title: Genotype IM4 Time 3 Biorep C


title: Col0 vs myb2 KO timepoint1 biorep B

status: Public on Apr 23 2013

type: RNA

city: Norwich

first: Jonathan

middle: David

last: Moore

address: Norwich Research Park

department: Platforms and Pipelines

country: United Kingdom

institute: The Genome Analysis Centre

description: Col0 WT vs myb2 KO at timepoint1

hyb_protocol: The microarray experiments were carried out using the CATMA (version 4) microarray (Allemeersh et al., 2005; http://www.catma.org). Labelled samples were hybridized to slides overnight at 42oC.

scan_protocol: Following hybridization, slides were washed and scanned using an Affymetrix 428 array scanner at 532nm (Cy3) and 635nm (Cy5).

data_processing:
Scanned data were quantified using Imagene 7.5.0 software (BioDiscovery, Inc.).
Analysis of expression differences between Col-0 and myb2 and Col-0 and myb108 under each condition was performed using the R Bioconductor package limmaGUI (Wettenhall and Smyth, 2004). Raw data were normalized within arrays using a PrintTip lowess transformation and normalized between arrays using the quantile-normalization. The data were fitted to a linear model using a least squares method. P-values were adjusted for multiple testing using Benjamini and Hochberg method to control the false discovery rate (Benjamini and Hochberg, 1995).

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Col0 t1

label_protocol: Cy3 and Cy5 labelled cDNA probes were prepared by reverse transcribing 5µg of aRNA with Cy3- or Cy5- dCTP (GE Healthcare) and a modified dNTP mix (10mM each dATP, dGTP and dTTP; 2mM dCTP) using random primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen), with the inclusion of RNase inhibitor (RNaseOUT, Invitrogen) and DTT. Labelled probes were purified using QiaQuick PCR Purification columns (Qiagen), freeze-dried, and resuspended in 50µl hybridization buffer (25% formamide, 5xSSC, 0.1% SDS, 0.5µg/µl yeast tRNA [Invitrogen]). Four biological replicates were pooled and labelled twice with each dye giving four technical replicates. Comparisons were made pairwise between WT and mutant under each condition.

growth_protocol: Arabidopsis plants Col-0, myb2 and myb108 were grown under a 16:8 hr light:dark cycle (lights on 04:00 to 20:00) at 20°C, 60% humidity and light intensity of 100 μmol photons.m-2.s-1. Arabidopsis seed was stratified for three days in 0.1% agar at 4°C before sowing onto Arabidopsis soil mix (Scotts Levingtons F2s compost:sand:fine grade vermiculite in a ratio of 6:1:1). The myb2, myb108 lines were T-DNA insertion lines Salk_045455, Salk_024059 respectively (obtained from the Nottingham Arabidopsis Seed Centre).

extract_protocol: Total RNA was isolated from four individual leaves from each sampled time point (arbitrarily labelled as biological replicates A, B, C and D) using TRIzol reagent (Invitrogen), purified with RNeasy columns (Qiagen) and amplified using the MessageAmp II aRNA Amplification kit (Ambion) in accordance with the kit protocol with a single round of amplification.

treatment_protocol: Nine 3-week old Col-0, myb2 (genotype IM24) and myb108 (genotype BOS1) rosettes, cut from the root, were transferred to 3 Petri dishes containing water-saturated filter paper and stored at 20oC in complete darkness. Plates were photographed daily and RGB values calculated for leaf 5 of each rosette using the Color Histogram function in ImageJ. RGB intensities were normalized using a white-background reference point and average red/green ratios provided a quantitative measure of leaf yellowing. A red-green ratio of around 0.8 indicates the initiation of senescence. When the average ratio of Col-0 samples was >0.8, leaf 5 for Col-0, myb2 and myb108 lines was harvested (4 biological replicates). The same sampling procedure was then performed on consecutive days to sample as senescence progressed.

tag: genotype

value: Col0 WT

tag: time

source_name: myb2 t1


title: Col0 vs myb2 KO timepoint2 biorep B

description: Col0 WT vs myb2 KO at timepoint2

source_name: Col0 t2

source_name: myb2 t2


title: Genotype IM4 Time 2 Biorep D

description: Randomised loop design providing dye-swaps between genotypes, time points and bioreps

data_processing:
Scanned data were quantified using Imagene 7.5.0 software (BioDiscovery, Inc.).
Quantified microarray data were Lowess normalied within pintip groups and within arrays, then variation due to arrays and dyes was removed by a random effects model, and averaged, in log space, using R/MAANOVA (MicroArray ANalysis Of VAriance) (Wu et al. 2003).

label: Cy5, Cy3

label_protocol: Cy3 and Cy5 labelled cDNA probes were prepared by reverse transcribing 5µg of aRNA with Cy3- or Cy5- dCTP (GE Healthcare) and a modified dNTP mix (10mM each dATP, dGTP and dTTP; 2mM dCTP) using random primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen), with the inclusion of RNase inhibitor (RNaseOUT, Invitrogen) and DTT. Labelled probes were purified using QiaQuick PCR Purification columns (Qiagen), freeze-dried, and resuspended in 50µl hybridization buffer (25% formamide, 5xSSC, 0.1% SDS, 0.5µg/µl yeast tRNA [Invitrogen]).

growth_protocol: Arabidopsis plants were grown under a 16:8 hr light:dark cycle (lights on 04:00 to 20:00) at 20°C, 60% humidity and light intensity of 100 μmol photons.m-2.s-1. Arabidopsis seed was stratified for three days in 0.1% agar at 4°C before sowing onto Arabidopsis soil mix (Scotts Levingtons F2s compost:sand:fine grade vermiculite in a ratio of 6:1:1). The anac055 line (genotype IM4, col0 background) was T-DNA insertion line Salk_011069 (obtained from the Nottingham Arabidopsis Seed Centre). The anac019 dSpm insertion mutant (genotype 9C11, col5 background) was identified in a pool of SLAT line DNA screened with gene specific primers (Tissier et al., 1999).

treatment_protocol: Leaf 7 was tagged with cotton 18 days after sowing (DAS) and harvested from five randomly selected plants, 8 h into the light period, at 23, 29, 31, 33 and 35 DAS (full senescence).


title: Genotype IM4 Time 1 Biorep B


title: Genotype DM Time 5 Biorep C

value: DM


title: Genotype IM4 Time 1 Biorep A


title: Genotype IM4 Time 1 Biorep C


title: Genotype DM Time 5 Biorep A


title: Genotype IM4 Time 2 Biorep A


title: Genotype DM Time 3 Biorep D


title: Genotype DM Time 2 Biorep D


title: myb2 KO vs Col0 time 30hpi biorep D

description: myb2 KO vs Col0 WT at 30hpi

treatment_protocol: B. cinerea pepper strain spores (Denby et al., 2004) were prepared and Arabidopsis leaves treated as described in Windram et al., Plant Cell 2012 Sep;24(9):3530-57. PMID: 23023172. Col-0, myb2 and myb108 leaves were inoculated with 4-6 (depending on leaf size) evenly spaced 10μl droplets of B. cinerea spores. Infected leaves were harvested to provide 4 biological replicates. Samples for the comparison between myb108 and Col-0 were harvested at 26 and 30 hpi. Samples for the comparison between myb2 knockout line and Col-0 or myb2 knockout line and Col-0 were harvested at 26 and 30 hpi or 24 and 30 hpi respectively.

value: myb2 KO


title: Genotype DM Time 3 Biorep B


title: Genotype DM Time 2 Biorep A


title: Genotype DM Time 4 Biorep B


title: Genotype IM4 Time 2 Biorep B


title: Genotype DM Time 2 Biorep B


title: Genotype DM Time 5 Biorep B


title: Genotype DM Time 4 Biorep A


title: Genotype DM Time 4 Biorep C


title: Genotype DM Time 2 Biorep C


title: Genotype IM4 Time 1 Biorep D


title: Genotype DM Time 5 Biorep D


title: Genotype DM Time 3 Biorep C


title: Genotype DM Time 3 Biorep A


title: Genotype DM Time 1 Biorep D


title: Genotype DM Time 4 Biorep D


title: Genotype DM Time 1 Biorep C


title: Genotype DM Time 1 Biorep B


title: Genotype DM Time 1 Biorep A


title: Genotype Col5 Time 5 Biorep D


title: Genotype Col5 Time 3 Biorep B


title: Genotype Col5 Time 4 Biorep C


title: Genotype Col5 Time 5 Biorep C


title: Genotype Col5 Time 4 Biorep D


title: Genotype Col5 Time 1 Biorep D


title: Genotype Col5 Time 2 Biorep A


title: Genotype Col5 Time 2 Biorep B


title: Genotype Col5 Time 3 Biorep D


title: Genotype Col5 Time 3 Biorep A


title: Genotype Col5 Time 1 Biorep B


title: Genotype Col5 Time 5 Biorep A


title: Genotype Col5 Time 4 Biorep A


title: Genotype IM4 Time 2 Biorep C


title: Genotype Col5 Time 2 Biorep D


title: Genotype Col0 Time 5 Biorep C


title: Genotype Col5 Time 1 Biorep A


title: Genotype Col0 Time 5 Biorep B


title: Genotype Col5 Time 4 Biorep B


title: Genotype Col5 Time 5 Biorep B


title: Genotype Col5 Time 1 Biorep C


title: Genotype Col0 Time 4 Biorep B


title: Genotype Col0 Time 5 Biorep A


title: Genotype Col0 Time 4 Biorep C


title: Genotype Col0 Time 3 Biorep B


title: Genotype Col0 Time 5 Biorep D


title: Genotype Col0 Time 3 Biorep A


title: Genotype Col0 Time 2 Biorep D


title: Genotype Col5 Time 3 Biorep C


title: Genotype Col0 Time 3 Biorep C


title: Genotype Col5 Time 2 Biorep C


title: Genotype Col0 Time 3 Biorep D


title: Genotype Col0 Time 2 Biorep B


title: Genotype Col0 Time 4 Biorep D


title: Genotype 9C11 Time 5 Biorep C


title: Genotype 9C11 Time 4 Biorep C


title: Genotype Col0 Time 2 Biorep C


title: Genotype Col0 Time 1 Biorep C


title: Genotype Col0 Time 1 Biorep A


title: Genotype 9C11 Time 5 Biorep A


title: Genotype Col0 Time 1 Biorep D


title: Genotype Col0 Time 1 Biorep B


title: Genotype 9C11 Time 5 Biorep B


title: Genotype 9C11 Time 4 Biorep B


title: Genotype Col0 Time 2 Biorep A


title: Genotype 9C11 Time 4 Biorep D


title: Genotype 9C11 Time 5 Biorep D


title: Genotype 9C11 Time 3 Biorep D


title: Genotype 9C11 Time 2 Biorep D


title: Genotype Col0 Time 4 Biorep A


title: Genotype 9C11 Time 4 Biorep A


title: Genotype 9C11 Time 2 Biorep A


title: Genotype 9C11 Time 3 Biorep C


title: Genotype 9C11 Time 3 Biorep B


title: Genotype 9C11 Time 2 Biorep C


title: Genotype 9C11 Time 3 Biorep A


title: Genotype 9C11 Time 1 Biorep D


title: Sle1b.BACSlamf6-H1 CD4+ T cells aCD3 24h biological Rep1

city: Boston

first: Marton

last: Keszei

state: MA

address: 3 Blackfan Cir., CLS building room 928

department: Medicine

country: USA

institute: Beth Israel Deaconess Medical Center

description: Gene expression data of splenic total CD4+  T cells after 24h aCD3 stimulation

hyb_protocol: Affymetrix GeneChip Array Station (GCAS) HT system

scan_protocol: standard Affymetrix HT Scanner protocol

data_processing: Array quality was assessed using the R/Bioconductor package. All arrays passed visual inspection and no technical outliers were identified. Raw CEL files were processed using the robust multiarray average (RMA) algorithm.

label: biotin

organism: Mus musculus

source_name: total CD4+

label_protocol: standard Affymetrix protocol

growth_protocol: Cells were incubated in complete RPMI medium at 37 degree C.

extract_protocol: RNA was isolated with Qiagen Total RNA isolation kit.

treatment_protocol: CD4+ T cells were activated with plate-bound  (0.1μg/ml) αCD3 (145-2C11) for 4 hours or  24 hours in 96 well U bottom plates.

tag: strain

tag: cell type

value: CD4+ T cell

tag: treatment


title: Genotype 9C11 Time 1 Biorep C


title: Genotype 9C11 Time 2 Biorep B


title: Genotype 9C11 Time 1 Biorep B


title: Genotype 9C11 Time 1 Biorep A


title: Sle1b.BACSlamf6-H1 CD4+ T cells aCD3 24h biological Rep2


title: Sle1b.BACSlamf6-H1 CD4+ T cells aCD3 24h biological Rep3


title: Sle1b CD4+ T cells aCD3 24h biological Rep3


title: WT CD4+ T cells aCD3 24h biological Rep2


title: WT CD4+ T cells aCD3 24h biological Rep1


title: Sle1b CD4+ T cells aCD3 24h biological Rep2


title: Sle1b CD4+ T cells aCD3 24h biological Rep1


title: Sle1b.BACSlamf6-H1 CD4+ T cells aCD3 4h biological Rep3

description: Gene expression data of splenic total CD4+  T cells after 4h aCD3 stimulation


title: WT CD4+ T cells aCD3 24h technical Rep4


title: 36h_30nMTSA_rep2

city: Noda

first: Hitoshi

last: Sasaki

state: Chiba

address: 2641 Yamazaki

department: Department of Biological Science and Technology

country: Japan

institute: Tokyo University of Science

description:
Technical replicate 2 of 4
The sample-dye assignment applies to both raw data files.

hyb_protocol: cDNA microarrays with varied spotting patterns (with the same total number of cDNA clones) were used. For HMBA and TSA experiments, 22k cDNAs were separately spotted on two glass  slides for one analysis, clone ID H3001A01 to H3120H12 (approx. 11k cDNA clones) were spotted on one slide, and H3121A11 to H4079G07 (approx. 11k cDNA clones) were spotted on the other  slide. For DMSO experiment, 22k cDNAs were separately spotted on two glass slides for one analysis, clone ID H3001A01 to H3159G07 (approx. 15k cDNA clones) were spotted on one slide, and H4001A11 to H4079G07 (approx. 7k cDNA clones) were spotted on the other slide. Therefore, raw data files have varied counts for data rows.  Microarray was pre-hybrized at 50°C, 60 minutes in 5 x saline sodium citrate buffer (SSC) contained 0.1% sodium dodecyl sulfate (SDS)and 0.1% bovine serum albumin (BSA), washed with water, and rinsed with isopropanol. Mixed Cy3 and Cy5 labeled cDNA solution was denaturation at 95°C, 5 minutes in 5 x SSC contained 1.67 mg/mL acetylated BSA. After cooling, SDS was added to final concentration 0.33%. The microarray was covered with a Gap cover glass (Matsunami), hybridization solution was injected, and the microarray was placed in a hybridization cassette (TeleChem). Hybridization was performed at 50°C for 14 hours. After hybridization, the microarray was washed using a Wash Station (TeleCham) as follow; at 42°C 5 minutes in 2 x SSC contained 0.1%SDS, at room temperature 10 minutes in 0.1 x SSC contained 0.1%SDS, and finally twice in 0.1 x SSC at room temperature for 2min. The microarray was dried by centrifugation.

scan_protocol: Hybridization images were scanned using a ScanArray 5000(Perkin-Elmer). Fluorescence intensity of the microarray was quantified using QuantArray 3.0 software (Perkin-Elmer).

data_processing: The microarray data was analyzed using GeneSpring 6.0 (Silicon Genetics). Intensity difference between Cy3 and Cy5 was normalized by LOWESS method. Signal intensities were higher than negative spot.

source_name: HD-MEL_before chemical treatment

label_protocol: Twenty ug of the total RNA was labeled with amino-modified dNTP using a SuperScript Indirect cDNA Labeling System (Invitrogen). The amino-modified cDNA was purified with a S.N.A.P column (Invitrogen) and ethanol precipitation. The purified cDNA was labeled with Cye3 Mono-Reactive Dye Pack (Amersham Biosciences) or Cye5 Mono-Reactive Dye Pack (Amersham Biosciences) by coupling reaction. The labeled cDNA was purified with a QIAquick PCR Purification Kit (Qiagen).

growth_protocol: MEL cells were cultured in RPMI1640 medium with 10% fetal calf serum at 37 °C with 5% CO2 concentration.

extract_protocol: Total RNA of MEL cells was extracted using RNeasy Mini Kit (Qiagen).

treatment_protocol: MEL cells were washed in PBS, and stored at -80 °C.

tag: cell line

value: T-3-Cl-2-0.fl (Riken Cell No. RCB0561)

value: High differentiation-inducible murine erythroleukemia cells

tag: time point

value: before chemical treatment

source_name: HD-MEL_at 36h after 30nM TSA treatment

value: at 36h after 30nM TSA treatment


title: 24h_30nMTSA_rep3

description:
Technical replicate 3 of 4
The sample-dye assignment applies to both raw data files.

source_name: HD-MEL_at 24h after 30nM TSA treatment

value: at 24h after 30nM TSA treatment


title: Sle1b.BACSlamf6-H1 CD4+ T cells aCD3 4h biological Rep2


title: 36h_30nMTSA_rep4

description:
Technical replicate 4 of 4
The sample-dye assignment applies to both raw data files.


title: 36h_30nMTSA_rep1

description:
Technical replicate 1 of 4
The sample-dye assignment applies to both raw data files.


title: WT CD4+ T cells aCD3 24h technical Rep3


title: 24h_30nMTSA_rep2


title: Sle1b CD4+ T cells aCD3 4h biological Rep3


title: Sle1b.BACSlamf6-H1 CD4+ T cells aCD3 4h biological Rep1


title: 24h_30nMTSA_rep1


title: WT CD4+ T cells aCD3 4h biological Rep1


title: Sle1b CD4+ T cells aCD3 4h biological Rep2


title: 12h_30nMTSA_rep1

source_name: HD-MEL_at 12h after 30nM TSA treatment

value: at 12h after 30nM TSA treatment


title: Sle1b.BACSlamf6-H1 CD4+ T cells non-stimulated biological Rep3

description: Gene expression data of splenic total CD4+  T cells

value: non-stimulated

value: control


title: 36h_30nMTSA_rep3


title: 24h_30nMTSA_rep4


title: 12h_30nMTSA_rep4


title: Sle1b CD4+ T cells aCD3 4h biological Rep1


title: WT CD4+ T cells aCD3 4h biological Rep2


title: Rat Carotid artery - Injury

city: Hwasun

first: Nakwon

last: Choe

state: Seoyang-ro 322

address: Baekseo-ro 160

department: Pharmacology

country: South Korea

institute: Chonnam Univ. Med. Sch.

description: Gene expression in rat carotid artery 10days after balloon injury

hyb_protocol: Agilent's miRNA Hybridization Kit was used for hybridization.

scan_protocol: Agilent's DNA microarray scanner and Feature Extraction Software was used for scaning and data acquisition.

data_processing: The data was normalized and clustered using Agilent's GeneSpring Software.

organism: Rattus norvegicus

source_name: Rat Carotid artery - Balloon Injury Model

label_protocol: Agilent's miRNA Labeling Reagent was used for Cyanine-3 labeling

extract_protocol: Total RNA was extracted using Trizol reagent following manufacturer's protocol. Quality was monitored using Agilent 2100 Bioanalyzer.

treatment_protocol: Balloon injury was induced in the carotid arteries.

tag: gender

value: male

tag: weight

tag: tissue

value: Carotid artery

value: Sprague-Dawley

tag: stress

value: balloon injury


title: Sle1b.BACSlamf6-H1 CD4+ T cells non-stimulated biological Rep2


title: Rat Carotid artery - Control

description: Gene expression in rat carotid artery

hyb_protocol: Agilent's miRNA Hybridization Kit was used for Cyanine-3 labeling and hybridization.

source_name: Rat Carotid artery - Control

label_protocol: Agilent's miRNA Labeling Reagent was used for Cyanine-3 labeling and hybridization.

value: non-injury


title: WT CD4+ T cells aCD3 4h biological Rep3


title: 36h_5mMHMBA_rep4

source_name: HD-MEL_at 36h after 5mM HMBA treatment

value: at 36h after 5mM HMBA treatment


title: 12h_30nMTSA_rep2


title: 6h_30nMTSA_rep4

source_name: HD-MEL_at 6h after 30nM TSA treatment

value: at 6h after 30nM TSA treatment


title: 1h_30nMTSA_rep1

source_name: HD-MEL_at 1h after 30nM TSA treatment

value: at 1h after 30nM TSA treatment


title: 6h_30nMTSA_rep1


title: 36h_5mMHMBA_rep3


title: Col-0 veg rep1

city: Cologne

first: Fernando

last: Andres

address: Carl von Linne 10

department: Plant Developmental Biology

country: Germany

institute: Max Planck Institute for Plant Breeding Research

hyb_protocol: After fragmentation, 7.5 ug of ds-cDNA was hybridized for 16 hr at 45C on GeneChip Arabidopsis Tiling 1.0R Array. GeneChips were washed and stained with Fluidics Script FS450_0001 in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: Data was processed in R as described in Naouar et al. Quantitative RNA expression analysis with Affymetrix Tiling 1.0R arrays identifies new E2F target genes. Plant J (2009) vol. 57 (1) pp. 184-94. Probe-level data were pre-processed using the RMA algorithm (Irizarry et al., 2003), which involves three steps: (i) background correction – where an error component of the intensities is estimated and eliminated; (ii) quantile normalization – where every slide is normalized to have the same cumulative frequency distribution; and (iii) summarization, using the median polish algorithm – where the median values per probe set, adjusted for slide differences, are calculated. RMA ignores the MM probes. On the basis of an empirical Bayes moderated t-statistic for the contrasts (Smyth, 2004), as implemented in the Bioconductor package limma, P values were calculated and then transformed into false-discovery rates, or Q values according to the method described by Storey and Tibshirani (2003), as implemented in the R package qvalue.

source_name: Col-0 veg

label_protocol: 1 μg of total RNA was reverse transcribed into cDNA using an oligo(dT)-T7 primer, and was then converted into cRNA and linearly amplified by T7 in vitro transcription reaction using the standard Ambion protocol (MessageAmp aRNA Kit, Ambion). cRNA was then reverse transcribed with random primers to dUTP-containing ds cDNA (WT ds cDNA Synthesis Kit, catalog no. 900813; Affymetrix). Fragmentation and labeling was performed with the GeneChip WT double-stranded DNA Terminal Labeling Kit (catalog no. 900812, Affymetrix)

growth_protocol: Col-0 seedlings grown for 2 weeks in Short Day (SD) conditions (8 h light/16 h dark)

extract_protocol: RNA was extracted using the RNA Plant Mini kit, QIAGEN (www1.qiagen.com/). (The amount of total RNA was quantified by NanoDrop).

tag: genetic background

value: wt

value: seedlings-aerial part

tag: age

value: 2 weeks old


title: WT CD4+ T cells non-stimulated biological Rep3

value: CD4+ T cell


title: 12h_30nMTSA_rep3

value: T-3-Cl-2-0.fl (Riken Cell No. RCB0561)

value: High differentiation-inducible murine erythroleukemia cells

value: before chemical treatment


title: 36h_5mMHMBA_rep2


title: Col-0 veg rep3


title: Col-0 veg rep2


title: 1h_30nMTSA_rep3


title: svp veg rep1

source_name: svp veg

growth_protocol: svp-41 seedlings (described in Hartmann PMID: 10758486) grown for 2 weeks in Short Day (SD) conditions (8 h light/16 h dark)


title: 6h_30nMTSA_rep2


title: 6h_30nMTSA_rep3


title: Sle1b CD4+ T cells non-stimulated biological Rep1

value: non-stimulated


title: svp veg rep3


title: Sle1b.BACSlamf6-H1 CD4+ T cells non-stimulated biological Rep1

value: control


title: 24h_5mMHMBA_rep4

source_name: HD-MEL_at 24h after 5mM HMBA treatment

value: at 24h after 5mM HMBA treatment


title: WT CD4+ T cells non-stimulated biological Rep1


title: svp veg rep2


title: 1h_30nMTSA_rep2


title: svp ap1 agl24 inf rep1

source_name: svp ap1 agl24 inf

growth_protocol: svp-41 agl24-2 ap1-12 (described in Gregis et al, 2009 - PMID:19656343) triple mutant inflorescences grown for 2 weeks in SD conditions and then moved in (LD) conditions (16 h light/16 h dark). The inflorescences were collected at 2 weeks after bolting.

value: seedlings-inflorescences

value: 4 weeks old


title: Sle1b CD4+ T cells non-stimulated biological Rep3


title: 1h_30nMTSA_rep4


title: Sle1b CD4+ T cells non-stimulated biological Rep2


title: svp ap1 agl24 inf rep2


title: 24h_5mMHMBA_rep2


title: Col-0 inf rep1

source_name: Col-0 inf


title: svp ap1 agl24 inf rep3


title: Col-0 inf rep3


title: Col-0 inf rep2


title: 24h_5mMHMBA_rep3


title: 12h_5mMHMBA_rep4

source_name: HD-MEL_at 12h after 5mM HMBA treatment

value: at 12h after 5mM HMBA treatment


title: 24h_5mMHMBA_rep1


title: WT CD4+ T cells non-stimulated biological Rep2


title: 12h_5mMHMBA_rep2


title: 6h_5mMHMBA_rep4

source_name: HD-MEL_at 6h after 5mM HMBA treatment

value: at 6h after 5mM HMBA treatment


title: 12h_5mMHMBA_rep3


title: Shoot apex, CB2009304-C, biological rep1

city: Canberra

first: xiaohui

last: yang

address: Ross

country: Australia

institute: CSIRO

description: Expression data from two-year-old shoot apex of Populus tomentosa.

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

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

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Populus tomentosa

source_name: Populus tomentosa shoot apex from natural condition

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: The seedlings were planted in the field of Xiaotangshan, Beijing, China. After growth for about two years, all the plantation for sampling with approximately the same crown size and equal height were chosen.

extract_protocol: Total RNAs were extracted using the RNeasy Plant Mini Kits (Qiagen, Inc. Valencia, CA, USA).

treatment_protocol: Five trees grew under natural condition.

value: two years old

value: Shoot apex


title: 6h_5mMHMBA_rep2

source_name: HD-MEL_before chemical treatment


title: 36h_1.5%DMSO_rep4

source_name: HD-MEL_at 36h after 1.5% DMSO treatment

value: at 36h after 15% DMSO treatment


title: 36h_1.5%DMSO_rep2


title: 36h_1.5%DMSO_rep1


title: 1h_5mMHMBA_rep3

source_name: HD-MEL_at 1h after 5mM HMBA treatment

value: at 1h after 5mM HMBA treatment


title: 6h_5mMHMBA_rep3


title: Sox17(+) 5

city: Lyon

first: Irene

last: Aksoy

address: 18 avenue du Doyen Lepine

country: France

institute: Stem Cell and Brain Research Institute

description: Replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

label: Biotin

source_name: ES cells

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

growth_protocol: mouse ES cells culture condtion

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.

treatment_protocol: Doxycycline

value: Sox17-V5 expression


title: Sox17(+) 2

description: Replicate 2


title: 1h_5mMHMBA_rep4


title: 1h_5mMHMBA_rep1


title: Sox17(+) 4

description: Replicate 1


title: 36h_1.5%DMSO_rep3


title: 12h_5mMHMBA_rep1


title: 1h_5mMHMBA_rep2


title: Sox17(-) 5

description: Replicate 2


title: Sox17(+) 1

description: Replicate 1


title: 6h_5mMHMBA_rep1


title: 24h_1.5%DMSO_rep4

source_name: HD-MEL_at 24h after 1.5% DMSO treatment

value: at 24h after 15% DMSO treatment


title: Shoot apex, CB2009304-D, biological rep 2


title: Sox17(+) 3

description: Replicate 3


title: Sox17(-) 4

description: Replicate 1


title: 36h_5mMHMBA_rep1

value: at 36h after 5mM HMBA treatment


title: 24h_1.5%DMSO_rep3

value: T-3-Cl-2-0.fl (Riken Cell No. RCB0561)


title: Sox17(-) 3

description: Replicate 3


title: 12h_1.5%DMSO_rep1

value: High differentiation-inducible murine erythroleukemia cells

source_name: HD-MEL_at 12h after 1.5% DMSO treatment

value: at 12h after 15% DMSO treatment


title: 12h_1.5%DMSO_rep2

value: before chemical treatment


title: 24h_1.5%DMSO_rep2


title: 6h_1.5%DMSO_rep3

source_name: HD-MEL_at 6h after 1.5% DMSO treatment

value: at 6h after 15% DMSO treatment


title: 1h_1.5%DMSO_rep3

source_name: HD-MEL_at 1h after 1.5% DMSO treatment

value: at 1h after 15% DMSO treatment


title: IRF3/5/7 TKO 6a

city: Cleveland

first: Peter

middle: A

last: Wilkinson

state: Ohio

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

institute: Case Western Reserve University

description: bmDC from Mouse_16, mock infected

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to Human RefSeq-8 V2 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol

scan_protocol: The arrays were scanned using an Illumina iScan scanner and quantified using GenomeStudio software (Illumina).

data_processing: Analysis of the GenomeStudio output data was conducted using the R statistical language and various software packages from Bioconductor. Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation

source_name: RPMI + rmGM-CSF purified BM-DC populations, mock and WNV infected with insect derived virus and RNA isolated 24 hours post infection.

label_protocol: The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.

growth_protocol: Bone marrow was cultured in RPMI supplemented with 10% fetal bovine serum, penicillin/streptomycin, L-glutamine, non-essential amino acids, 55 μM β-mercaptoethanol and 20 ng/ml  recombinant mouse GM-CSF (eBioscience) for 6 days in non-tissue culture treated plates.

extract_protocol: The DC/Mac populations were harvested at each desired post-infection time point. The cells were washed once with RT 1XPBS (about 2ml/Well). Then 0.5ml added of warmed trypsin to each well, incubate 10 min at 37°C. Once this was done, 5 ml added of cold PBS w/ 10% serum or use 10% complete medium. The cells were then collected in 15ml conical tube. Cells were spun down at 1000-1200 RPM x 5 minutes at 4°C.

treatment_protocol: GM-CSF was replenished after 2 days and non-adherent cells were sub-cultured after 4 days. Sub-cultured cells were infected at an MOI of 25 with WNV-NY. To determine the percentage of cells infected, mDC were detached 24 h after WNV inoculation. Non-specific binding of antibody to Fc-γR was blocked with anti-CD16/CD32 (Biolegend), and all subsequent surface staining (I-Ab-FITC, CD86-PE, and CD11c-APC (all from Biolegend)) was performed in PBS supplemented with 2% fetal calf serum. Cells were fixed, permeabilized, and then stained with Alexa-647 conjugated anti-WNV E16 anti-WNV MAb. For microarray analysis, total RNA was harvested at 24 hours post-infection.

tag: subject

value: IRF3/5/7 TKO

value: bone marrow derived myeloid DC bmDCs

tag: infection

value: mock

value: 24 hours


title: 12h_1.5%DMSO_rep3


title: IRF3/5/7 TKO 6b

description: bmDC from Mouse_16, wnv infected

value: West Nile Virus


title: IRF3/5/7 TKO 5b

description: bmDC from Mouse_15, mock infected


title: 12h_1.5%DMSO_rep4


title: MAVS KO 3b

description: bmDC from Mouse_9, wnv infected

value: MAVS KO


title: 24h_1.5%DMSO_rep1


title: IRF3/7 DKO 2

description: bmDC from Mouse_12, wnv infected

value: IRF3/7 DKO


title: IRF3/7 DKO 1b

description: bmDC from Mouse_11, wnv infected


title: 6h_1.5%DMSO_rep4


title: 6h_1.5%DMSO_rep2


title: 1h_1.5%DMSO_rep1


title: 1h_1.5%DMSO_rep4


title: Sox17(-) 2

description: Replicate 2

value: control


title: 1h_1.5%DMSO_rep2


title: CD133+CD140+ (C)

city: Buffalo

first: Fraser

middle: James

last: Sim

state: NY

address: 3435 Main Street

institute: University at Buffalo

hyb_protocol: Standard Illumina hybridization protocol @ 48 deg Hyb

data_processing: analysis performed in R. background adjustment was performed using 'bgAdjust.affy' algorithm, expression values were normalized using 'vsn', poor-quality data was removed using lumi detectionCall function, such that probes were retained if there were at least 2 P present cells among the samples in any cell type group

organism: Homo sapiens

source_name: fetal brain

label_protocol: cDNA was amplified using NuGEN WTA Pico amplification kit and labeled using NuGen/UNG enzyme protocol (per manufacturer's instructions).

growth_protocol: cells were extracted immediately following FACS sorting

extract_protocol: total RNA extraction was performed using Omega-Bio RNA Mini Extraction Kit (per manufacturer's instructions).

value: fetal brain

tag: facs population

tag: sample id

value: C


title: IRF3/5/7 TKO 4a

description: bmDC from Mouse_14, mock infected

tag: genotype


title: 6h_1.5%DMSO_rep1


title: IRF3/5/7 TKO 5a

description: bmDC from Mouse_15, wnv infected


title: Sox17(-) 1

description: Replicate 1


title: CD133+CD140+ (B)

value: B


title: IRF3/7 DKO 1a

description: bmDC from Mouse_11, mock infected


title: 36h_TSA_rep4

description:
Technical replicate 4 of 4. 36 hours after 15nM TSA treatment.
control LD-MEL
target HD-MEL

hyb_protocol: Microarray was pre-hybrized at 50°C, 60 minutes in 5 x saline sodium citrate buffer (SSC) contained 0.1% sodium dodecyl sulfate (SDS)and 0.1% bovine serum albumin (BSA), washed with water, and rinsed with isopropanol. Mixed Cy3 and Cy5 labeled cDNA solution was denaturation at 95°C, 5 minutes in 5 x SSC contained 1.67 mg/mL acetylated BSA. After cooling, SDS was added to final concentration 0.33%. The microarray was covered with a Gap cover glass (Matsunami), hybridization solution was injected, and the microarray was placed in a hybridization cassette (TeleChem). Hybridization was performed at 50°C for 14 hours. After hybridization, the microarray was washed using a Wash Station (TeleCham) as follow; at 42°C 5 minutes in 2 x SSC contained 0.1%SDS, at room temperature 10 minutes in 0.1 x SSC contained 0.1%SDS, and finally twice in 0.1 x SSC at room temperature for 2min. The microarray was dried by centrifugation.

data_processing:
The microarray data was analyzed using GeneSpring 6.0 (Silicon Genetics). Intensity difference between Cy3 and Cy5 was normalized by LOWESS method.
Signal intensities were higher than negative spot.

source_name: LD-MEL cells

label_protocol: Twenty mg of the total RNA was labeled with amino-modified dNTP using a SuperScript Indirect cDNA Labeling System (Invitrogen). The amino-modified cDNA was purified with a S.N.A.P column (Invitrogen) and ethanol precipitation. The purified cDNA was labeled with Cye3 Mono-Reactive Dye Pack (Amersham Biosciences) or Cye5 Mono-Reactive Dye Pack (Amersham Biosciences) by coupling reaction. The labeled cDNA was purified with a QIAquick PCR Purification Kit (Qiagen).

value: Low differentiation-inducible murine erythroleukemia cells, A clone of T-3-Cl-2-0.fl.

value: TSA

tag: time

value: T-3-Cl-2-0.fl (Riken Cell No. RCB0561)

source_name: HD-MEL cells

value: High differentiation-inducible murine erythroleukemia cells, A clone of T-3-Cl-2-0.fl.


title: CD133+CD140- (A)

value: A


title: CD133+CD140- (C)


title: MAVS KO 2b

description: bmDC from Mouse_8, wnv infected


title: CD133+CD140+ (A)


title: CD133+CD140- (B)


title: 36h_TSA_rep3

description:
Technical replicate 3 of 4. 36 hours after 15nM TSA treatment.
control LD-MEL
target HD-MEL


title: 36h_TSA_rep2

description:
Technical replicate 2 of 4. 36 hours after 15nM TSA treatment.
target HD-MEL
control LD-MEL


title: 36h_TSA_rep1

description:
Technical replicate 1 of 4. 36 hours after 15nM TSA treatment.
target HD-MEL
control LD-MEL


title: MAVS KO 1b

description: bmDC from Mouse_7, wnv infected


title: 24h_TSA_rep1

description:
Technical replicate 1 of 4. 24 hours after 15nM TSA treatment.
target HD-MEL
control LD-MEL


title: MAVS KO 1a

description: bmDC from Mouse_7, mock infected


title: 12h_TSA_rep3

description:
Technical replicate 3 of 4. 12 hours after 15nM TSA treatment.
control LD-MEL
target HD-MEL


title: 12h_TSA_rep2

description:
Technical replicate 2 of 4. 12 hours after 15nM TSA treatment.
target HD-MEL
control LD-MEL


title: 24h_TSA_rep3

description:
Technical replicate 3 of 4. 24 hours after 15nM TSA treatment.
control LD-MEL
target HD-MEL


title: 12h_TSA_rep4

description:
Technical replicate 4 of 4. 12 hours after 15nM TSA treatment.
control LD-MEL
target HD-MEL


title: CD133-CD140+ (C)


title: MAVS KO 2a

description: bmDC from Mouse_8, mock infected


title: 24h_TSA_rep4

description:
Technical replicate 4 of 4. 24 hours after 15nM TSA treatment.
control LD-MEL
target HD-MEL


title: CD133-CD140+ (B)


title: CD133-CD140+ (A)


title: 24h_TSA_rep2

description:
Technical replicate 2 of 4. 24 hours after 15nM TSA treatment.
target HD-MEL
control LD-MEL


title: IRF3/7 DKO 3a

description: bmDC from Mouse_13, mock infected


title: IRF3/7 DKO 3b

description: bmDC from Mouse_13, wnv infected


title: 6h_TSA_rep3

description:
Technical replicate 3 of 4. 6 hours after 15nM TSA treatment.
control LD-MEL
target HD-MEL


title: 6h_TSA_rep2

description:
Technical replicate 2 of 4. 6 hours after 15nM TSA treatment.
target HD-MEL
control LD-MEL


title: IFNAR KO 3b

description: bmDC from Mouse_6, wnv infected

value: IFNAR KO


title: 6h_TSA_rep4

description:
Technical replicate 4 of 4. 6 hours after 15nM TSA treatment.
control LD-MEL
target HD-MEL


title: IFNAR KO 3a

description: bmDC from Mouse_6, mock infected


title: 12h_TSA_rep1

description:
Technical replicate 1 of 4. 12 hours after 15nM TSA treatment.
target HD-MEL
control LD-MEL


title: 36h_HMBA_rep3

description:
Technical replicate 3 of 4. 36 hours after 3.0mM HMBA treatment.
control LD-MEL
target HD-MEL

value: HMBA


title: CD133-CD140- (B)


title: 36h_HMBA_rep4

description:
Technical replicate 4 of 4. 36 hours after 3.0mM HMBA treatment.
control LD-MEL
target HD-MEL


title: 6h_TSA_rep1

description:
Technical replicate 1 of 4. 6 hours after 15nM TSA treatment.
target HD-MEL
control LD-MEL


title: IFNAR KO 2b

description: bmDC from Mouse_5, wnv infected

value: bone marrow derived myeloid DC bmDCs


title: 36h_HMBA_rep2

description:
Technical replicate 2 of 4. 36 hours after 3.0mM HMBA treatment.
target HD-MEL
control LD-MEL


title: CD133-CD140- (A)


title: 24h_HMBA_rep4

description:
Technical replicate 4 of 4. 24 hours after 3.0mM HMBA treatment.
control LD-MEL
target HD-MEL


title: IFNAR KO 1b

description: bmDC from Mouse_4, wnv infected


title: 24h_HMBA_rep1

description:
Technical replicate 1 of 4. 24 hours after 3.0mM HMBA treatment.
target HD-MEL
control LD-MEL


title: Sox7/Sox17 KD 3

description: Replicate 3

source_name: F9 cells

growth_protocol: F9 cells culture condtion

treatment_protocol: Retinoic Acid

value: Sox7 and Sox17 knocked-down cells


title: 12h_HMBA_rep4

description:
Technical replicate 4 of 4. 12 hours after 3.0mM HMBA treatment.
control LD-MEL
target HD-MEL


title: IFNAR KO 2a

description: bmDC from Mouse_5, mock infected

value: mock

value: 24 hours


title: WT 3b

description: bmDC from Mouse_3, wnv infected

value: WT

value: West Nile Virus


title: 36h_HMBA_rep1

description:
Technical replicate 1 of 4. 36 hours after 3.0mM HMBA treatment.
target HD-MEL
control LD-MEL


title: 12h_HMBA_rep2

description:
Technical replicate 2 of 4. 12 hours after 3.0mM HMBA treatment.
target HD-MEL
control LD-MEL


title: 24h_HMBA_rep2

description:
Technical replicate 2 of 4. 24 hours after 3.0mM HMBA treatment.
target HD-MEL
control LD-MEL


title: 24h_HMBA_rep3

description:
Technical replicate 3 of 4. 24 hours after 3.0mM HMBA treatment.
control LD-MEL
target HD-MEL


title: Sox7/Sox17 KD 2

description: Replicate 2


title: IFNAR KO 1a

description: bmDC from Mouse_4, mock infected


title: 12h_HMBA_rep1

description:
Technical replicate 1 of 4. 12 hours after 3.0mM HMBA treatment.
target HD-MEL
control LD-MEL


title: IRF3/5/7 TKO 4b

description: bmDC from Mouse_14, wnv infected

value: IRF3/5/7 TKO


title: WT 2b

description: bmDC from Mouse_2, wnv infected


title: 12h_HMBA_rep3

description:
Technical replicate 3 of 4. 12 hours after 3.0mM HMBA treatment.
control LD-MEL
target HD-MEL


title: CD133-CD140- (C)

value: fetal brain


title: 6h_HMBA_rep4

description:
Technical replicate 4 of 4. 6 hours after 3.0mM HMBA treatment.
control LD-MEL
target HD-MEL


title: 6h_HMBA_rep3

description:
Technical replicate 3 of 4. 6 hours after 3.0mM HMBA treatment.
control LD-MEL
target HD-MEL


title: Sox7/Sox17 KD 1

description: Replicate 1


title: MAVS KO 3a

description: bmDC from Mouse_9, mock infected

value: MAVS KO


title: WT 3a

description: bmDC from Mouse_3, mock infected


title: 36h_DMSO_rep2

description:
Technical replicate 2 of 4. 36 hours after 1.0% DMSO treatment.
target HD-MEL
control LD-MEL

value: DMSO


title: HEK293DYG cell line treated for 12 h with 1 µg/mL doxycycline and 10µM trimethoprim Replicate #3

city: La Jolla

first: R.

middle: Luke

last: Wiseman

state: CA

address: 10550 N. Torrey Pines Rd. MEM 220

department: Molecular & Experimental Medicine

institute: The Scripps Research Institute

hyb_protocol: 2.5 ug labeled and fragmented cDNA was used to prepare a hybridization cocktail which was hybridized for 16 hr at 45C on HuGene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Standard Affymetrix scan protocol on the GCS7000 for GeneArray 1.0 ST

data_processing: Using the HuGene-1_0-st-v1 Affymetrix chip the data normalization was performed using RMA Express 1.0 (http://rmaexpress.bmbolstad.com) with quantile normalization, median polish and background adjustment.

source_name: Human Cell line HEK293

label_protocol: 200 ng total RNA was used with the Ambion WT Expression amplification kit following manufacturer's protocol.

extract_protocol: RNeasy Mini Kit (Qiagen)

value: HEK293T-Rex cells expressing tet-inducible GFP and DHFR.YFP


title: WT 2a

description: bmDC from Mouse_2, mock infected


title: 6h_HMBA_rep2

description:
Technical replicate 2 of 4. 6 hours after 3.0mM HMBA treatment.
target HD-MEL
control LD-MEL

value: Low differentiation-inducible murine erythroleukemia cells, A clone of T-3-Cl-2-0.fl.


title: HEK293DYG cell line treated for 12 h with 1 µg/mL doxycycline and 10µM trimethoprim Replicate #1


title: 36h_DMSO_rep4

description:
Technical replicate 4 of 4. 36 hours after 1.0% DMSO treatment.
control LD-MEL
target HD-MEL

value: T-3-Cl-2-0.fl (Riken Cell No. RCB0561)


title: WT 1a

description: bmDC from Mouse_1, mock infected


title: Control 2

description: Replicate 2

value: control cells


title: 6h_HMBA_rep1

description:
Technical replicate 1 of 4. 6 hours after 3.0mM HMBA treatment.
target HD-MEL
control LD-MEL

value: High differentiation-inducible murine erythroleukemia cells, A clone of T-3-Cl-2-0.fl.


title: 24h_DMSO_rep2

description:
Technical replicate 2 of 4. 24 hours after 1.0% DMSO treatment.
target HD-MEL
control LD-MEL


title: 24h_DMSO_rep4

description:
Technical replicate 4 of 4. 24 hours after 1.0% DMSO treatment.
control LD-MEL
target HD-MEL


title: 24h_DMSO_rep1

description:
Technical replicate 1 of 4. 24 hours after 1.0% DMSO treatment.
target HD-MEL
control LD-MEL


title: 24h_DMSO_rep3

description:
Technical replicate 3 of 4. 24 hours after 1.0% DMSO treatment.
control LD-MEL
target HD-MEL


title: 36h_DMSO_rep1

description:
Technical replicate 1 of 4. 36 hours after 1.0% DMSO treatment.
target HD-MEL
control LD-MEL


title: WT 1b

description: bmDC from Mouse_1, wnv infected


title: Control 1

description: Replicate 1


title: HEK293DYG cell line treated for 12 h with DMSO Replicate #2

value: 12 h with DMSO


title: 36h_DMSO_rep3

description:
Technical replicate 3 of 4. 36 hours after 1.0% DMSO treatment.
control LD-MEL
target HD-MEL


title: 12h_DMSO_rep4

description:
Technical replicate 4 of 4. 12 hours after 1.0% DMSO treatment.
control LD-MEL
target HD-MEL


title: 12h_DMSO_rep3

description:
Technical replicate 3 of 4. 12 hours after 1.0% DMSO treatment.
control LD-MEL
target HD-MEL


title: HEK293DYG cell line treated for 12 h with DMSO Replicate #1


title: HEK293DYG cell line treated for 12 h with DMSO Replicate #3


title: HEK293DAX cell line treated for 12 h with 1 µg/mL doxycycline and 10 µM trimethoprim. Replicate #2

value: HEK293T-Rex cells expressing tet-inducible XBP1s and DHFR.ATF6


title: 12h_DMSO_rep2

description:
Technical replicate 2 of 4. 12 hours after 1.0% DMSO treatment.
target HD-MEL
control LD-MEL


title: DLA3 (WT) cells with 15min HPUra Replicate 9

city: Groningen

first: Jelle

last: Slager

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

description: Technical replicate 3 of 4

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 sequential

scan_protocol: Fluorescence signals were detected by a GenePix 4200AL microarray scanner (Axon Instruments), with detection of excitation/emission at 562/576 nm for DyLight550 and excitation/emission at 652/672 nm for DyLight650

data_processing: Selection of correct intensity for slides was performed with a scatterplot of the logarithm of the netto intensities of both channels, yielding a flattened plot when images were oversaturated. Assigning a value to the intensity of each spot and identification of the spots was performed in ArrayPro as previously described (de Jong et al., 2012). Spots with a background value of above 1000 were discarded or corrected for the mean background if the spot was not connected to the background signal. The produced data was prepared for further statistical analysis using MicroPrep (van Hijum et al., 2003). For the Lowess normalization an unchanged fraction of 0.7 was used. Further settings were used as previously described (de Jong et al., 2012). In the raw data files, A always refers to Cy3 (DyLight550) and B to Cy5 (DyLight650). Each 3 Samples share one raw data file. The order of the Sample is identical to the order of the spot replicates.

label: Dylight 550

organism: Streptococcus pneumoniae D39

source_name: WT without HPUra (15min)

label_protocol: After quantification, around 15 µg of total RNA was converted into cDNA using reverse transcriptase and subsequently purified and labeled as has been described previously (de Jong et al., 2012). The random nonamers for the annealing were purchased from Bioké. For the transcription, the Superscript III and DTT were purchased from Invitrogen and AA-dUTP from Ambion. The amino allyl-modified cDNA was purified with the NucleoSpin Gel and PCR Clean-up kit (ref 740609.250, Macherey-Nagel). The cDNA concentrations were measured by spectrophotometry (NanoDrop ND-1000, Thermo Scientific). The purified cDNA samples were labeled either with DyLight550 (ref 62262, Thermo Scientific) or DyLight650 (ref 62265, Thermo Scientific). The DyLight labeled cDNA was purified, according to the previously described protocol (de Jong et al, 2012), using the similar kit from Macherey-Nagel. After incorporation of DyLight dyes in the cDNA, we measured the cDNA concentrations as described above.

growth_protocol: S. pneumoniae D39 bgaA::PssbB-luc (DLA3) was grown as standing culture without aeration at 37 °C to an optical density at 600nm of 0.15 in 50 ml C+Y medium, adjusted to pH 7.0 with 1M HCl.

extract_protocol: The cells were collected by centrifugation at 8000 rpm for 5 min and frozen in liquid nitrogen for RNA isolation. The macaloïd method and the RNA isolation kit (ref 11828665001 Roche) were used, according to the previously described protocol (de Jong et al., 2012), for isolation of the total RNA. RNA concentrations and quality were measured by spectrophotometry (NanoDrop ND-1000, Thermo Scientific) and capillary electrophoresis (Agilent RNA 6000 Nano Assay Kit and Agilent 2100 Bioanalyzer, Agilent Technologies).

treatment_protocol: DLA was treated either with HPUra (0.15 µg/ml final concentration in the medium) (Brown, 1970) dissolved in 10 mM NaOH or with 10 mM NaOH as a control. The cells were collected 15 min after addition of HPUra to the medium.

tag: sample type

value: Bacterium, Wild-type resembling

label: Dylight 650

source_name: WT with HPUra (15min)

value: with 15min HPUra


title: DLA3 (WT) cells with 15min HPUra Replicate 10

description: Technical replicate 4 of 4 (dye swap)

tag: cell type


title: DLA3 (WT) cells with 15min HPUra Replicate 11

description: Technical replicate 4 of 4 (dye swap)

tag: treatment


title: DLA3 (WT) cells with 15min HPUra Replicate 12

description: Technical replicate 4 of 4 (dye swap)


title: HEK293DAX cell line treated for 12 h with 1 µg/mL doxycycline and 10 µM trimethoprim. Replicate #1


title: HEK293DAX cell line treated for 12 h with 1 µg/mL doxycycline and 10 µM trimethoprim. Replicate #3


title: DLA3 (WT) cells with 15min HPUra Replicate 8

description: Technical replicate 3 of 4


title: HEK293DYG cell line treated for 12 h with 1 µg/mL doxycycline and 10µM trimethoprim Replicate #2


title: DLA3 (WT) cells with 15min HPUra Replicate 7

description: Technical replicate 3 of 4


title: HEK293DAX cell line treated for 12 h with 10 µM trimethoprim. Replicate #3

value: 12 h with 10 µM trimethoprim


title: 6h_DMSO_rep4

description:
Technical replicate 4 of 4. 6 hours after 1.0% DMSO treatment.
control LD-MEL
target HD-MEL

tag: cell line


title: 12h_DMSO_rep1

description:
Technical replicate 1 of 4. 12 hours after 1.0% DMSO treatment.
target HD-MEL
control LD-MEL


title: HEK293DAX cell line treated for 12 h with 10 µM trimethoprim. Replicate #2


title: HEK293DAX cell line treated for 12 h with 10 µM trimethoprim. Replicate #1


title: 6h_DMSO_rep1

description:
Technical replicate 1 of 4. 6 hours after 1.0% DMSO treatment.
target HD-MEL
control LD-MEL


title: 6h_DMSO_rep3

description:
Technical replicate 3 of 4. 6 hours after 1.0% DMSO treatment.
control LD-MEL
target HD-MEL


title: 6h_DMSO_rep2

description:
Technical replicate 2 of 4. 6 hours after 1.0% DMSO treatment.
target HD-MEL
control LD-MEL


title: DLA3 (WT) cells with 15min HPUra Replicate 6

description: Technical replicate 2 of 4 (dye swap)


title: DLA3 (WT) cells with 15min HPUra Replicate 5

description: Technical replicate 2 of 4 (dye swap)


title: DLA3 (WT) cells with 15min HPUra Replicate 4

description: Technical replicate 2 of 4 (dye swap)


title: HEK293DAX cell line treated for 12 h with DMSO control. Replicate #3

value: 12 h with DMSO control


title: DLA3 (WT) cells with 15min HPUra Replicate 3

description: Technical replicate 1 of 4


title: HEK293DAX cell line treated for 12 h with 1 µg/mL doxycycline. Replicate #1

value: 12 h with 1 µg/mL doxycycline


title: HEK293DAX cell line treated for 12 h with 1 µg/mL doxycycline. Replicate #3


title: DLA3 (WT) cells with 15min HPUra Replicate 2

description: Technical replicate 1 of 4


title: Heifer 987

city: Columbia

first: Thomas

last: Spencer

state: MO

address: 920 East Campus Drive

department: Animal Sciences

institute: University of Missouri

hyb_protocol: Antisense cRNA (1650 ng) was hybridized on the Agilent-manufactured EmbryoGENE slides.  Microarray slides were hybridized for 17 hours at 65°C, then washed for 1 min in gene Expression Wash Buffer 1 at room temperature, 3 min in gene Expression Wash Buffer 2 at 42°C, 10 sec in 100% acetonitrile at room temperature, and 30 sec in Stabilization and Drying Solution (Agilent Technologies).

scan_protocol: Slides were scanned with the PowerScanner (Tecan, San Jose, CA), and data extraction was performed with Array-Pro Analyzer 6.3 (MediaCybernatics, Bethesda, MD).

data_processing: Probes were filtered based on background-corrected signals to remove probes, which did not show hybridization signals above background levels. Probes which passed the filter needed to have background-corrected signals of >9 in the samples of at least one of the experimental groups (in at least 11 samples out of 14 in the ‘HF’ group, in at least 7 samples out of 8 in the ‘IF’ group, or in at least 11 samples out of 14 in the ‘SF’ group, respectively).

organism: Bos taurus

source_name: day 14 cyclic heifer

label_protocol: Preparation of cDNA was performed according to Agilent’s one-color microarray-based gene expression analysis instructions.  Briefly, 150 ng total RNA from each heifer was amplified by T7 RNA polymerase and labeled with cyanine 3-labeled CTP (Agilent Technologies).

extract_protocol: Total cellular RNA was isolated from frozen endometrium using Isol-RNA lysis reagent (5 Prime, Gaithersburg, MD) according to manufacturer’s instructions

treatment_protocol: Endometrium was isolated by physical dissection from the uterus on day 14 of the estrous cycle.

value: endometrium

tag: fertility class

value: Highly Fertile


title: Heifer 986


title: Heifer 989

value: Subfertile


title: HEK293DAX cell line treated for 12 h with DMSO control. Replicate #2


title: Heifer 988

value: Infertile


title: HEK293DAX cell line treated for 12 h with 1 µg/mL doxycycline. Replicate #2


title: Heifer 991


title: Heifer 998


title: DLA3 (WT) cells with 15min HPUra Replicate 1

description: Technical replicate 1 of 4


title: HEK293DAX cell line treated for 12 h with DMSO control. Replicate #1


title: Heifer 992


title: Heifer 912


title: Midtrimester_AF_sample_8_female_15_weeks

city: Medford

first: Heather

middle: C

last: Wick

address: 161 College Ave

department: Department of Computer Science

institute: Tufts University

description: gene expression data from normal second trimester fetus

hyb_protocol: Arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: Arrays were scanned on a GeneArray Scanner, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).

data_processing: Normalization was performed with the threestep command from the AffyPLM package in BioConductor, using ideal-mismatch background/signal adjustment, quantile normalization, and the Tukey biweight summary method.  To obtain detection calls consistent with those produced by Affymetrix' 5.0 software, we used the mas5calls function from the Bioconductor affy package.

source_name: cell free mRNA from second trimester amniotic fluid

label_protocol: Samples were labeled using the Encore Biotin Module (NuGEN, San Carlos, CA)

extract_protocol: RNA was extracted from 5-10 mL AF.All samples were processed using the Qiagen Circulating Nucleic Acid kit with an on-column DNase digestion step to remove genomic DNA. The RNA was then purified and concentrated with the RNeasy MinElute Clean up kit and eluted in RNasefree water. RNA was converted to cDNA and amplified using the Ovation Pico WTA kit V2 and then purified with the QIAquick PCR Purification kit.

tag: gender

value: female

tag: Stage

value: second trimester


title: Heifer 995

tag: tissue


title: Heifer 990


title: Heifer 993


title: Midtrimester_AF_sample_7_male_16_weeks

value: male


title: plasma miRNAs S11_A_2.5

city: Milan

first: Maurizio

last: Callari

address: Via Amadeo, 42

country: Italy

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

description: miRNA profile of archival plasma sample S11

hyb_protocol: Hybridization for 20 h at 55 °C. The arrays were washed in Agilent GE Wash Buffers, following the manufacturer’s instructions

scan_protocol: All slides were immediately scanned at 2 mm resolution using an Agilent DNA microarray scanner

data_processing: The resulting images were analyzed using Agilent's Feature Extraction software v10.7. The total gene signal for each miRNA was obtained by summing the gTotalProbeSignal of all probes. Before log2 transformation an offset of 16 was added in order to avoid negative data. Then, data were log2 transformed.

source_name: plasma

label_protocol: First, samples were dephosphorylated with calf intestinal alkaline phosphatase, followed by denaturation in the presence of dimethyl sulfoxide. A dye, cyanine 3-pCp, was then coupled to the dephosphorylated single-stranded RNA by T4 RNA ligase

growth_protocol: Plasma samples used in this study belong to the human plasma collection of the Fenretinide Breast Cancer Prevention Trial and RNA was extracted from 350 µl.

extract_protocol: Total RNA was extracted from plasma using the commercial column-based system Qiagen miRNeasy® Mini Kit (Qiagen, Valencia, CA, USA), slightly modified by Exiqon (Vedbaek, Denmark. The eluate was digested using 1 u/µl heparinase I (Sigma-Aldrich, St. Luis, MO, USA), in the presence of an RNase inhibitor, (RNAsin; Promega, Madison, WI, USA) for 1 hour at room temperature, and RNA was stored at −80 °C.

tag: plasmid

tag: replicate

value: A

tag: hybridizaton

tag: quantity (ul)

tag: year of storage


title: Heifer 911


title: plasma miRNAs S11_B_2.5

value: B


title: PediatricLowGradeGlioma39

type: genomic

first: Peleg

middle: Moshe

last: Horowitz

address: 44 Binney St. SM1010

department: Cancer Biology

institute: Dana-Farber Cancer Institute

hyb_protocol: Detailed in Craig, et al., 2012 PLoS One. The entire volumes of the Cy5-labeled sample DNA and the Cy3-labeled reference DNA were combined together with 37.8 uL H2O, 50 uL Cot-1 DNA (Invitrogen, cat. no. 15279-011, Carlsbad, CA), 5.2 uL 100X Blocking Agent (Agilent Technologies, Oligo aCGH Hybridization Kit cat. no. 5188-5220), and 260 uL 2X Hi-RPM Hybridization Buffer (Agilent Technologies, cat. no. 5190-0403) before denaturation (3 min at 95C) and pre-hybridization (30 min at 37C). 130 uL Agilent-CGHblock (Agilent Technologies, cat. no. 5190-0421) was added to each hybridization solution before 490 uL of the combined solution was applied to a gasket slide (Agilent Technologies, cat. no. G2534-60003). A 1x1 M SurePrint G3 Human CGH Microarray (Agilent Technologies, cat. no. G4447A) was paired with each gasket slide in a SureHyb Enabled Hybridization Chamber (Agilent Technologies, cat. no. G2534A) and the differentially labeled DNA samples were hybridized (65C) to the microarray for 40–72 hrs in a hybridization oven (Agilent Technologies, cat. no. G2545A). During hybridization the slides were rotated at 19 rpm.

scan_protocol: Detailed in Craig, et al., 2012 PLoS One. Microarrays and gaskets were disassembled at room temperature in Wash Buffer 1 (Agilent Technologies, cat. no. 5188-5221) and quickly moved to a second dish containing Wash Buffer 1 and a stir bar rotating at speed sufficient for gentle agitation of the liquid’s surface. After 5–30 minutes, slides were moved to a dish containing Wash Buffer 2 (Agilent Technologies, cat. no. 5188-5222) and a stir bar and agitated at 37C for 1 minute. Slides were then washed in anhydrous acetonitrile (Sigma- Aldrich, cat. no. 271004, St. Louis, MO) for 10–15 sec before being removed and placed in a slide holder (Agilent Technologies, cat. no. G2505-60525) with an Ozone-Barrier Slide Cover (Agilent Technologies, cat. no. G2505-60550). Microarrays were scanned immediately with a DNA Microarray Scanner (Agilent Technol- ogies, cat. no. G2505C) at 3 um resolution.

data_processing: Detailed in Craig, et al., 2012 PLoS One. Scanned images were processed using Agilent Feature Extraction v10.7 and FE Protocol CGH_107_Sep09. Quality control dLRsd statistics were recorded as reported in the QC Metrics file generated by the software. Copy number analysis was performed using the DNA Analytics module of Agilent Genomic Workbench 6.5. Log2 ratios were corrected for a periodic ‘‘wave’’ artifact that correlates with GC content using the software’s GC correction tool with a GC window size of 2 kb. The ADM-2 algorithm was used with a threshold of 6.0 to detect significantly aberrant genomic regions and detected regions were filtered for those spanning more than five probes (,10 kb) with an average absolute log2 ratio .0.3.

molecule: genomic DNA

source_name: Pediatric Low-Grade Glioma

label_protocol: Detailed in Craig, et al., 2012 PLoS One. Purified DNA extracts from FFPE tissues, frozen tissues, and frozen cells were heat fragmented as indicated by FSM analysis. Subsequently, ULS labeling (Agilent Technologies, Genomic DNA ULS Labeling Kit cat. no. 5190-0419, Santa Clara, CA) was performed according to the manufacturer’s suggested protocol. Briefly, 2 ug DNA from each sample was combined with 2 uL ULS-Cy5 Reagent (Genomic DNA ULS Labeling Kit) and 2 uL 10X Labeling Solution (Genomic DNA ULS Labeling Kit) prior to 30 min at 85C and >10 min at 4C in a PCR thermocycler. An equal mass of either male or female reference DNA was heat-fragmented according to FSM predictions and then labeled with the ULS-Cy3 Reagent (Genomic DNA ULS Labeling Kit). Unincorporated dye was removed using Genomic DNA Purification Modules (Agilent Technologies, cat. no. 5190-0418).

extract_protocol: Detailed in Craig, et al., 2012 PLoS One. Briefly, 1 mm cores (two to five cores total) or 20 um sections (three to five sections total) were taken from regions estimated to contain greater than 50% tumor cells based on previous pilot studies showing accurate detection of single copy gains and losses in samples with .40% tumor nuclei by pathologist estimate of H&E slides. Cores or sections were placed in sterile nuclease-free microcentrifuge tubes and paraffin was removed by treating the tissue in (1.2 ml) xylene. Samples were rinsed twice with 1.2 ml 100% ethanol and allowed to dry at room temperature before the addition of 0.9 ml 1 M NaSCN and overnight incubation at 37C. After 12–24 hrs, samples were rinsed twice in 0.9 ml 1X PBS. 0.34 ml of Buffer ATL (Qiagen, QIAamp DNA FFPE Tissue Kit cat. no. 56404, Valencia, CA) and 40 ml of Proteinase K (20 mg/ mL) (Qiagen, cat. no. 19131) were added and samples were incubated in a thermomixer (Eppendorf, cat. no. 022670000, Hamburg, Germany) set at 56–58C and 450 rpm. An additional 40 ul Proteinase K was added every 8–12 hrs for a period of 48–72 hrs. Samples were allowed to cool to room temperature before the addition of 10–20 ul RNase A (100 mg/mL) (Qiagen, cat. no. 19101) and a 5–10 minute incubation at room temperature. After adding 400 ul of Buffer AL (Qiagen QIAamp DNA FFPE Tissue Kit), samples were placed in thermomixer at 60C for 10 minutes. 440 ul of 100% ethanol was added and each sample was split between two QIAamp MinElute Columns (Qiagen QIAamp DNA FFPE Tissue Kit). Following successive washes with 500 ul Buffer AW1 (Qiagen QIAamp DNA FFPE Tissue Kit) and 500 ul 80% ethanol, DNA was eluted in 50–100 ul H2O.

tag: tissue type

value: Pediatric Low-Grade Glioma

source_name: pooled normal genomic DNA

value: pooled normal genomic DNA


title: PediatricLowGradeGlioma37


title: PediatricLowGradeGlioma42


title: PediatricLowGradeGlioma36


title: PediatricLowGradeGlioma44


title: PediatricLowGradeGlioma35


title: Heifer 997


title: PediatricLowGradeGlioma43


title: PediatricLowGradeGlioma41


title: PediatricLowGradeGlioma38


title: plasma miRNAs S9_A_2.5

description: miRNA profile of archival plasma sample S9


title: plasma miRNAs S10_A_2.5

description: miRNA profile of archival plasma sample S10


title: Heifer 996


title: PediatricLowGradeGlioma30


title: PediatricLowGradeGlioma33


title: Midtrimester_AF_sample_1_male_16_weeks


title: plasma miRNAs S9_B_2.5


title: PediatricLowGradeGlioma40


title: Heifer 913


title: PediatricLowGradeGlioma32


title: Term_AF_sample_8_female_39_weeks

description: gene expression data from normal term fetus

source_name: cell free mRNA from term amniotic fluid

value: term


title: plasma miRNAs S10_B_2.5


title: plasma miRNAs S8_B_2.5

description: miRNA profile of archival plasma sample S8


title: PediatricLowGradeGlioma29


title: Heifer 920


title: plasma miRNAs S8_A_2.5


title: Term_AF_sample_7_female_39_weeks


title: Heifer 926


title: plasma miRNAs S7_B_2.5

description: miRNA profile of archival plasma sample S7


title: plasma miRNAs S7_A_2.5


title: PediatricLowGradeGlioma28


title: Heifer 919


title: Term_AF_sample_6_male_37_weeks


title: PediatricLowGradeGlioma27


title: Term_AF_sample_5_male_39_weeks


title: PediatricLowGradeGlioma26


title: PediatricLowGradeGlioma24


title: plasma miRNAs S6_A_2.5

description: miRNA profile of archival plasma sample S6


title: plasma miRNAs S6_B_2.5


title: Term_AF_sample_4_male_37_weeks


title: Heifer 918


title: plasma miRNAs S4_C_2.5

description: miRNA profile of archival plasma sample S4

value: C


title: Heifer 916


title: Term_AF_sample_1_male_37_weeks


title: Term_AF_sample_3_male_39_weeks


title: Heifer 915


title: plasma miRNAs S4_B_2.5


title: Term_AF_sample_2_female_37_weeks


title: plasma miRNAs S4_A_2.5


title: Heifer 917


title: H

city: Kagoshima

first: Masahiro

last: Sato

state: Kagoshima

address: 8-35-1 Sakuragaoka

department: Frontier Science Research Center

institute: Kagoshima University

hyb_protocol: cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 array, washed and stained according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with median polish summarization and quantile normalization by Affymetrix® Expression Console™ 1.1 software, and obtained normalized intensity values.

source_name: Hela cells, ALP-positive and negative

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

growth_protocol: All these cells were grown in high glucose-DMEM (#11995; Invitrogen Co., Carlsbad, CA) with 10% fetal bovine serum (FBS) and 100 U/mL penicillin/streptomycin at 37C in a humidified atmosphere of 5% CO2 in air

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

treatment_protocol: Confluent cells (HeLa cells and H-1 cells) were subjected to direct lysis as described in the extract protocol

value: HeLa


title: plasma miRNAs S3_C_2.5

description: miRNA profile of archival plasma sample S3


title: Heifer 923


title: H-1

source_name: Hela cells, ALP-negative


title: PediatricLowGradeGlioma34


title: plasma miRNAs S3_B_2.5


title: Heifer 933


title: Heifer 914


title: plasma miRNAs S3_A_2.5


title: PediatricLowGradeGlioma25


title: Heifer 999


title: plasma miRNAs S5_B_2.5

description: miRNA profile of archival plasma sample S5


title: Heifer 994


title: PediatricLowGradeGlioma22


title: PediatricLowGradeGlioma23


title: Heifer 921


title: plasma miRNAs S5_A_2.5


title: PediatricLowGradeGlioma19


title: PediatricLowGradeGlioma31


title: PediatricLowGradeGlioma21


title: Heifer 929


title: plasma miRNAs S2_C_2

description: miRNA profile of archival plasma sample S2


title: plasma miRNAs S2_B_2


title: plasma miRNAs S2_B_2.5


title: Heifer 924


title: Heifer 928


title: Heifer 927


title: PediatricLowGradeGlioma17


title: PediatricLowGradeGlioma16


title: Heifer 932


title: Heifer 931


title: plasma miRNAs S2_A_2.5


title: plasma miRNAs S2_A_2


title: Heifer 930


title: plasma miRNAs S1_B_2.5

description: miRNA profile of archival plasma sample S1


title: plasma miRNAs S1_B_2


title: plasma miRNAs S1_C_2


title: plasma miRNAs S1_A_2


title: PediatricLowGradeGlioma18


title: Heifer 934


title: plasma miRNAs S1_C_2.5


title: PediatricLowGradeGlioma20


title: PediatricLowGradeGlioma13


title: plasma miRNAs S2_C_2.5


title: ZR 75-30 21904

status: Public on Apr 22 2013

city: Rotterdam

first: Marcel

last: Smid

address: Dr. Molewaterplein 50

department: Medical Oncology

institute: Erasmus MC

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: The data were using Affymetrix software Expression Console with default analysis settings and RMA as normalization method.

source_name: Breast cancer cell line

label_protocol: Standard Affymetrix protocol

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Total RNA was extracted with RNABee (Campro, Veenendaal, the Netherlands) according to the manufacturer procedure


title: ZR 75-30 21901


title: ZR 75-30 21831


title: UACC 893 21837

value: UACC 893


title: ZR 75-1 21895


title: UACC 893 21915


title: UACC 812 21887

value: UACC 812


title: UACC 893 21859


title: UACC 812 21906


title: plasma miRNAs S1_A_2.5


title: T47D 21858


title: PediatricLowGradeGlioma07


title: T47D 21926


title: SUM 52 PE 21875

value: SUM 52 PE


title: T47D 21969


title: PediatricLowGradeGlioma15


title: PediatricLowGradeGlioma09


title: PediatricLowGradeGlioma11


title: SUM 44 PE 21903

value: SUM 44 PE


title: PediatricLowGradeGlioma12


title: SUM 44 PE 21951


title: PediatricLowGradeGlioma08


title: PediatricLowGradeGlioma05


title: SUM 44 PE 21936


title: SUM 229 PE 21894

value: SUM 229 PE


title: PediatricLowGradeGlioma04


title: PediatricLowGradeGlioma06


title: SUM 229 PE 21919


title: SUM 229 PE 21967


title: SUM 225 PE 21980

value: SUM 225 PE


title: UACC 812 21946


title: ZR 75-1 21964


title: SUM 225 PE 21832


title: PediatricLowGradeGlioma03


title: SUM 190 PT 21893

value: SUM 190 PT


title: SUM 225 PE 21934


title: SUM 190 PT 21921


title: SUM 185 PE 21911

value: SUM 185 PE


title: SUM 149 PT 21956

value: SUM 149 PT


title: SUM 159 PT 21961

value: SUM 159 PT


title: SUM 185 PE 21947


title: SUM 185 PE 21860


title: PediatricLowGradeGlioma02


title: SUM 190 PT 21902


title: PediatricLowGradeGlioma14


title: SUM 149 PT 21970


title: SUM 52 PE 21927


title: SUM 1315 M02 21879


title: SUM 159 PT 21846


title: SUM 1315 M02 21971


title: SK-BR-5 21833


title: SUM 1315 M02 21944


title: SK-BR-5 21923


title: SK-BR-7 21874


title: SK-BR-7 21939


title: SK-BR-7 21838


title: SUM 102PT 21948

value: SUM 102PT


title: SK-BR-5 21857


title: SUM 102PT 21852


title: ZR 75-1 21928


title: SK-BR-3 21839


title: SUM 149 PT 21935


title: PediatricLowGradeGlioma01


title: OCUB-M 21922

value: OCUB-M


title: OCUB-F 21957

value: OCUB-F


title: OCUB-M 21972


title: MPE600 21842


title: MDA-MB-468 21848


title: MPE600 21853


title: OCUB-M 21871


title: MDA-MB-468 21861


title: PediatricLowGradeGlioma10

value: Pediatric Low-Grade Glioma

value: pooled normal genomic DNA


title: MDA-MB-453 21889


title: OCUB-F 21933


title: MDA-MB-468 21845


title: MDA-MB-453 21856


title: MDA-MB-453 21910


title: SK-BR-3 21955


title: OCUB-F 21882


title: MDA-MB-436 21925


title: MDA-MB-435S 21973


title: MDA-MB-415 21942


title: MDA-MB-415 21930


title: MPE600 21959


title: SUM 52 PE 21977


title: MDA-MB-435S 21912


title: MDA-MB-361 21862


title: MDA-MB-436 21978


title: MDA-MB-415 21963


title: MDA-MB-435S 21877


title: MDA-MB-436 21954


title: SUM 159 PT 21868


title: MDA-MB-361 21880


title: MDA-MB-330 21913


title: MDA-MB-231 21914


title: MDA-MB-231 21850


title: MDA-MB-157 21899


title: MDA-MB-175 VII 21881

value: MDA-MB-175 VII


title: MDA-MB-175 VII 21950


title: MDA-MB-330 21872


title: MDA-MB-330 21897


title: MDA-MB-175 VII 21905


title: MDA-MB-157 21945


title: MDA-MB-134VI 21888


title: MDA-MB-361 21958


title: Hs578T 21983


title: MDA-MB-231 21941


title: MDA-MB-134VI 21834


title: Hs578T 21931


title: MDA-MB-134VI 21844


title: MDA-MB-157 21864


title: HCC38 21909


title: HCC202 21865


title: HCC70 21966


title: HCC70 21918


title: MCF 7 21898

value: MCF 7


title: HCC38 21869


title: MCF 7 21938


title: HCC202 21866


title: HCC38 21908


title: HCC1954 21841


title: HCC1954 21867


title: HCC1937 21929


title: HCC1954 21975


title: HCC70 21835


title: MCF 7 21960


title: HCC1937 21870


title: HCC1569 21863


title: HCC1806 21892


title: HCC1569 21920


title: HCC202 21965


title: HCC1500 21974


title: HCC1937 21836


title: HCC1569 21943


title: HCC1806 21949


title: HCC1419 21981


title: HCC1419 21876


title: HCC1500 21891


title: HCC1419 21932


title: HCC1395 21886


title: EVSA-T 21952

value: EVSA-T


title: HCC1143 21873


title: HCC1395 21884


title: HCC1500 21855


title: HCC1806 21854


title: DU4475 21940


title: DU4475 21916


title: HCC1143 21976


title: HCC1143 21896


title: BT 483 21878


title: EVSA-T 21900


title: BT 483 21962


title: BT 483 21849


title: HCC1395 21885


title: EVSA-T 21843


title: DU4475 21883


title: CAMA-1 21968


title: CAMA-1 21917


title: CAMA-1 21840


title: BT 549 21890


title: BT 549 21907


title: BT 549 21847


title: BT 474 21851


title: BT 474 21953


title: fhMSC week 1

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: Differentiated using BMP2 and TGFB

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 3.1, from SAS. Gene expression profiling was performed using arrays of human genome 133 Plus 2.0 -type from Affymetrix. A Custom CDF Version 10 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization.

source_name: bone marrow derived fetal mesenchymal stromal cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: hfMSCs (2Ã—105 cells/well) were cultured in cell pellets. Pellets were formed by centrifugation of the cells at 1200 rpm for 4 minutes in U-shaped 96-well suspension culture plates (Greiner). To induce chondrogenesis the pellets were cultured at 37Â°C with 5% CO2 in 200 ul of serum-free chondrogenic medium consisting of high-glucose (25 mM) Dulbeccoâ€™s modified Eagleâ€™s medium (DMEM; Gibco) supplemented with 40 ug/ml proline (Sigma), 100 ug/ml sodium pyruvate (Sigma, USA), 50 mg/ml ITS (insulin-transferrin-selenic acid) with Premix (BD Biosciences), 1% Glutamax (Gibco), 1% penicillin/streptavidin, 50 ug/ml ascorbate-2-phosphate (Sigma), 10-7 M dexamethasone (Sigma), 10 ng/ml transforming growth factor-beta 3 (TGF-beta 3; R&D Systems), 500 ng/ml bone morphogenetic protein 6 (BMP6) and antibiotic and antimycotic mix (0.06% polymixin, 0.2% kanamycin, 0.2% penicillin, 0.2% streptavidin, 0.02% nystatin and 0.5% amphotericin) as described by Sekiya et al., 2001. The medium was changed twice per week for 5 weeks.

extract_protocol: Total RNA isolation was performed with an optimized method for RNA extraction from cartilage as described by Heinrichs et al. (1994) except that the protocol was started by homogenizing the sections in 1 ml guanidine thiocyanate solution. RNA extraction was followed by purification with a RNeasy kit according to the manufacturers protocol (Qiagen)

value: week 1

value: Differentiation fhMSCs


title: BT 474 21982


title: fhMSC week 4

description: Differentiated using BMP2 and TGFB

value: week 4


title: Growth plate - 4

description: direct isolation

source_name: growth plate cartilage

tag: growth plate

value: Hyaline cartilage


title: fhMSC week 3

description: Differentiated using BMP2 and TGFB

value: week 3


title: BT 20 21937

value: BT 20


title: Growth plate - 3

description: direct isolation


title: BT 20 21924


title: fhMSC week 2

description: Differentiated using BMP2 and TGFB

value: week 2


title: Growth plate - 2

description: direct isolation


title: fhMSC week 5

description: Differentiated using BMP2 and TGFB

value: week 5


title: LP_3000_13w_483_NDPA3000_10012_Bladder_Urinary

city: RTP

first: Longlong

last: Yang

state: NC

address: 6 Davis Dr.

institute: CIIT Centers for Health Research

description: LP_3000_13w_483_NDPA3000_10012_Bladder_(HT_Rat230_PM)_B05_Rep2: 1470 rats were used in this study:  6 chemicals, 4 time points, and 6 dose groups (including control).  10 animals per group and 5 extra control animals.  Timepoints were 5d, 2w, 4w, and 13 weeks.  Doses varied with compound (Tribromobenzene: 0, 2.5, 5, 10, 25, 75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Methylenebis(N,N-dimethyl)benzen amine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300).  Animals were dosed through gavage or diet.  Two of the protocols had female rats and the rest were male rats (see protocols).  F344 and Sprague Dawley rats were used.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: RMA normalization with Partek software program

label_protocol: standard Affymetrix protocol

extract_protocol: Extraction Method: Qiagen

treatment_protocol: in vivo Treatment: N-Nitrosodiphenylamine, Treatment Repeat: 7, Units of Treatment Repeat: Days/Week, Treatment Duration: 13, Units of Duration: Weeks, Treatment Time: ad lib, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 3000, Units of Dose or Concentration: ppm

tag: array type

tag: amount to core

tag: units of amount

value: ul

tag: ratio

tag: rna integrity number

tag: bioanalyzer results

value: Excellent

tag: sample preservation

value: RNA Later

tag: strain or line

tag: ncbi taxonomy id

tag: individual

tag: developmental state

value: Adult

tag: sacrifice method

value: Pentobarbital, Exsanguinated

tag: Sex

value: Female

tag: age

tag: units of age

value: Weeks

value: Urinary Bladder

tag: tissue harvest methods

value: The organ was longitudinally bisected, a slice was removed for histology and the remainder of the organ was minced and used for microarray analysis


title: BT 20 21979

tag: cell line


title: LP_3000_13w_482_NDPA3000_10012_Bladder_Urinary

description: LP_3000_13w_482_NDPA3000_10012_Bladder_(HT_Rat230_PM)_A07_Rep2: 1470 rats were used in this study:  6 chemicals, 4 time points, and 6 dose groups (including control).  10 animals per group and 5 extra control animals.  Timepoints were 5d, 2w, 4w, and 13 weeks.  Doses varied with compound (Tribromobenzene: 0, 2.5, 5, 10, 25, 75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Methylenebis(N,N-dimethyl)benzen amine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300).  Animals were dosed through gavage or diet.  Two of the protocols had female rats and the rest were male rats (see protocols).  F344 and Sprague Dawley rats were used.

tag: array type

tag: tissue


title: LP_2000_13w_475_NDPA2000_10012_Bladder_Urinary

description: LP_2000_13w_475_NDPA2000_10012_Bladder_(HT_Rat230_PM)_H05_Rep2: 1470 rats were used in this study:  6 chemicals, 4 time points, and 6 dose groups (including control).  10 animals per group and 5 extra control animals.  Timepoints were 5d, 2w, 4w, and 13 weeks.  Doses varied with compound (Tribromobenzene: 0, 2.5, 5, 10, 25, 75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Methylenebis(N,N-dimethyl)benzen amine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300).  Animals were dosed through gavage or diet.  Two of the protocols had female rats and the rest were male rats (see protocols).  F344 and Sprague Dawley rats were used.

treatment_protocol: in vivo Treatment: N-Nitrosodiphenylamine, Treatment Repeat: 7, Units of Treatment Repeat: Days/Week, Treatment Duration: 13, Units of Duration: Weeks, Treatment Time: ad lib, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 2000, Units of Dose or Concentration: ppm

tag: amount to core

tag: units of amount


title: LP_4000_13w_494_NDPA4000_10012_Bladder_Urinary

description: LP_4000_13w_494_NDPA4000_10012_Bladder_(HT_Rat230_PM)_D07_Rep2: 1470 rats were used in this study:  6 chemicals, 4 time points, and 6 dose groups (including control).  10 animals per group and 5 extra control animals.  Timepoints were 5d, 2w, 4w, and 13 weeks.  Doses varied with compound (Tribromobenzene: 0, 2.5, 5, 10, 25, 75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Methylenebis(N,N-dimethyl)benzen amine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300).  Animals were dosed through gavage or diet.  Two of the protocols had female rats and the rest were male rats (see protocols).  F344 and Sprague Dawley rats were used.

treatment_protocol: in vivo Treatment: N-Nitrosodiphenylamine, Treatment Repeat: 7, Units of Treatment Repeat: Days/Week, Treatment Duration: 13, Units of Duration: Weeks, Treatment Time: ad lib, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 4000, Units of Dose or Concentration: ppm

tag: ratio

tag: rna integrity number


title: LP_2000_13w_473_NDPA2000_10012_Bladder_Urinary

description: LP_2000_13w_473_NDPA2000_10012_Bladder_(HT_Rat230_PM)_G07_Rep2: 1470 rats were used in this study:  6 chemicals, 4 time points, and 6 dose groups (including control).  10 animals per group and 5 extra control animals.  Timepoints were 5d, 2w, 4w, and 13 weeks.  Doses varied with compound (Tribromobenzene: 0, 2.5, 5, 10, 25, 75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Methylenebis(N,N-dimethyl)benzen amine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300).  Animals were dosed through gavage or diet.  Two of the protocols had female rats and the rest were male rats (see protocols).  F344 and Sprague Dawley rats were used.

tag: bioanalyzer results

tag: sample preservation


title: LP_4000_13w_493_NDPA4000_10012_Bladder_Urinary

description: LP_4000_13w_493_NDPA4000_10012_Bladder_(HT_Rat230_PM)_D05_Rep2: 1470 rats were used in this study:  6 chemicals, 4 time points, and 6 dose groups (including control).  10 animals per group and 5 extra control animals.  Timepoints were 5d, 2w, 4w, and 13 weeks.  Doses varied with compound (Tribromobenzene: 0, 2.5, 5, 10, 25, 75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Methylenebis(N,N-dimethyl)benzen amine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300).  Animals were dosed through gavage or diet.  Two of the protocols had female rats and the rest were male rats (see protocols).  F344 and Sprague Dawley rats were used.

tag: strain or line

tag: ncbi taxonomy id


title: LP_3000_13w_481_NDPA3000_10012_Bladder_Urinary

description: LP_3000_13w_481_NDPA3000_10012_Bladder_(HT_Rat230_PM)_A05_Rep2: 1470 rats were used in this study:  6 chemicals, 4 time points, and 6 dose groups (including control).  10 animals per group and 5 extra control animals.  Timepoints were 5d, 2w, 4w, and 13 weeks.  Doses varied with compound (Tribromobenzene: 0, 2.5, 5, 10, 25, 75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Methylenebis(N,N-dimethyl)benzen amine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300).  Animals were dosed through gavage or diet.  Two of the protocols had female rats and the rest were male rats (see protocols).  F344 and Sprague Dawley rats were used.

tag: individual

tag: developmental state


title: LP_3000_13w_484_NDPA3000_10012_Bladder_Urinary

description: LP_3000_13w_484_NDPA3000_10012_Bladder_(HT_Rat230_PM)_B07_Rep2: 1470 rats were used in this study:  6 chemicals, 4 time points, and 6 dose groups (including control).  10 animals per group and 5 extra control animals.  Timepoints were 5d, 2w, 4w, and 13 weeks.  Doses varied with compound (Tribromobenzene: 0, 2.5, 5, 10, 25, 75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Methylenebis(N,N-dimethyl)benzen amine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300).  Animals were dosed through gavage or diet.  Two of the protocols had female rats and the rest were male rats (see protocols).  F344 and Sprague Dawley rats were used.

tag: sacrifice method

tag: Sex


title: Growth plate - 1

description: direct isolation

tag: growth plate


title: fhMSC week 0

description: Differentiated using BMP2 and TGFB

tag: time

value: week 0

tag: cell type


title: LP_4000_13w_495_NDPA4000_10012_Bladder_Urinary

description: LP_4000_13w_495_NDPA4000_10012_Bladder_(HT_Rat230_PM)_E05_Rep2: 1470 rats were used in this study:  6 chemicals, 4 time points, and 6 dose groups (including control).  10 animals per group and 5 extra control animals.  Timepoints were 5d, 2w, 4w, and 13 weeks.  Doses varied with compound (Tribromobenzene: 0, 2.5, 5, 10, 25, 75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Methylenebis(N,N-dimethyl)benzen amine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300).  Animals were dosed through gavage or diet.  Two of the protocols had female rats and the rest were male rats (see protocols).  F344 and Sprague Dawley rats were used.

tag: array type

tag: age

tag: units of age

tag: tissue harvest methods


title: LP_4000_13w_496_NDPA4000_10012_Bladder_Urinary

description: LP_4000_13w_496_NDPA4000_10012_Bladder_(HT_Rat230_PM)_E07_Rep2_2: 1470 rats were used in this study:  6 chemicals, 4 time points, and 6 dose groups (including control).  10 animals per group and 5 extra control animals.  Timepoints were 5d, 2w, 4w, and 13 weeks.  Doses varied with compound (Tribromobenzene: 0, 2.5, 5, 10, 25, 75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Methylenebis(N,N-dimethyl)benzen amine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300).  Animals were dosed through gavage or diet.  Two of the protocols had female rats and the rest were male rats (see protocols).  F344 and Sprague Dawley rats were used.

tag: amount to core

tag: units of amount

tag: ratio

tag: tissue


title: LP_4000_13w_492_NDPA4000_10012_Bladder_Urinary

description: LP_4000_13w_492_NDPA4000_10012_Bladder_(HT_Rat230_PM)_C07_Rep2: 1470 rats were used in this study:  6 chemicals, 4 time points, and 6 dose groups (including control).  10 animals per group and 5 extra control animals.  Timepoints were 5d, 2w, 4w, and 13 weeks.  Doses varied with compound (Tribromobenzene: 0, 2.5, 5, 10, 25, 75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Methylenebis(N,N-dimethyl)benzen amine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300).  Animals were dosed through gavage or diet.  Two of the protocols had female rats and the rest were male rats (see protocols).  F344 and Sprague Dawley rats were used.

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: strain or line


title: LP_2000_13w_476_NDPA2000_10012_Bladder_Urinary

description: LP_2000_13w_476_NDPA2000_10012_Bladder_(HT_Rat230_PM)_H07_Rep2: 1470 rats were used in this study:  6 chemicals, 4 time points, and 6 dose groups (including control).  10 animals per group and 5 extra control animals.  Timepoints were 5d, 2w, 4w, and 13 weeks.  Doses varied with compound (Tribromobenzene: 0, 2.5, 5, 10, 25, 75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Methylenebis(N,N-dimethyl)benzen amine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300).  Animals were dosed through gavage or diet.  Two of the protocols had female rats and the rest were male rats (see protocols).  F344 and Sprague Dawley rats were used.

tag: ncbi taxonomy id

tag: individual

tag: developmental state

tag: sacrifice method


title: LP_2000_13w_471_NDPA2000_10012_Bladder_Urinary

description: LP_2000_13w_471_NDPA2000_10012_Bladder_(HT_Rat230_PM)_F07_Rep2: 1470 rats were used in this study:  6 chemicals, 4 time points, and 6 dose groups (including control).  10 animals per group and 5 extra control animals.  Timepoints were 5d, 2w, 4w, and 13 weeks.  Doses varied with compound (Tribromobenzene: 0, 2.5, 5, 10, 25, 75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Methylenebis(N,N-dimethyl)benzen amine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300).  Animals were dosed through gavage or diet.  Two of the protocols had female rats and the rest were male rats (see protocols).  F344 and Sprague Dawley rats were used.

tag: Sex


title: LP_3000_13w_486_NDPA3000_10012_Bladder_Urinary

description: LP_3000_13w_486_NDPA3000_10012_Bladder_(HT_Rat230_PM)_C05_Rep2: 1470 rats were used in this study:  6 chemicals, 4 time points, and 6 dose groups (including control).  10 animals per group and 5 extra control animals.  Timepoints were 5d, 2w, 4w, and 13 weeks.  Doses varied with compound (Tribromobenzene: 0, 2.5, 5, 10, 25, 75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Methylenebis(N,N-dimethyl)benzen amine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300).  Animals were dosed through gavage or diet.  Two of the protocols had female rats and the rest were male rats (see protocols).  F344 and Sprague Dawley rats were used.

tag: array type


title: LP_2000_13w_472_NDPA2000_10012_Bladder_Urinary

description: LP_2000_13w_472_NDPA2000_10012_Bladder_(HT_Rat230_PM)_G05_Rep2: 1470 rats were used in this study:  6 chemicals, 4 time points, and 6 dose groups (including control).  10 animals per group and 5 extra control animals.  Timepoints were 5d, 2w, 4w, and 13 weeks.  Doses varied with compound (Tribromobenzene: 0, 2.5, 5, 10, 25, 75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Methylenebis(N,N-dimethyl)benzen amine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300).  Animals were dosed through gavage or diet.  Two of the protocols had female rats and the rest were male rats (see protocols).  F344 and Sprague Dawley rats were used.

tag: age


title: LP_1000_13w_461_NDPA1000_10012_Bladder_Urinary

description: LP_1000_13w_461_NDPA1000_10012_Bladder_(HT_Rat230_PM)_D05_Rep2: 1470 rats were used in this study:  6 chemicals, 4 time points, and 6 dose groups (including control).  10 animals per group and 5 extra control animals.  Timepoints were 5d, 2w, 4w, and 13 weeks.  Doses varied with compound (Tribromobenzene: 0, 2.5, 5, 10, 25, 75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Methylenebis(N,N-dimethyl)benzen amine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300).  Animals were dosed through gavage or diet.  Two of the protocols had female rats and the rest were male rats (see protocols).  F344 and Sprague Dawley rats were used.

treatment_protocol: in vivo Treatment: N-Nitrosodiphenylamine, Treatment Repeat: 7, Units of Treatment Repeat: Days/Week, Treatment Duration: 13, Units of Duration: Weeks, Treatment Time: ad lib, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 1000, Units of Dose or Concentration: ppm

tag: units of age


title: LP_1000_13w_466_NDPA1000_10012_Bladder_Urinary

description: LP_1000_13w_466_NDPA1000_10012_Bladder_(HT_Rat230_PM)_F05_Rep2: 1470 rats were used in this study:  6 chemicals, 4 time points, and 6 dose groups (including control).  10 animals per group and 5 extra control animals.  Timepoints were 5d, 2w, 4w, and 13 weeks.  Doses varied with compound (Tribromobenzene: 0, 2.5, 5, 10, 25, 75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Methylenebis(N,N-dimethyl)benzen amine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300).  Animals were dosed through gavage or diet.  Two of the protocols had female rats and the rest were male rats (see protocols).  F344 and Sprague Dawley rats were used.

tag: tissue harvest methods


title: LP_1000_13w_462_NDPA1000_10012_Bladder_Urinary

description: LP_1000_13w_462_NDPA1000_10012_Bladder_(HT_Rat230_PM)_D07_Rep2: 1470 rats were used in this study:  6 chemicals, 4 time points, and 6 dose groups (including control).  10 animals per group and 5 extra control animals.  Timepoints were 5d, 2w, 4w, and 13 weeks.  Doses varied with compound (Tribromobenzene: 0, 2.5, 5, 10, 25, 75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Methylenebis(N,N-dimethyl)benzen amine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300).  Animals were dosed through gavage or diet.  Two of the protocols had female rats and the rest were male rats (see protocols).  F344 and Sprague Dawley rats were used.

tag: amount to core


title: LP_1000_13w_464_NDPA1000_10012_Bladder_Urinary

description: LP_1000_13w_464_NDPA1000_10012_Bladder_(HT_Rat230_PM)_E05_Rep2: 1470 rats were used in this study:  6 chemicals, 4 time points, and 6 dose groups (including control).  10 animals per group and 5 extra control animals.  Timepoints were 5d, 2w, 4w, and 13 weeks.  Doses varied with compound (Tribromobenzene: 0, 2.5, 5, 10, 25, 75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Methylenebis(N,N-dimethyl)benzen amine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300).  Animals were dosed through gavage or diet.  Two of the protocols had female rats and the rest were male rats (see protocols).  F344 and Sprague Dawley rats were used.

tag: units of amount


title: LP_250_13w_453_NDPA250_10012_Bladder_Urinary

description: LP_250_13w_453_NDPA250_10012_Bladder_(HT_Rat230_PM)_B05_Rep2: 1470 rats were used in this study:  6 chemicals, 4 time points, and 6 dose groups (including control).  10 animals per group and 5 extra control animals.  Timepoints were 5d, 2w, 4w, and 13 weeks.  Doses varied with compound (Tribromobenzene: 0, 2.5, 5, 10, 25, 75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Methylenebis(N,N-dimethyl)benzen amine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300).  Animals were dosed through gavage or diet.  Two of the protocols had female rats and the rest were male rats (see protocols).  F344 and Sprague Dawley rats were used.

treatment_protocol: in vivo Treatment: N-Nitrosodiphenylamine, Treatment Repeat: 7, Units of Treatment Repeat: Days/Week, Treatment Duration: 13, Units of Duration: Weeks, Treatment Time: ad lib, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 250, Units of Dose or Concentration: ppm

tag: ratio

value: Good


title: LP_4000_5d_316_NDPA4000_10012_Bladder_Urinary

description: LP_4000_5d_316_NDPA4000_10012_Bladder_(HT_Rat230_PM)_C06: 1470 rats were used in this study:  6 chemicals, 4 time points, and 6 dose groups (including control).  10 animals per group and 5 extra control animals.  Timepoints were 5d, 2w, 4w, and 13 weeks.  Doses varied with compound (Tribromobenzene: 0, 2.5, 5, 10, 25, 75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Methylenebis(N,N-dimethyl)benzen amine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300).  Animals were dosed through gavage or diet.  Two of the protocols had female rats and the rest were male rats (see protocols).  F344 and Sprague Dawley rats were used.

treatment_protocol: in vivo Treatment: N-Nitrosodiphenylamine, Treatment Repeat: 7, Units of Treatment Repeat: Days/Weeks, Treatment Duration: 5, Units of Duration: Days, Treatment Time: ad lib, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 4000, Units of Dose or Concentration: ppm

tag: tissue


title: LP_250_13w_455_NDPA250_10012_Bladder_Urinary

description: LP_250_13w_455_NDPA250_10012_Bladder_(HT_Rat230_PM)_C05_Rep2: 1470 rats were used in this study:  6 chemicals, 4 time points, and 6 dose groups (including control).  10 animals per group and 5 extra control animals.  Timepoints were 5d, 2w, 4w, and 13 weeks.  Doses varied with compound (Tribromobenzene: 0, 2.5, 5, 10, 25, 75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Methylenebis(N,N-dimethyl)benzen amine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300).  Animals were dosed through gavage or diet.  Two of the protocols had female rats and the rest were male rats (see protocols).  F344 and Sprague Dawley rats were used.

tag: rna integrity number


title: LP_0_13w_445_RCC2_10012_Bladder_Urinary

description: LP_0_13w_445_RCC2_10012_Bladder_(HT_Rat230_PM)_H11: 1470 rats were used in this study:  6 chemicals, 4 time points, and 6 dose groups (including control).  10 animals per group and 5 extra control animals.  Timepoints were 5d, 2w, 4w, and 13 weeks.  Doses varied with compound (Tribromobenzene: 0, 2.5, 5, 10, 25, 75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Methylenebis(N,N-dimethyl)benzen amine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300).  Animals were dosed through gavage or diet.  Two of the protocols had female rats and the rest were male rats (see protocols).  F344 and Sprague Dawley rats were used.

treatment_protocol: in vivo Treatment: Rodent Chow Control 2, Treatment Repeat: 7, Units of Treatment Repeat: Days/Week, Treatment Duration: 13, Units of Duration: Weeks, Treatment Time: ad lib, Vehicle for Chemical: Rodent Chow, Route of Exposure: Diet, Dose or Concentration: 0, Units of Dose or Concentration: ppm

tag: bioanalyzer results


title: LP_0_13w_443_RCC2_10012_Bladder_Urinary

description: LP_0_13w_443_RCC2_10012_Bladder_(HT_Rat230_PM)_H09: 1470 rats were used in this study:  6 chemicals, 4 time points, and 6 dose groups (including control).  10 animals per group and 5 extra control animals.  Timepoints were 5d, 2w, 4w, and 13 weeks.  Doses varied with compound (Tribromobenzene: 0, 2.5, 5, 10, 25, 75; Bromobenzene: 0, 25, 100, 200, 300, 400; Tetrachlorophenol: 0, 10, 25, 50, 100, 200; Methylenebis(N,N-dimethyl)benzen amine: 0, 50, 200, 375, 500, 750; Nitrosodiphenylamine: 0, 250, 1000, 2000, 3000, 4000; Hydrazobenzene: 0, 5, 20, 80, 200, 300).  Animals were dosed through gavage or diet.  Two of the protocols had female rats and the rest were male rats (see protocols).  F344 and Sprague Dawley rats were used.

tag: sample preservation