.


title: TL6-Infant

value: Infant


title: plasma-treated HaCaT (w2)

city: Greifswald

first: Anke

last: Schmidt

state: MV

address: Felix-Hausdorff-Str. 2

department: Plasma Life Science

institute: INP Greifswald

description: gene expression of plasma-treated cells (w2)

hyb_protocol: 600 ng of Cy3-labeled cRNA (specific activity >15.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays for 17 hours at 65Â°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), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner  using one color scan setting for 8x60k array slides (Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocolGE1_1105 and Grid: 06247_D_F_20131210) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: plasma-treated HaCaT cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Germany).  Dye incorporation and cRNA yield were checked with the NanoDrop and Bioanalyzer (Agilent, USA).

growth_protocol: HaCaT cells were cultured in  Roswell Park Memorial Institute medium (RPMI; Lonza, Switzerland) supplemented with 8 % fetal calf serum (FCS; Sigma, USA), 2 mM L-glutamine, 0.1 mg∙L-1 streptomycin and 100 U∙mL-1 penicillin (Lonza, Switzerland).

extract_protocol: After two, six, eight, ten, and twelve weeks, cells were either subjected to microscopic experiments and RNA isolation.  RNA were isolated according to the manufacturer’s instruction (Bio&SELL, Germany). Then, RNA was reversely transcribed using Transcriptor First Strand Synthesis Kit the cDNA synthesis (Roche, Germany). cDNA was conjugated with a fluorescence dye and applied onto whole genome chips (OaksLab, Germnany).

treatment_protocol: Cold physical plasma treated cell culture medium was generated by 60 s exposure of five milliliter of fully supplemented medium to the plasma of an atmospheric pressure argon plasma jet (kINPen; neoplas tools, Germany). Three standard liters per minute of highly pure argon (99.99 %; Air Liquide, France) were used as feed gas. The plasma was generated by applying a voltage of 2-6 kVpp with a frequency of 1.0-1.1 MHz to the central electrode. Three millions HaCaT keratinocytes were exposed to 15 ml of plasma treated medium twice a week and passaged once a week

value: plasma-treated

tag: time (weeks)

tag: cell line

value: HaCat

value: keratinocyte cell line


title: plasma-treated HaCaT (w4)

description: gene expression of plasma-treated cells (w4)


title: plasma-treated HaCaT (w10)

description: gene expression of plasma-treated cells (w10)


title: PA-824-4x

city: Seattle

first: Shuyi

last: Ma

state: Washington

address: 1900 9th Avenue

department: Department of Pediatrics

institute: University of Washington

hyb_protocol: Each pair of differentially labeled probes was resuspended in 60 ml of hybridization buffer (500 ml formamide, 250 ml 20X SSC, 5 ml 10% SDS, 245 ml ultrapure water) and hybridized to the microarray slide overnight in a 42uC incubator.

scan_protocol: Slides were washed in increasingly stringent wash conditions (5 min 1X SSC 0.1% SDS, 10 min 0.1X SSC 0.1% SDS, 4 times 1 minute in 0.1 X SSC and a final 10 second wash in 0.01X SSC).

data_processing: Arrays were scanned and spots were quantified using Genepix 4000B with GenePix 6.0 software.

organism: Mycobacterium tuberculosis

source_name: H37Rv liquid culture_PA-824

label_protocol: Three mg of total RNA was used to create cDNA labeled with aminoallyl dUTP (Fermentas). Fluores- cent Cy3 and Cy5 dyes (Amersham) were then covalently attached to the aminoallyl tags.

growth_protocol: Mycobacteria tuberculosis strain H37Rv (ATCC 27294) were grown on Middlebrook 7H9 medium (Difco) with 0.05% Tween 80 and ADC supplement.

extract_protocol: RNA was isolated and applied to arrays provided by TIGR under the NIAID contract N01-AI-15447 using published protocols (Rustad TR, Harrell MI, Liao R, Sherman DR (2008) The Enduring Hypoxic Response of Mycobacterium tuberculosis. PLoS ONE 3(1): e1502). In summary, frozen cell pellets Pellets were resuspended in Trizol, transferred to a tube containing Lysing Matrix B (QBiogene, Inc.), and vigorously shaken at max speed for 30 sec in a FastPrep 120 homogenizer (Qbiogene) three times, with cooling on ice between steps. This mixture was centrifuged at max speed for 1 min and the supernatant was transferred to a tube containing 300 mL chloroform and Heavy Phase Lock Gel (Eppendorf North America, Inc.), inverted for one minute, and centrifuged at max speed. The aqueous phase was then precipitated with 270 mL isopropanol and 270 mL high salt solution (0.8M Na citrate, 1.2M NaCl). RNA was cleaned using an RNeasy kit following manufacturer’s recommendations (Qiagen).

treatment_protocol: Bacteria were exposed for 16 hrs to various concentrations of each drug (different multiples of the compound's MIC), as noted in the title of each sample.

tag: drug

tag: mic

source_name: H37Rv liquid culture_control

tag: exposed to

value: none (untreated control)


title: plasma-treated HaCaT (w6)

description: gene expression of plasma-treated cells (w6)


title: PA-824-8x


title: PA-824-2x


title: Moxifloxacin-8x

source_name: H37Rv liquid culture_Moxifloxacin

value: Moxifloxacin


title: untreated HaCaT 2

description: gene expression of untreated control

source_name: HaCaT untreated  control

value: control


title: G1

description: Gene expression paternal strain

tag: age

tag: tissue


title: Streptomycin-8x(dead)

source_name: H37Rv liquid culture_Streptomycin

value: Streptomycin


title: Streptomycin-4x


title: Streptomycin-8x_8/10


title: untreated HaCaT 1

description: gene expression of untreated control

tag: treatment

tag: cell type


title: plasma-treated HaCaT (w12)

description: gene expression of plasma-treated cells (w12)


title: Moxifloxacin-4x


title: plasma-treated HaCaT (w8)

description: gene expression of plasma-treated cells (w8)


title: Streptomycin-2x_8/10


title: Rifampicin-4x

source_name: H37Rv liquid culture_Rifampicin

value: Rifampicin


title: Streptomycin-2x


title: TL27-Adolescent

value: Adolescent

value: Thymocytes

value: T cell lymphoma

source_name: Ear obtained from the same individual

value: Ear


title: Moxifloxacin-2x


title: Kanamycin-4x

source_name: H37Rv liquid culture_Kanamycin

value: Kanamycin


title: INH-8x

source_name: H37Rv liquid culture_Isoniazid

value: Isoniazid


title: INH-4x


title: INH-2x


title: TL10-Infant


title: INH-2x(redone)


title: IMTB047-4x

source_name: H37Rv liquid culture_IMTB047 (GATB - Biodura*)

value: IMTB047 (GATB - Biodura*)


title: IMTB044-4x

source_name: H37Rv liquid culture_IMTB044 (Guanosine analog)

value: IMTB044 (Guanosine analog)


title: Kanamycin-8x


title: IMTB044-2x


title: IMTB045-4x

source_name: H37Rv liquid culture_IMTB045 (GATB - Biodura*)

value: IMTB045 (GATB - Biodura*)


title: IMTB047-2x


title: TL5-Infant

value: Infant


title: Kanamycin-2x


title: SUDHL6_siNFYB_A_rep3

city: New York

first: Mukesh

last: Bansal

state: NY

address: 1130 St. Nicholas Ave. Room 908

institute: Columbia University

scan_protocol: Standard Illumina hybridization protocol

data_processing: VST RSN normalization

source_name: SUDHL6 DLBCL cell line, 20 hrs siRNA post-nucleoporation

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep-96 RNA Amplification Kit according to the manufacturers protocol

growth_protocol: SUDHL6 cell line was maintained in IMDM medium supplemented with 10%FBS and antibiotics (Pen/Strep).

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

treatment_protocol: Silencing experiments in B lymphoma cells with SmartPool siRNA (Dharmacon) were performed using Amaxa Nucleofector technology from LONZA Cologne AG, Germany. 1x10^6 cell were resuspended in SF solution and 80 pmol of siRNA pool was added. Cells were nucleoporated using DC-100 program.

value: SUDHL6 DLBCL

value: siNFYB


title: SUDHL6_siNFYB_A_rep2


title: SUDHL6_siFOXM1_A_rep3


title: SUDHL6_siNT4_control_A_rep2


title: SUDHL6_siNT4_control_A_rep3


title: SUDHL6_siFOXM1_A_rep1


title: SUDHL6_siFOXM1_A_rep2


title: SUDHL6_siNT4+siNT4_control_A_rep3


title: Rifampicin-2x

value: none (untreated control)


title: SUDHL6_siNT4_control_A_rep1


title: IMTB041-8x

source_name: H37Rv liquid culture_IMTB041 (GATB - UIC)

value: IMTB041 (GATB - UIC)


title: IMTB042-4x

source_name: H37Rv liquid culture_IMTB042 (GATB - UIC)

value: IMTB042 (GATB - UIC)


title: IMTB042-8x


title: IMTB041-2x


title: IMTB038-8x

source_name: H37Rv liquid culture_IMTB038 (GATB - UIC)

value: IMTB038 (GATB - UIC)


title: IMTB042-2x


title: SUDHL6_siNFYB_A_rep1


title: IMTB038-4x


title: IMTB041-4x


title: SUDHL6_siNFYB+siFOXM1_A_rep3


title: IMTB036-4x

source_name: H37Rv liquid culture_IMTB036 (GATB - Biodura*)

value: IMTB036 (GATB - Biodura*)


title: IMTB038-2x


title: IMTB036-8x


title: SUDHL6_siNT4+siNT4_control_rep3


title: SUDHL6_siNFYB+siFOXM1_A_rep2


title: SUDHL6_siTFDP1+siATF5_rep2


title: IMTB035-8x

source_name: H37Rv liquid culture_IMTB035 (GATB - Biodura*)

value: IMTB035 (GATB - Biodura*)


title: SUDHL6_siHMGA1+siTFDP1_rep3


title: SUDHL6_siHMGA1+siATF5_rep2


title: IMTB035-4x

source_name: H37Rv liquid culture_control


title: SUDHL6_siHMGA1+siTFDP1_rep4


title: SUDHL6_siTFDP1+siATF5_rep3


title: SUDHL6_siHMGA1+siATF5_rep3


title: SUDHL6_siHMGA1+siFOXM1_rep3


title: SUDHL6_siNT4+siNT4_control_A_rep1


title: IMTB033-4x

source_name: H37Rv liquid culture_IMTB033 (GATB - Biodura*)

value: IMTB033 (GATB - Biodura*)


title: Streptomycin-4x_8/10

value: Streptomycin


title: IMTB036-2x


title: IMTB035-2x


title: SUDHL6_siNFYB+siFOXM1_A_rep1


title: IMTB033-2x


title: IMTB032-4x

source_name: H37Rv liquid culture_IMTB032 (GATB - Biodura*)

value: IMTB032 (GATB - Biodura*)


title: IMTB031-2x

source_name: H37Rv liquid culture_IMTB031 (Chloroxine)

value: IMTB031 (Chloroxine)


title: IMTB032-2x


title: SUDHL6_siHMGA1+siATF5_rep1


title: IMTB031-4x


title: SUDHL6_siNT4_control_rep3


title: SUDHL6_siNT4+siNT4_control_rep2


title: SUDHL6_siHMGA1+siTFDP1_rep2


title: SUDHL6_siATF5_rep3


title: SUDHL6_siHMGA1_rep3


title: IMTB029-8x

source_name: H37Rv liquid culture_IMTB029


title: IMTB029-4x


title: SUDHL6_siNT4_control_rep4


title: SUDHL6_siTFDP1_rep3


title: IMTB030-2x

source_name: H37Rv liquid culture_IMTB030 (methoxy-methylellipticinium )

value: IMTB030 (methoxy-methylellipticinium )


title: SUDHL6_siFOXM1_rep3


title: IMTB030-8x


title: IMTB030-4x


title: SUDHL6_siNT4_control_rep2


title: IMTB028-2x

source_name: H37Rv liquid culture_IMTB028


title: IMTB028-4x


title: SUDHL6_siHMGA1_rep2


title: SUDHL6_siHMGA1+siTFDP1_rep1


title: SUDHL6_siHMGA1+siFOXM1_rep2


title: SUDHL6_siHMGA1+siFOXM1_rep1


title: SUDHL6_siNT4_control_rep1


title: IMTB029-2x


title: IMTB027-8x

source_name: H37Rv liquid culture_IMTB027


title: IMTB027-4x


title: IMTB027-2x


title: IMTB026-8x

source_name: H37Rv liquid culture_IMTB026


title: IMTB026-4x


title: IMTB025-8x

source_name: H37Rv liquid culture_IMTB025 (Disulfiram)

value: IMTB025 (Disulfiram)


title: IMTB028-8x


title: IMTB026-2x


title: IMTB011-4x

source_name: H37Rv liquid culture_IMTB011 (Acivicin)

value: IMTB011 (Acivicin)


title: IMTB014-2x

source_name: H37Rv liquid culture_IMTB014 (Iodotubercidin)

value: IMTB014 (Iodotubercidin)


title: IMTB025-2x


title: SUDHL6_siTFDP1_rep2

source_name: SUDHL6 DLBCL cell line, 20 hrs siRNA post-nucleoporation


title: SUDHL6_siFOXM1_rep2


title: IMTB025-4x


title: IMTB025-2x_0hr


title: IMTB014-8x


title: IMTB009-4x(Needs repeat)

source_name: H37Rv liquid culture_IMTB009 (Coumarin analog)

value: IMTB009 (Coumarin analog)


title: IMTB025-2x_8hr


title: SUDHL6_siFOXM1_rep1

value: SUDHL6 DLBCL


title: SUDHL6_siTFDP1_rep1


title: SUDHL6_siHMGA1_rep1


title: IMTB009-8x


title: SUDHL6_siNT4+siNT4_control_A_rep2


title: IMTB011-2x


title: IMTB025-2x_2hr


title: IMTB045-2x

source_name: H37Rv liquid culture_IMTB045 (GATB - Biodura*)

value: IMTB045 (GATB - Biodura*)


title: SUDHL6_siATF5_rep1


title: IMTB009-4x

value: none (untreated control)


title: IMTB007-8x?

source_name: H37Rv liquid culture_IMTB007 (Amidinobenzoate)

value: IMTB007 (Amidinobenzoate)


title: IMTB026-0x


title: IMTB014-4x


title: IMTB012-4x

source_name: H37Rv liquid culture_IMTB012 (Fenamisal)

value: IMTB012 (Fenamisal)


title: IMTB009-2x

source_name: H37Rv liquid culture_control


title: IMTB012-2x


title: IMTB007-2x?


title: IMTB007-4x?


title: IMTB006-2x

source_name: H37Rv liquid culture_IMTB006 (Salicylanilide (prev. Diarylamide))


title: IMTB006-2x_7/8/10

value: IMTB006 (Salicylanilide (prev. Diarylamide))


title: IMTB006-8x


title: IMTB006-4x(BAD)


title: IMTB006-1x_7/8/10


title: IMTB006-0.5x_7/8/10


title: IMTB004-8x

source_name: H37Rv liquid culture_IMTB004 (Tunicamycin)

value: IMTB004 (Tunicamycin)


title: IMTB001-8x

source_name: H37Rv liquid culture_IMTB001 (LY-83583, IDR10013)


title: IMTB001-2x


title: IMTB001-4x


title: SUDHL6_siATF5_rep2


title: IMTB004-4x


title: IMTB002-4x

source_name: H37Rv liquid culture_IMTB002 (Aminothiadiazole)

value: IMTB002 (Aminothiadiazole)


title: Cycloserine-4x

source_name: H37Rv liquid culture_cycloserine

value: cycloserine


title: IMTB002-8x


title: Ethionamide-2x

source_name: H37Rv liquid culture_ethionamide

value: ethionamide


title: Cycloserine-2x(poor)


title: Capreomycin-2x

source_name: H37Rv liquid culture_capreomycin

value: capreomycin


title: IMTB002-2x


title: Capreomycin-4x


title: Cycloserine-2x


title: IMTB004-2x


title: Ethionamide-4x


title: SkinTissue_ShortPhotoperiod vs LongPhotoperiod_rep1

city: Hohhot

first: cunfa

last: zhao

address: zhaojun Road

country: China

institute: Academy of Agriculture and Stockbreeding Sciences

description: Gene expression after ShortPhotoperiod vs natural Photoperiod goat skin

hyb_protocol: The labeled DNA was dissolved in 80 μl of hybridization buffer (3× saline sodium citrate [SSC], 0.2% sodium dodecyl sulfate [SDS], 5× Denhardt's solution, and 25% formamide) overnight at 42 °C. After the hybridization, the gene chips were washed for 5 min (0.2% SDS, 2 x SSC) at 42 °C and then washed for 5 min (0.2 x SSC) at room temperature.

scan_protocol: The labeled cRNAs were hybridized onto the Whole Genome Oligo Array (4x44K, Agilent Technologies). This study used the G2519F sheep gene expression profile chip from Agilent, whose size is 8×15k and contains 15,208 sheep genes for expression profiling. an Agilent G2565CA Microarray Scanner was used to obtain the hybridization images of the gene chips.

data_processing: Feature Extraction software was used to transform the image signal into a digital signal, and the original data were then normalized (fold change ≥ 2 or ≤ 0.5) using the Lowess method (locally weighted scatterplot smoothing). If there were more than three biological replicates, the samples were analyzed with SAM (Significance Analysis of Microarrays) software to select the differentially expressed genes

organism: Capra hircus

source_name: Short Photoperiod Skin Tissue

label_protocol: The control group was labeled with Cy3, and the experimental group was labeled with Cy5. The samples were sent to CapitalBio Corporation (Beijing, China) for hybridization to an Agilent Sheep Gene Expression Microarray (Santa Clara, CA, USA).

extract_protocol: TRIzol (Invitrogen, Gaithersburg, MD, USA) was used for the total RNA extractions according to the manufacturer’s protocol. The RNA quantity and quality were measured using a NanoDrop ND-1000 spectrophotometer. The mRNAs were purified with a NucleoSpin® RNA Clean-up Kit (MACHEREY-NAGEL, Germany). The concentrations of the RNAs present in the samples and the OD 260/280 ratios of the samples were determined using a NanoDrop ND – 2000 spectrophotometer. The quality was assessed by standard denaturing agarose gel electrophoresis. Reverse transcription of the first strand of the complementary DNAs (cDNAs) was performed using an oligo dT primer with T7 promoter sequences.

treatment_protocol: We took samples from one side of the body. After iodine disinfection and alcohol deiodination, we cut skin samples using sterile blades, quickly placed them into liquid nitrogen and stored them in a freezer (-80°C).

value: Short Photoperiod Skin

value: female

source_name: Natural Photoperiod Skin Tissue

value: Natural Photoperiod Skin


title: Oleic acid a1

city: Leon

first: Silvio

last: Zaina

state: Gto

address: 20 de Enero no. 929

department: Department of Medical Sciences

country: Mexico

institute: University of Guanajuato

hyb_protocol: The labeled samples were hybridized to the Human Genome U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA, USA). The arrays were washed and stained with phycoerytrin conjugated streptavidin (SAPE) using the Affymetrix Fluidics Station® 450.

scan_protocol: The arrays were scanned in the Affymetrix GeneArray® 3000 scanner to generate fluorescent images, as described in the Affymetrix GeneChip® protocol.

data_processing: Cell intensity files (CEL files) were generated in the GeneChip® Command Console® Software (AGCC) (Affymetrix, Santa Clara, CA, USA). The data were modeled using the RMA (Robust Multichip Average) approach, followed by mean one step Probe Set summarization giving each gene a single expression value, all done using the software package Partek Genomics Suite 6.5.

source_name: THP-1 monocytes, 24h-stimulation, 50microM fatty acid

label_protocol: RNA was amplified and labeled using the Ambion WT Expression Kit (Applied Biosystems) according to manufactures instructions. 250 ng total RNA was used as input.

growth_protocol: Growth conditions: RPMI-1640 (Gibco), 10% FCS (Gibco), 1% PenStrep (Gibco), 2mM L-Glutamine (Sigma), 37C, 5% CO2

extract_protocol: Trizol-based RNA extraction

treatment_protocol: Cells were challenged with BSA-fatty acid complexes (1:6 ratio)

value: THP-1 monocytes

value: 24 h stimulation with 50 microM Oleic acid


title: SkinTissue_ShortPhotoperiod vs LongPhotoperiod_rep3


title: Oleic acid c1


title: Axin2- cells, biological rep1

city: Cambridge

first: Wei

last: Hsu

state: MA

address: 245 First St

department: Mineralized TIssue Biology

institute: Forsyth Institute

hyb_protocol: Samples were hybridized with GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix) and scanned at the SUNY Albany microarray core facility (USA).

scan_protocol: Affymetrix standard procedure

data_processing: RMA background correction and normalization using R software v.3.2.1.

source_name: non-Axin2 expressing cells in suture mesenchyme at P28

label_protocol: samples were processed with the Whole Transcript Assay Kit as recommended by the manufacterer (Affymetrix)

growth_protocol: Mice carrying Axin2rtTA and TRE-H2BGFP transgenes were used to isolate Axin2+/GFP+ and Axin2-/GFP- cells population in calvarial suture mesenchyme

extract_protocol: Total RNA extraction was performed by RNeasy Mini Kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: Axin2rtTA;TRE-H2BGFP mice were treated with Doxycycline from P25 to P28. Calvarial suture mesenchymal cells were digested by 0.2% collagenase, and then sorted by GFP intensity.

tag: strain background

value: mixed; C57BL/6J, CD-1 and B6CBAF2

tag: genotype/variation

tag: treated with

value: Doxycycline from P25 to P28

value: Calvarial suture

value: Axin2-/GFP- cells in suture mesenchyme


title: Elaidic acid a1

value: 24 h stimulation with 50 microM Elaidic acid


title: Elaidic acid b1