title: AC (L1)


title: W2 (L2)

status: Public on Dec 31 2016

type: RNA

city: Rennes

first: Aurelie

last: LE CAM

address: Campus de Beaulieu

department: PHASE

country: France

institute: INRA

hyb_protocol: Hybridization was carried out for 17 hours at 65°C in a rotating hybridization oven prior to washing.

scan_protocol: Scanning was performed with an Agilent Scanner (Agilent DNA Microarray Scanner, Agilent Technologies, Massy, France) using the standard parameters for a gene expression 8x60K oligoarray (channels: Green, resolution: 3µm, TIFF: 20 bit)

data_processing: Data were then obtained with the Agilent Feature Extraction software (v10.7.3.1) according to the appropriate GE protocol (GE1_107_Sep09). Before analysis, saturated spot, non-uniform spots and spots not significantly different from background (k=5) were flagged using the Agilent GeneSpring GX software (v.10.0.2). Probes were considered valid when corresponding spots remained present in at least 80% of the replicates of each experimental condition after the flagging procedure. Data were subsequently scale-normalized using the median value of each array.

molecule: total RNA

organism: Dicentrarchus labrax

source_name: Low quality_eggs

label_protocol: 150 ng of total RNA was amplified and labeled using Cy3-CTP. Yield (>0.825µg cRNA) and specific activity (> 6pmol of Cy3 per µg of cRNA) of Cy3-cRNA produced were checked with the Nanodrop. 600 ng of Cy3-cRNA was fragmented and hybridized on a sub-array.

growth_protocol: For the experiment 16 egg batches obtained from cultured European seabass (with average weight of 3.24 kg ±1.2 SD) resulting from a standard protocol including female stimulation, artificial spawning, artificial fertilization and incubation of the embryos as follows.

extract_protocol: RNA was extracted from 16 egg batches collected using Tri-reagent as previously described for rainbow trout (Bonnet et al., 2007). A NanoDrop® NP-1000 spectrophotometer (NanoDrop technologies, Wilmington, DE, USA) was used to measure the quantity and quality of the RNA samples. The quality of the RNA samples was checked also using a 2100 Bioanalyzer (Agilent Technologies Inc. Santa Clara, USA), and samples with RIN value higher than 8.5 were used for further analysis.

treatment_protocol: During spawning season, female genital state was regularly controlled through the observation of an ovarian biopsy. Only females at postvitellogenic stage were chosen for further procedures and subject to intraperitoneally injection of LHRHa (D-Trp6, SIGMA) solution at a dose of 10 µg kg-1. After induction, females were individually kept  indoor in 1m3 tanks at a temperature of 12.9-13.5°C, salinity of 34.8-36.2 ppt , pH 7.9-8.1 and photoperiod 8/16 (light/dark). After ovulation occurring between 68 and 75 h following hormonal injection) the eggs from each female separately were stripped exhaustively into dry containers the time after stimulation and the total volume of the collected egg batch was recorded. Then eggs were dispatched into aliquots for different treatments. One portion of 500 µl (approx. 500 eggs) was deep frozen in duplicate in liquid nitrogen and stored at -80°C until molecular analysis. Batches of 5 ml of eggs were fertilized in triplicates with an aliquot of a large pool (n=20) cryopreserved sperm created to cover the needs for all the crosses in order to exclude possible paternal effect in the analysis of embryonic development course [33]. During fertilization the amount of sperm was always adjusted to 2 105 of spermatozoa per egg. Fertilization was performed with sea water as an activating solution.

tag: tissue

value: eggs

tag: egg quality

value: Low quality


title: EBV_M_2015_1_C57BLL6_Mu_Mock_Li_D3_3

city: New York

first: Angela

last: Rasmussen

state: NY

department: Center for Infection and Immunity

country: USA

institute: Columbia University

hyb_protocol: ). Individual cRNA samples were hybridized to Agilent mouse whole-genome oligonucleotide 4-by-44 microarrays (approximately 39,000 unique mouse genes) according to the manufacturer's instructions. To enable examination of animal-to-animal variation as part of the data analysis, samples from individual animals were not pooled; included were samples from three animals per time point for each virus (60 animals total). Select samples were hybridized a second time (n = 2 technical replicates) to verify the quality of the process.

scan_protocol: Slides were scanned with an Agilent DNA microarray scanner, and the resulting images were analyzed using Agilent Feature Extractor version 8.1.1.1. This software was used to perform image analysis, including significance of signal and spatial detrending and to apply a universal error model. For these hybridizations, the most conservative error model was applied.

data_processing: standard Agilent protocol

organism: Mus musculus

label_protocol: cRNA probes were generated from each sample by the use of an Agilent one-color LowInput Quick Amp labeling kit (Agilent Technologies, Santa Clara, CA).

growth_protocol: Six to nine week-old male mice (C57Bl/6J, MAVS-/-) were used in all experiments.  Mice were housed in microisolator cages and allowed to acclimatize to the BSL4 environment for a least 5 days prior to use in experiments.

extract_protocol: RNA was extracted from mouse spleens and livers using a Qiagen RNeasy Minikit with RNAlater solution (Qiagen, Valencia, CA) according to the manufacturer's instructions. RNA was further purified using RNeasy columns (Qiagen, Valencia, CA). RNA samples were spectroscopically verified for purity, and the quality of the intact RNA was assessed using an Agilent 2100 Bioanalyzer. For each set of treatment conditions, three of the five RNA samples exhibiting the highest RNA integrity number (RIN) determined using the Bioanalyzer were used for microarray analysis.

treatment_protocol: Mice were infected by intraperitoneal (i.p.) injection with 100 focus-forming units (ffu) of either MA-ZEBOV or WT ZEBOV diluted in 0.2 ml of Dulbecco’s minimum essential medium (DMEM).  Mock-infected mice were i.p. inoculated with DMEM alone. Mice were humanely euthanized on days 3 and 5 post-infection, and spleens and livers removed and incubated in RNAlater (Qiagen, Valencia, CA). Tissues were then homogenized in Trizol reagent (ThermoFisher Scientific, Waltham, MA) to both inactivate virus and stabilize RNA, and stored at -80 C until RNA extraction.

value: Microarray


title: EBV_M_2015_1_MAVSKO_Mu_MAZEBOV_Li_D5_2


title: AR (L5)


title: V (H5)

source_name: High quality_eggs

value: High quality


title: T (H4)


title: EBV_M_2015_1_C57BLL6_Mu_MAZEBOV_Sp_D3_3


title: EBV_M_2015_1_C57BLL6_Mu_WTZEBOV_Li_D5_3


title: Ketoconazole 2 uM 5-R1

status: Public on Dec 30 2016

city: Torino

first: Irene

last: Stefanini

address: via Accademia Albertina

country: Italy

institute: University of Turin

hyb_protocol: Arrays were hybridized as described by the manufacturer. Hybridization took place at 63 °C for 14–16 h.

scan_protocol: Fluorescent cDNA bound to the microarray was detected with a GenePix 4000B microarray scanner (Axon Instruments), using the GenePixPro6.1 software package to quantify microarray fluorescence.

data_processing: Data were normalized using the limma R package and DEGs (Differentially Expressed Genes) were identified with the RankProduct R package

organism: Saccharomyces cerevisiae

source_name: antifungal treatment-high concentration

label_protocol: The labeling method used was the indirect method described by DeRisi (see the University of California San Francisco DeRisi laboratory Web site).

growth_protocol: Yeast cells were stored in glycerol 15% at -80°C, then tawned and growth in YPD (pH 4.8). The treatments were carried out after at least two inoculations to let cells recover.

extract_protocol: RNA was extracted from about 1 *109 cells using the hot acid phenol/chloroform protocol. RNAs were quantified spectrophotometrically using Nanodrop and by measuring the absorbance at 230, 260, and 280 nm and then calculating the 260/230 and 260/280 ratios and considering good data to be values of 1.8–2.2. RNA integrity was checked by electrophoresis in 1% agarose gel stained with ethidium bromide.

treatment_protocol: Yeast cells were treated in YPD (pH 4.8) supplemented with the antifungal at the indicated concentration or with DMSO andincubated at 28 °C with shaking for 4 h.

tag: treatment

value: 2.5 uM ketoconazole

tag: genetic background

source_name: control treatment

value: DMSO


title: EBV_M_2015_1_MAVSKO_Mu_MAZEBOV_Li_D3_2


title: 089 R1

source_name: novel antifungal treatment


title: IgG2b rep2 SNP

type: genomic

city: Innsbruck

first: Mirjana

last: Efremova

address: Innrain 80-82

country: Austria

institute: Medical University of Innsbruck

description: Affymetrix Mouse Diversity Array

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing:
The SNP arrays were processed, quantile-normalized, and median-polished using the Aroma Affymetrix CRMAv2 algorithm. Copy number alteration (CNA) for each probe were computed as log2-ratios between the probe signal intensities of each sample and the reference skin sample and then those ratios were segmented using the circular binary segmentation algorithm implemented in the R package DNAcopy
*_cna.txt: Segmented CNA - output from DNAcopy

label: biotin

molecule: genomic DNA

source_name: tumor cells

label_protocol: standard Affymetrix protocol

extract_protocol: Genome-wide copy number profiles of two wt samples (day 23 and day 46), two RAG1-/- samples (day 13 and day 23), three aPD-L1 and three IgG2b samples, MC38 and skin germline DNA were obtained using the Affymetrix Mouse Diversity Array. The genotyping analyses were carried out at Eurofins Genomics (Ebersberg, Germany) using Affymetrix Mouse Diversity Array.

tag: strain background

tag: genotype/variation

value: wild type

tag: cell type

value: tumor cells

tag: time point

value: day 14


title: skin rep1 SNP

description: Affymetrix Mouse Diversity Array

source_name: skin

value: skin

value: day 23


title: IgG2b rep1 SNP

description: Affymetrix Mouse Diversity Array


title: aPDL1 rep3 SNP

description: Affymetrix Mouse Diversity Array


title: RAG1 day23 rep3 SNP

description: Affymetrix Mouse Diversity Array

value: immunodeficient Rag1-/-


title: aPDL1 rep2 SNP

description: Affymetrix Mouse Diversity Array


title: Ketoconazole 50 uM R2

source_name: antifungal treatment-low concentration

value: 50 uM ketoconazole


title: MC38 SNP

description: Affymetrix Mouse Diversity Array

value: day 0


title: IgG2b rep3 SNP

description: Affymetrix Mouse Diversity Array


title: Ketoconazole 50 uM R1


title: iPSC-derived neurons, biological rep2

city: Baltimore

first: Hongkai

last: Ji

state: Maryland

address: 615 North Wolfe Street, Rm E3638

department: Department of Biostatistics

institute: Johns Hopkins Bloomberg School of Public Health

description: Human iPSC-derived neurons

hyb_protocol: The labeled sense strand DNA was hybridized to the Affymetrix GeneChip human Exon 1.0 ST arrays for 17hr at 45 C with constant rotation (60 rpm). Affymetrix Fluidics Station 450 was used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinilated cDNA. The staining was further amplified using goat IgG as blocking reagent and biotinilated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.

scan_protocol: Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner and image analysis of each GeneChip was perfomed through the Affymetrix GeneChip Command Console version 2.0 (AGCC v2.0) software from Affymetrix, using the standard default settings.

data_processing: Data were processed using GeneBASE software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.

label: Biotin

organism: Homo sapiens

source_name: dopaminergic neurons derived from iPSCs

label_protocol: RNA samples were labeled using the Whole Transcript Sense Target Labeling protocol described by Affymetrix and reagent from Affymetrix. Briefly, ribosomal RNA was reduced from the samples using Ribominus Human/Mouse Transcriptome isolation kit (Invitrogen, Carlsbad, California) from 1 micrograms of total RNA. The isolated RNA was then used to synthesize first strand cDNA using random oligonucleotides with T7 promoter as primer and the SuperScript Choice System (Invitrogen, Carlsbad, California). Following the double stranded cDNA synthesis, the product was purified using cDNA clean-up column, and cRNA was generated through in vitro transcription. 10 ug of cRNA was then used to generate sense strand cDNA using random primer, dNTP-dUTP mix, and Superscript II reverse transcriptase (Invitrogen, Carlsbad, California). Sense strand cDNA was then purified using cDNA clean-up column, fragmented using UDG and APE at 37C for 60 minutes, and terminal labeled with biotinylated nucleotide and terminal DNA transferase at 37C for 60 minutes.

growth_protocol: We followed a dual-SMAD inhibition protocol (1) for differentiating human iPSCs into dopaminergic (DA) neurons. iPSCs are plated (35 × 103–40 × 103 cells per cm2) and grown for 11 days on matrigel (BD) in knockout serum replacement medium (KSR) containing DMEM, 15% knockout serum replacement, 2 mM L-glutamine and 10 μM β-mercaptoethanol. KSR medium was gradually shifted to N2 medium starting from day 5 of differentiation. On day 11, media is changed to Neurobasal medium with B27 supplement and L-Glutamine (Invitrogen) supplemented with CHIR (until day 13) and with BDNF (brain-derived neurotrophic factor, 20 ng/ml, R&D), ascorbic acid (0.2 mM, Sigma), GDNF (glial cell line-derived neurotrophic factor, 20 ng/ml; R&D), TGFβ3 (transforming growth factor type β3, 1 ng/ml; R&D), dibutyryl cAMP (0.5 mM; Sigma), and DAPT (10 μM; Tocris) for 9 days. On day 20, cells are dissociated using Accutase (Sigma-Aldrich) and replated under high cell density conditions (300 × 103–400 × 103 cells per cm2) on dishes pre-coated with polyornithine (15 μg/ml) and laminin (1 μg/ml) in differentiation medium (Neurobasal medium plus B27 supplement, BDNF, ascorbic acid, GDNF, dibutyryl cAMP, TGFβ3 and DAPT) until the desired maturation stage for RNA preparation.

extract_protocol: Total RNA were extracted using a Qiagen RNeasy kit.

value: iPSC-derived neurons


title: iPSCs, biological rep1

description: Human iPSCs, undifferentiated

source_name: human induced pluripotent stem cells

value: undifferentiated iPSCs


title: RAG1 day13 rep2 SNP

description: Affymetrix Mouse Diversity Array

value: day 13


title: iPSCs, biological rep2

description: Human iPSCs, undifferentiated


title: C. miR520, biological rep3

city: Nijmegen

first: Gerald

middle: W

last: Verhaegh

address: Geert Grooteplein Zuid 28

department: Urology

country: Netherlands

institute: Radboudumc

description: mirVana #4464066

hyb_protocol: Hybridization was performed using the GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix). Hybridization was performed for 16 hours at 45° at 60 rpm. Arrays were washed in the GeneChip® Fluidics station FS 450 (Affymetrix).

scan_protocol: Affymetrix GeneChip® Scanner 3000 7G.

data_processing:
Partek Genomics Suite 6.6. Robust Multiarray Average (RMA) algorithm was used for background correction of probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: PANC-1 + miR-520f

label_protocol: cDNA synthesis, amplification and biotin labeling were performed using the GeneChip® WT PLUS Reagent kit (Affymetrix).

growth_protocol: PANC-1 cells were grown in RPMI-1640 medium supplemented with 10% FCS and 2 mM glutamine.

extract_protocol: 72 hours after transfection total RNA was extracted using TRIzol reagent (Invitrogen).

treatment_protocol: Cells were transfected with 20 nM miRNA mimics (mirVana, Ambion) using Lipofectamine RNAiMAX Transfection Reagent (Invitrogen).

tag: cell line

tag: cell line origin

value: pancreatic carcinoma


title: iPSC-derived neurons, biological rep1

description: Human iPSC-derived neurons


title: WT day46 rep1 SNP

description: Affymetrix Mouse Diversity Array

value: day 46


title: B. NC, biological rep1

description: mirVana #4464058

source_name: PANC-1 + negative control

value: negative control


title: C. miR520, biological rep2

description: mirVana #4464066


title: A. NT, biological rep1

description: Lipofectamine RNAiMAX only

source_name: PANC-1 non-transfected

value: non-transfected


title: aPDL1 rep1 SNP

description: Affymetrix Mouse Diversity Array


title: B. NC, biological rep3

description: mirVana #4464058


title: C. miR520, biological rep1

description: mirVana #4464066


title: WT day23 rep1 SNP

description: Affymetrix Mouse Diversity Array


title: A. NT, biological rep2

description: Lipofectamine RNAiMAX only


title: A. NT, biological rep3

description: Lipofectamine RNAiMAX only


title: B. NC, biological rep2

description: mirVana #4464058


title: blood_Q35_59

city: Kodaira

first: Daimei

last: Sasayama

address: 4-1-1 Ogawahigashi-machi

country: Japan

institute: National Center of Neurology and Psychiatry

hyb_protocol: As described elsewhere (Adler, A. J., Wiley, G. B., Gaffney, P. M. Infinium Assay for Large-scale SNP Genotyping Applications. J. Vis. Exp. (81), e50683, doi:10.3791/50683 (2013).).

scan_protocol: Genotypes were examined using the HumanOmniExpressExome-8 v1.2 BeadChip (Illumina, Inc., San Diego).

data_processing:
A total of 954,703 SNPs were assessed for quality using the PLINK v1.07 software [20]. All SNPs with a call rate below 90%, a deviation from Hardy-Weinberg equilibrium at an error level of P < 0.001, or a minor allele frequency of less than 5% were excluded, and duplicated SNPs were removed. The remaining 514,227 SNPs were used for subsequent analyses.
The "Matrix processed" file contains the Genotype, Score, Theta, R, B allele frequency and log R ratio.  The "Matrix_signal_intensities" contains the X raw, X, Y raw, Y values. Both of these files are available on the series record.

label: Cy3 and Cy5

source_name: venous blood

extract_protocol: Genomic DNA was prepared from venous blood according to standard procedures.

value: venous blood

tag: age

tag: Sex

value: female

tag: physical status

value: healthy


title: blood_Q35_61

label_protocol: As described elsewhere (Adler, A. J., Wiley, G. B., Gaffney, P. M. Infinium Assay for Large-scale SNP Genotyping Applications. J. Vis. Exp. (81), e50683, doi:10.3791/50683 (2013).).

value: male


title: blood_Q35_58


title: blood_Q35_64


title: blood_Q35_63


title: blood_Q35_60


title: blood_Q35_62


title: blood_Q35_54


title: blood_Q35_53


title: blood_Q35_56


title: blood_Q35_51


title: blood_Q35_57


title: blood_Q35_52


title: blood_Q35_55


title: blood_Q35_50


title: blood_Q35_49


title: blood_Q35_48


title: blood_Q35_47


title: blood_Q35_45


title: blood_Q35_46


title: blood_Q35_43


title: blood_Q35_44


title: blood_Q35_42


title: EBV_M_2015_1_C57BLL6_Mu_MAZEBOV_Li_D5_1

value: Microarray


title: MSC180314 P6  co-cul

city: Hannover

first: Ralf

last: Hass

state: Germany

address: Carl-Neuberg-Str. 1

department: Gynecology

country: Germany

institute: Hannover Medical School

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol V5.7’, except that 500ng of each fluorescently labeled cRNA population were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ using the extraction protocol file ‘GE1_107_Sep09.xml’. Processed intensity values of the green channel, ‘gProcessedSignal’ (gPS) were normalized by global linear scaling: All gPS values of one sample were multiplied by an array-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the particular Microarray (‘Array I’ in the formula shown below). Accordingly, normalized gPS values for all samples (microarray data sets) were calculated by the following formula:   normalized gPSArray i = gPSArray i  x (1500 / 75th PercentileArray i)  Measurements of on-chip replicates (quintuplicates) were averaged using the geometric mean of normalized gPS values to retrieve one resulting value per probe and sample. Measurements that lay outside the interval of ‘1.42 x interquartile range‘ regarding the normalized gPS distribution of the respective on-chip replicate population, were excluded from averaging.   A lower intensity threshold (surrogate value) was defined as 1% of the reference 75th Percentile value (= 15). All of those normalized gPS values that fell below this intensity border, were substituted by the respective surrogate value of 15.

source_name: human mesenchymal stroma/stem cells (type 180314)  in passage 6 (P6), GFP-transduced after 7d co-culture with NIH:OVCAR-3 in passage 145 (P145) and double FACS sorting for GFP

label_protocol: 100 ng of total RNA were used to prepare aminoallyl-UTP-modified (aaUTP) cRNA (Amino Allyl MessageAmp™ II Kit; #AM1753; Life Technologies) as directed by the company (applying one-round of amplification). The labeling of aaUTP-cRNA was performed by use of CY3 POST-Labelling Reactive Dyes (25-8010-79; GE Healthcare Biosciences). Prior to the reverse transcription reaction, 1µl of a 1:10000 dilution of Agilent’s ‘One-Color spike-in Kit stock solution’ (#5188-5282, Agilent Technologies) were added to each total RNA sample.

extract_protocol: Total RNA was extracted by use of the RNeasy Mini Kit (Qiagen).

tag: gender

tag: protocol

value: mesenchymal stroma/stem cells (type 180314) in passage 6 (P6),  co-culture


title: NIH:OVCAR-3 P145 wt

source_name: human NIH:OVCAR-3 cells in passage 145 (P145), mcherry-transduced

value: NIH:OVCAR-3 cells in passage 145 (P145), wt


title: NIH:OVCAR-3 P145 co-cul

source_name: human mesenchymal stroma/stem cells (type 180314)  in passage 6 (P6), GFP-transduced after 7d co-culture with NIH:OVCAR-3 in passage 145 (P145), mcherry-transduced and double FACS sorting for mcherry

value: NIH:OVCAR-3 cells in passage 145 (P145), co-culture


title: blood_Q35_41


title: MSC180314 P6 wt

source_name: human mesenchymal stroma/stem cells (type 180314)  in passage 6 (P6), GFP-transduced

value: mesenchymal stroma/stem cells (type 180314) in passage 6 (P6), wt


title: blood_Q35_39


title: blood_Q35_37


title: blood_Q35_38


title: blood_Q35_36


title: Unstimulated MDA231 #3

city: Oxford

first: Zhichao

last: Ai

address: Roosevelt Drive

department: Kennedy Institute of Rheumatology

country: United Kingdom

institute: University of Oxford

data_processing: For each gene, ΔCt was calculated using the same threshold (0.2) for all genes and Ct>35 considered as no expression, followed by normalization to 5 housekeeping genes (Hsp90ab1, Gusb, Hprt1, Gapdh, and Actb) included in each array, followed by calculation of ΔΔCt for each gene from two arrays: ΔΔCt = ΔCt1 – ΔCt2, where ΔCt1 is the DSS-treated mice group and ΔCT2 is the untreated mice group, using the program provided by Qiagen/SA Biosciences

label: SYBR Green

source_name: MDA-MB-231(ATCC® HTB-26™)

label_protocol: Quantitative reverse transcription real-time PCR (qRT-PCR) was used to quantify the amounts of mRNA in the colon using inflammatory gene RT2 Profiler PCR Arrays manufactured by Qiagen/SA Biosciences. The arrays included 84 assay genes, 5 housekeeping genes, and reverse transcription efficiency and DNA contamination controls. cDNA synthesis was performed from 1 µg of total RNAs using RT2 PCR Array First Strand Kit(Qiagen/SA Biosciences).

extract_protocol:
Total RNA was extracted and reverse-transcribed using, and loaded onto RT² Profiler™ PCR Arrays. Quantitative real-time PCR was performed for the expression of genes that encodeseveral classes of protein factors including cell adhesion, ECM components, cell cycle, cell growth and proliferation, apoptosis, transcription factors and regulators and other genes related to tumor metastasis.
Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

value: unstimulated

tag: sample type

value: control


title: Unstimulated MDA468 #3

source_name: MDA-MB-468(ATCC® HTB-132™)


title: blood_Q35_35


title: MDA468 under MDMs conditioned medium #4

value: conditioned medium

value: test


title: blood_Q35_40


title: MDA468 under MDMs conditioned medium #3


title: blood_Q35_34


title: Unstimulated MDA231 #4


title: Unstimulated MDA468 #4


title: blood_Q35_33


title: HP_7

city: Paris

first: Martin

last: BEAUMONT

address: 16  rue Claude Bernard

department: INRA AgroParisTech

institute: UMR914 PNCA

hyb_protocol: For each sample, 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug ) were fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 25x Agilent Fragmentation Buffer (Agilent Technologies) and 10x Agilent Blocking Agent (Agilent Technologies)following the manufacturer's instructions. Afterwards, for each sample 25 µl of 2x Agilent hybridization buffer (Agilent Technologies) were added to the fragmentation mixture and hybridized to the microarrays for 17 hours at 65°C in a rotating Agilent Hybridization Oven (Agilent Technologies.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the G2565CA Scanner system (Agilent Technologies) using a scan protocol with a resolution of 3 µm and a dynamic range of 20 bit.

data_processing: The scanned images were analyzed using the Feature Extraction Software v.10.7.3.1 (Agilent  Technologies) with default parameters (protocol: GE1_107_Sep09 and Grid: 028279_D_F_20120224). Signal intensities were normalized with a log2 transformation and centered by array (limma function in R).  The gene name-level data are available on the series record. The sample table includes normalized data for all probes on the array.

organism: Rattus norvegicus

source_name: Colonocyte_Male Wistar rat

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Low Input Quick Amp Labeling kit  (Agilent Technologies), followed by a purification step using RNAeasy columns(QIAGEN).  Specific activities and RNA yields were determined using a NanoDrop ND-1000 (Thermo Fisher Scientific).

growth_protocol: Wistar male  rats were fed ad libitum with a normal or a high protein isocaloric diet (14 vs 55 % of energy provided by protein) during 15 days. . The animals were maintained in a 12:12-h light-dark cycle with the dark period beginning at 7:00 PM. At the end of the experiments, rats were anesthetized with pentobarbital sodium (40 mg/kg body weight)

extract_protocol: RNA was extracted with trizol extraction and then purified with Rneasy easy mini kit and DNAse I (Qiagen). RNA quality was checked by determination of RNA Integrity Number was with 2100 Bioanalyser (Agilent Technologies).

treatment_protocol: Colon was flushed with a NaCl 9 g/l solution and then with a Ca2+ and Mg2+ -free Krebs Henseleit bicarbonate (pH 7.4) buffer solution containing 10mM HEPES, 5mM DTT, and 2.5g bovine serum albumin and equilibrated against a mixture of O2 and CO2 (19:1, vol/vol). Then, colon was perfused for 20 min at 37°C with the same buffer containing 10 mM EDTA. Colonocytes were detached by tapping gently the colon and washed  three times in PBS by centrifugation (200 g, 3 min)

tag: strain

value: Wistar

value: colon

value: Colonocyte

tag: diet

value: High protein diet


title: MDA231 under MDMs conditioned medium #3


title: NP_7

tag: tissue

value: Normal protein diet


title: HP_6


title: Unstimulated MDA468 #2

tag: treatment


title: blood_Q35_31

value: venous blood


title: NP_6


title: MDA468 under MDMs conditioned medium #2


title: NP_5


title: HP_4


title: HP_5


title: NP_4


title: HP_3


title: NP_3


title: blood_Q35_29

value: healthy


title: HP_1

value: male


title: blood_Q35_28


title: blood_Q35_32


title: blood_Q35_26

value: female


title: blood_Q35_27


title: Unstimulated MDA231 #2


title: NP_2


title: HP_2


title: blood_Q35_25


title: blood_Q35_24


title: blood_Q35_30


title: blood_Q35_23


title: blood_Q35_21


title: blood_Q35_22


title: MDA231 under MDMs conditioned medium #2


title: blood_Q35_19


title: blood_Q35_20


title: blood_Q35_18


title: lateral_fluid_percussion_trauma_rat_1month_frontal_cortex_rep_3

city: Marseille

first: PABAN

last: Veronique

address: 3 place V. Hugo

institute: Aix-Marseille Universite

description: Gene expression in rat  frontal cortex  1 month after lateral fluid percussion trauma

hyb_protocol: Hybridization was performed in a hybridization oven at 65◦C for 17 hr  at 10rpm into SurePrint G3 Rat GE microarray slides (8×60K G4853A, Agilent Technologies, Santa Clara, CA) containing 60,000 oligonucleotide probes.

scan_protocol: Hybridized microarray slides were then washed according to manufacturer’s instructions and scanned using an AgilentMicroarray Scanner, using the Agilent Feature Extraction Software (Agilent Technologies).

data_processing: Quantification files derived from the Agilent Feature Extraction Software were analyzed using the AgiND package (http://tagc.univmrs.fr/AgiND). We also used the AgiND R package for quality control and normalization. Quantile methods and a background correction were used for data normalization.

source_name: lateral fluid percussion trauma

label_protocol: Sample amplification and labeling followed the one-color microarray-based gene expression analysis (low input quick amp labeling) protocol (version 6.5, May 2010) recommended by Agilent Technologies.  In brief, 200 ng of each total RNA sample was reverse transcribed into cDNA using oligo dT-T7 promoter primer. Labeled cRNA was synthesized from the cDNA. The reaction was performed in a solution containing dNTP mix, cyanine 3-dCTP, and T7 RNA Polymerase, and incubated at 40◦C for 2 hr. Qiagen’s RNeasy mini spin columns are used for purification of the amplified cRNA samples. cRNA are quantited using NanoDrop Spectrophotometer version 3.2.1. 600ng of cyanine 3-labeled, linearly amplified cRNA are used for hybrization.

extract_protocol: Frontal cortex tissues were homogenized and purified with mirVana miRNA Kit (AB Applied-Ambion, France) according to the manufacturer’s protocol.

value: Sprague–Dawley

value: frontal cortex

tag: post trauma time

value: 1 month


title: sham_lateral_fluid_percussion_trauma_rat_1month_frontal_cortex_rep_2

description: Gene expression in  frontal cortex  of sham rat. Rat was sacrificed 1 month after surgery

source_name: sham rat


title: blood_Q35_17


title: lateral_fluid_percussion_trauma_rat_1month_frontal_cortex_rep_2


title: blood_Q35_16


title: NP_1


title: rotational_trauma_rat_1month_frontal_cortex_rep_3

description: Gene expression in rat  frontal cortex   1 month after head acceleration rotational trauma

source_name: head acceleration rotational trauma


title: sham_lateral_fluid_percussion_trauma_rat_1month_frontal_cortex_rep_4


title: blood_Q35_15


title: sham_lateral_fluid_percussion_trauma_rat_1month_frontal_cortex_rep_3


title: rotational_trauma_rat_1month_frontal_cortex_rep_2


title: Lm_7C_Anaerobic_Rep2

city: Northampton

first: Stuart

middle: C

last: Allen

state: Northamptonshire

address: Boughton Green Road

department: Faculty of Health and Society

institute: University of Northampton

description: Gene expression in exponential phase cells grown at 7C under limited oxygen

hyb_protocol: 600ng of labelled RNA was prepared using the Hybridisation kit (Agilent  5188-5242  ) Briefly, 600ng RNA was mixed with 5ul 10X GE blocking reagent and water added to 24ul, 1ul Fragmentation buffer was added and the samples incubated at 60C for 30 minutes. Samples were then cooled on ice before a further 25ul of hybridisation buffer was added. Samples were mixed by pipetting and centrifuged at 8000rpm for 1 minute to remove any bubbles. 40ul of each sample was used per individual array.

scan_protocol: The slides were scanned on an Agilent Technologies Scanner (G2505C) using the Agilent 1 colour HD setting for 15K arrays, using a scan resolution of 5um. The resultant scan image was imported into Agilent Feature Extraction software and the data extracted.

data_processing: Raw data had background subtracted and were then normalised using oligo's ordinary quantile normalisation.

organism: Listeria monocytogenes

source_name: Microbiological culture

label_protocol: 50ng of RNA was labelled using the Agilent Low Input Quick Amp WT kit (Agilent 5190-2943). Briefly, 50ng RNA plus Spike-Ins** were used for the 1st step of cDNA synthesis using WT primers. WT primers consist of a mixture of oligo dT- and random nucleotide-based T7 promoter primers. cRNA is then transcribed and amplified from this 1st step cDNA, incorporating CY3 in the process

growth_protocol: Overnight cultures were prepared by addition of a single colony into 100ml of BHI broth followed by overnight incubation at 37°C under static, aerobic conditions. Overnight cultures were diluted 1:100 (~5 x 10e5 cfu/ml) into pre-tempered and/or pre-reduced BHI broth and at regular intervals, 100μl aliquots were taken, serially diluted in PBS and plated by drop plate method. Plates were air dried and total viable counts obtained after aerobic incubation at 37°C for 24 hours. For low temperature and low temperature/anaerobic conditions samples were taken for the first 12 hours at two hourly intervals. Samples were then taken at 24 hours intervals.

extract_protocol: Upon reaching exponential phase under test conditions (anaerobiosis, refrigeration, anaerobiosis/refrigeration combined) 3ml aliquots of cultures were transferred into centrifuge tubes containing 2 volumes (6 ml) RNA Protect solution (Qiagen, Manchester, UK) for RNA stabilisation. Cells were pelleted by centrifugation (5000x g, 10 minutes, 4°C), supernatants discarded, and pellets resuspended in 700μl of TE buffer (10 mM Tris–HCl pH 8.0 and 1 mM EDTA pH 8.0). Suspensions were transferred to matrix B lysis tubes (MP Biomedicals, UK) and underwent three rounds of mechanical disruption using a Fastprep device at speed setting 6 for 45 seconds. Tubes were briefly centrifuged to pellet the matrix and supernatant was transferred to a new microtube. Extracted RNA was purified by use of RNeasy kits as per manufacturer’s instructions.

treatment_protocol: Anaerobic conditions were generated through the use of an anaerobic cabinet (Don Whitley Scientific Limited, West Yorkshire, UK). Anaerobic indicator strips were used to ensure anaerobic conditions were generated and maintained throughout testing (Oxoid, Basingstoke, UK). Test broths were pre-reduced overnight before use. Low temperature environments (7°C) were achieved through the use of a refrigerated incubator. For low temperature and anaerobic conditions in combination media were first pre-reduced overnight in an anaerobic cabinet. Upon inoculation with test cultures broths were transferred to anaerojars (Oxoid, Basingstoke, UK) containing anaerogen sachets (Oxoid, Basingstoke, UK).

tag: serotype

value: serotype 1/2a


title: lateral_fluid_percussion_trauma_rat_1month_frontal_cortex_rep_1


title: sham_rotational_trauma_rat_1month_frontal_cortex_rep_1

source_name: sham rotational trauma rat


title: rotational_trauma_rat_1month_frontal_cortex_rep_1


title: Lm_7C_Aerobic_Rep4

description: Gene expression in exponential phase cells grown at 7C aerobically


title: sham_lateral_fluid_percussion_trauma_rat_1month_frontal_cortex_rep_1


title: Lm_7C_Anaerobic_Rep4


title: sham_rotational_trauma_rat_1month_frontal_cortex_rep_2


title: blood_Q35_13


title: sham_rotational_trauma_rat_1month_frontal_cortex_rep_3


title: blood_Q35_14


title: Lm_7C_Aerobic_Rep3


title: blood_Q35_12


title: Lm_7C_Anaerobic_Rep1


title: 24h WT and KO replicate 1

city: Tampere

first: Ville

middle: Kalle Tapio

last: Kytölä

address: Finn-Medi 2, Biokatu 8

department: BioMediTech

country: Finland

institute: University of Tampere

description:
Furin treated time point 24h WT and KO biological replicate 1
US83400189_252800514373_S01_GE2_107_Sep09_2_3

hyb_protocol: Hybridizations were performed with Agilent ”Gene Expression Hybridization” kit (Product number 5188-5242). The chips were washed with the Gene Expression Wash Pack according to the instructions.

scan_protocol: Scanning was performed with Agilent Technologies Scanner, model G2565CA.

data_processing: Scan results were converted into numerical data by the Agilent Feature Extraction software version 10.7.3. The data was analyzed using the R software. Raw probe level intensity values were background corrected and normalized with loess regression and quantile normalization using R package “limma”.

source_name: WT_LPS for 24h

growth_protocol: C57BL/6 mice were euthanized by CO2 inhalation. Cells were elicited from the peritoneal cavity by injecting 5 ml of cold, sterile PBS supplemented with 3% FBS (Gibco) and 2 mM EDTA. A gentle massage of the peritoneum was performed to dislodge any attached cells into the PBS solution. The fluid was then aspirated through a syringe and immediately transferred to 50-ml polypropylene tubes kept on ice. This procedure was repeated twice. Peritoneal cells were then centrifuged and resuspended in RPMI 1640 medium supplemented with 10% (vol/vol) heat-inactivated FBS (Gibco), penicillin (100 U/ml), streptomycin (100 μg/ml), glutamine (2 mM), 50 μM 2-mercaptoethanol, and 10 mM HEPES (Sigma-Aldrich). The cells were counted, seeded on six-well plates at a density of 1 × 106 cells/ml, and cultured for 24 h at 37°C in a 5% CO2 humidified atmosphere. After 24 h, cells were washed three times with PBS to remove nonadherent cells, and fresh RPMI 1640 medium supplemented with 1% FBS was added to adherent cells. After 1 h of incubation at 37°C in a 5% CO2 humidified atmosphere, the macrophages were stimulated for 4 h. Subsequently, the cells were scraped and collected for RNA extraction.

extract_protocol: The samples were collected and the RNA was isolated using Qiagen RNeasy on-column DNase (Qiagen, Düsseldorf, Germany). 50 ng of purified RNA was amplified and dye labeled using Agilent’s Low Input Quick Amp Labeling kit and RNA Spike In kit (Agilent Technologies, California, USA). Initial and purified RNA contents along with dyed and amplified cRNA contents were measured with a NanoDrop ND-2000 (Thermo Fisher Scientific, Massachusetts, USA). RNA and cRNA quality was inspected using the Agilent 2100 Bioanalyzer RNA 6000 Nano kit (Agilent Technologies, California, USA)

tag: strain background

tag: genotype/variation

value: WT

value: peritoneal macrophages

tag: stimulated with

value: LPS for 24h

source_name: FURIN KO_LPS for 24h

value: FURIN KO


title: Lm_7C_Anaerobic_Rep3


title: 24h WT and KO replicate 2

description:
Furin treated time point 24h WT and KO biological replicate 2
US83400189_252800514373_S01_GE2_107_Sep09_2_4

label_protocol: 50 ng of purified RNA was amplified and dye labeled using Agilent’s Low Input Quick Amp Labeling kit and RNA Spike In kit (Agilent Technologies, California, USA)

tag: cell type


title: blood_Q35_11


title: 4h WT and KO replicate 1

description:
Furin treated time point 4h WT and KO biological replicate 1
US83400189_252800514373_S01_GE2_107_Sep09_2_1

source_name: WT_LPS for 4h

value: LPS for 4h

source_name: FURIN KO_LPS for 4h


title: blood_Q35_10

source_name: venous blood


title: blood_Q35_9


title: Lm_7C_Aerobic_Rep2


title: Lm_37C_Anaerobic_Rep3

description: Gene expression in exponential phase cells grown at 37C under limited oxygen


title: blood_Q35_7


title: blood_Q35_8


title: 4h WT and KO replicate 2

description:
Furin treated time point 4h WT and KO biological replicate 2
US83400189_252800514373_S01_GE2_107_Sep09_2_2


title: blood_Q35_6


title: Lm_7C_Aerobic_Rep1


title: Lm_37C_Anaerobic_Rep2


title: 1h WT and KO replicate 2

description:
Furin treated time point 1h WT and KO biological replicate 2
US83400189_252800514373_S01_GE2_107_Sep09_1_4

source_name: FURIN KO_LPS for 1h

value: LPS for 1h

source_name: WT_LPS for 1h


title: Lm_37C_Anaerobic_Rep4


title: Untreated WT and KO replicate 2

description:
Furin untreated WT and KO biological replicate 2
US83400189_252800514373_S01_GE2_107_Sep09_1_2

source_name: FURIN KO_none (untreated)

value: none (untreated)

source_name: WT_none (untreated)


title: blood_Q35_4


title: CSF_Q35_64

type: protein

description: Sample name: RG64

hyb_protocol: As described elsewhere [SomaLogic. Somascan technical white paper 2014. http://www.somalogic.com/somalogic/media/Assets/PDFs/SSM-002-Rev-2-SOMAscan-Technical-White-Paper-3-7-15.pdf].

scan_protocol: Proteomic assessments were performed as described elsewhere [De Groote MA et al. PLoS One. 2013;8(4):e61002;.Gold L et al. N Biotechnol. 2012 Jun 15;29(5):543-9.].

data_processing: Normalization and interrun calibration were performed as described elsewhere [SomaLogic. Somascan technical white paper 2014. http://www.somalogic.com/somalogic/media/Assets/PDFs/SSM-002-Rev-2-SOMAscan-Technical-White-Paper-3-7-15.pdf]. In brief, correction for systematic effects on the data introduced during the hybridization step, median normalization within an array, and calibration between plates were performed.

label: not provided

molecule: protein

source_name: cerebrospinal fluid

extract_protocol: Non-fasting CSF was drawn between 1000 h and 1600 h from the L4-L5 or L3-L4 interspace, with the subject in the left decubitus position. The samples were immediately transferred on ice, centrifuged at 4000 × g, aliquoted and stored at −80°C until they were assayed.

value: cerebrospinal fluid


title: CSF_Q35_62

description: Sample name: RG62

label_protocol: As described elsewhere [SomaLogic. Somascan technical white paper 2014. http://www.somalogic.com/somalogic/media/Assets/PDFs/SSM-002-Rev-2-SOMAscan-Technical-White-Paper-3-7-15.pdf].


title: Lm_37C_Aerobic_Rep4

description: Gene expression in exponential phase cells grown at 37C aerobically


title: CSF_Q35_63

description: Sample name: RG63


title: Ketoconazole 50 uM R3

source_name: antifungal treatment-low concentration

value: 50 uM ketoconazole

tag: genetic background

source_name: control treatment

value: DMSO


title: Lm_37C_Aerobic_Rep3


title: 089 R2

source_name: novel antifungal treatment


title: blood_Q35_3

value: venous blood

tag: age

value: healthy


title: Lm_37C_Aerobic_Rep1


title: Lm_37C_Aerobic_Rep2


title: 1h WT and KO replicate 1

description:
Furin treated time point 1h WT and KO biological replicate 1
US83400189_252800514373_S01_GE2_107_Sep09_1_3


title: Untreated WT and KO replicate 1

description:
Furin untreated WT and KO biological replicate 1
US83400189_252800514373_S01_GE2_107_Sep09_1_1


title: Lm_37C_Anaerobic_Rep1


title: blood_Q35_5

tag: Sex

value: male


title: blood_Q35_2

tag: physical status


title: blood_Q35_1

value: female


title: Ketoconazole 2 uM 5-R2

source_name: antifungal treatment-high concentration

value: 2.5 uM ketoconazole


title: CSF_Q35_59

description: Sample name: RG59


title: CSF_Q35_61

description: Sample name: RG61


title: CSF_Q35_56

description: Sample name: RG56


title: CSF_Q35_57

description: Sample name: RG57


title: CSF_Q35_60

description: Sample name: RG60


title: CSF_Q35_51

description: Sample name: RG51


title: CSF_Q35_49

description: Sample name: RG49


title: CSF_Q35_54

description: Sample name: RG54


title: CSF_Q35_52

description: Sample name: RG52


title: CSF_Q35_44

description: Sample name: RG44


title: CSF_Q35_45

description: Sample name: RG45


title: CSF_Q35_43

description: Sample name: RG43


title: CSF_Q35_46

description: Sample name: RG46


title: CSF_Q35_41

description: Sample name: RG41


title: CSF_Q35_42

description: Sample name: RG42


title: CSF_Q35_40

description: Sample name: RG40


title: CSF_Q35_38

description: Sample name: RG38


title: CSF_Q35_39

description: Sample name: RG39


title: CSF_Q35_58

description: Sample name: RG58


title: CSF_Q35_50

description: Sample name: RG50


title: CSF_Q35_31

description: Sample name: RG31


title: CSF_Q35_22

description: Sample name: RG22


title: CSF_Q35_34

description: Sample name: RG34


title: CSF_Q35_33

description: Sample name: RG33


title: blood_Q17_90

scan_protocol: Genotypes were examined using the HumanOmniExpressExome-8 v1.1 BeadChip (Illumina, Inc., San Diego).


title: CSF_Q35_25

description: Sample name: RG25


title: CSF_Q35_37

description: Sample name: RG37


title: CSF_Q35_20

description: Sample name: RG20


title: blood_Q17_89


title: CSF_Q35_21

description: Sample name: RG21


title: CSF_Q35_47

description: Sample name: RG47


title: blood_Q17_87


title: blood_Q17_86


title: blood_Q17_88


title: blood_Q17_85


title: CSF_Q35_19

description: Sample name: RG19


title: blood_Q17_82


title: blood_Q17_83


title: CSF_Q35_16

description: Sample name: RG16


title: CSF_Q35_17

description: Sample name: RG17


title: CSF_Q35_15

description: Sample name: RG15


title: CSF_Q35_18

description: Sample name: RG18


title: blood_Q17_81


title: CSF_Q35_11

description: Sample name: RG11


title: CSF_Q35_8

description: Sample name: RG8


title: CSF_Q35_9

description: Sample name: RG9


title: CSF_Q35_7

description: Sample name: RG7


title: blood_Q17_79


title: blood_Q17_80


title: blood_Q17_77


title: CSF_Q35_5

description: Sample name: RG5


title: blood_Q17_84


title: blood_Q17_78


title: blood_Q17_76


title: CSF_Q35_2

description: Sample name: RG2


title: CSF_Q17_88

description: Sample name: 88


title: CSF_Q17_89

description: Sample name: 89


title: CSF_Q17_87

description: Sample name: 87


title: CSF_Q17_84

description: Sample name: 84


title: CSF_Q35_3

description: Sample name: RG3


title: blood_Q17_72


title: blood_Q17_74


title: blood_Q17_75


title: blood_Q17_71


title: blood_Q17_73


title: CSF_Q17_83

description: Sample name: 83


title: CSF_Q17_85

description: Sample name: 85


title: Root, GS transgenic, recovery, replicate 2

city: Málaga

first: Juan Jesus

last: Molina-Rueda

state: Spain

address: Facultad de ciencias, campus universitario de teatinos, SN

department: Molecular biology and Biochemistry

country: Spain

institute: University of Málaga

description:
MR_T_Rec.2
Gene expression in root of GS transgenic under recovery condition, replicate 2

hyb_protocol: Hybridization (10-17 hours at 65ºC) and washing were carried out using the Gene Expression Hybridization kits (Agilent, Santa Clara CA, USA) with 1 µg of cRNA in 110 µL of hybridization buffer.

scan_protocol: Scan settings for one‐color scans were selected. Slide ID = <Auto detect>. Channels = G (green for Cy3). Scan region = 61 x 21.6 mm. Resolution = 5 μm. TIFF = 20 bit. PMT = 100%. XDR = <NoXDR>. Profile = AgilentHD_GX_1color

data_processing: The scanned images were analyzed with Feature Extraction Software v10.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Populus tremula x Populus alba

source_name: Root, GS transgenic, recovery

label_protocol: The protocol used for cRNA synthesis is a scaled‐down version of Agilent’s One‐color QuickAmp Labeling kit, adapted from Syed and Threadgill (2006)(Enhanced oligonucleotide microarray labeling and hybridization. Biotechniques 41: 685–686).  The Quick Amp Labeling Kit and RNA Spike‐in Kit (One‐color) (Agilent) were used for cDNA and cRNA synthesis, respectively, employing 250 ng of RNA, and Qiagen RNeasy Plant Mini Kit for cRNA purification.  Quantification of RNA synthesis and Cy3 incorporation was carried out using a nanodrop.  The yields (µg) and specific activities ([pmol Cy3 incorporated/ng RNA] x 103) were higher than 4.8 and 6.2, respectively, in all samples.

growth_protocol: Hybrid poplar (Populus tremula x P. alba, INRA 717-1B4) expressing ectopically the pine glutamine synthetase gene (GS1a) were generated and maintained as previously described (Gallardo, F. et al. (1999). Expression of a conifer glutamine synthetase gene in transgenic poplar. Planta 210: 19–26). Rooted cuttings (9–12-months old) of a fast-growing GS transgenic clone of poplar and the non-transgenic wild type  were planted in 6-inch pots containing a peat-based commercial growth medium (Metro-Mix 200, Scotts, Marysville, OH) without supplementary nutrients and raised in a growth chamber (24–26°C) supplying a 16h photoperiod (295–330 μmol m−2 s−1).

extract_protocol: RNA extraction was carried out as described in Liao et al. (2004) (Rapid Isolation of High‐Quality Total RNA from Taxus and Ginkgo. Prep. Biochem. Biotechnol. 34: 209–214). All RNA samples were treated with DNases (Turbo DNA Free kit, Applied Biosystems/Ambion, Austin TX), following the manufacturer’s protocol, and stored at -80°C. After DNase treatment, the quality of RNA was assessed both on agarose gels and spectrophotometrically. RNA quality in aliquots was additionally assessed using a 2100 Bioanalyzer using the RNA 6000 Nano Chip kit (Agilent, Santa Clara CA, USA); all samples presented RNA integration values higher than 7.

treatment_protocol: Water stress (drought) treatments and conditions of recovery from drought were as described in  El-Khatib et al. (2004) (Transgenic poplar characterized by ectopic expression of a pine cytosolic glutamine synthetase gene exhibits enhanced tolerance to water stress. Tree Physiol. 24: 729–36). Soil samples were weighed after drying overnight at 60°C and volumetric soil moisture contents (θ) were calculated.  Soil water potential was used as a proxy measure of plant water status.  Plants were watered every day until θ was between 50 and 55%, equivalent to a soil water potential of –1 to 0 MPa for well-watered conditions.  Drought stress was applied to plants by withholding irrigation for 7 days, by which time θ was between 15 and 20%, equivalent to a soil water potential of –2 to –3 MPa.  This level of water stress typically resulted in a decline in leaf stomatal conductance in wild type poplars from 0.138 mol m-2s-1 (SE 0.025) for well-watered leaves to 0.018 mol m-2s-1 (SE 0.002) during drought conditions (unpublished data).  After drought treatment, plants were watered every day for 5 days to recover the well-watered condition in soil.  Plant heights ranged from 45 to 55 cm at the collection day.

value: Root

tag: genotype

value: glutamine synthetase (GS1a) transgenic

tag: growth condition

value: Recovery


title: Root, wild type, recovery, replicate 2

description:
MR_C_Rec.2
Gene expression in root of wild type under recovery condition, replicate 2

source_name: Root, wild type, recovery

value: Wild type


title: Root, GS transgenic, recovery, replicate 1

description:
MR_T_Rec.1
Gene expression in root of GS transgenic under recovery condition, replicate 1


title: Root, wild type, recovery, replicate 1

description:
MR_C_Rec.1
Gene expression in root of wild type under recovery condition, replicate 1


title: blood_Q17_70


title: CSF_Q17_86

description: Sample name: 86


title: blood_Q17_69


title: blood_Q17_68


title: Root, GS transgenic, drought, replicate 1

description:
MR_T_Max.1
Gene expression in root of GS transgenic under drought condition, replicate 1

source_name: Root, GS transgenic, drought

value: Drought


title: blood_Q17_66


title: CSF_Q17_81

description: Sample name: 81


title: CSF_Q17_82

description: Sample name: 82


title: CSF_Q17_80

description: Sample name: 80


title: CSF_Q17_79

description: Sample name: 79


title: blood_Q17_67


title: Root, wild type, drought, replicate 1

description:
MR_C_Max.1
Gene expression in root of wild type under drought condition, replicate 1

source_name: Root, wild type, drought


title: Root, GS transgenic, well-watered, replicate 1

description:
MR_T_Pre.1
Gene expression in root of GS transgenic under well-watered condition, replicate 1

source_name: Root, GS transgenic, well-watered

value: Well-watered


title: Dermal fibroblast - control no peptide, 1hnrL-15 incubation+ 24h wait rep1

city: College Station

first: Jean-Philippe

last: Pellois

state: Texas

address: 300 Olsen Blvd

department: Biochemistry and Biophysics

institute: Texas A&M university

description:
replicate 1
SAMPLE 3

hyb_protocol: Biotin labeled cRNA are hybridized with Illumina Beadchips using Illumina standard protocol

scan_protocol: The beadchips are scanned using Illumina HiScanSQ scanner

data_processing: The data is analyzed using Illumina GenomeStudio software

source_name: Dermal fibroblast

label_protocol: The RNA samples are labeled with Biotin using Illumina TotalPrep RNA Amplification Kit

extract_protocol: Total RNAs were isolated with Trizol reagent (Invitrogen)

value: Normal human primary fibroblast

value: neonatal

value: foreskin


title: Root, wild type, well-watered, replicate 2

description:
MR_C_Pre.2
Gene expression in root of wild type under well-watered condition, replicate 2

source_name: Root, wild type, well-watered


title: MCH58 - control no peptide, 1hnrL-15 incubation+ 24h wait rep1

description:
replicate 1
SAMPLE 8

source_name: Fibroblast

tag: cell line

value: Immortalized MCH58 human fibroblast

value: skin


title: MCH58 - D-dTAT 5uM, 1h incubation+ 24 h wait rep2

description:
replicate 2
SAMPLE 7


title: Root, wild type, drought, replicate 2

description:
MR_C_Max.2
Gene expression in root of wild type under drought condition, replicate 2


title: Root, wild type, well-watered, replicate 1

description:
MR_C_Pre.1
Gene expression in root of wild type under well-watered condition, replicate 1


title: MCH58 - dTAT 5uM, 1h incubation+ 24 h wait rep1

description:
replicate 1
SAMPLE 4


title: Stem, wild type, recovery, replicate 2

description:
ST_C_Rec.2
Gene expression in stem of wild type under recovery condition, replicate 2

source_name: Stem, wild type, recovery

value: Stem


title: MCH58 - dTAT 5uM, 1h incubation+ 24 h wait rep2

description:
replicate 2
SAMPLE 5


title: MCH58 - D-dTAT 5uM, 1h incubation+ 24 h wait rep1

description:
replicate 1
SAMPLE 6


title: Stem, GS transgenic, recovery, replicate 1

description:
ST_T_Rec.1
Gene expression in stem of GS transgenic under recovery condition, replicate 1

source_name: Stem, GS transgenic, recovery


title: Stem, wild type, recovery, replicate 1

description:
ST_C_Rec.1
Gene expression in stem of wild type under recovery condition, replicate 1


title: blood_Q17_65

source_name: venous blood

value: venous blood


title: blood_Q17_64

value: healthy


title: CSF_Q17_78

description: Sample name: 78

value: cerebrospinal fluid

value: male


title: CSF_Q17_77

description: Sample name: 77

value: female


title: CSF_Q17_76

description: Sample name: 76


title: blood_Q17_63


title: CSF_Q17_75

description: Sample name: 75


title: blood_Q17_61


title: blood_Q17_60


title: Stem, GS transgenic, recovery, replicate 2

description:
ST_T_Rec.2
Gene expression in stem of GS transgenic under recovery condition, replicate 2


title: Root, GS transgenic, well-watered, replicate 2

description:
MR_T_Pre.2
Gene expression in root of GS transgenic under well-watered condition, replicate 2

value: Root


title: CSF_Q17_73

description: Sample name: 73


title: Root, GS transgenic, drought, replicate 2

description:
MR_T_Max.2
Gene expression in root of GS transgenic under drought condition, replicate 2

value: glutamine synthetase (GS1a) transgenic


title: Stem, GS transgenic, drought, replicate 2

description:
ST_T_Max.2
Gene expression in stem of GS transgenic under drought condition, replicate 2

source_name: Stem, GS transgenic, drought


title: CSF_Q17_72

description: Sample name: 72

source_name: cerebrospinal fluid


title: CSF_Q17_70

description: Sample name: 70


title: blood_Q17_59


title: Dermal fibroblast - D-dTAT 5uM, 1h incubation+ 24 h wait rep1

description:
replicate 1
SAMPLE 2


title: Stem, GS transgenic, drought, replicate 1

description:
ST_T_Max.1
Gene expression in stem of GS transgenic under drought condition, replicate 1


title: blood_Q17_58


title: CSF_Q17_74

description: Sample name: 74


title: lymph node unstable 5

city: Los Angeles

first: Katie

last: Chun

state: CA

address: 300 Medical Plaza

institute: University of California, Los Angeles

description:
Human Ref 8 v 3.0
4887770048_E

hyb_protocol: Standard Illumina hybridization protocol (carried out by UCLA Neuroscience Genomics Core).

scan_protocol: Standard Illumina scan protocol for gene expression profiling (carried out by UCLA Neuroscience Genomics Core).

data_processing: Raw probe intensity values and quantile-normalized gene expression values were generated by Illumina GenomeStudio software using Gene Expression module 1.1.1.  All probe and gene values are provided, with no additional filtering.

organism: Macaca mulatta

source_name: Rhesus macaque lymph node_unstable

label_protocol: Biotinylated cRNA were prepared with Ambion TotalPrep for Illumina arrays (carried out by UCLA Neuroscience Genomics Core).

extract_protocol: Total RNA was extracted from lymph node samples lysed in RLT buffer following the protocol from a QIAGEN RNeasy mini kit on a QIACube instrument and included DNase I treatment.

value: lymph node

value: Male

tag: social condition

value: unstable


title: Stem, GS transgenic, well-watered, replicate 1

description:
ST_T_Pre.1
Gene expression in stem of GS transgenic under well-watered condition, replicate 1

source_name: Stem, GS transgenic, well-watered

value: Well-watered


title: blood_Q17_57


title: lymph node unstable 4

description:
Human Ref 8 v 3.0
4887770048_D


title: CSF_Q17_71

description: Sample name: 71


title: CSF_Q17_69

description: Sample name: 69


title: lymph node unstable 3

description:
Human Ref 8 v 3.0
4887770041_G


title: Stem, wild type, drought, replicate 2

description:
ST_C_Max.2
Gene expression in stem of wild type under drought condition, replicate 2

source_name: Stem, wild type, drought

value: Wild type

value: Drought


title: FLRT2 overexpression

city: goyang

first: seungyeon

last: lee

address: dongguk-ro 32

department: life science

country: South Korea

institute: dongguk unversity

description: Sample name: SAMPLE 4

hyb_protocol: Following fragmentation, 0.75ug of cRNA were hybridized to the Illumina HumanHT-12 Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner

data_processing: Array data export processing and analysis was performed using Illumina Genomestudio v2011.1(Gene Expresion Module v1.9.0)

source_name: FLRT2 overexpression

label_protocol: Biotinylated cRNA were prepared from 0.55ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX).

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


title: ORF vector negative control

description: Sample name: SAMPLE 3

source_name: ORF vector negative control


title: CSF_Q17_68

description: Sample name: 68


title: FLRT2 downregulation

description: Sample name: SAMPLE 2

source_name: FLRT2 downregulation


title: lymph node unstable 2

description:
Human Ref 8 v 3.0
4887770041_F


title: Dermal fibroblast - dTAT 5uM, 1h incubation+ 24 h wait rep1

description:
replicate 1
SAMPLE 1

value: Normal human primary fibroblast

value: neonatal

value: foreskin


title: blood_Q17_56


title: Stem, wild type, drought, replicate 1

description:
ST_C_Max.1
Gene expression in stem of wild type under drought condition, replicate 1

value: Stem


title: Stem, wild type, well-watered, replicate 1

description:
ST_C_Pre.1
Gene expression in stem of wild type under well-watered condition, replicate 1

source_name: Stem, wild type, well-watered


title: blood_Q17_55

value: venous blood


title: CSF_Q17_66

description: Sample name: 66

value: healthy


title: blood_Q17_62


title: Mature Leave, GS transgenic, recovery, replicate 2

description:
ML_T_Rec.2
Gene expression in mature leaves of GS transgenic under recovery condition, replicate 2

source_name: Mature Leave, GS transgenic, recovery

value: Mature Leave

value: Recovery


title: blood_Q17_53

value: male


title: siRNA negative control

description: Sample name: SAMPLE 1

source_name: siRNA negative control


title: blood_Q17_52


title: CSF_Q17_64

description: Sample name: 64

value: cerebrospinal fluid

value: female


title: lymph node unstable 1

description:
Human Ref 8 v 3.0
4887770041_D

value: lymph node


title: Stem, wild type, well-watered, replicate 2

description:
ST_C_Pre.2
Gene expression in stem of wild type under well-watered condition, replicate 2


title: Stem, GS transgenic, well-watered, replicate 2

description:
ST_T_Pre.2
Gene expression in stem of GS transgenic under well-watered condition, replicate 2

value: glutamine synthetase (GS1a) transgenic


title: CSF_Q17_67

description: Sample name: 67


title: blood_Q17_51


title: CSF_Q17_63

description: Sample name: 63


title: blood_Q17_50


title: CSF_Q17_62

description: Sample name: 62


title: Mature Leave, GS transgenic, recovery, replicate 1

description:
ML_T_Rec.1
Gene expression in mature leaves of GS transgenic under recovery condition, replicate 1


title: blood_Q17_54


title: lymph node stable 3

description:
Human Ref 8 v 3.0
4887770042_E

source_name: Rhesus macaque lymph node_stable

value: Male

value: stable


title: blood_Q17_49


title: lymph node stable 2

description:
Human Ref 8 v 3.0
4887770042_C


title: CSF_Q17_61

description: Sample name: 61


title: lymph node stable 4

description:
Human Ref 8 v 3.0
4887770042_H


title: Mature Leave, wild type, recovery, replicate 2

description:
ML_C_Rec.2
Gene expression in mature leaves of wild type under recovery condition, replicate 2

source_name: Mature Leave, wild type, recovery

value: Wild type


title: CSF_Q17_65

description: Sample name: 65


title: blood_Q17_48


title: CSF_Q17_60

description: Sample name: 60


title: Mature Leave, wild type, recovery, replicate 1

description:
ML_C_Rec.1
Gene expression in mature leaves of wild type under recovery condition, replicate 1


title: lymph node stable 5

description:
Human Ref 8 v 3.0
4887770041_B


title: CSF_Q17_59

description: Sample name: 59


title: blood_Q17_47


title: lymph node stable 1

description:
Human Ref 8 v 3.0
4887770042_B


title: blood_Q17_46


title: CSF_Q17_58

description: Sample name: 58


title: CSF_Q17_57

description: Sample name: 57


title: Mature Leave, wild type, drought, replicate 2

description:
ML_C_Max.2
Gene expression in mature leaves of wild type under drought condition, replicate 2

source_name: Mature Leave, wild type, drought

value: Drought


title: blood_Q17_45


title: blood_Q17_44


title: Mature Leave, GS transgenic, drought, replicate 1

description:
ML_T_Max.1
Gene expression in mature leaves of GS transgenic under drought condition, replicate 1

source_name: Mature Leave, GS transgenic, drought


title: Mature Leave, wild type, drought, replicate 1

description:
ML_C_Max.1
Gene expression in mature leaves of wild type under drought condition, replicate 1


title: CSF_Q17_56

description: Sample name: 56


title: Hippocampus_High-CPF_rep20

city: Ft. Detrick

first: Christine

last: Baer

state: MD

address: 568 Doughten Drive

department: Environmental Health Program

institute: Excet, Inc. / USACEHR

description: Hippocampus RNA of rats administered with 10mg/kg/day CPF for 21 days

hyb_protocol: 10ug of biotinylated cRNA were fragmented and hybridized onto Affymetrix GeneChip Rat Genome 230 2.0 Arrays for 16 h at 45C.

scan_protocol: Hybridized GeneChip arrays were washed and stained using the Affymetrix Fluidic Station 450, and then scanned using the Affymetrix GeneChip scanner.

data_processing: Probe intensity data were summarized and normalized using the Robust Multichip Array (RMA) method using the Partek Genomics Suite v6.6.

source_name: Hippocampus, 10 mg/kg/day CPF

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip 3' IVT Express Kit User Manual, 2008, Affymetrix).

growth_protocol: All animals used in this study were housed and maintained in the animal facilities at WIL Research Laboratories, LLC (Ashland, OH) that are fully accredited by the Association for Assessment and Accreditation of Laboratory Animal Care International (AAALAC International). Research was conducted in compliance with the Animal Welfare Act, and other Federal statutes and regulations relating to animals and experiments involving animals and adheres to principles stated in the Guide for the Care and Use of Laboratory Animals (National Research Council 2011). Nine-week old Long Evans (LE) male rats were received from Charles River Laboratories, Inc. (Raleigh, NC) and acclimated for at least ten days. The animals were housed individually in suspended stainless steel wire mesh cages in a humidity and temperature-controlled room (50% ± 20% and 25 °C) with a 12-hour (h) light/12-h dark cycle (lights on at 0600). Rats were provided ad libitum access to rodent chow (Certified Rodent LabDiet 5002, PMI Nutrition International, LLC, St. Louis, MO) and reverse-osmosis treated water throughout the study. Individual body weights were recorded twice weekly.

extract_protocol: Total RNA including small non-coding RNA was isolated from the CA1 region of rat hippocampus using miRNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol.

treatment_protocol: Rats were 11 weeks old at the initiation of dosing, and individual body weights ranged from 350 g to 450 g. Two CPF formulations (3 or 10 mg/kg b.w./day) and the vehicle control (peanut oil) were administered by subcutaneous (s.c.) injection for 21 consecutive days (study days 1 - 20), approximately 24 h apart.

tag: strain

value: Long Evans

tag: gender

value: 14 wk

value: Hippocampus


title: CSF_Q17_55

description: Sample name: 55

tag: tissue


title: blood_Q17_43

source_name: venous blood


title: Mature Leave, GS transgenic, drought, replicate 2

description:
ML_T_Max.2
Gene expression in mature leaves of GS transgenic under drought condition, replicate 2


title: Mature Leave, GS transgenic, well-watered, replicate 1

description:
ML_T_Pre.1
Gene expression in mature leaves of GS transgenic under well-watered condition, replicate 1

value: Well-watered


title: Mature Leave, GS transgenic, well-watered, replicate 2

description:
ML_T_Pre.2
Gene expression in mature leaves of GS transgenic under well-watered condition, replicate 2


title: CSF_Q17_54

description: Sample name: 54


title: blood_Q17_42

value: venous blood


title: Mature Leave, wild type, well-watered, replicate 1

description:
ML_C_Pre.1
Gene expression in mature leaves of wild type under well-watered condition, replicate 1

source_name: Mature Leave, wild type, well-watered


title: Mature Leave, wild type, well-watered, replicate 2

description:
ML_C_Pre.2
Gene expression in mature leaves of wild type under well-watered condition, replicate 2


title: Hippocampus_High-CPF_rep19


title: Hippocampus_High-CPF_rep17


title: Hippocampus_High-CPF_rep15


title: blood_Q17_39

value: healthy


title: Young Leave, GS transgenic, recovery, replicate 1

description:
YL_T_Rec.1
Gene expression in young leaves of GS transgenic under recovery condition, replicate 1

source_name: Young Leave, GS transgenic, recovery

value: Young Leave


title: CSF_Q17_53

description: Sample name: 53

source_name: cerebrospinal fluid


title: Hippocampus_High-CPF_rep18


title: CSF_Q17_52

description: Sample name: 52


title: Hippocampus_High-CPF_rep14


title: Hippocampus_High-CPF_rep16


title: blood_Q17_40


title: Hippocampus_High-CPF_rep11


title: Hippocampus_High-CPF_rep12


title: blood_Q17_41


title: Young Leave, GS transgenic, drought, replicate 1

description:
YL_T_Max.1
Gene expression in young leaves of GS transgenic under drought condition, replicate 1

source_name: Young Leave, GS transgenic, drought


title: blood_Q17_37


title: CSF_Q17_51

description: Sample name: 51


title: Hippocampus_High-CPF_rep13


title: Young Leave, wild type, recovery, replicate 2

description:
YL_C_Rec.2
Gene expression in young leaves of wild type under recovery condition, replicate 2

source_name: Young Leave, wild type, recovery

value: Recovery


title: blood_Q17_38


title: Young Leave, wild type, drought, replicate 1

description:
YL_C_Max.1
Gene expression in young leaves of wild type under drought condition, replicate 1

source_name: Young Leave, wild type, drought


title: blood_Q17_36

value: male


title: Hippocampus_Low-CPF_rep20

description: Hippocampus RNA of rats administered with 3mg/kg/day CPF for 21 days

source_name: Hippocampus, 3 mg/kg/day CPF


title: Young Leave, wild type, recovery, replicate 1

description:
YL_C_Rec.1
Gene expression in young leaves of wild type under recovery condition, replicate 1


title: Young Leave, wild type, drought, replicate 2

description:
YL_C_Max.2
Gene expression in young leaves of wild type under drought condition, replicate 2


title: blood_Q17_35


title: blood_Q17_34


title: CSF_Q17_50

description: Sample name: 50

value: cerebrospinal fluid


title: Hippocampus_Low-CPF_rep18


title: CSF_Q17_46

description: Sample name: 46


title: CSF_Q17_47

description: Sample name: 47


title: CSF_Q17_49

description: Sample name: 49

value: female


title: CSF_Q17_45

description: Sample name: 45


title: CSF_Q17_44

description: Sample name: 44


title: CSF_Q17_48

description: Sample name: 48


title: blood_Q17_32


title: Hippocampus_Low-CPF_rep19


title: blood_Q17_33


title: Young Leave, GS transgenic, drought, replicate 2

description:
YL_T_Max.2
Gene expression in young leaves of GS transgenic under drought condition, replicate 2


title: Young Leave, wild type, well-watered, replicate 2

description:
YL_C_Pre.2
Gene expression in young leaves of wild type under well-watered condition, replicate 2

source_name: Young Leave, wild type, well-watered


title: Young Leave, GS transgenic, well-watered, replicate 1

description:
YL_T_Pre.1
Gene expression in young leaves of GS transgenic under well-watered condition, replicate 1


title: Hippocampus_Low-CPF_rep16


title: Young Leave, GS transgenic, well-watered, replicate 2

description:
YL_T_Pre.2
Gene expression in young leaves of GS transgenic under well-watered condition, replicate 2


title: Hippocampus_Low-CPF_rep15


title: Young Leave, wild type, well-watered, replicate 1

description:
YL_C_Pre.1
Gene expression in young leaves of wild type under well-watered condition, replicate 1


title: Hippocampus_Low-CPF_rep17


title: Hippocampus_Low-CPF_rep13


title: Hippocampus_Low-CPF_rep12


title: CSF_Q17_43

description: Sample name: 43


title: blood_Q17_31


title: blood_Q17_30


title: Hippocampus_Low-CPF_rep11


title: blood_Q17_29


title: blood_Q17_28


title: blood_Q17_27


title: CSF_Q17_40

description: Sample name: 40


title: blood_Q17_23


title: CSF_Q17_38

description: Sample name: 38


title: CSF_Q17_39

description: Sample name: 39


title: CSF_Q17_37

description: Sample name: 37


title: blood_Q17_21


title: blood_Q17_25


title: CSF_Q17_34

description: Sample name: 34


title: blood_Q17_24


title: CSF_Q17_36

description: Sample name: 36


title: Hippocampus_Control_rep20

description: Hippocampus RNA of rats administered with vehicle control for 21 days

source_name: Hippocampus, vehicle control


title: CSF_Q17_42

description: Sample name: 42


title: Hippocampus_Control_rep19


title: Hippocampus_Control_rep17


title: Hippocampus_Control_rep14


title: Hippocampus_Control_rep18


title: CSF_Q17_35

description: Sample name: 35


title: Hippocampus_Control_rep15


title: Hippocampus_Control_rep13


title: Hippocampus_Control_rep16


title: CSF_Q17_32

description: Sample name: 32


title: CSF_Q17_41

description: Sample name: 41


title: blood_Q17_22


title: Hippocampus_Control_rep12


title: CSF_Q17_33

description: Sample name: 33


title: blood_Q17_20


title: CSF_Q17_30

description: Sample name: 30


title: blood_Q17_26


title: Hippocampus_Control_rep11


title: Hippocampus_High-CPF_rep10

description: Hippocampus RNA of rats administered with 10mg/kg/day CPF for 21 days


title: CSF_Q17_29

description: Sample name: 29


title: blood_Q17_14


title: CSF_Q17_31

description: Sample name: 31


title: blood_Q17_19


title: blood_Q17_16


title: blood_Q17_18


title: CSF_Q17_28

description: Sample name: 28


title: Hippocampus_High-CPF_rep7


title: Hippocampus_High-CPF_rep9


title: CSF_Q17_27

description: Sample name: 27


title: blood_Q17_15


title: CSF_Q17_26

description: Sample name: 26


title: blood_Q17_13


title: CSF_Q17_25

description: Sample name: 25


title: Hippocampus_High-CPF_rep3


title: Hippocampus_High-CPF_rep4


title: blood_Q17_11


title: Hippocampus_High-CPF_rep8


title: blood_Q17_10


title: Hippocampus_High-CPF_rep5


title: blood_Q17_9


title: blood_Q17_17


title: blood_Q17_8


title: CSF_Q17_24

description: Sample name: 24


title: CSF_Q17_21

description: Sample name: 21


title: blood_Q17_7


title: Hippocampus_High-CPF_rep6


title: blood_Q17_12


title: CSF_Q17_20

description: Sample name: 20


title: CSF_Q17_19

description: Sample name: 19


title: blood_Q17_4


title: Young Leave, GS transgenic, recovery, replicate 2

description:
YL_T_Rec.2
Gene expression in young leaves of GS transgenic under recovery condition, replicate 2


title: CSF_Q17_22

description: Sample name: 22


title: CSF_Q17_23

description: Sample name: 23


title: blood_Q17_6


title: CSF_Q17_18

description: Sample name: 18


title: CSF_Q17_15

description: Sample name: 15


title: blood_Q17_3


title: blood_Q17_2


title: blood_Q17_5


title: Hippocampus_High-CPF_rep1


title: CSF_Q17_17

description: Sample name: 17


title: Hippocampus_High-CPF_rep2


title: CSF_Q17_13

description: Sample name: 13


title: Hippocampus_Low-CPF_rep7


title: Hippocampus_Low-CPF_rep9


title: CSF_Q17_16

description: Sample name: 16


title: Hippocampus_Low-CPF_rep8


title: Hippocampus_Low-CPF_rep10


title: Hippocampus_Low-CPF_rep6


title: blood_Q17_1


title: CSF_Q17_12

description: Sample name: 12


title: CSF_Q17_14

description: Sample name: 14


title: CSF_Q17_11

description: Sample name: 11


title: CSF_Q17_10

description: Sample name: 10


title: CSF_Q17_9

description: Sample name: 9


title: Hippocampus_Low-CPF_rep5


title: MDMs MDA468 Donor#4

source_name: Monocyte-derived macrophages

extract_protocol: Total RNA was extracted and reverse-transcribed using, and loaded onto RT² Profiler™ PCR Arrays. Quantitative real-time PCR was performed for the expression of 84 key genes mediating the inflammatory response.

value: Monocyte-derived macrophages


title: MDMs Control Donor#4

value: control


title: MDMs MDA231 Donor#4


title: CSF_Q17_7

description: Sample name: 7


title: CSF_Q17_8

description: Sample name: 8


title: MDMs MDA468 Donor#3


title: CSF_Q17_5

description: Sample name: 5


title: CSF_Q17_6

description: Sample name: 6


title: MDMs Control Donor#3


title: Hippocampus_Low-CPF_rep1


title: MDMs MDA231 Donor#3


title: Hippocampus_Control_rep9


title: Hippocampus_Control_rep10


title: Hippocampus_Control_rep5


title: Hippocampus_Control_rep6


title: Hippocampus_Low-CPF_rep3


title: MDMs Control   Donor#2


title: CSF_Q17_3

description: Sample name: 3


title: MDMs MDA468 Donor#2


title: CSF_Q17_2

description: Sample name: 2


title: Hippocampus_Control_rep7


title: Hippocampus_Control_rep8


title: Hippocampus_Control_rep4


title: CSF_Q17_4

description: Sample name: 4


title: MDMs MDA231 Donor#2


title: Hippocampus_Control_rep2


title: CSF_Q17_1

description: Sample name: 1


title: Hippocampus_Low-CPF_rep14


title: Hippocampus_Low-CPF_rep4


title: Hippocampus_Control_rep3


title: Hippocampus_Control_rep1


title: IL0RA-Impaired

city: Hamburg

first: Babett

last: Steglich

address: Martinistrasse 52

institute: Universitätsklinikum Hamburg-Eppendorf

hyb_protocol: Hybridised to Affymetrix Mouse Gene 1.0 ST Arrays according to standard Affymetrix protocols.

scan_protocol: Scanned according to standard Affymetrix protocols.

data_processing: Data was analyzed using R and the Bioconductor package affy. Samples were normalized by RMA with standard parameters.

source_name: IL0RA-Impaired Tr1-cells isolated from small intestine

label_protocol: Biotin-labeled according to standard Affymetrix protocols.

extract_protocol: RNA from cells was isolated with TRIzol LS reagent (Life Technologies) in accordance with the manufacturer’s protocol. RNA was subjected to reverse transcription with Superscript II (Invitrogen) with oligo (dT) primer in accordance with the manufacturer’s protocol.

treatment_protocol: Mice were injected with anti-CD3 (clone 2C11, 15μg,) i.p. two times every other day, and sacrificed 4 hours or 48 hours after the second injection.

value: CD4-DNIL-10R transgenic


title: LSCC adjacent non-neoplastic tissue sample N3

status: Public on Dec 29 2016

city: Beijing

first: Lin

last: Feng

state: Beijing

address: No.1, Dong Jiao Min Xiang Street  Dong Cheng District

country: China

institute: Beijing Tongren Hospital

description:
Gene expression in LSCC non-neoplastic tissue
surgically removed tissue sample

hyb_protocol: The labeled cRNAs were hybridized onto the microarray based on the manufacturer’s standard protocols.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg 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, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

treatment_protocol: A total number of 9 pairs of LSCC cancer tissues and adjacent non-neoplastic tissues were surgically removed between the years of 2012 to 2014 in Beijing Tongren Hospital. All tissue samples were stored at -80˚C refrigerator within 10 minutes after the resection.

tag: disease state

value: LSCC

tag: pair

tag: tumor stage

value: IV

value: adjacent non-neoplastic tissue


title: LSCC adjacent non-neoplastic tissue sample N7


title: IL10RA wildtype

source_name: IL10RA wildtype Tr1-cells isolated from small intestine

tag: genotype/variation

value: wildtype


title: LSCC adjacent non-neoplastic tissue sample N2


title: LSCC adjacent non-neoplastic tissue sample N9


title: LSCC adjacent non-neoplastic tissue sample N4


title: LSCC adjacent non-neoplastic tissue sample N5


title: LSCC adjacent non-neoplastic tissue sample N6


title: LSCC cancer tissue sample  C9

description:
Gene expression in LSCC cancer tissue
surgically removed tissue sample

source_name: LSCC cancer tissue sample

value: LSCC cancer tissue


title: LSCC cancer tissue sample  C4


title: LSCC cancer tissue sample  C6


title: LSCC adjacent non-neoplastic tissue sample N1


title: LSCC cancer tissue sample  C3


title: LSCC cancer tissue sample  C1


title: LSCC adjacent non-neoplastic tissue sample N8


title: LSCC cancer tissue sample  C8


title: LSCC cancer tissue sample  C2


title: LSCC cancer tissue sample  C7


title: NHT9

first: Tengxu

last: Wang

address: Tsinghua Yuan Street, No.1

department: School of Environment

institute: Tsinghua University

description: GeoChip data for sludge sample collected in Ninghai, thermophilic tank, September

hyb_protocol: Subsequently, the mixed solution was kept at 90 °C for 3 min for denaturation, and incubated at 37°C for 30 min before GeoChip hybridization was carried out at 67 °C for 24 hrs with a rotation at 20rpm in Agilent hybridization oven.

scan_protocol: After hybridization, Agilent Wash Buffers were applied to wash away unbounded DNA at ordinary temperature, and the arrays were scanned with a NimbleGen MS200 Microarray Scanner (Roche NimbleGen, Madison, WI, USA) at 633 nm. Eventually the images data were extracted by Agilent Feature Extraction program.

data_processing: The raw microarray data was analyzed by GeoChip Microarray Data Manager pipeline (http://ieg.ou.edu/microarray/) as previously described (Xu et al., 2010). We processed raw GeoChip data using the following steps: (i) remove the spots with a signal-to-noise ratio (SNR) less than 2.0; (ii) log-transformed the data and then, on each microarray, divide them by the mean intensity of all the genes; and (iii) remove genes detected only once in each digester. Finally we acquired GeoChip data for further analysis.

organism: uncultured bacterium

source_name: sludge microbes in anaerobic digestion systems

label_protocol: Purified DNA was first labeled with the fluorescent dye Cy-3 (GE Healthcare, CA, USA) using random priming as described previously (Cong et al., 2015), then purified by a QIAquick Purification kit (Qiagen, Valencia, CA, USA), and dried in a SpeedVac (Thermo Savant, NY, USA) at 45 °C for 45 min. The dried DNA was then resuspended into ??? μl of DNase/RNase-free distilled water and evenly mixed with ??? μl of hybridization solution, which contains 1 × Acgh blocking, 1 × HI-RPM hybridization buffer, 10 pM universal standard DNA, 0.05 μg/μl Cot-1 DNA, and 10% formamide (final concentrations).

extract_protocol:
Sludge samples were collected on the monthly basis from during October, 2012 to September, 2013. Briefly, 2 liters of each sludge sample were obtained near the outlets of anaerobic tanks, stored in a portable dry ice container and immediately transported to laboratory. A small part of each sample was kept at 4°C for physicochemical properties analysis, while others were precipitated by centrifugation at 14,000 g for 10 minutes. After centrifugation, the pellet was air dried for 30 min and stored at -80°C for DNA extraction, while the supernatant was decanted. It was noted that the solid content of all 48 samples was less than 10%.
DNA was extracted by MoBio PowerSoil DNA isolation kit (MoBio Laboratories, Carlsbad, CA, USA) and then purified by agarose gel electrophoresis followed by extractions with phenol and chloroform, and precipitation with butanol. After purifying, NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) were applied to access DNA quality, confirming that the A260/A280 ratio was between 1.8 to 2.0 and A260/A230 over 1.5.

tag: collected

value: Ninghai, thermophilic, Sep


title: LSCC cancer tissue sample  C5


title: NHT2

description: GeoChip data for sludge sample collected in Ninghai, thermophilic tank, February

value: Ninghai, thermophilic, Feb


title: NHT5

description: GeoChip data for sludge sample collected in Ninghai, thermophilic tank, May

value: Ninghai, thermophilic, May


title: NHT7

description: GeoChip data for sludge sample collected in Ninghai, thermophilic tank, July

value: Ninghai, thermophilic, Jul


title: NHT3

description: GeoChip data for sludge sample collected in Ninghai, thermophilic tank, March

value: Ninghai, thermophilic, Mar


title: NHT8

description: GeoChip data for sludge sample collected in Ninghai, thermophilic tank, August

value: Ninghai, thermophilic, Aug


title: NHT12

description: GeoChip data for sludge sample collected in Ninghai, thermophilic tank, December

value: Ninghai, thermophilic, Dec


title: NHT6

description: GeoChip data for sludge sample collected in Ninghai, thermophilic tank, June

value: Ninghai, thermophilic, Jun


title: NHT11

description: GeoChip data for sludge sample collected in Ninghai, thermophilic tank, November

value: Ninghai, thermophilic, Nov


title: NHM6

description: GeoChip data for sludge sample collected in Ninghai, mesophilic tank, June

value: Ninghai, mesophilic, Jun


title: NHM7

description: GeoChip data for sludge sample collected in Ninghai, mesophilic tank, July

value: Ninghai, mesophilic, Jul


title: NHT1

description: GeoChip data for sludge sample collected in Ninghai, thermophilic tank, January

value: Ninghai, thermophilic, Jan


title: NHT4

description: GeoChip data for sludge sample collected in Ninghai, thermophilic tank, April

value: Ninghai, thermophilic, Apr


title: NHT10

description: GeoChip data for sludge sample collected in Ninghai, thermophilic tank, October

value: Ninghai, thermophilic, Oct


title: NHM9

description: GeoChip data for sludge sample collected in Ninghai, mesophilic tank, September

value: Ninghai, mesophilic, Sep


title: NHM4

description: GeoChip data for sludge sample collected in Ninghai, mesophilic tank, April

value: Ninghai, mesophilic, Apr


title: QD7

description: GeoChip data for sludge sample collected in Qingdao WWTP, July

value: Qingdao, Jul


title: NHM2

description: GeoChip data for sludge sample collected in Ninghai, mesophilic tank, February

value: Ninghai, mesophilic, Feb


title: NHM5

description: GeoChip data for sludge sample collected in Ninghai, mesophilic tank, May

value: Ninghai, mesophilic, May


title: NHM3

description: GeoChip data for sludge sample collected in Ninghai, mesophilic tank, March

value: Ninghai, mesophilic, Mar


title: QD8

description: GeoChip data for sludge sample collected in Qingdao WWTP, August

value: Qingdao, Aug


title: NHM12

description: GeoChip data for sludge sample collected in Ninghai, mesophilic tank December

value: Ninghai, mesophilic, Dec


title: NHM11

description: GeoChip data for sludge sample collected in Ninghai, mesophilic tank, November

value: Ninghai, mesophilic, Nov


title: NHM1

description: GeoChip data for sludge sample collected in Ninghai, mesophilic tank, January

value: Ninghai, mesophilic, Jan


title: A549 cells treated with 5 mM sodium butyrate

city: Wenzhou

first: xiaoqiang

last: xiao

state: zhejiang

address: No 270.Xueyuan road

institute: Wenzhou Medical University

description: Gene expression data from 5 mM sodium butyrate treated A549 cell line

hyb_protocol: Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45oC on PrimeView™ Human Gene Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using Affymetrix Genechip Scanner 3000.

data_processing: The data were analyzed with Expression Console software  and Partek software. Gene expression in mRNA transcription more than 2 Fold is thought to significantly difference.

source_name: 5mM sodium butyrate treated A549 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15ug total RNA (GeneChip® 3’ IVT Express Kit User Manual, Affymetrix)

growth_protocol: A549 cells were loaded on 10 cm cell culture plate and cultured in RPMI 1640 medium containing 10% fetal bovine serium and 100 mg/ml streptomycin, and 100 U/ml penicillin for 24 hours .Cells were grown at 37oC under 5% CO2.

extract_protocol: Total RNAs were extracted with Trizol based on the manufacture's instruction.

treatment_protocol: 9mM sodium butyrate were added into the medium after 24 hours loading and cells were harvested after 24 hours sodium butyrate treatment.

tag: cell type

value: non-small cell lung cancer

tag: treatment

value: 5 mM sodium butyrate


title: QD6

description: GeoChip data for sludge sample collected in Qingdao WWTP, June

value: Qingdao, Jun


title: QD9

description: GeoChip data for sludge sample collected in Qingdao WWTP, September

value: Qingdao, Sep


title: NHM10

description: GeoChip data for sludge sample collected in Ninghai, mesophilic tank, October

value: Ninghai, mesophilic, Oct


title: QD5

description: GeoChip data for sludge sample collected in Qingdao WWTP, May

value: Qingdao, May


title: QD4

description: GeoChip data for sludge sample collected in Qingdao WWTP, April

value: Qingdao, Apr


title: A549 cells no treatment

description: Gene expression data from no normal A549 cell line

source_name: no treated A549 cells


title: Hippocampus_Low-CPF_rep2

description: Hippocampus RNA of rats administered with 3mg/kg/day CPF for 21 days

value: Long Evans

value: male

tag: age

value: 14 wk

value: Hippocampus


title: breast tumor_relapse lesion_patient 1

city: Chengdu

first: Xiaorong

last: Zhong

state: Sichuan

address: 5 Gongxing Lane, Wuhou District

institute: West China Hospital, Sichuan University

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal. Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm.

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. Shapiro-Wilk test using open source software R (function “shapiro.test()”), Paired t-test and Wilcoxon-test in Matlab computation environment were performed to determine statistical significance of expressed miRNAs.

source_name: breast tumor, relapse lesion

label_protocol: After RNA isolation from the samples, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling. One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.

extract_protocol: Total RNA was extracted from deparaffinized FFPE tissue sections using TRIzol (Invitrogen, Carlsbad, CA, USA) and miRNeasy mini kit (QIAGEN, Hilden, Germany) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) .

treatment_protocol: 6 hormone receptor positive BC women (stage I~III) relapsed after standard adjuvant tamoxifen treatment in West China Hospital. MiRNA expression profiles in the primary tumors and their matched recurrent/metastatic lesions from those patients were compared.

tag: age at diagnosis

tag: Sex

value: Female

tag: clincal stage

tag: tumor histology

value: Invasive ductal carcinoma

tag: er

value: positive

tag: pr

value: negative

tag: menopause when receiving tamoxifen

value: Premenopause

tag: adjuvant chemotherapy

value: Yes

tag: disease-free survival following tamoxifen treatment_months

tag: death

value: Alive


title: QD2

description: GeoChip data for sludge sample collected in Qingdao WWTP, February

value: Qingdao, Feb


title: breast tumor_primary lesion_patient 1

source_name: breast tumor, primary lesion

value: IIIA


title: QD3

description: GeoChip data for sludge sample collected in Qingdao WWTP, March

value: Qingdao, Mar


title: breast tumor_relapse lesion_patient 6


title: breast tumor_primary lesion_patient 6

value: IIB


title: QD1

description: GeoChip data for sludge sample collected in Qingdao WWTP, January

value: Qingdao, Jan


title: breast tumor_relapse lesion_patient 5

value: Postmenopause


title: QD10

description: GeoChip data for sludge sample collected in Qingdao WWTP, October

value: Qingdao, Oct


title: QD11

description: GeoChip data for sludge sample collected in Qingdao WWTP, November

value: Qingdao, Nov


title: BJ9

description: GeoChip data for sludge sample collected in Beijing WWTP, September

value: Beijing, Sep


title: BJ8

description: GeoChip data for sludge sample collected in Beijing WWTP, August

value: Beijing, Aug


title: Normal

city: Toyama

first: Takeshi

last: Yamamoto

address: 2630 Sugitani

institute: University of Toyama

hyb_protocol: Standard protocols for Affymetrix GeneChip® Mouse Gene 1.0 ST Array

scan_protocol: The Genechip was scanned with a GeneChip Scanner 3000 (Affymetrix), and the gene expression was analyzed using GeneChip Analysis Suite Software (Affymetrix).

data_processing: GeneChip Analysis Suite, affymetrix-algorithm-name = rma, affymetrix-algorithm-version = 1.0, program = Expression Console version 1.3.1.187

source_name: vehicle-treated normal mice

label_protocol: Samples were biotin-labelled using the Affymetrix WT labeling kit (www.affymetrix.com) per manufacturer's protocol.

extract_protocol: RNeasy Mini Kit (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

tag: tissue

value: proximal colon

tag: strain

value: BALB/C

tag: gender

value: Male

tag: disease state

value: Normal

value: vehicle


title: Combined therapy of Oral immunotherapy and Kakkonto

source_name: Oral immunotherapy and Kakkonto-treated food allergy mice

value: FOOD ALLERGY

value: Oral immunotherapy and Kakkonto


title: NRVCM_24 h stretch_2

city: Kiel

first: Ashraf

middle: Yusuf

last: Rangrez

address: Arnold-Heller Str. 3 (Haus 6)

institute: University Medical Center Kiel

description:
Neonatal rat cardiomyocyte, stretched for 24 hours, replicate 2
Gene expression in stretched cardiomyocytes for 24 hours
356_11

hyb_protocol: Hybridization was performed using laboratory standarized protocol by Comprehensive Biomarker Center (Heidelberg)

scan_protocol: Scanning was performed on Latest high-resolution microarray scanner GS2505_C commercially by Comprehensive Biomarker Center (Heidelberg)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent). The software automatically finds and places microarray grids, rejects outlier pixels, accurately determines feature intensities and ratios, flags outlier pixels, and calculates statistical confidences.

label_protocol: Labeling was performed by using Agilent’s Low Input Quick Amp Labeling Kit commercially by Comprehensive Biomarker Center (Heidelberg)

growth_protocol: Isolated cardiomyocytes were cultured in DMEM supplemented with 10% (v/v) FCS, 100 U/ml penicillin and 100 µg/ml streptomycin (Life Technologies), and 2 mmol/L L-glutamine (Life Technologies) for 24 h prior to stretch treatment.

extract_protocol: Total RNA was isolated from NRVCMs using QIAzol (Qiagen) according to manufacturer’s instructions

treatment_protocol: Phasic biomechanical stretch was used as the primary stimulus in NRVCMs for microarray and other experiments used in this manuscript. NRVCMs were seeded in 0.02 inch thick, collagen type I coated silicone Bioflex 6-well plates (Dunn Labortechnik), in DMEM containing 10% FCS supplemented with penicillin/streptomycin, and L-glutamine. Cells were washed and incubated in a special incubation chamber to apply biaxial pulsatile stretch to a total of 120% (+20%) for 24 h (or a specified time period) composed of a CO2 series incubator (SHEL LAB) and FlexLink FX5000T (Dunn Labortechnik). Non-stimulated and un-stretched NRVCMs plated in similar silicone-membrane 6-well plates were served as controls in the respective experiments.

tag: developmental stage

value: neonate

tag: cell type

value: Cardiomyocytes

value: stretched

tag: time

value: 24 hours


title: Oral immunotherapy-treated

source_name: Oral immunotherapy-treated food allergy mice

tag: treatment

value: Oral immunotherapy


title: BJ5

description: GeoChip data for sludge sample collected in Beijing WWTP, May

tag: collected

value: Beijing, May


title: NRVCM_24 h stretch_3

description:
Neonatal rat cardiomyocyte, stretched for 24 hours, replicate 3
Gene expression in stretched cardiomyocytes for 24 hours
356_12


title: Food allergy

source_name: vehicle-treated food allergy mice


title: QD12

description: GeoChip data for sludge sample collected in Qingdao WWTP, December

value: Qingdao, Dec


title: NRVCM_24 h stretch_1

description:
Neonatal rat cardiomyocyte, stretched for 24 hours, replicate 1
Gene expression in stretched cardiomyocytes for 24 hours
356_10