title: SDT-2

city: Harbin

first: Zheng

last: Hu

address: 92 West Dazhi Street , Nan Gang District, Harbin

country: China

institute: Harbin Institute of Technology

description: miRNA

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

scan_protocol: 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. After normalization, significant differentially expressed miRNAs were identified through Volcano Plot filtering. Hierarchical clustering was performed using MEV software (v4.6, TIGR).

data_processing:
The box plots are convenient way to quickly visualize the distribution of a dataset. They are most useful for comparing the distributions of samples. After normalization, the distributions of log2-ratios across every sample are nearly the same. (Left: non-normalized log2-ratio data; right: Median normalized log2-ratio data) .A correlation matrix describes correlation among replicate experiments. The scatter-plot is a visualization that is useful for assessing the variation (or reproducibility) between chips. The axes of the scatter-plot are the normalized signal values of the samples (Ratio scale).
To identify differentially expressed miRNAs with statistical significance, we performed a Volcano Plot filtering between the two groups from the experiment. The threshold we used to screen Up or Down regulated miRNAs is Fold Change>=2.0 and P-value<=0.05.
Non-normalized/Raw and normalized data are located on the series record.

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.

growth_protocol: Female BALB/c athymic nude mice 6-8 weeks of age were obtained from SLAC Laboratory Animal Company (Shanghai, China). To create the tumor model, B16-F10 tumor cells (1 × 10^5 cells in 100 μL of serum-free culture medium) were implanted subcutaneously on to the right-side flanks of the mice.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

treatment_protocol: When the tumor grew to a volume of ~100 mm3, approximately 5 days after implantation, mice were randomized into four groups with 12 mice per group. The groups were as follows: C, the untreated control mice; ALA, mice received 200 mg/kg ALA by intraperitoneal injection alone; US, mice treated with ultrasound (1.1 MHz, 1 W/cm2, 10 % duty cycle) alone; SDT, mice were treated with ultrasound plus ALA. After 4 hours of administration of ALA, the mice in the US and SDT groups were sonicated by ultrasound for 10 minutes in the dark. All mice were sacrificed when tumor diameter exceeded 10 millimeters after 11 days.To study the differential miRNAs expression in tissue samples, we performed miRNAs expression profiling of the tissue samples from 4 groups (Control, ALA, US, and SDT group) with 2 samples per group.

tag: strain

value: BALB/c athymic nude

value: B16-F10 transplanted melanoma

value: 6-8 weeks

tag: Sex

value: Female

tag: status

value: Sacrificed


title: SDT-1

status: Public on Jan 29 2015

type: RNA

description: miRNA

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: age


title: MCF7 IGF1R exposed for 1 h to vehicle solution replicate 2

city: Leiden

first: Steven

last: Wink

state: Zuid Holland

address: Einsteinweg 55

department: Division of Toxicology

country: Netherlands

institute: LACDR

hyb_protocol: cRNA was denaturized to prepare for the hybridization on the array. The fragmented cRNA with a concentration of 0.0375 μg/μl was finally utilized for the hybridization on the Affymetrix HT HG U133 plus PM.  The Affymetrix HWS Kit (#901530) was used for the hybridization, washing and staining of the chips.

scan_protocol: Scanning of the Array Plates was performed using the Affymetrix GeneTitan scanner

data_processing: BRB Array Tools software was used to normalize the CEL data using the Robust Multichip Average (RMA) method. Significantly differentially expressed genes (p-value < 0.001) between the various experimental conditions were identified with an ANOVA test followed by calculation according to Benjamini and Hochberg (Benjamini and Hochberg, 1995).

label: biotin

organism: Homo sapiens

source_name: MCF7 IGF1R

label_protocol: The Affymetrix 3' IVT-Express Labeling Kit (#901229) was used to synthesize Biotin-labeled cRNA. From each RNA sample 100 ng was used as input for the labeling reactions.

growth_protocol: MCF7 IRA, MCF7 IRB or MCF7 IGF1R cells (as described in Arch Toxicol. 2014 Apr;88(4):953-66. doi: 10.1007/s00204-014-1201-2. Epub 2014 Jan 25.) were cultured in RPMI supplemented with 5% (v/v) CDFBS (Hyclone) and used for experiments. Cells have been exposed for 1 or 6 hours to 10 nM of the indicated insulin-like molecule. As a control sample a vehicle stimulation was performed that contained everything except the active compound.

extract_protocol: RNA was isolated using the RNeasy® Plus Mini Kit (Qiagen, Venlo, the Netherlands) and RNA integrity and quality was assessed using the Agilent bioanalyser (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: Prior to compound stimulation the cells were starved in 5% charcoal/dextran-stripped fetal bovine serum (CDFBS) containing medium. Stimulations included: insulin NPH (Insuman Basal, Sanofi Aventis), insulin glargine (Lantus, Sanofi Aventis), M1 (metabolite of glargine, Sanofi Aventis), M2 (metabolite of glargine, Sanofi Aventis), glulisine (Apidra, Sanofi Aventis), lispro (Humalog, Elly Lilly), Insulin X10 (not marketed, Novo Nordisk), aspart (B28Asp, Novo Nordisk), detemir (Levemir, Novo Nordisk) and IGF1 (Increlex, Ipsen). All insulin analogues were dissolved in their original vehicle solutions [18]. For the in vitro experiments 1000x stock concentrations were prepared. Except for the first exposure experiment (Figure 1C) in which a dose response of 10, 33 and 100 nM was used, all exposures have been performed with a concentration of 10 nM

tag: cell line

tag: receptor

tag: treatment

value: vehicle solution

tag: time point

value: 1 hr


title: MCF7 IRA exposed for 1 h to vehicle solution replicate 1

source_name: MCF7 IRA

value: IRA


title: US-1

description: miRNA


title: MCF7 IGF1R exposed for 1 h to vehicle solution replicate 1


title: US-2

description: miRNA


title: MCF7 IRB exposed for 6 h to IGF1 replicate 3

source_name: MCF7 IRB

value: IRB

value: 6 hrs


title: ALA-2

description: miRNA


title: MCF7 IRA exposed for 6 h to IGF1 replicate 3


title: MCF7 IRA exposed for 6 h to X10 replicate 3


title: MCF7 IGF1R exposed for 6 h to X10 replicate 3


title: C-2

description: miRNA


title: MCF7 IRB exposed for 6 h to X10 replicate 3


title: C-1

description: miRNA


title: MCF7 IGF1R exposed for 6 h to insulin replicate 3

value: insulin


title: MCF7 IRB exposed for 6 h to glargine replicate 3

value: glargine


title: MCF7 IGF1R exposed for 6 h to glargine replicate 3


title: MCF7 IRA exposed for 6 h to glargine replicate 3


title: MCF7 IRA exposed for 6 h to vehicle solution replicate 2


title: ALA-1

description: miRNA


title: MCF7 IRB exposed for 6 h to insulin replicate 3


title: MCF7 IGF1R exposed for 6 h to IGF1 replicate 2


title: MCF7 IRB exposed for 6 h to IGF1 replicate 2


title: MCF7 IRA exposed for 6 h to insulin replicate 3


title: MCF7 IGF1R exposed for 6 h to X10 replicate 2


title: MCF7 IRA exposed for 6 h to IGF1 replicate 2


title: MCF7 IRB exposed for 6 h to glargine replicate 2


title: MCF7 IGF1R exposed for 6 h to glargine replicate 2


title: MCF7 IRA exposed for 6 h to X10 replicate 2


title: MCF7 IGF1R exposed for 6 h to insulin replicate 2


title: MCF7 IRB exposed for 6 h to X10 replicate 2


title: MCF7 IGF1R exposed for 6 h to IGF1 replicate 1


title: Parental genomic DNA (BAB4540)

type: genomic

city: Houston

first: James

last: Lupski

address: One Baylor Plaza, 604B

country: USA

institute: Baylor College of Medicine

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed following the manufacturer’s protocol.

scan_protocol: Scanned on an Agilent G2505C  scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1)

data_processing: Agilent Feature Extraction Software (version 10.7.3.1) was used for background subtraction and normalization.

molecule: genomic DNA

source_name: Mother to BAB4539- Not a carrier

label_protocol: 1.2 ug of genomic patient and reference DNA were digested with AluI (5 U) and RsaI (5 U) (Promega, R6281 and R6371) for 2 hr at 37°C. Labeling reactions were performed according to the manufacturer’s instructions (BioPrime Array CGH Genomic Labeling Module,Invitrogen Corporation, #18095-012; Perkin-Elmer Las Inc. Cyanine Smart Pack dCTP,  PerkinElmer, #NEL620001KT) with Cy5-dCTP for patient DNA and Cy3-dCTP for reference DNA.

extract_protocol: DNA was isolated from peripheral blood with a Puregene kit (Gentra Systems), following the manufacturer’s protocol

value: whole blood

source_name: Reference sample


title: MCF7 IRA exposed for 6 h to glargine replicate 2


title: MCF7 IRA exposed for 6 h to insulin replicate 2


title: Patient genomic DNA (BAB4539)

source_name: Patient carries a 21.8 Mb triplication + 50.3 Mb AOH


title: MCF7 IRB exposed for 6 h to insulin replicate 2


title: MCF7 IRB exposed for 6 h to IGF1 replicate 1


title: MCF7 IRA exposed for 6 h to X10 replicate 1


title: MCF7 IRB exposed for 6 h to glargine replicate 1


title: MCF7 IRA exposed for 6 h to glargine replicate 1


title: MCF7 IRB exposed for 6 h to X10 replicate 1


title: MCF7 IRA exposed for 6 h to IGF1 replicate 1


title: MCF7 IGF1R exposed for 6 h to glargine replicate 1


title: MCF7 IGF1R exposed for 6 h to insulin replicate 1


title: L-540_Sorafenib 5µM_24hrs_3C

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

description: SAMPLE 9

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were processed and normalised using quantile normalisation with BeadStudio software

source_name: L-540_Sorafenib 5µM_24hrs

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

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

tag: cell type

value: Human Hodgkin Lymphoma

value: 5 µM Sorafenib for 24hrs


title: L-540_Perifosine 10µM+Sorafenib 5µM_24hrs_4B

description: SAMPLE 11

value: 10 µM Perifosine + 5 µM Sorafenib for 24hrs


title: MCF7 IRB exposed for 6 h to insulin replicate 1


title: MCF7 IRA exposed for 6 h to insulin replicate 1


title: L-540_Sorafenib 5µM_24hrs_3A

description: SAMPLE 7


title: L-540_Perifosine 10µM+Sorafenib 5µM_24hrs_4C

description: SAMPLE 12


title: L-540_Perifosine 10µM_24hrs_2B

description: SAMPLE 5

source_name: L-540_Perifosine 10µM_24hrs

value: 10 µM Perifosine for 24hrs


title: MCF7 IRB exposed for 1 h to IGF1 replicate 3


title: Parental genomic DNA (BAB4541)

source_name: Father to BAB4539- Not a carrier


title: L-540_Perifosine 10µM+Sorafenib 5µM_24hrs_4A

description: SAMPLE 10


title: MCF7 IGF1R exposed for 6 h to X10 replicate 1


title: L-540_Sorafenib 5µM_24hrs_3B

description: SAMPLE 8


title: L-540_CTRL_24hrs_1C

description: SAMPLE 3


title: MCF7 IGF1R exposed for 1 h to IGF1 replicate 3


title: MCF7 IRA exposed for 1 h to IGF1 replicate 3


title: L-540_Perifosine 10µM_24hrs_2C

description: SAMPLE 6


title: tissue fetal stomach 15wk

city: La Jolla

first: Kristopher

middle: L.

last: Nazor

state: CA

address: 10550 North Torrey Pines Road

department: Regenerative Medicine

institute: The Scripps Research Institute

hyb_protocol: 750 ng labeled RNA/sample was hybridized to HT-12v4 Expression BeadChips (Illumina, Inc.).

scan_protocol: Arrays were imaged using HiScan using standard recommended Illumina scanner settings.

data_processing: In GenomeStudio, probes were filtered for those detected at p<0.01 in at least 1 sample and exported for normalization in R using robust spline normalization (RSN).

source_name: tissue fetal stomach 15wk_PP_101.412.1.2

label_protocol: 200 ng RNA per sample was amplified using the Total PrepTM RNA Amplification Kit (Illumina, Inc.) according to manufacturer’s protocol.

growth_protocol: iPSCs were grown on gamma-irradiated mouse embryonic fibroblasts (GlobalStem) in DMEM/F-12 with 20% KnockOut serum replacement, 1 mM glutamine, 1% nonessential amino acids, 1% antibiotic/antimycotic, 0.1 mM beta-mercaptoethanol, and 20 ng/ml basic FGF and passaged manually every 7 or 8 days. For neuronal differentiation, iPSC colonies were passaged onto high-density -irradiated mouse embryonic fibroblasts (at 60 103 cells/cm2) with 10uM ROCK inhibitor. Induction was performed with noggin (0.5 g/ml) and SB431542 (10 uM) in ESC medium. During induction, FRDA iPSCs were maintained for 2 weeks without passage. Subsequently, induced colonies were dissected and transferred to suspension culture as neurospheres in Neurobasal-A medium with EGF (20 ng/ml) and basic FGF (20 ng/ml). Neurospheres were maintained as a suspension culture and passaged manually every 4–5 days. Neural differentiation was performed by dissociating neurospheres with Accutase (Life technologies) and replating onto polylysine/laminin-coated plates at 5 104 cells/cm2. Neurons were maintained in Neurobasal-A medium without EGF or FGF for 7 or 8 days after replating. Neuronal cells were grown on laminin (0.5ug/cm2) in Neurobasal-A medium with 2% B-27 supplement, 1% ITS-A supplement, 1% N-2 supplement, 2mM glutamine and 1% antibiotic/antimycotic.

extract_protocol: Total RNA was extracted from snap-frozen sample pellets (Ambion mirVana Kit, Life Technologies, Inc.) according to the manufacturer’s protocol. RNA quantity (QubitTM RNA BR Assay Kits, Life Technologies, Inc.) and quality (RNA6000 Nano Kit and Bioanalyzer 2100, Agilent) was determined to be optimal for each sample prior to further processing.

tag: differentiation or tissue type

value: stomach fetal


title: MCF7 IRB exposed for 1 h to X10 replicate 3


title: MCF7 IRB exposed for 1 h to vehicle solution replicate 1


title: tissue fetal spleen 18wk

source_name: tissue fetal spleen 18wk_MR_91.1441.1.2

value: spleen fetal


title: MCF7 IGF1R exposed for 1 h to X10 replicate 3


title: L-540_Perifosine 10µM_24hrs_2A

description: SAMPLE 4


title: tissue fetal pancreas 21wk

source_name: tissue fetal pancreas 21wk_MR_220.1857.1.1

value: pancreas fetal


title: tissue fetal small intestine 20wk

source_name: tissue fetal small intestine 20wk_MR_146.1442.1.2

value: small intestine fetal


title: tissue fetal spleen 20wk

source_name: tissue fetal spleen 20wk_MR_91.1440.1.2


title: tissue fetal spleen 14wk

source_name: tissue fetal spleen 14wk_PP_91.414.1.2


title: L-540_CTRL_24hrs_1B

description: SAMPLE 2


title: MCF7 IGF1R exposed for 1 h to glargine replicate 3


title: HD-MyZ_Perifosine 10µM+Sorafenib 5µM_24hrs_4C

value: HD-MyZ


title: L-540_CTRL_24hrs_1A

description: SAMPLE 1


title: tissue fetal pancreas 20wk

source_name: tissue fetal pancreas 20wk_MR_220.1850.1.1


title: HD-MyZ_Perifosine 10µM+Sorafenib 5µM_24hrs_4B


title: tissue fetal lung 8wk

source_name: tissue fetal lung 8wk_PP_94.416.1.1

value: lung fetal


title: MCF7 IRA exposed for 1 h to X10 replicate 3

value: 1 hr


title: tissue fetal pancreas 19wk

source_name: tissue fetal pancreas 19wk_MR_220.1840.1.1


title: tissue fetal lung 18wk

source_name: tissue fetal lung 18wk_MR_94.1441.1.2


title: tissue fetal pancreas 18wk

source_name: tissue fetal pancreas 18wk_MR_220.1841.1.1


title: MCF7 IRA exposed for 1 h to glargine replicate 3

source_name: MCF7 IRA

value: IRA


title: MCF7 IRB exposed for 1 h to glargine replicate 3

source_name: MCF7 IRB

value: IRB


title: HD-MyZ_Sorafenib 5µM_24hrs_3C

source_name: HD-MyZ_Sorafenib 5µM_24hrs


title: tissue fetal lung 15wk

source_name: tissue fetal lung 15wk__94.412.1.2


title: HD-MyZ_Perifosine 10µM+Sorafenib 5µM_24hrs_4A


title: HD-MyZ_Sorafenib 5µM_24hrs_3B


title: tissue fetal lung 14wk

source_name: tissue fetal lung 14wk_PP_94.414.1.2


title: MCF7 IGF1R exposed for 1 h to insulin replicate 3

source_name: MCF7 IGF1R


title: tissue fetal lung 10wk

source_name: tissue fetal lung 10wk__94.409.1.1


title: HD-MyZ_Sorafenib 5µM_24hrs_3A


title: MCF7 IRB exposed for 1 h to insulin replicate 3


title: tissue fetal liver 18wk

source_name: tissue fetal liver 18wk_MR_147.1441.1.2

value: liver fetal


title: tissue fetal liver 14wk

source_name: tissue fetal liver 14wk_PP_147.414.1.2


title: tissue fetal heart 18wk

source_name: tissue fetal heart 18wk_MR_111.1441.1.2

value: heart fetal


title: tissue fetal adrenal 15wk

source_name: tissue fetal adrenal 15wk_PP_95.412.1.3

value: adrenal fetal


title: tissue fetal brain 10wk

source_name: tissue fetal brain 10wk_MR_21.1846.1.1

value: brain fetal


title: tissue fetal brain 19wk

source_name: tissue fetal brain 19wk_MR_21.1849.1.1


title: HD-MyZ_Perifosine 10µM_24hrs_2C

source_name: HD-MyZ_Perifosine 10µM_24hrs

value: Human Hodgkin Lymphoma


title: tissue fetal brain 14wk

source_name: tissue fetal brain 14wk_MR_21.1847.1.1


title: MCF7 IGF1R exposed for 1 h to IGF1 replicate 2


title: MCF7 IRA exposed for 1 h to insulin replicate 3

value: insulin


title: HD-MyZ_Perifosine 10µM_24hrs_2B


title: tissue fetal kidney 18wk

source_name: tissue fetal kidney 18wk_MR_143.1441.1.2

value: kidney fetal


title: HD-MyZ_Perifosine 10µM_24hrs_2A

value: 10 µM Perifosine for 24hrs


title: MCF7 IRB exposed for 1 h to IGF1 replicate 2


title: tissue fetal adrenal 14wk

source_name: tissue fetal adrenal 14wk_PP_95.414.1.2


title: HD-MyZ_CTRL_24hrs_1C


title: tissue fetal adrenal 20wk

source_name: tissue fetal adrenal 20wk_MR_95.1440.1.2


title: tissue fetal thymus 20wk rep2

value: thymus fetal


title: tissue fetal adrenal 10wk

source_name: tissue fetal adrenal 10wk__95.409.1.1


title: hPSC_iPS.4078.1A2

value: undifferentiated


title: hPSC_iPS.3816.5


title: HD-MyZ_CTRL_24hrs_1B


title: hPSC_iPS.4078.1B3


title: MCF7 IGF1R exposed for 1 h to X10 replicate 2


title: HD-MyZ_CTRL_24hrs_1A


title: MCF7 IRA exposed for 1 h to IGF1 replicate 2

source_name: MCF7 IRA


title: MCF7 IRB exposed for 1 h to X10 replicate 2

source_name: MCF7 IRB


title: MCF7 IRA exposed for 1 h to X10 replicate 2


title: HDLM-2_Perifosine 10µM+Sorafenib 5µM_24hrs_4C

value: 10 µM Perifosine + 5 µM Sorafenib for 24hrs


title: tissue fetal thymus 20wk rep1


title: HDLM-2_Perifosine 10µM+Sorafenib 5µM_24hrs_4A


title: tissue fetal stomach 14wk rep1

source_name: tissue fetal stomach 14wk_PP_101.407.1.1

value: stomach fetal


title: tissue fetal small intestine 15wk rep2

source_name: tissue fetal small intestine 15wk_PP_146.412.1.2

value: small intestine fetal


title: tissue fetal small intestine 15wk rep1

source_name: tissue fetal small intestine 15wk_MR_146.1836.1.3


title: MCF7 IGF1R exposed for 1 h to glargine replicate 2

source_name: MCF7 IGF1R

value: glargine


title: MCF7 IRB exposed for 1 h to glargine replicate 2

value: 1 hr


title: tissue fetal lung 20wk rep2

source_name: tissue fetal lung 20wk_MR_94.1442.1.2

value: lung fetal


title: HDLM-2_Perifosine 10µM+Sorafenib 5µM_24hrs_4B


title: HDLM-2_Sorafenib 5µM_24hrs_3C

source_name: HDLM-2_Sorafenib 5µM_24hrs

value: 5 µM Sorafenib for 24hrs


title: tissue fetal pancreas 10wk rep2

source_name: tissue fetal pancreas 10wk_PP_220.422.1.1

value: pancreas fetal


title: MCF7 IRA exposed for 1 h to glargine replicate 2

value: IRA


title: HDLM-2_Sorafenib 5µM_24hrs_3B


title: tissue fetal pancreas 10wk rep1

source_name: tissue fetal pancreas 10wk_PP_220.417.1.1


title: tissue fetal lung 20wk rep1

source_name: tissue fetal lung 20wk_MR_94.1440.1.2


title: tissue fetal liver 20wk rep1

source_name: tissue fetal liver 20wk_MR_147.1440.1.2

value: liver fetal


title: MCF7 IGF1R exposed for 1 h to insulin replicate 2


title: MCF7 IRA exposed for 1 h to insulin replicate 2


title: MCF7 IRB exposed for 1 h to insulin replicate 2

value: IRB


title: tissue fetal heart 20wk rep2

source_name: tissue fetal heart 20wk_MR_111.1442.1.2

value: heart fetal


title: tissue fetal kidney 20wk rep2

source_name: tissue fetal kidney 20wk_MR_143.1442.1.3


title: tissue fetal brain 17wk rep2

source_name: tissue fetal brain 17wk_MR_21.1366.1.1

value: brain fetal


title: HDLM-2_Perifosine 10µM_24hrs_2C

source_name: HDLM-2_Perifosine 10µM_24hrs

value: Human Hodgkin Lymphoma


title: tissue fetal kidney 20wk rep1

source_name: tissue fetal kidney 20wk_MR_143.1440.1.2

value: kidney fetal


title: HDLM-2_Perifosine 10µM_24hrs_2A

value: 10 µM Perifosine for 24hrs


title: tissue fetal brain 17wk rep1

source_name: tissue fetal brain 17wk_MR_21.1365.1.1


title: HDLM-2_Perifosine 10µM_24hrs_2B


title: MCF7 IRB exposed for 1 h to IGF1 replicate 1

source_name: MCF7 IRB


title: MCF7 IGF1R exposed for 1 h to IGF1 replicate 1


title: HDLM-2_Sorafenib 5µM_24hrs_3A


title: HDLM-2_CTRL_24hrs_1B


title: MCF7 IGF1R exposed for 1 h to X10 replicate 1


title: MCF7 IRA exposed for 1 h to IGF1 replicate 1

source_name: MCF7 IRA


title: tissue fetal brain 18wk rep2

source_name: tissue fetal brain 18wk_MR_21.1441.1.4


title: tissue fetal liver 20wk rep2

source_name: tissue fetal liver 20wk_MR_147.1442.1.2


title: tissue fetal brain 18wk rep3

source_name: tissue fetal brain 18wk_MR_21.1841.1.1


title: tissue fetal heart 20wk rep1

source_name: tissue fetal heart 20wk_MR_111.1440.1.2


title: neuronal.diff KIPS68 d24 rep3

value: neural progenitors


title: tissue fetal brain 18wk rep1

source_name: tissue fetal brain 18wk_MR_21.1441.1.2


title: neuronal.diff KIPS68 d24 rep2


title: HDLM-2_CTRL_24hrs_1C


title: MCF7 IRB exposed for 1 h to X10 replicate 1


title: neuronal.diff KIPS68 d24 rep1


title: HDLM-2_CTRL_24hrs_1A


title: neuronal.diff iPS.4078.1B3 d24 rep3


title: neuronal.diff iPS.4078.1B3 d24 rep2


title: neuronal.diff iPS.4078.1B3 d24 rep1


title: MCF7 IRA exposed for 1 h to X10 replicate 1


title: hPSC_iPS.8.2A4R rep2

value: undifferentiated


title: hPSC_iPS.8.2A4R rep3


title: MCF7 IGF1R exposed for 1 h to glargine replicate 1

source_name: MCF7 IGF1R


title: U-87 glioma cell line with shcontrol and TMZ treatment, biological rep1

city: Chicago

first: Bakhtiar

last: Yamini

state: IL

address: 956 E 57th street

department: Neurosurgery

institute: Univeristy of Chicago

description: Gene expression data from U-87 MG cells after stable transfection with sh-control RNA and 16 hours of TMZ treatment

hyb_protocol: Array hybridization was performed in the UCLA Bioinformatics Institute Core Laboratory Facility (Los Angeles, CA) according to Affymetrix (Sata Clara, CA) protocols. Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Array d scanning wasperformed in the UCLA Bioinformatics Institute Core Laboratory Facility (Los Angeles, CA) according to Affymetrix (Sata Clara, CA) protocolsGeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The raw data generated were processed using the Affymetrix Power Tools. The probe intensities were quantile normalized over all samples, summarized with the robust multi-array average (RMA) algorithm and log2 transformed with a median polish

source_name: U-87 cells transfected with sh-control RNA  and treated with 100uM TMZ for 16 hours

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: U-87 MG cells were grown in Eagle's minimum essential medium + 10% FBS + 100 U/mL penicllin + 100ug/mL streptomycin

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

treatment_protocol: Cells were treated with 100uM TMZ or a control (DMSO)

value: U-87 MG

value: glioma


title: neuronal.diff iPS.8333.1D1 d24 rep5


title: hPSC_iPS.8.2A4R rep1


title: U-87 glioma cell line with shcontrol, biological rep3

description: Gene expression data from U-87 MG cells after stable transfection with sh-control RNA and 16 hours of control DMSO treatment

source_name: U-87 cells transfected with sh-control RNA and treated with DMSO for 16 hours


title: U-87 glioma cell line with shcontrol and TMZ treatment, biological rep2


title: U-87 glioma cell line with shcontrol and TMZ treatment, biological rep3


title: MCF7 IRB exposed for 1 h to glargine replicate 1

value: glargine


title: neuronal.diff iPS.8333.1D1 d24 rep1


title: neuronal.diff iPS.8333.1D1 d24 rep3


title: U-87 glioma cell line with shcontrol, biological rep2


title: tissue fetal brain 20wk rep6

source_name: tissue fetal brain 20wk_MR_21.1852.1.1


title: neuronal.diff iPS.8333.1D1 d24 rep4


title: MCF7 IRA exposed for 1 h to glargine replicate 1

value: 1 hr


title: neuronal.diff iPS.8333.1D1 d24 rep2


title: MCF7 IGF1R exposed for 1 h to insulin replicate 1

value: insulin


title: MCF7 IRB exposed for 1 h to insulin replicate 1


title: IPMN High Risk sample18

city: Tampa

first: Jennifer

middle: Permuth

last: Wey

state: FL

address: 12902 Magnolia Dr

institute: Moffitt Cancer Center

description: microRNA data from High-risk IPMN tissue

hyb_protocol: according to manufacturer's procedures

data_processing: Data was processed using the software ABI Sequence Detection software v2.3 from Applied Biosystems.  The cut off value for Ct was set in 32 cycles taking into account that these samples were pre-amplified. Therefore, for miRNAs with undetermined expression and Ct values higher than 32 cycles, the miRNA was considered as non-expressed.  Ct for cycle threshold meaning the cycle in which the specific miRNA starts to be detected. ddCt for delta delta Ct, defined by the formula (Ct of the specific miRNA in the target sample-Ct of the endogenous control RNU44 in the target sample)-(Ct of the specific miRNA in the control sample-Ct of the endogenous control RNU44 in the control sample) for each human pancreas preparation. RQ for relative quantification, defined by the formula 2^-ddCt . Small nuclear RNA (RNU44) was used as endogenous control.

label: FAM

source_name: Microdissected IPMN tissue

extract_protocol: miRNeasy™ FFPE Isolation Kit (Qiagen)

value: pancreas ductal epithelium

tag: risk

value: High-risk IPMN tissue


title: IPMN High Risk sample19


title: U-87 glioma cell line with shcontrol, biological rep1


title: tissue fetal stomach 14wk rep2

source_name: tissue fetal stomach 14wk_PP_101.414.1.2

value: stomach fetal


title: U-87 glioma cell line with shp105 and TMZ treatment, biological rep3

description: Gene expression data from U-87 MG cells after stable transfection with sh-p105 RNA and 16 hours of TMZ treatment

source_name: U-87 cells transfected with sh-p105 RNA and treated with TMZ for 16 hours


title: MCF7 IRA exposed for 1 h to insulin replicate 1

value: IRA


title: tissue fetal brain 20wk rep5

source_name: tissue fetal brain 20wk_MR_21.1851.1.5


title: IPMN High Risk sample17


title: tissue fetal brain 20wk rep4

source_name: tissue fetal brain 20wk_MR_21.1850.1.1


title: tissue fetal brain 20wk rep3

source_name: tissue fetal brain 20wk_MR_21.1839.1.6


title: IPMN High Risk sample16


title: U-87 glioma cell line with shp105 and TMZ treatment, biological rep1


title: U-87 glioma cell line with shp105 and TMZ treatment, biological rep2


title: IPMN High Risk sample15


title: neuronal.diff iPS.8.2A4R d24 rep4


title: U-87 glioma cell line with shp105, biological rep2

description: Gene expression data from U-87 MG cells after stable transfection with sh-p105 RNA and 16 hours of control DMSO treatment

source_name: U-87 cells transfected with sh-p105 RNA and treated with DMSO for 16 hours


title: IPMN High Risk sample14


title: U-87 glioma cell line with shp105, biological rep3


title: tissue fetal brain 20wk rep2

source_name: tissue fetal brain 20wk_MR_21.1442.1.2


title: IPMN High Risk sample13


title: tissue fetal brain 20wk rep1

source_name: tissue fetal brain 20wk_MR_21.1440.1.2


title: neuronal.diff iPS.8.2A4R d24 rep3


title: neuronal.diff iPS.8.2A4R d24 rep2


title: neuronal.diff iPS.8.2A4R d24 rep5


title: IPMN High Risk sample11


title: IPMN Low Risk sample9

description: microRNA data from Low-risk IPMN tissue

value: Low-risk IPMN tissue


title: IPMN High Risk sample10


title: neuronal.diff iPS.8.2A4R_d24 rep6


title: IPMN High Risk sample12


title: IPMN Low Risk sample8

description: microRNA data from Low-risk IPMN tissue


title: neuronal.diff iPS.8.2A4R d24 rep1


title: U-87 glioma cell line with shp105, biological rep1


title: H157-Rapamycin-6h

city: Bethesda

first: Phillip

middle: A

last: Dennis

state: MD

address: 37 Convent Dr.

department: MOB, CCR

institute: NCI

description:
Analysis used the RNA sample from DMSO-treated H157 cells at 6h as control for comparison to that from Rapamycin-treated H157 cells at the same time point.

This Sample represents two dye-swapped samples.

HV33730.txt: Rapamycin-Cy5/DMSO-Cy3
HV33494.txt: Rapamycin-Cy3/DMSO-Cy5

hyb_protocol: The combined Cy3- and Cy5-labeled cDNAs were put in a total volume of 250 ul DEPC H20 and 250 ul of 2x Agilent hybridization buffer. The mixture was then denatured for 2 minutes and applied on the Agillent hybridization chamber/gasket slide in sandwich with the array slide. The hybridization was performed at 65 °C for 16 hours.

scan_protocol: Agilent High-Resolution Microarray Scanner (Cat# G2565CA).

data_processing: IPLab/DeArray image microarray analysis software. The data went through a linear normalization process. No filtering was done on the raw result files. The values in the Sample data table represent the log2 ratio of the calRatio column in the raw data files.

source_name: H157 cells treated with Rapamycin for 6h

label_protocol: 15 microgram of total RNA was reverse transcribed with Anchor Oligo-dT and Aminoallyl dUTP, after NaOH RNA hydrolysis, the labeled Aminoallyl dUTP cDNA was purified with Qiagen, QIAQuick PCR Purification Kit (Cat. # 28104). The Aminoallyl dUTP cDNAs were then coupled with either Cy3 or Cy5 mono NHS Ester Dyes. The CyDye-labeled cDNAs were then purified with the QIAQuick PCR Purification Kit (QIAGEN, Cat. # 28104).

growth_protocol: H157 cells were plated 2x10^6 in T-75 flasks in RPMI 1640 containing 10% FBS and incubated for 24h at 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol: Total RNA was extracted from cells treated in T-75 flasks using TRIzol reagent (Invitrogen) and chloroform and purified according to the RNeasy midiprep spin kit protocol (QIAGEN).

treatment_protocol: The medium was changed to RPMI 1640 with 0.1% FBS and the cells were incubated overnight. The following morning, cells were treated with 10 microM of LY294002, OSU-03012, PIA23, Perifosine, Miltefosine, API-2, DZ-50, or 100 nM of Wortmannin and Rapamycin for 6 hours, or an equal amount of DMSO as a control.

value: non-small cell lung cancer cells

value: Rapamycin

tag: treatment duration

value: 6 hrs

source_name: H157 cells treated with DMSO for 6h

value: DMSO


title: H157-DZ-50-6h

description:
Analysis used the RNA sample from DMSO-treated H157 cells at 6h as control for comparison to that from DZ-50-treated H157 cells at the same time point.

This Sample represents two dye-swapped samples.

HV33729.txt: DZ-50-Cy5/DMSO-Cy3
HV33493.txt: DZ-50-Cy3/DMSO-Cy5

source_name: H157 cells treated with DZ-50 for 6h


city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description: RNA from tolerogenic monocyte derived dendritic cells:x8

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol using a Gene chip scanner 3000

data_processing: Data processing cel files were normalized with 'rma' function of the Bioconductor package (v2.4)  in R.2.9.1

label_protocol: Standard Affymetrix protocol

extract_protocol: Total RNA was isolated using RNeasy Mini Kit columns with on-column DNase I  treatment (QIAGEN). RNA yield and purity were measured using the NanoDrop ND- 1000 Spectrophotometer and the Agilent 2100 Bioanalyzer.

tag: group

tag: monocyte derived dendritic cell

value: tolerogenic

tag: lps treatment

value: no

tag: dexamethasone treatment


description: RNA from tolerogenic monocyte derived dendritic cells:x25


title: IPMN Low Risk sample7

description: microRNA data from Low-risk IPMN tissue


title: H157-API-2-6h

description:
Analysis used the RNA sample from DMSO-treated H157 cells at 6h as control for comparison to that from API-2-treated H157 cells at the same time point.

This Sample represents two dye-swapped samples.

HV33728.txt: API-Cy5/DMSO-Cy3
HV33492.txt: API-Cy3/DMSO-Cy5

source_name: H157 cells treated with API-2 for 6h


title: H157-OSU-03012-6h

description:
Analysis used the RNA sample from DMSO-treated H157 cells at 6h as control for comparison to that from OSU-03012-treated H157 cells at the same time point.

This Sample represents two dye-swapped samples.

HV33719.txt: OSU-03012-Cy5/DMSO-Cy3
HV33487.txt: OSU-03012-Cy3/DMSO-Cy5

source_name: H157 cells treated with OSU-03012 for 6h


description: RNA from tolerogenic monocyte derived dendritic cells:x9


title: H157-PIA23-6h

description:
Analysis used the RNA sample from DMSO-treated H157 cells at 6h as control for comparison to that from PIA23-treated H157 cells at the same time point.

This Sample represents two dye-swapped samples.

HV33724.txt: PIA23-Cy5/DMSO-Cy3
HV33488.txt: PIA23-Cy3/DMSO-Cy5

source_name: H157 cells treated with PIA23 for 6h


title: H157-Miltefosine-6h

description:
Analysis used the RNA sample from DMSO-treated H157 cells at 6h as control for comparison to that from Miltefosine-treated H157 cells at the same time point.

This Sample represents two dye-swapped samples.

HV33726.txt: Miltefosine-Cy5/DMSO-Cy3
HV33496.txt: Miltefosine-Cy3/DMSO-Cy5

source_name: H157 cells treated with Miltefosine for 6h

value: Miltefosine


title: IPMN High Risk sample9


description: RNA from mature monocyte derived dendritic cells:x24

source_name: mature monocyte derived dendritic cells

value: mature monocyte derived dendritic cells

value: mature


description: RNA from mature monocyte derived dendritic cells:x4


description: RNA from mature monocyte derived dendritic cells:x7


title: H157-Perifosine-6h

description:
Analysis used the RNA sample from DMSO-treated H157 cells at 6h as control for comparison to that from Perifosine-treated H157 cells at the same time point.

This Sample represents two dye-swapped samples.

HV33725.txt: Perifosine-Cy5/DMSO-Cy3
HV33489.txt: Perifosine-Cy3/DMSO-Cy5

source_name: H157 cells treated with Perifosine for 6h

value: Perifosine


title: H157-Wortmannin-6h

description:
Analysis used the RNA sample from DMSO-treated H157 cells at 6h as control for comparison to that from Wortmannin-treated H157 cells at the same time point.

This Sample represents two dye-swapped samples.

HV33722.txt: Wortmannin-Cy5/DMSO-Cy3
HV33486.txt: Wortmannin-Cy3/DMSO-Cy5

source_name: H157 cells treated with Wortmannin for 6h

value: Wortmannin


description: RNA from tolerogenic monocyte derived dendritic cells:x5


description: RNA from immature monocyte derived dendritic cells:x23

value: immature


title: IPMN High Risk sample8

description: microRNA data from High-risk IPMN tissue

source_name: Microdissected IPMN tissue

value: pancreas ductal epithelium


title: IPMN High Risk sample7

value: High-risk IPMN tissue


title: H157-LY294002-6h

description:
Analysis used the RNA sample from DMSO-treated H157 cells at 6h as control for comparison to that from LY294002-treated H157 cells at the same time point.

This Sample represents two dye-swapped samples.

HV33721.txt: LY294002-Cy5/DMSO-Cy3
HV33485.txt: LY294002-Cy3/DMSO-Cy5

source_name: H157 cells treated with LY294002 for 6h


title: IPMN High Risk sample6


description: RNA from immature monocyte derived dendritic cells:x6


description: RNA from immature monocyte derived dendritic cells:x1


title: IPMN High Risk sample4


title: IPMN Low Risk sample5

description: microRNA data from Low-risk IPMN tissue


title: Liver 021 (50mg.kg GSK932121)

city: London

first: Ashley

last: Broom

address: Du Cane Road

country: United Kingdom

institute: Imperial College London

description: Gene expression data from livers of rats treated with GSK932121A for 5 hours

hyb_protocol: Fragmented and labeled DNA was added to a hybridization cocktail containing, 20X Eukaryotic Hyb-Controls, 2X Hybridization mix, control oligonucleotide B2, DMSO and nuclease free water (at concentrations defined by Affymetrix Ltd). The hybridization cocktail was heated at 99°C for 5 minutes and then 45°C for a further 5 minutes in a heat block before centrifuging at 14,000g for 1 minute.  Affymetrix Rat Gene 2.0 Sense Target (ST) Genechips were equilibrated to room temperature immediately before use and 130µL of hybridization cocktail was injected into the array though the septa on the reverse of the chip. The arrays were then placed in a hybridization oven (with rotating arm) at 45°C (60rpm) for 17 hours. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Samples were scanned using the Affymetrix Genechip Scanner 3000. The scanner was turned on ~10 minutes prior to scanning to warm the laser. In the AGCC, autoloader function was selected and arrays were firstly wiped clean using a non-abrasive tissue before loading onto the scanner carousel (up to 30 at a time).

data_processing: Once scanning was complete the hybridization image was inspected to ensure no gross scan-errors could be detected. CEL.files were then transferred from the PC and differential gene expression analysis was performed using Array Studio version 7.0 (www.omicsoft.com). Affymetrix data was normalised using the robust multichip average (RMA) method (Irizarry, Hobbs et al. 2003) and differentially expressed genes were defined as those with greater than 1.5 fold change in expression, at p<0.05.

label: Biotin

organism: Rattus norvegicus

source_name: Liver Median Lobe - Excised Fresh and Snap Frozen in Liquid Nitrogen

label_protocol: Fragmented single-stranded DNA was labelled by terminal deoxynucleotidyl transferase (TdT) with Biotin Allonamide Triphosphate using the Affymetrix WT Terminal Labelling and Hybridization Kit (#901524, Affymetrix, Santa Clara, CA, USA)

growth_protocol: Twenty-four female Crl:CD(SD) rats were obtained from Charles River UK (Margate, Kent), and were housed under controlled environmental conditions (19-23°C, 55% ± 10% relative humidity, 12h dark-light cycles), with free access to both water and 5LF2 EURodent Diet (Purina Mills International, St Louis, MO, USA). All animals were implanted with a Plexx™ microchip (Plexx B.V., Elst, The Netherlands) on arrival for the purposes of identification and body temperature measurement. Animals were acclimatised for at least 12 days prior to dose administration, and were 10 to 14 weeks old on the day of dosing.

extract_protocol: Total RNA was isolated from snap frozen median lobe of liver using the SV Total RNA isolation system (Promega, Madison, WI, USA) according to manufacturers recommendations.

treatment_protocol: Rats were divided into 2 groups of 12 animals, each of which received a single intraperitoneal (IP) dose of either vehicle or GSK932121A.  All doses and concentrations expressed are in terms of the parent compound. A nanomilled and spray-dried formulation of GSK932121A, containing mannitol, hydroxypropylmethylcellulose (Pharmacoat 603) and sodium dodecyl sulphate was suspended in sterile water for IP administration.  A dose of 50 mg/kg was selected based on data generated in previous GSK932121A single-dose tolerability studies (known to cause acute toxicity in rats).   A single dose of either 50 mg/kg GSK932121A or vehicle (described above minus test article) was administered to female rats (12/group) at a dose volume of 10 mL/kg.

value: Female

tag: strain

value: 12 weeks

tag: tissue type

value: Liver


description: RNA from mature monocyte derived dendritic cells:B66 5

value: yes


title: Liver 020 (50mg.kg GSK932121)

tag: Sex


title: Liver 024 (50mg.kg GSK932121)


title: IPMN High Risk sample5

tag: tissue


description: RNA from tolerogenic monocyte derived dendritic cells:B66 6


description: RNA from mature monocyte derived dendritic cells:B66 3


title: Liver 023 (50mg.kg GSK932121)

tag: age


title: Liver 018 (50mg.kg GSK932121)


title: Liver 022 (50mg.kg GSK932121)


title: Parental genomic DNA (BAB4153)

source_name: Mother to BAB3923- Not a carrier

value: whole blood

source_name: Reference sample

tag: cell line


title: Patient genomic DNA (BAB3924)

source_name: Patient carries a 5.9 Mb triplication + 8.6 Mb AOH

value: fetal DNA cultured amniocytes


description: RNA from tolerogenic monocyte derived dendritic cells:B66 4


title: Parental genomic DNA (BAB4154)

source_name: Father to BAB3923- Not a carrier


title: Parental genomic DNA (BAB4156)

source_name: Father to BAB3922- Not a carrier


title: IPMN High Risk sample3


title: Parental genomic DNA (BAB4155)

source_name: Mother to BAB3922- Not a carrier


title: Liver 016 (50mg.kg GSK932121)


title: IPMN Low Risk sample6

description: microRNA data from Low-risk IPMN tissue

value: Low-risk IPMN tissue


title: IPMN High Risk sample2


title: IPMN High Risk sample1


description: RNA from dexamethasone immature monocyte derived dendritic cells:B66 2


title: IPMN Low Risk sample4

description: microRNA data from Low-risk IPMN tissue


title: Patient genomic DNA (BAB3923)

source_name: Patient carries a 3.8 Mb triplication + 5.9 Mb AOH


description: RNA from immature monocyte derived dendritic cells:B66 1


description: RNA from tolerogenic monocyte derived dendritic cells:B55 4

value: tolerogenic


title: Parental genomic DNA (BAB3926)

source_name: Father to BAB3924- Not a carrier


title: Patient genomic DNA (BAB3922)

source_name: Patient carries a 3.8 Mb triplication + 24.7 Mb AOH


title: Liver 017 (50mg.kg GSK932121)


description: RNA from dexamethasone immature monocyte derived dendritic cells:B55 2

value: no


title: IPMN Low Risk sample3

description: microRNA data from Low-risk IPMN tissue


title: Liver 013 (50mg.kg GSK932121)


title: Liver 014 (50mg.kg GSK932121)


title: Parental genomic DNA (BAB3925)

source_name: Mother to BAB3924- Not a carrier


title: Liver 012 (Control)

description: Gene expression data from control rat livers


title: Liver 008 (Control)


description: RNA from immature monocyte derived dendritic cells:B55 1


title: IPMN Low Risk sample2

description: microRNA data from Low-risk IPMN tissue


title: Liver 007 (Control)


title: Liver 010 (Control)


title: Liver 009 (Control)


title: Liver 011 (Control)


title: Liver 005 (Control)


description: RNA from tolerogenic monocyte derived dendritic cells:B54 4


title: Liver 006 (Control)


description: RNA from mature monocyte derived dendritic cells:B55 3


description: RNA from mature monocyte derived dendritic cells:B54 3


title: IPMN Low Risk sample1

description: microRNA data from Low-risk IPMN tissue


title: Liver 004 (Control)


title: Liver 003 (Control)


description: RNA from immature monocyte derived dendritic cells:B54 1


title: Vpara_VBNC_rep8

status: Public on Jan 28 2015

city: Berlin

first: Stephan

last: Huehn

address: Koenigsweg 69

country: Germany

institute: Freie Universität Berlin

description: bacterial cell culture incubated at 4°C for 40 days

hyb_protocol: Finally 600 ng of the labelled and linear amplified cRNA (specific activity 9,0 pmol Cy3/µg cRNA) was fragmented, added to 25 µl Agilent-hybridization buffer resulting in 480 ng loaded on a microarray in a hybridization chamber (following manufacturers instructions). The hybridization was performed at 65°C for 17 hours and 10 rpm.  Washing of the slides was performed using preheated washing buffer (Gene expression wash buffer kit, Agilent). First the chamber was rinsed with washing buffer. Then the slides were washed once followed by a second wash using washing buffer containing 0.01% Triton X-102 (Agilent). The slides were dried using acetonitrile.

scan_protocol: Scanning was carried out immediately after washing using the Agilent G2565CA scanner with a resolution of 5 µm.

data_processing: After scanning, tiff-files were analysed and raw data was extracted using Feature Extraction Software (Agilent). Data processing was performed using Bioconductor V 2.12 package of the software R. At first, filtering of bad quality spots was performed and the data was background corrected with normexp method using offset = 50.

organism: Vibrio parahaemolyticus RIMD 2210633

source_name: bacterial cell culture incubated at 4°C

label_protocol: Reverse transcription of the RNA was performed. Briefly 200 ng of RNA were linear amplified using the full spectrum MultiStart primer (Biocat, Heidelberg, Germany) and Moloney murine leukemia virus (MMLV) reverse transcriptase (Agilent). The amplification was performed at 40°C for 2 hours followed by 65°C for 15 minutes and stored at 4°C. Labelling was performed using the Quick Amp Labeling Kit (Agilent). Briefly the amplified cDNA, the full spectrum MultiStart primer and T7 RNA polymerase were used along with Cyanine 3-CTP. Labeled cRNA was purified using the Qiagen RNeasy Mini Kit (Qiagen). A 3 µl-aliquot was used for quality control (NanoDrop 2000, Thermo Scientific).

growth_protocol: Prior use, the strain was stored in cryovials at -80°C (Cryobank; Mast Diagnostica, Bootle, England). For initial growth, cells were grown using a rotary shaker (Unimax 1010 and Incubator 1000; Heidolph, Schwabach, Germany) in alkaline peptone water (APW; 0.3% Yeast-Extract, 1% Peptone, 2% NaCl; pH 8.6) at 37°C overnight.A 50 μL aliquot of the resulting culture was then diluted into 50 mL APW and grown at 37 °C for 4 h and 7 h, respectively, in order to generate exponential phase and early stationary phase cultures.  For VBNC state, bacterial cells were cultured at 37 °C on thiosulfate citrate bile salts sucrose (TCBS) agar overnight. Then one single colony was inoculated in 10 mL APW (2% NaCl) under constant shaking (200 rpm) for 5 h. Then 100 µL of 5 h V. parahaemolyticus culture was diluted in 1 L APW (2% NaCl) followed by incubating overnight at 37 °C. Stationary phase cells were harvested by centrifugation at 7,830 g for 15 min at 4 °C and washed twice using fresh APW. Cells were resuspended in sterile APW at a final density of 106 cells mL-1 and maintained at 4 °C (over 40 days) without shaking to induce the VBNC state.

extract_protocol: Total RNA was isolated using the peqGold Bacterial RNA Kit (Peqlab, Erlangen, Germany). Obtained RNA was eluted into 43 µl of DEPC-treated, DNase- and RNase-free water (Carl Roth, Karlsruhe, Germany). Samples were then treated by DNase I along with an RNase-A, -B and -C inhibitor (Fermentas, Vilnius, Lithuania). RNA quantity was measured by spectrophotometry (NanoDrop 2000, Thermo Scientific). RNA quality of each sample was monitored via gel electrophoresis. Additionally, the RNA quality was assessed using the Agilent RNA 6000 Nano Kit on a 2100 Bioanalyzer (Agilent, Santa Clara, US).

treatment_protocol: The cultures were centrifuged (2 minutes, 8000 x g) and the supernatant was discarded. The pellet was immediately resuspended in 1.5 ml RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany) to minimize RNA degradation.

tag: cell

value: whole cell

tag: growth phase

value: VBNC state


title: Vpara_VBNC_rep4


title: Vpara_VBNC_rep5


description: RNA from dexamethasone immature monocyte derived dendritic cells:B54 2


title: Vpara_stationary_rep7

description: bacterial cell culture incubated at 37°C for 7 h

value: early stationary phase


title: Vpara_VBNC_rep1


title: Vpara_VBNC_rep7


title: Vpara_stationary_rep6

source_name: bacterial cell culture incubated at 37°C


title: Vpara_VBNC_rep2


title: Vpara_stationary_rep8


title: Liver 002 (Control)


title: Vpara_stationary_rep4


title: Vpara_stationary_rep1


title: Vpara_VBNC_rep3


title: Vpara_exponential_rep3

description: bacterial cell culture incubated at 37°C for 4 h

value: exponential phase


title: Vpara_stationary_rep5


title: Liver 001 (Control)


title: Vpara_exponential_rep7


title: Vpara_exponential_rep6


title: Vpara_stationary_rep2


title: Vpara_exponential_rep4


title: Vpara_VBNC_rep6


title: Vpara_stationary_rep3


title: Vpara_exponential_rep8


title: Vpara_exponential_rep2


title: Vpara_exponential_rep5


title: Vpara_exponential_rep1


title: NM_TFGB1-_rep2

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

institute: Parc Taulí Research and Innovation Institute (I3PT)

hyb_protocol: cDNA was hybridized to GeneAtlas Human Genome HG-133+PM strip arrays for 16 hours at 45ºC.Washing and staining of microarrays was performed using a GeneAtlas Fluidics Station (Affymetrix, Santa Clara, CA)

scan_protocol: GeneChips were scanned in a GeneAtlas Imaging Station (Affymetrix, Santa Clara, CA)

data_processing: RMA normalization method as implemented in affy Bioconductor R package

source_name: Fibroblasts from morphological normal mucosa (NM) adjacent to colorectal cancer, Recombinant TGFB1 not treated (-)

label_protocol: 25 ng total RNA was amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2) and 8 µg of cDNA was  subsequently fragmented and labeled using GeneChip Human Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

growth_protocol: Human colon fibroblasts were obtained from patient treated at Hospital del Mar, Barcelona. Normal mucosa was minced and incubated with DMEM plus DNAse (10 μg mL-1; Sigma Aldrich) and Collagenase IV (100 U mL-1; R&D) for half an hour. Pieces were seeded in plates and incubated at 37ºC in complete FGM (Lonza) supplemented with 2% FBS. Once fibroblasts adhered to the plate, pieces were removed. Fibroblasts were grown using standard methods at 37ºC and 5% CO2.

extract_protocol: RNA extraction was done in TRIZOL and washed with Qiagen kit following manufacturer's instructions.

treatment_protocol: Fibroblasts were seeded at 60% confluence and treated with TGF-β1 (Peprotech; 5 ng mL-1) for 8 hours in FGM basal medium + 0.2%FBS.

tag: recombinant tgfb1

value: Recombinant TGFB1 not treated (-)


title: NM_TFGB1-_rep1


title: NM_TFGB1+_rep1

source_name: Fibroblasts from morphological normal mucosa (NM) adjacent to colorectal cancer, Recombinant TGFB1 treated (+)

value: Recombinant TGFB1 treated (+)


title: NM_TFGB1+_rep2


title: PERS-UK-112

city: Los Angeles

first: Steve

last: Cole

address: 11-934 Factor Bldg, UCLA

department: Medicine

institute: UCLA School of Medicine

description:
8381661006_B.AVG_Signal
Age=24/Male=1/BMI=20/Caucasian=0/CigDay=0/AlcDay=6/ExerDay=0.1/Neuroticism=1.32/Extraversion=-0.57/Openness=0.73/Agreeableness=-3.19/Conscientiousness=-2.45
Illumina Human HT-12 BeadArray

hyb_protocol: Illumina cDNA hybridization protocol for gene expression profiling (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 available data are provided, with no additional filtering.

source_name: PBMC

label_protocol: Low mass NuGEN PicoSL cDNA synthesis with biotin labeling for gene expression profiling (carried out UCLA Neuroscience Genomics Core).

extract_protocol: Primary peripheral blood mononuclear cells were isolated and total RNA was extracted using Qiagen RNEasy.

tag: male

tag: bmi

tag: caucasian

tag: cigday

tag: alcday

tag: exerday

tag: minorsymptom

tag: birthcontrol

tag: antidepressant

tag: othermedication

tag: negativeaffect

tag: neuroticism

tag: extraversion

tag: openness

tag: agreeableness

tag: conscientiousness


title: PERS-UK-117

description:
8381661006_G.AVG_Signal
Age=27/Male=1/BMI=22/Caucasian=missing/CigDay=0/AlcDay=0.4/ExerDay=0.7/Neuroticism=1.57/Extraversion=0.6/Openness=1.52/Agreeableness=0.62/Conscientiousness=-1.29
Illumina Human HT-12 BeadArray

tag: age

value: missing


title: PERS-UK-114

description:
8381661006_D.AVG_Signal
Age=26/Male=0/BMI=20/Caucasian=1/CigDay=0/AlcDay=0.6/ExerDay=0.7/Neuroticism=0.56/Extraversion=-0.13/Openness=0.11/Agreeableness=0.78/Conscientiousness=-0.25
Illumina Human HT-12 BeadArray

tag: male


title: PERS-UK-115

description:
8381661006_E.AVG_Signal
Age=22/Male=0/BMI=22/Caucasian=1/CigDay=0/AlcDay=1/ExerDay=1/Neuroticism=-0.2/Extraversion=0.75/Openness=0.11/Agreeableness=1.41/Conscientiousness=0.66
Illumina Human HT-12 BeadArray

tag: bmi


title: PERS-UK-105

description:
8381661005_G.AVG_Signal
Age=34/Male=1/BMI=28/Caucasian=missing/CigDay=0/AlcDay=0.1/ExerDay=1/Neuroticism=1.95/Extraversion=-1.01/Openness=-0.2/Agreeableness=0.14/Conscientiousness=-1.42
Illumina Human HT-12 BeadArray

tag: caucasian


title: PERS-UK-109

description:
8381661005_K.AVG_Signal
Age=21/Male=1/BMI=19/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=0.6/Neuroticism=-1.09/Extraversion=-0.87/Openness=0.11/Agreeableness=0.14/Conscientiousness=0.53
Illumina Human HT-12 BeadArray

tag: cigday


title: PERS-UK-104

description:
8381661005_F.AVG_Signal
Age=51/Male=0/BMI=23/Caucasian=1/CigDay=0/AlcDay=2/ExerDay=0.5/Neuroticism=0.18/Extraversion=1.04/Openness=-0.36/Agreeableness=1.1/Conscientiousness=1.18
Illumina Human HT-12 BeadArray

tag: alcday


title: PERS-UK-106

description:
8381661005_H.AVG_Signal
Age=51/Male=0/BMI=22/Caucasian=1/CigDay=0/AlcDay=1/ExerDay=0.6/Neuroticism=0.94/Extraversion=-1.16/Openness=0.11/Agreeableness=-0.33/Conscientiousness=1.05
Illumina Human HT-12 BeadArray

tag: exerday


title: PERS-UK-111

description:
8381661006_A.AVG_Signal
Age=29/Male=0/BMI=23/Caucasian=0/CigDay=0/AlcDay=0.1/ExerDay=1/Neuroticism=0.3/Extraversion=1.19/Openness=0.42/Agreeableness=-0.17/Conscientiousness=0.92
Illumina Human HT-12 BeadArray

tag: minorsymptom


title: PERS-UK-100

description:
8381661005_B.AVG_Signal
Age=59/Male=0/BMI=24/Caucasian=1/CigDay=0/AlcDay=1.3/ExerDay=1/Neuroticism=-1.22/Extraversion=0.31/Openness=-2.08/Agreeableness=0.46/Conscientiousness=1.96
Illumina Human HT-12 BeadArray

tag: birthcontrol


title: PERS-UK-118

description:
8381661006_H.AVG_Signal
Age=22/Male=1/BMI=24/Caucasian=1/CigDay=0/AlcDay=0/ExerDay=1/Neuroticism=-0.96/Extraversion=0.75/Openness=-0.2/Agreeableness=0.3/Conscientiousness=-1.03
Illumina Human HT-12 BeadArray

tag: antidepressant


title: PERS-UK-120

description:
8381661006_J.AVG_Signal
Age=18/Male=1/BMI=24/Caucasian=1/CigDay=0/AlcDay=0/ExerDay=1/Neuroticism=0.56/Extraversion=0.75/Openness=-0.98/Agreeableness=-0.97/Conscientiousness=-0.25
Illumina Human HT-12 BeadArray

tag: othermedication


title: PERS-UK-110

description:
8381661005_L.AVG_Signal
Age=25/Male=0/BMI=30/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=2/Neuroticism=1.06/Extraversion=-0.87/Openness=-2.7/Agreeableness=-0.81/Conscientiousness=0.66
Illumina Human HT-12 BeadArray

tag: negativeaffect


title: PERS-UK-121

description:
8381661006_K.AVG_Signal
Age=20/Male=0/BMI=36/Caucasian=1/CigDay=0/AlcDay=1.3/ExerDay=0.4/Neuroticism=0.05/Extraversion=0.46/Openness=-1.14/Agreeableness=0.62/Conscientiousness=1.05
Illumina Human HT-12 BeadArray

tag: neuroticism


title: PERS-UK-101

description:
8381661005_C.AVG_Signal
Age=22/Male=0/BMI=27/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=1/Neuroticism=1.95/Extraversion=0.16/Openness=0.27/Agreeableness=0.3/Conscientiousness=1.18
Illumina Human HT-12 BeadArray

tag: extraversion


title: PERS-UK-103

description:
8381661005_E.AVG_Signal
Age=35/Male=0/BMI=35/Caucasian=1/CigDay=0/AlcDay=2/ExerDay=0.75/Neuroticism=2.08/Extraversion=-1.46/Openness=0.42/Agreeableness=0.78/Conscientiousness=0.4
Illumina Human HT-12 BeadArray

tag: openness


title: PERS-UK-108

description:
8381661005_J.AVG_Signal
Age=21/Male=0/BMI=21/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=0/Neuroticism=0.68/Extraversion=-0.87/Openness=-1.14/Agreeableness=1.1/Conscientiousness=-1.42
Illumina Human HT-12 BeadArray

tag: agreeableness


title: PERS-UK-119

description:
8381661006_I.AVG_Signal
Age=26/Male=1/BMI=23/Caucasian=1/CigDay=0/AlcDay=0/ExerDay=1/Neuroticism=-1.34/Extraversion=-0.43/Openness=1.52/Agreeableness=-0.81/Conscientiousness=1.83
Illumina Human HT-12 BeadArray

tag: conscientiousness


title: PERS-UK-116

description:
8381661006_F.AVG_Signal
Age=32/Male=1/BMI=21.9/Caucasian=0/CigDay=0/AlcDay=0.1/ExerDay=1.1/Neuroticism=-1.09/Extraversion=1.19/Openness=-0.83/Agreeableness=0.78/Conscientiousness=-0.38
Illumina Human HT-12 BeadArray

tag: age


title: PERS-UK-113

description:
8381661006_C.AVG_Signal
Age=20/Male=1/BMI=24/Caucasian=1/CigDay=0/AlcDay=0.2/ExerDay=0.1/Neuroticism=1.06/Extraversion=-0.13/Openness=-0.98/Agreeableness=-0.02/Conscientiousness=-0.25
Illumina Human HT-12 BeadArray

tag: male


title: PERS-UK-107

description:
8381661005_I.AVG_Signal
Age=50/Male=0/BMI=27/Caucasian=1/CigDay=0/AlcDay=0.1/ExerDay=0.6/Neuroticism=-0.08/Extraversion=-0.28/Openness=0.11/Agreeableness=1.1/Conscientiousness=1.31
Illumina Human HT-12 BeadArray

tag: bmi


title: PERS-UK-102

description:
8381661005_D.AVG_Signal
Age=22/Male=0/BMI=24/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=0.5/Neuroticism=1.44/Extraversion=-1.75/Openness=-0.83/Agreeableness=0.62/Conscientiousness=-1.42
Illumina Human HT-12 BeadArray

tag: caucasian


title: PERS-UK-99

description:
8381661005_A.AVG_Signal
Age=45/Male=0/BMI=30/Caucasian=1/CigDay=20/AlcDay=1/ExerDay=0.5/Neuroticism=-1.85/Extraversion=-1.16/Openness=-1.77/Agreeableness=1.73/Conscientiousness=0.4
Illumina Human HT-12 BeadArray

tag: cigday


title: PERS-UK-97

description:
8381653100_K.AVG_Signal
Age=21/Male=1/BMI=24/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=0.7/Neuroticism=-0.08/Extraversion=0.75/Openness=-0.2/Agreeableness=-1.6/Conscientiousness=1.05
Illumina Human HT-12 BeadArray

tag: alcday


title: PERS-UK-95

description:
8381653100_I.AVG_Signal
Age=20/Male=0/BMI=27/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=0.7/Neuroticism=0.3/Extraversion=1.63/Openness=1.05/Agreeableness=1.89/Conscientiousness=-0.12
Illumina Human HT-12 BeadArray

tag: exerday


title: PERS-UK-92

description:
8381653100_F.AVG_Signal
Age=22/Male=0/BMI=24/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=0.3/Neuroticism=-1.09/Extraversion=1.04/Openness=0.11/Agreeableness=0.94/Conscientiousness=1.18
Illumina Human HT-12 BeadArray

tag: minorsymptom


title: PERS-UK-89

description:
8381653100_C.AVG_Signal
Age=22/Male=0/BMI=24/Caucasian=1/CigDay=0/AlcDay=1.5/ExerDay=0.4/Neuroticism=0.18/Extraversion=1.34/Openness=-0.36/Agreeableness=1.41/Conscientiousness=-0.38
Illumina Human HT-12 BeadArray

tag: birthcontrol


title: PERS-UK-94

description:
8381653100_H.AVG_Signal
Age=20/Male=0/BMI=20/Caucasian=1/CigDay=0/AlcDay=2.2/ExerDay=1/Neuroticism=0.3/Extraversion=1.49/Openness=0.42/Agreeableness=0.62/Conscientiousness=-0.51
Illumina Human HT-12 BeadArray

tag: antidepressant


title: PERS-UK-91

description:
8381653100_E.AVG_Signal
Age=21/Male=0/BMI=24/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=0.5/Neuroticism=-0.08/Extraversion=0.75/Openness=0.42/Agreeableness=0.3/Conscientiousness=-0.51
Illumina Human HT-12 BeadArray

tag: othermedication


title: PERS-UK-87

description:
8381653100_A.AVG_Signal
Age=20/Male=0/BMI=27/Caucasian=1/CigDay=0/AlcDay=1/ExerDay=1/Neuroticism=0.05/Extraversion=-0.13/Openness=0.11/Agreeableness=0.62/Conscientiousness=-0.12
Illumina Human HT-12 BeadArray

tag: negativeaffect


title: PERS-UK-84

description:
8381653098_J.AVG_Signal
Age=19/Male=0/BMI=21/Caucasian=0/CigDay=0/AlcDay=0.3/ExerDay=2/Neuroticism=-0.2/Extraversion=-0.13/Openness=-0.2/Agreeableness=-2.24/Conscientiousness=0.4
Illumina Human HT-12 BeadArray

tag: neuroticism


title: PERS-UK-96

description:
8381653100_J.AVG_Signal
Age=21/Male=0/BMI=22/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=1.5/Neuroticism=-0.08/Extraversion=-0.43/Openness=0.89/Agreeableness=-1.29/Conscientiousness=0.79
Illumina Human HT-12 BeadArray

tag: extraversion


title: PERS-UK-86

description:
8381653098_L.AVG_Signal
Age=24/Male=0/BMI=22/Caucasian=1/CigDay=0/AlcDay=2.3/ExerDay=0/Neuroticism=1.19/Extraversion=-0.87/Openness=-0.2/Agreeableness=0.94/Conscientiousness=-0.25
Illumina Human HT-12 BeadArray

tag: openness


title: PERS-UK-90

description:
8381653100_D.AVG_Signal
Age=20/Male=0/BMI=25/Caucasian=1/CigDay=0/AlcDay=2/ExerDay=0.5/Neuroticism=0.56/Extraversion=0.9/Openness=0.89/Agreeableness=0.94/Conscientiousness=-0.38
Illumina Human HT-12 BeadArray

tag: agreeableness


title: PERS-UK-85

description:
8381653098_K.AVG_Signal
Age=21/Male=1/BMI=25/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=3/Neuroticism=-0.46/Extraversion=1.34/Openness=-0.05/Agreeableness=-0.02/Conscientiousness=1.18
Illumina Human HT-12 BeadArray

tag: conscientiousness


title: PERS-UK-93

description:
8381653100_G.AVG_Signal
Age=19/Male=0/BMI=27/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=0.3/Neuroticism=0.43/Extraversion=-0.13/Openness=-0.67/Agreeableness=0.94/Conscientiousness=-1.42
Illumina Human HT-12 BeadArray

tag: age


title: PERS-UK-79

description:
8381653098_E.AVG_Signal
Age=19/Male=1/BMI=22/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=2/Neuroticism=-0.46/Extraversion=-0.43/Openness=-2.23/Agreeableness=-1.13/Conscientiousness=0.14
Illumina Human HT-12 BeadArray

tag: male


title: PERS-UK-98

description:
8381653100_L.AVG_Signal
Age=22/Male=0/BMI=24/Caucasian=1/CigDay=0/AlcDay=0/ExerDay=0.5/Neuroticism=-0.58/Extraversion=0.16/Openness=-0.67/Agreeableness=0.46/Conscientiousness=-0.77
Illumina Human HT-12 BeadArray

tag: bmi


title: PERS-UK-82

description:
8381653098_H.AVG_Signal
Age=25/Male=0/BMI=20/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=0.3/Neuroticism=-0.84/Extraversion=0.6/Openness=0.27/Agreeableness=0.78/Conscientiousness=0.01
Illumina Human HT-12 BeadArray

tag: caucasian


title: PERS-UK-80

description:
8381653098_F.AVG_Signal
Age=18/Male=1/BMI=24/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=0.4/Neuroticism=-0.58/Extraversion=1.93/Openness=-0.67/Agreeableness=-0.49/Conscientiousness=0.92
Illumina Human HT-12 BeadArray

tag: cigday


title: PERS-UK-77

description:
8381653098_C.AVG_Signal
Age=20/Male=1/BMI=30/Caucasian=1/CigDay=0/AlcDay=1/ExerDay=3/Neuroticism=-1.09/Extraversion=1.19/Openness=-0.83/Agreeableness=0.14/Conscientiousness=-1.16
Illumina Human HT-12 BeadArray

tag: alcday


title: PERS-UK-81

description:
8381653098_G.AVG_Signal
Age=21/Male=0/BMI=22/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=0.3/Neuroticism=-0.08/Extraversion=-1.46/Openness=0.11/Agreeableness=-0.97/Conscientiousness=-0.77
Illumina Human HT-12 BeadArray

tag: exerday


title: PERS-UK-75

description:
8381653098_A.AVG_Signal
Age=22/Male=0/BMI=22/Caucasian=1/CigDay=0/AlcDay=1/ExerDay=0.7/Neuroticism=0.43/Extraversion=0.46/Openness=-0.98/Agreeableness=0.62/Conscientiousness=0.01
Illumina Human HT-12 BeadArray

tag: minorsymptom


title: PERS-UK-74

description:
8381653097_L.AVG_Signal
Age=19/Male=0/BMI=23/Caucasian=1/CigDay=0/AlcDay=2/ExerDay=2/Neuroticism=1.44/Extraversion=-1.31/Openness=-1.14/Agreeableness=-1.29/Conscientiousness=0.4
Illumina Human HT-12 BeadArray

tag: birthcontrol


title: PERS-UK-72

description:
8381653097_J.AVG_Signal
Age=28/Male=0/BMI=24/Caucasian=1/CigDay=0/AlcDay=1.3/ExerDay=0.6/Neuroticism=0.05/Extraversion=-0.28/Openness=0.58/Agreeableness=-0.33/Conscientiousness=0.14
Illumina Human HT-12 BeadArray

tag: antidepressant


title: PERS-UK-71

description:
8381653097_I.AVG_Signal
Age=23/Male=1/BMI=23/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=0.3/Neuroticism=-0.33/Extraversion=-1.16/Openness=0.89/Agreeableness=-0.97/Conscientiousness=-0.12
Illumina Human HT-12 BeadArray

tag: othermedication


title: PERS-UK-88

description:
8381653100_B.AVG_Signal
Age=20/Male=0/BMI=24/Caucasian=1/CigDay=0/AlcDay=0.6/ExerDay=1/Neuroticism=-0.96/Extraversion=0.31/Openness=0.11/Agreeableness=0.46/Conscientiousness=0.01
Illumina Human HT-12 BeadArray

tag: negativeaffect


title: PERS-UK-76

description:
8381653098_B.AVG_Signal
Age=20/Male=0/BMI=24/Caucasian=1/CigDay=0/AlcDay=1/ExerDay=1/Neuroticism=-0.84/Extraversion=0.6/Openness=-1.61/Agreeableness=1.1/Conscientiousness=0.14
Illumina Human HT-12 BeadArray

tag: neuroticism


title: PERS-UK-73

description:
8381653097_K.AVG_Signal
Age=19/Male=0/BMI=17/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=0.4/Neuroticism=0.05/Extraversion=-0.13/Openness=-1.3/Agreeableness=-0.02/Conscientiousness=-0.25
Illumina Human HT-12 BeadArray

tag: extraversion


title: PERS-UK-69

description:
8381653097_G.AVG_Signal
Age=29/Male=0/BMI=23/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=1/Neuroticism=-0.33/Extraversion=-0.43/Openness=-0.36/Agreeableness=0.3/Conscientiousness=0.66
Illumina Human HT-12 BeadArray

tag: openness


title: PERS-UK-66

description:
8381653097_D.AVG_Signal
Age=38/Male=1/BMI=29/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=1.4/Neuroticism=-0.08/Extraversion=0.6/Openness=1.83/Agreeableness=-0.49/Conscientiousness=0.4
Illumina Human HT-12 BeadArray

tag: agreeableness


title: PERS-UK-68

description:
8381653097_F.AVG_Signal
Age=26/Male=0/BMI=23/Caucasian=1/CigDay=0/AlcDay=0.4/ExerDay=0.3/Neuroticism=-1.97/Extraversion=2.22/Openness=1.2/Agreeableness=1.89/Conscientiousness=-0.38
Illumina Human HT-12 BeadArray

tag: conscientiousness


title: PERS-UK-64

description:
8381653097_B.AVG_Signal
Age=33/Male=1/BMI=19/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=2/Neuroticism=-0.84/Extraversion=2.07/Openness=1.36/Agreeableness=-1.13/Conscientiousness=0.14
Illumina Human HT-12 BeadArray

tag: age


title: PERS-UK-61

description:
8381653096_K.AVG_Signal
Age=45/Male=0/BMI=29/Caucasian=0/CigDay=0/AlcDay=0.3/ExerDay=0.1/Neuroticism=-0.58/Extraversion=0.46/Openness=0.11/Agreeableness=-0.49/Conscientiousness=0.27
Illumina Human HT-12 BeadArray

tag: male


title: PERS-UK-83

description:
8381653098_I.AVG_Signal
Age=18/Male=1/BMI=25/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=1/Neuroticism=-0.46/Extraversion=0.16/Openness=-0.52/Agreeableness=-1.44/Conscientiousness=0.01
Illumina Human HT-12 BeadArray

tag: bmi


title: PERS-UK-78

description:
8381653098_D.AVG_Signal
Age=19/Male=0/BMI=22/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=1/Neuroticism=-0.96/Extraversion=-0.13/Openness=1.36/Agreeableness=0.14/Conscientiousness=0.27
Illumina Human HT-12 BeadArray

tag: caucasian


title: PERS-UK-58

description:
8381653096_H.AVG_Signal
Age=19/Male=1/BMI=23/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=0.75/Neuroticism=-0.08/Extraversion=1.93/Openness=0.73/Agreeableness=1.1/Conscientiousness=-1.29
Illumina Human HT-12 BeadArray

tag: cigday


title: PERS-UK-62

description:
8381653096_L.AVG_Signal
Age=19/Male=0/BMI=35/Caucasian=1/CigDay=0/AlcDay=0.1/ExerDay=0.9/Neuroticism=-0.33/Extraversion=-0.13/Openness=0.27/Agreeableness=-0.02/Conscientiousness=0.79
Illumina Human HT-12 BeadArray

tag: alcday


title: PERS-UK-59

description:
8381653096_I.AVG_Signal
Age=20/Male=0/BMI=22/Caucasian=1/CigDay=0/AlcDay=0/ExerDay=1/Neuroticism=-0.84/Extraversion=1.63/Openness=1.05/Agreeableness=0.3/Conscientiousness=-0.77
Illumina Human HT-12 BeadArray

tag: exerday


title: PERS-UK-70

description:
8381653097_H.AVG_Signal
Age=30/Male=1/BMI=30/Caucasian=1/CigDay=0/AlcDay=0/ExerDay=0.5/Neuroticism=-1.97/Extraversion=-0.57/Openness=1.83/Agreeableness=-0.81/Conscientiousness=-0.38
Illumina Human HT-12 BeadArray

tag: minorsymptom


title: PERS-UK-54

description:
8381653096_D.AVG_Signal
Age=21/Male=0/BMI=25/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=0.7/Neuroticism=0.81/Extraversion=0.16/Openness=0.27/Agreeableness=-0.33/Conscientiousness=0.53
Illumina Human HT-12 BeadArray

tag: birthcontrol


title: PERS-UK-60

description:
8381653096_J.AVG_Signal
Age=23/Male=0/BMI=28/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=0.3/Neuroticism=2.08/Extraversion=-0.13/Openness=1.52/Agreeableness=0.3/Conscientiousness=0.01
Illumina Human HT-12 BeadArray

tag: antidepressant


title: PERS-UK-51

description:
8381653096_A.AVG_Signal
Age=23/Male=0/BMI=missing/Caucasian=1/CigDay=0/AlcDay=0/ExerDay=0.5/Neuroticism=-0.84/Extraversion=0.6/Openness=1.2/Agreeableness=0.94/Conscientiousness=0.4
Illumina Human HT-12 BeadArray

tag: othermedication


title: PERS-UK-63

description:
8381653097_A.AVG_Signal
Age=19/Male=0/BMI=25/Caucasian=1/CigDay=0/AlcDay=0.1/ExerDay=1.5/Neuroticism=0.68/Extraversion=0.46/Openness=1.36/Agreeableness=0.94/Conscientiousness=-1.42
Illumina Human HT-12 BeadArray

tag: negativeaffect


title: PERS-UK-49

description:
8381653090_K.AVG_Signal
Age=22/Male=0/BMI=21/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=0.8/Neuroticism=-1.34/Extraversion=0.31/Openness=-1.3/Agreeableness=1.25/Conscientiousness=0.4
Illumina Human HT-12 BeadArray

tag: neuroticism


title: PERS-UK-55

description:
8381653096_E.AVG_Signal
Age=22/Male=1/BMI=22/Caucasian=1/CigDay=0/AlcDay=1.7/ExerDay=0.9/Neuroticism=-1.34/Extraversion=0.01/Openness=0.27/Agreeableness=-0.81/Conscientiousness=1.31
Illumina Human HT-12 BeadArray

tag: extraversion


title: PERS-UK-65

description:
8381653097_C.AVG_Signal
Age=22/Male=1/BMI=28/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=0.3/Neuroticism=2.46/Extraversion=-1.31/Openness=0.58/Agreeableness=0.46/Conscientiousness=-0.9
Illumina Human HT-12 BeadArray

tag: openness


title: CD8+_Memory_3

city: Philadelphia

first: Christopher

last: Snyder

state: PA

address: 233 South Tenth Street

department: Department of Microbiology and Immunology

institute: Thomas Jefferson University

description:
Memory-3
Gene expression in mouse CD8+ T-cells that exhibit reactivity to MCMV antigens and a memory phenotype.

hyb_protocol: Affymetrix GeneChips, Mouse Gene 1.0 ST array (Affymetrix) were hybridized with 2.5 μg fragmented and biotinylated cDNA in hybridization cocktail.

scan_protocol: Chips were scanned on an Affymetrix GeneChip Scanner 3000, using Command Console Software.

data_processing: Data was analyzed using the R programming language and various packages from Bioconductor. The oligo package was used to extract expression data from the Affymetrix CEL files and perform background and RMA normalization. Annotation information was added using the mogene10sttranscriptcluster.db package and probes without valid annotations were removed before differential expression analysis using the limma package’s linear modeling and Bayes methods.

source_name: CD8+ T-cells, memory

label_protocol: 50 μg of total RNA was reverse transcribed into cDNA. 2.5 μg cDNA was fragmented and biotinylated using FL-Ovation cDNA biotin module (NuGen Technologies, Inc).

growth_protocol: C57BL/6 mice were bred and housed under specific pathogen-free conditions at Thomas Jefferson University (Philadelphia, PA). Between 6-16 weeks of age, mice were infected intraperitoneally (i.p.) with 2 x 10^5 pfu of MCMV strain MW97.01. Mice were considered chronically-infected at 8 weeks post-infection.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy Plus Kit.

treatment_protocol: Splenocytes were isolated from chronically-infected mice, stained with fluorescently conjugated antibodies, and sorted on a MoFlo cell sorter.

tag: strain/background

tag: cell type

value: CD8+ T-cells

tag: cell subset

value: memory

tag: sorting markers

value: CD8+, CD44hi,tetramer binding,KLRG1+

tag: replicate

value: biological replicate 3


title: PERS-UK-67

description:
8381653097_E.AVG_Signal
Age=19/Male=1/BMI=23/Caucasian=0/CigDay=0/AlcDay=0.1/ExerDay=0.7/Neuroticism=-0.2/Extraversion=0.46/Openness=0.89/Agreeableness=-0.33/Conscientiousness=0.14
Illumina Human HT-12 BeadArray

tag: age

tag: male

tag: bmi

tag: caucasian

tag: agreeableness

tag: conscientiousness


title: PERS-UK-57

description:
8381653096_G.AVG_Signal
Age=21/Male=1/BMI=22/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=2/Neuroticism=-0.33/Extraversion=-0.57/Openness=-0.2/Agreeableness=-1.92/Conscientiousness=0.79
Illumina Human HT-12 BeadArray

tag: cigday

tag: alcday

tag: exerday

tag: minorsymptom

tag: birthcontrol

tag: antidepressant


title: CD8+_Memory_2

description:
Memory-2
Gene expression in mouse CD8+ T-cells that exhibit reactivity to MCMV antigens and a memory phenotype.

tag: strain/background

value: biological replicate 2


title: PERS-UK-48

description:
8381653090_J.AVG_Signal
Age=25/Male=0/BMI=16/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=1/Neuroticism=0.81/Extraversion=-1.01/Openness=-1.14/Agreeableness=-0.49/Conscientiousness=1.44
Illumina Human HT-12 BeadArray

tag: othermedication

tag: negativeaffect

tag: neuroticism

tag: extraversion

tag: openness


title: PERS-UK-53

description:
8381653096_C.AVG_Signal
Age=26/Male=0/BMI=24/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=0.5/Neuroticism=1.19/Extraversion=-0.28/Openness=-0.98/Agreeableness=0.14/Conscientiousness=-1.29
Illumina Human HT-12 BeadArray

tag: age

tag: male


title: PERS-UK-50

description:
8381653090_L.AVG_Signal
Age=22/Male=0/BMI=24/Caucasian=1/CigDay=1.4/AlcDay=1.7/ExerDay=0.4/Neuroticism=1.95/Extraversion=-1.16/Openness=0.58/Agreeableness=-0.49/Conscientiousness=-2.71
Illumina Human HT-12 BeadArray

tag: bmi

tag: caucasian


title: CD8+_Memory_1

description:
Memory-1
Gene expression in mouse CD8+ T-cells that exhibit reactivity to MCMV antigens and a memory phenotype.

tag: cell type

tag: cell subset

tag: sorting markers

tag: replicate

value: biological replicate 1


title: PERS-UK-56

description:
8381653096_F.AVG_Signal
Age=34/Male=0/BMI=26/Caucasian=1/CigDay=0/AlcDay=0.9/ExerDay=1/Neuroticism=-0.71/Extraversion=0.16/Openness=-1.14/Agreeableness=0.14/Conscientiousness=-0.12
Illumina Human HT-12 BeadArray

tag: cigday

tag: alcday

tag: exerday

tag: minorsymptom

tag: agreeableness

tag: conscientiousness


title: PERS-UK-52

description:
8381653096_B.AVG_Signal
Age=19/Male=0/BMI=20/Caucasian=1/CigDay=0/AlcDay=0.3/ExerDay=1/Neuroticism=1.06/Extraversion=-1.6/Openness=-0.05/Agreeableness=0.46/Conscientiousness=-0.25
Illumina Human HT-12 BeadArray

tag: birthcontrol

tag: antidepressant

tag: othermedication

tag: negativeaffect

tag: neuroticism


title: CD8+_Effector_3

description:
Effector-3
Gene expression in mouse CD8+ T-cells that exhibit reactivity to MCMV antigens and an effector phenotype.

source_name: CD8+ T-cells, effector

tag: strain/background

value: effector

value: CD8+, CD44hi,tetramer binding,CD127+


title: CD8+_Effector_2

description:
Effector-2
Gene expression in mouse CD8+ T-cells that exhibit reactivity to MCMV antigens and an effector phenotype.


title: CD8+_Naive_3

description:
Naive-3
Gene expression in mouse CD8+ T-cells that do not exhibit signs of activation.

source_name: CD8+ T-cells, naïve

value: naïve


title: PERS-UK-45

description:
8381653090_G.AVG_Signal
Age=21/Male=0/BMI=22/Caucasian=0/CigDay=0/AlcDay=0.6/ExerDay=0.4/Neuroticism=-0.71/Extraversion=-0.13/Openness=-0.52/Agreeableness=0.46/Conscientiousness=-0.51
Illumina Human HT-12 BeadArray

tag: age

tag: male

tag: bmi

tag: caucasian

tag: extraversion

tag: openness


title: Rep9_S_T_82

city: Umea

first: Johannes

last: Hanson

address: KBC

department: Plant Physiology, Umeå University

country: Sweden

institute: Umeå Plant Science Centre

description: Total mRNA

hyb_protocol: 5.5 µg fragmented sscDNA were used for hybridization on the Affymetrix GeneChips Arabidopsis AGRONOMICS Genome Array. Hybridization, washing, and staining were performed with the GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: the scanned array images were analyzed using Affymetrix Command Console Viewer software.

data_processing: The GeneChip data were analyzed using the R statistical programming environment and the Bioconductor packages. The aroma.affymetrix package was used to perform RMA background correction, normalization, probe summarization, and quality check of the data. The LIMMA package was used to obtain gene expression data.

organism: Arabidopsis thaliana

source_name: seedling

label_protocol: Labeled sense stranded cDNA was synthesized with the Ambion WT Expression kit using 100 ng RNA. Fragmentation and terminal labeling with 5.5 µg sscDNA was performed using the Affymetrix Terminal Labeling Kit.

growth_protocol: Liquid culture Arabidopsis seedling, 7 days old

extract_protocol: RNA was extracted using Guanidine-HCl extraction, followed by a clean-up step using the Spectrum Plant Total RNA Kit (Sigma Aldrich). To each sample (single or pooled fractions), 50 pg of luciferase RNA was added prior to mRNA extraction to allow normalization independent of the original RNA content of the sample.

treatment_protocol: Sucrose was added by change to succrose containing medium

tag: treatment group

value: Sucrose treated

tag: sample type

value: total RNA


title: PERS-UK-46

description:
8381653090_H.AVG_Signal
Age=22/Male=0/BMI=21/Caucasian=1/CigDay=0/AlcDay=0.7/ExerDay=0.1/Neuroticism=0.81/Extraversion=-1.16/Openness=0.73/Agreeableness=0.94/Conscientiousness=-0.12
Illumina Human HT-12 BeadArray

tag: cigday

tag: alcday

tag: exerday

tag: minorsymptom


title: PERS-UK-43

description:
8381653090_E.AVG_Signal
Age=22/Male=1/BMI=17.5/Caucasian=0/CigDay=0/AlcDay=0.6/ExerDay=0.1/Neuroticism=0.3/Extraversion=-0.43/Openness=2.45/Agreeableness=0.46/Conscientiousness=-0.25
Illumina Human HT-12 BeadArray

tag: birthcontrol

tag: antidepressant

tag: agreeableness

tag: conscientiousness


title: PERS-UK-38

description:
8381653088_L.AVG_Signal
Age=19/Male=0/BMI=18/Caucasian=1/CigDay=0/AlcDay=0.3/ExerDay=1/Neuroticism=-0.33/Extraversion=-0.28/Openness=-0.36/Agreeableness=0.94/Conscientiousness=1.18
Illumina Human HT-12 BeadArray

tag: othermedication

tag: negativeaffect

tag: neuroticism


title: PERS-UK-47

description:
8381653090_I.AVG_Signal
Age=21/Male=0/BMI=19/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=0.3/Neuroticism=-0.46/Extraversion=-0.28/Openness=-0.83/Agreeableness=0.3/Conscientiousness=1.57
Illumina Human HT-12 BeadArray

tag: age

tag: male

tag: bmi


title: PERS-UK-39

description:
8381653090_A.AVG_Signal
Age=27/Male=1/BMI=23/Caucasian=0/CigDay=0.1/AlcDay=1.1/ExerDay=0.6/Neuroticism=-0.84/Extraversion=-1.46/Openness=0.58/Agreeableness=-0.49/Conscientiousness=-1.16
Illumina Human HT-12 BeadArray

tag: caucasian

tag: extraversion

tag: openness


title: PERS-UK-40

description:
8381653090_B.AVG_Signal
Age=19/Male=1/BMI=21/Caucasian=1/CigDay=0/AlcDay=0.7/ExerDay=0.4/Neuroticism=-0.96/Extraversion=-0.87/Openness=0.11/Agreeableness=-0.02/Conscientiousness=1.96
Illumina Human HT-12 BeadArray

tag: cigday


title: PERS-UK-44

description:
8381653090_F.AVG_Signal
Age=20/Male=0/BMI=22/Caucasian=1/CigDay=0/AlcDay=0/ExerDay=0.5/Neuroticism=-1.34/Extraversion=-0.87/Openness=-0.67/Agreeableness=-0.17/Conscientiousness=1.83
Illumina Human HT-12 BeadArray

tag: alcday


title: PERS-UK-42

description:
8381653090_D.AVG_Signal
Age=21/Male=1/BMI=24/Caucasian=1/CigDay=0/AlcDay=0.4/ExerDay=1/Neuroticism=-0.46/Extraversion=-0.87/Openness=-0.67/Agreeableness=0.94/Conscientiousness=-0.9
Illumina Human HT-12 BeadArray

tag: exerday


title: CD8+_Naive_2

description:
Naive-2
Gene expression in mouse CD8+ T-cells that do not exhibit signs of activation.

tag: strain/background

tag: cell type

tag: cell subset

tag: sorting markers

tag: replicate


title: PERS-UK-37

description:
8381653088_K.AVG_Signal
Age=20/Male=0/BMI=23/Caucasian=1/CigDay=0/AlcDay=3/ExerDay=1/Neuroticism=0.05/Extraversion=0.31/Openness=-1.77/Agreeableness=0.14/Conscientiousness=0.79
Illumina Human HT-12 BeadArray

tag: minorsymptom

tag: birthcontrol

tag: antidepressant

tag: othermedication

tag: agreeableness

tag: conscientiousness


title: PERS-UK-41

description:
8381653090_C.AVG_Signal
Age=53/Male=0/BMI=24/Caucasian=1/CigDay=0/AlcDay=1/ExerDay=0.5/Neuroticism=-0.84/Extraversion=0.16/Openness=0.73/Agreeableness=0.78/Conscientiousness=1.7
Illumina Human HT-12 BeadArray

tag: age

tag: male

tag: bmi

tag: caucasian

tag: negativeaffect

tag: neuroticism


title: CD8+_Effector_1

description:
Effector-1
Gene expression in mouse CD8+ T-cells that exhibit reactivity to MCMV antigens and an effector phenotype.

tag: strain/background


title: Rep9_S_SP_84

type: other

description: Polysoma mRNA

molecule: other

tag: treatment group

tag: sample type

value: Polysoma mRNA


title: PERS-UK-36

description:
8381653088_J.AVG_Signal
Age=20/Male=0/BMI=24/Caucasian=1/CigDay=0/AlcDay=1.7/ExerDay=0.5/Neuroticism=-0.71/Extraversion=0.31/Openness=-0.36/Agreeableness=-0.17/Conscientiousness=0.4
Illumina Human HT-12 BeadArray

tag: cigday

tag: alcday

tag: exerday

tag: extraversion

tag: openness


title: CD8+_Naive_1

description:
Naive-1
Gene expression in mouse CD8+ T-cells that do not exhibit signs of activation.

tag: cell type

tag: cell subset

tag: sorting markers

tag: replicate


title: Rep9_DS_SP_92

description: Polysoma mRNA

value: Dark and Sucrose treated


title: Rep9_DS_T_90

description: Total mRNA


title: Arabidopsis thaliana shoots replicate 1

city: Montpellier

first: Patrick

last: Doumas

address: Place Viala

country: France

institute: INRA

description: Biological replicate 1 of 3. Transcriptional profiling of shoots from plants treated with 40 µM Pb(NO3)2 vs. not treated plants (control).

hyb_protocol: 825 ng of control_Cy3 and 825 ng test_Cy5 were applied to microarrays at 60°C during 17 hours.

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3).

source_name: shoots, without Pb treatment

label_protocol: 200 ng of total RNA were primed using the Low imput Quick Amp Labelling kit (Ailent technologies) according to the to the manufacturer’s instructions.

growth_protocol: Seeds were surface sterilized, sown on half MS medium with 1,2% agar and grown vertically in a growth chamber, after 2 weeks seedlings were transferred to hydroponic culture

extract_protocol: Total RNA extracted using RNeasy plant mini kit (Qiagen, USA) for roots and SV Total RNA isolation system (Promega, USA) for shoots, following manufacturer's instructions

treatment_protocol: 4 weeks old seedlings were treated in hydroponic cultures with Pb during 3 days, by adding 40 µM Pb(NO3)2 in a fresh growth medium without phosphate. In control experiments, growth medium was replaced by fresh growth medium without phosphate.

tag: tissue

value: shoots

tag: treatment

value: without Pb treatment

source_name: shoots, with 40 µM Pb(NO3)2 treatment

value: with 40 µM Pb(NO3)2 treatment


title: PERS-UK-34

description:
8381653088_H.AVG_Signal
Age=23/Male=0/BMI=18/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=0.3/Neuroticism=-0.2/Extraversion=1.34/Openness=-0.2/Agreeableness=-1.29/Conscientiousness=0.53
Illumina Human HT-12 BeadArray

tag: age

tag: male

tag: bmi

tag: caucasian

tag: minorsymptom

tag: birthcontrol

tag: antidepressant

tag: othermedication

tag: agreeableness

tag: conscientiousness


title: PERS-UK-35

description:
8381653088_I.AVG_Signal
Age=22/Male=0/BMI=19/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=0/Neuroticism=1.06/Extraversion=-2.19/Openness=-0.52/Agreeableness=-1.6/Conscientiousness=-0.64
Illumina Human HT-12 BeadArray

tag: cigday

tag: alcday

tag: exerday

tag: negativeaffect

tag: neuroticism

tag: extraversion

tag: openness


title: Rep9_D_T_86

description: Total mRNA

tag: treatment group

value: Dark treated

tag: sample type


title: PERS-UK-31

description:
8381653088_F.AVG_Signal
Age=20/Male=0/BMI=31/Caucasian=1/CigDay=0/AlcDay=2.9/ExerDay=2/Neuroticism=0.56/Extraversion=0.6/Openness=1.2/Agreeableness=0.3/Conscientiousness=-0.77
Illumina Human HT-12 BeadArray

tag: age

tag: male

tag: bmi


title: PERS-UK-32

description:
8381653088_G.AVG_Signal
Age=33/Male=1/BMI=21/Caucasian=1/CigDay=0/AlcDay=0.3/ExerDay=0.9/Neuroticism=0.43/Extraversion=0.01/Openness=1.52/Agreeableness=-0.81/Conscientiousness=-1.42
Illumina Human HT-12 BeadArray

tag: caucasian

tag: minorsymptom

tag: birthcontrol


title: Arabidopsis thaliana shoots replicate 3

description: Biological replicate 3 of 3. Transcriptional profiling of shoots from plants treated with 40 µM Pb(NO3)2 vs. not treated plants (control).

tag: tissue

tag: treatment


title: Arabidopsis thaliana shoots replicate 2

description: Biological replicate 2 of 3. Transcriptional profiling of shoots from plants treated with 40 µM Pb(NO3)2 vs. not treated plants (control).


title: PERS-UK-28

description:
8381653088_C.AVG_Signal
Age=20/Male=1/BMI=19/Caucasian=0/CigDay=5/AlcDay=0/ExerDay=0.1/Neuroticism=-0.84/Extraversion=0.9/Openness=-0.05/Agreeableness=-0.33/Conscientiousness=0.4
Illumina Human HT-12 BeadArray

tag: cigday

tag: antidepressant

tag: othermedication

tag: agreeableness

tag: conscientiousness


title: PERS-UK-29

description:
8381653088_D.AVG_Signal
Age=20/Male=0/BMI=19/Caucasian=1/CigDay=0/AlcDay=0.4/ExerDay=0.3/Neuroticism=-0.46/Extraversion=0.16/Openness=0.42/Agreeableness=-0.33/Conscientiousness=0.66
Illumina Human HT-12 BeadArray

tag: alcday

tag: exerday

tag: negativeaffect

tag: neuroticism

tag: extraversion


title: Arabidopsis thaliana roots replicate 2

description: Biological replicate 2 of 3. Transcriptional profiling of roots from plants treated with 40 µM Pb(NO3)2 vs. not treated plants (control).

source_name: roots, without Pb treatment

value: roots

source_name: roots, with 40 µM Pb(NO3)2 treatment


title: Arabidopsis thaliana roots replicate 3

description: Biological replicate 3 of 3. Transcriptional profiling of roots from plants treated with 40 µM Pb(NO3)2 vs. not treated plants (control).


title: PERS-UK-23

description:
8381653087_J.AVG_Signal
Age=21/Male=0/BMI=22/Caucasian=0/CigDay=0/AlcDay=1/ExerDay=1/Neuroticism=-0.2/Extraversion=0.01/Openness=-1.92/Agreeableness=0.78/Conscientiousness=0.92
Illumina Human HT-12 BeadArray

tag: age

tag: male

tag: openness


title: Arabidopsis thaliana roots replicate 1

description: Biological replicate 1 of 3. Transcriptional profiling of roots from plants treated with 40 µM Pb(NO3)2 vs. not treated plants (control).


title: Rep9_D_SP_88

description: Polysoma mRNA

tag: treatment group

tag: sample type


title: PERS-UK-26

description:
8381653088_A.AVG_Signal
Age=21/Male=0/BMI=22/Caucasian=1/CigDay=0/AlcDay=1.4/ExerDay=0.7/Neuroticism=-1.34/Extraversion=1.04/Openness=1.52/Agreeableness=0.3/Conscientiousness=0.4
Illumina Human HT-12 BeadArray

tag: bmi

tag: caucasian

tag: minorsymptom

tag: birthcontrol


title: Rep9_C_SP_80

description: Polysoma mRNA

value: Control


title: PERS-UK-27

description:
8381653088_B.AVG_Signal
Age=20/Male=1/BMI=missing/Caucasian=1/CigDay=0/AlcDay=1/ExerDay=1/Neuroticism=0.43/Extraversion=0.46/Openness=-0.67/Agreeableness=-2.08/Conscientiousness=-1.94
Illumina Human HT-12 BeadArray

value: missing

tag: cigday

tag: antidepressant

tag: othermedication


title: Rep8_S_SP_68

description: Polysoma mRNA


title: Hirschfeldia incana shoots replicate 3

description: Biological replicate 3 of 3. Transcriptional profiling of shoots from plants treated with 100 µM Pb(NO3)2 vs. not treated plants (control).

organism: Hirschfeldia incana

treatment_protocol: 4 weeks old seedlings were treated in hydroponic cultures with lead during 3 days, by adding 100 Pb (NO3)2 in a fresh growth medium without phosphate. In control experiments, growth medium was replaced by fresh growth medium without phosphate.

tag: tissue

tag: treatment

source_name: shoots, with 100 µM Pb(NO3)2 treatment

value: with 100 µM Pb(NO3)2 treatment


title: Hirschfeldia incana shoots replicate 1

description: Biological replicate 1 of 3. Transcriptional profiling of shoots from plants treated with 100 µM Pb(NO3)2 vs. not treated plants (control).


title: PERS-UK-24

description:
8381653087_K.AVG_Signal
Age=19/Male=0/BMI=24/Caucasian=1/CigDay=0/AlcDay=0.1/ExerDay=1/Neuroticism=-0.46/Extraversion=1.19/Openness=-0.83/Agreeableness=0.78/Conscientiousness=-0.12
Illumina Human HT-12 BeadArray

tag: alcday

tag: exerday

tag: negativeaffect

tag: agreeableness

tag: conscientiousness


title: PERS-UK-22

description:
8381653087_I.AVG_Signal
Age=20/Male=0/BMI=21/Caucasian=1/CigDay=0/AlcDay=0/ExerDay=0.5/Neuroticism=-0.46/Extraversion=-0.72/Openness=0.11/Agreeableness=0.14/Conscientiousness=-1.16
Illumina Human HT-12 BeadArray

tag: age

tag: male

tag: neuroticism

tag: extraversion

tag: openness


title: Hirschfeldia incana shoots replicate 2

description: Biological replicate 2 of 3. Transcriptional profiling of shoots from plants treated with 100 µM Pb(NO3)2 vs. not treated plants (control).


title: PERS-UK-30

description:
8381653088_E.AVG_Signal
Age=23/Male=0/BMI=25/Caucasian=1/CigDay=0/AlcDay=0.6/ExerDay=0.1/Neuroticism=1.19/Extraversion=-2.19/Openness=-0.52/Agreeableness=-0.17/Conscientiousness=-0.51
Illumina Human HT-12 BeadArray

tag: bmi

tag: caucasian

tag: minorsymptom


title: PERS-UK-25

description:
8381653087_L.AVG_Signal
Age=22/Male=1/BMI=23/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=0/Neuroticism=-1.09/Extraversion=-2.34/Openness=-2.39/Agreeableness=-2.87/Conscientiousness=-2.84
Illumina Human HT-12 BeadArray

tag: cigday

tag: birthcontrol

tag: antidepressant


title: Hirschfeldia incana roots replicate 2

description: Biological replicate 2 of 3. Transcriptional profiling of roots from plants treated with 100 µM Pb(NO3)2 vs. not treated plants (control).

tag: tissue

tag: treatment

source_name: roots, with 100 µM Pb(NO3)2 treatment


title: Rep8_S_T_66

description: Total mRNA

tag: treatment group

tag: sample type


title: Rep9_C_T_78

description: Total mRNA


title: PERS-UK-21

description:
8381653087_H.AVG_Signal
Age=21/Male=1/BMI=22/Caucasian=0/CigDay=3/AlcDay=0/ExerDay=0.9/Neuroticism=-0.46/Extraversion=0.9/Openness=1.67/Agreeableness=-0.33/Conscientiousness=-1.68
Illumina Human HT-12 BeadArray

tag: alcday

tag: exerday

tag: othermedication

tag: negativeaffect

tag: agreeableness


title: Hirschfeldia incana roots replicate 3

description: Biological replicate 3 of 3. Transcriptional profiling of roots from plants treated with 100 µM Pb(NO3)2 vs. not treated plants (control).


title: Rep8_DS_T_74

description: Total mRNA


title: Hirschfeldia incana roots replicate 1

description: Biological replicate 1 of 3. Transcriptional profiling of roots from plants treated with 100 µM Pb(NO3)2 vs. not treated plants (control).


title: PERS-UK-18

description:
8381653087_E.AVG_Signal
Age=23/Male=0/BMI=30/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=0/Neuroticism=-0.71/Extraversion=-1.6/Openness=0.11/Agreeableness=-1.13/Conscientiousness=-0.38
Illumina Human HT-12 BeadArray

tag: age

tag: male

tag: neuroticism

tag: extraversion

tag: conscientiousness


title: PERS-UK-19

description:
8381653087_F.AVG_Signal
Age=20/Male=0/BMI=24/Caucasian=1/CigDay=0/AlcDay=2/ExerDay=2/Neuroticism=-0.96/Extraversion=0.46/Openness=-0.2/Agreeableness=-3.67/Conscientiousness=1.31
Illumina Human HT-12 BeadArray

tag: bmi

tag: caucasian

tag: cigday

tag: minorsymptom

tag: openness


title: PERS-UK-17

description:
8381653087_D.AVG_Signal
Age=23/Male=0/BMI=23/Caucasian=1/CigDay=0/AlcDay=0.4/ExerDay=0.6/Neuroticism=-0.08/Extraversion=2.22/Openness=0.89/Agreeableness=0.3/Conscientiousness=0.79
Illumina Human HT-12 BeadArray

tag: birthcontrol

tag: antidepressant


title: PERS-UK-20

description:
8381653087_G.AVG_Signal
Age=34/Male=0/BMI=22/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=1.5/Neuroticism=0.81/Extraversion=-0.72/Openness=-1.14/Agreeableness=-0.97/Conscientiousness=-0.12
Illumina Human HT-12 BeadArray

tag: alcday


title: PERS-UK-15

description:
8381653087_B.AVG_Signal
Age=22/Male=0/BMI=24/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=0.3/Neuroticism=0.81/Extraversion=-1.31/Openness=-0.98/Agreeableness=-0.02/Conscientiousness=-0.77
Illumina Human HT-12 BeadArray

tag: exerday


title: PERS-UK-16

description:
8381653087_C.AVG_Signal
Age=22/Male=0/BMI=21/Caucasian=1/CigDay=0/AlcDay=2/ExerDay=0.5/Neuroticism=-0.96/Extraversion=2.22/Openness=1.67/Agreeableness=1.57/Conscientiousness=1.31
Illumina Human HT-12 BeadArray

tag: othermedication


title: Rep8_D_T_70

description: Total mRNA

tag: treatment group

tag: sample type


title: PERS-UK-13

description:
8381653086_L.AVG_Signal
Age=33/Male=0/BMI=23/Caucasian=1/CigDay=0/AlcDay=0.4/ExerDay=1/Neuroticism=-1.09/Extraversion=0.46/Openness=0.73/Agreeableness=0.14/Conscientiousness=1.05
Illumina Human HT-12 BeadArray

tag: age

tag: negativeaffect

tag: agreeableness


title: Rep8_D_SP_72

description: Polysoma mRNA


title: 5753677001_G

city: Westmead

first: Philip

middle: John

last: O'Connell

state: NSW

address: 176 Hawkesbury Rd

department: Centre for Transplant and Renal Research

country: Australia

institute: Westmead Millennium Institute

description: 12 month kidney biopsy post transplant

data_processing: The data were background-subtracted and normalised using quantile normalisation in GenomeStudio

source_name: 12 month kidney biopsy post transplant

label_protocol: The sample was labeled using Epicentre TargetAmp™ Nano-g™ Biotin-aRNA Labeling Kit  Nano-g Biotin-aRNA Labeling Kit

extract_protocol: Total RNA was extracted using the Qiagen Allprep DNA/RNA/protein Mini kit or the Invitrogen Micro-to-Midi kit

tag: ifta


title: PERS-UK-12

description:
8381653086_K.AVG_Signal
Age=21/Male=0/BMI=22/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=0.1/Neuroticism=0.43/Extraversion=0.9/Openness=-0.36/Agreeableness=-0.49/Conscientiousness=0.53
Illumina Human HT-12 BeadArray

tag: male

tag: neuroticism

tag: extraversion

tag: conscientiousness


title: PERS-UK-10

description:
8381653086_I.AVG_Signal
Age=23/Male=0/BMI=24/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=0.5/Neuroticism=2.46/Extraversion=-1.75/Openness=1.05/Agreeableness=1.41/Conscientiousness=-1.42
Illumina Human HT-12 BeadArray

tag: bmi

tag: caucasian

tag: cigday

tag: minorsymptom


title: 5753677001_I

description: 12 month kidney biopsy post transplant


title: 5753677001_F

description: 12 month kidney biopsy post transplant


title: PERS-UK-8

description:
8381653086_G.AVG_Signal
Age=23/Male=0/BMI=16/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=0.1/Neuroticism=0.3/Extraversion=-1.16/Openness=0.11/Agreeableness=-1.13/Conscientiousness=0.53
Illumina Human HT-12 BeadArray

tag: alcday

tag: birthcontrol

tag: antidepressant

tag: openness


title: Rep8_C_T_62

description: Total mRNA

tag: treatment group

tag: sample type


title: Rep8_DS_SP_76

description: Polysoma mRNA


title: PERS-UK-9

description:
8381653086_H.AVG_Signal
Age=23/Male=0/BMI=26/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=0.3/Neuroticism=0.94/Extraversion=0.16/Openness=0.89/Agreeableness=0.14/Conscientiousness=-0.38
Illumina Human HT-12 BeadArray

tag: age

tag: exerday

tag: othermedication

tag: negativeaffect


title: PERS-UK-14

description:
8381653087_A.AVG_Signal
Age=21/Male=0/BMI=18/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=1/Neuroticism=-1.47/Extraversion=1.04/Openness=0.27/Agreeableness=1.41/Conscientiousness=0.79
Illumina Human HT-12 BeadArray

tag: male

tag: neuroticism

tag: agreeableness


title: PERS-UK-7

description:
8381653086_F.AVG_Signal
Age=23/Male=0/BMI=22/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=0.1/Neuroticism=-0.46/Extraversion=-0.57/Openness=-1.14/Agreeableness=0.78/Conscientiousness=-0.38
Illumina Human HT-12 BeadArray

tag: bmi

tag: extraversion

tag: conscientiousness


title: Rep7_S_T_50

description: Total mRNA


title: 5753677001_D

description: 12 month kidney biopsy post transplant

tag: ifta


title: Rep8_C_SP_64

description: Polysoma mRNA


title: PERS-UK-11

description:
8381653086_J.AVG_Signal
Age=23/Male=0/BMI=31/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=0.5/Neuroticism=0.81/Extraversion=0.01/Openness=-0.2/Agreeableness=0.46/Conscientiousness=-0.77
Illumina Human HT-12 BeadArray

tag: caucasian

tag: cigday

tag: alcday

tag: minorsymptom